Building Blocks, Biological Pathways, and Networks (BBPN)
Building Blocks, Biological Pathways, and Networks (BBPN)
Program Publications
Publications Search by Program
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date | PubMedLink |
|---|---|---|---|---|---|
| Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. | Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T | Molecular & cellular proteomics : MCP | 25161197 | 2014 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/25161197 |
| Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. | Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Almo, Steven C; Rout, Michael; Sa | Molecular & cellular proteomics : MCP | 25139911 | 2014 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/25139911 |
| Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway. | Algret, Romain; Fernandez-Martinez, Javier; Shi, Yi; Kim, Seung Joong; Pellarin, Riccardo; Cimermancic, Peter; Cochet, Emilie; Sali, Andrej; Chait, Brian T; Rout, Michael P; Dokudovskaya, Svetlana | Molecular & cellular proteomics : MCP | 25073740 | 2014 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/25073740 |
| Metabolomics of ApcMin/+ mice genetically susceptible to intestinal cancer. | Dazard, Jean-Eudes J; Sandlers, Yana; Doerner, Stephanie K; Berger, Nathan A; Brunengraber, Henri | BMC systems biology | 24954394 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24954394 |
| Imaging mass spectrometry of diversified cardiolipin molecular species in the brain. | Amoscato, A A; Sparvero, L J; He, R R; Watkins, S; Bayir, H; Kagan, V E | Analytical chemistry | 24949523 | 2014 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24949523 |
| Enzyme inhibitor discovery by activity-based protein profiling. | Niphakis, Micah J; Cravatt, Benjamin F | Annual review of biochemistry | 24905785 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24905785 |
| A draft map of the human proteome. | Kim, Min-Sik; Pinto, Sneha M; Getnet, Derese; Nirujogi, Raja Sekhar; Manda, Srikanth S; Chaerkady, Raghothama; Madugundu, Anil K; Kelkar, Dhanashree S; Isserlin, Ruth; Jain, Shobhit; Thomas, Joji K; Muthusamy, Babylakshmi; Leal-Rojas, Pamela; Kumar, Prave | Nature | 24870542 | 2014 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/24870542 |
| Self-Checking Cell-Based Assays for GPCR Desensitization and Resensitization. | Fisher, Gregory W; Fuhrman, Margaret H; Adler, Sally A; Szent-Gyorgyi, Christopher; Waggoner, Alan S; Jarvik, Jonathan W | Journal of biomolecular screening | 24820110 | 2014 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/24820110 |
| A Selective Phenelzine Analogue Inhibitor of Histone Demethylase LSD1. | Prusevich, Polina; Kalin, Jay H; Ming, Shonoi A; Basso, Manuela; Givens, Jeffrey; Li, Xin; Hu, Jianfei; Taylor, Martin S; Cieniewicz, Anne M; Hsiao, Po-Yuan; Huang, Rong; Roberson, Heather; Adejola, Nkosi; Avery, Lindsay B; Casero Jr, Robert A; Taverna, S | ACS chemical biology | 24707965 | 2014 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/24707965 |
| Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. | Tan, Minjia; Peng, Chao; Anderson, Kristin A; Chhoy, Peter; Xie, Zhongyu; Dai, Lunzhi; Park, Jeongsoon; Chen, Yue; Huang, He; Zhang, Yi; Ro, Jennifer; Wagner, Gregory R; Green, Michelle F; Madsen, Andreas S; Schmiesing, Jessica; Peterson, Brett S; Xu, Guo | Cell metabolism | 24703693 | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24703693 |
| Increased Glucose Metabolism and Glycerolipid Formation by Fatty Acids and GPR40 Receptor Signaling Underlies the Fatty Acid Potentiation of Insulin Secretion. | El-Azzouny, Mahmoud; Evans, Charles R; Treutelaar, Mary K; Kennedy, Robert T; Burant, Charles F | The Journal of biological chemistry | 24675078 | 2014 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/24675078 |
| Functional annotation of proteome encoded by human chromosome 22. | Pinto, Sneha M; Manda, Srikanth S; Kim, Min-Sik; Taylor, KyOnese; Selvan, Lakshmi Dhevi Nagarajha; Balakrishnan, Lavanya; Subbannayya, Tejaswini; Yan, Fangfei; Prasad, T S Keshava; Gowda, Harsha; Lee, Charles; Hancock, William S; Pandey, Akhilesh | Journal of proteome research | 24669763 | 2014 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/24669763 |
| The multifunctional nuclear pore complex: a platform for controlling gene expression. | Ptak, Christopher; Aitchison, John D; Wozniak, Richard W | Current opinion in cell biology | 24657998 | 2014 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/24657998 |
| Human cytomegalovirus pUL37x1-induced calcium flux activates PKC*, inducing altered cell shape and accumulation of cytoplasmic vesicles. | Sharon-Friling, Ronit; Shenk, Thomas | Proceedings of the National Academy of Sciences of the United States of America | 24616524 | 2014 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/24616524 |
| An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. | Wurtmann, Elisabeth J; Ratushny, Alexander V; Pan, Min; Beer, Karlyn D; Aitchison, John D; Baliga, Nitin S | Molecular microbiology | 24612392 | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24612392 |
| Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. | Holden, Jennifer M; Koreny, Ludek; Obado, Samson; Ratushny, Alexander V; Chen, Wei-Ming; Chiang, Jung-Hsien; Kelly, Steven; Chait, Brian T; Aitchison, John D; Rout, Michael P; Field, Mark C | Molecular biology of the cell | 24600046 | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24600046 |
| Twist1-induced dissemination preserves epithelial identity and requires E-cadherin. | Shamir, Eliah R; Pappalardo, Elisa; Jorgens, Danielle M; Coutinho, Kester; Tsai, Wen-Ting; Aziz, Khaled; Auer, Manfred; Tran, Phuoc T; Bader, Joel S; Ewald, Andrew J | The Journal of cell biology | 24590176 | 2014 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/24590176 |
| TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. | Zhong, Jun; Sharma, Jyoti; Raju, Rajesh; Palapetta, Shyam Mohan; Prasad, T S Keshava; Huang, Tai-Chung; Yoda, Akinori; Tyner, Jeffrey W; van Bodegom, Diederik; Weinstock, David M; Ziegler, Steven F; Pandey, Akhilesh | Database : the journal of biological databases and curation | 24573880 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24573880 |
| Fluorogen-activating scFv biosensors target surface markers on live cells via streptavidin or single-chain avidin. | Gallo, Eugenio; Jarvik, Jonathan | Molecular biotechnology | 24562573 | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24562573 |
| Glutathionylated 4-hydroxy-2-(E)-alkenal enantiomers in rat organs and their contributions toward the disposal of 4-hydroxy-2-(E)-nonenal in rat liver. | Sadhukhan, Sushabhan; Han, Yong; Jin, Zhicheng; Tochtrop, Gregory P; Zhang, Guo-Fang | Free radical biology & medicine | 24556413 | 2014 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/24556413 |
| Real-Time Detection of Protein Trafficking with High-Throughput Flow Cytometry (HTFC) and Fluorogen-Activating Protein (FAP) Base Biosensor. | Wu, Yang; Tapia, Phillip H; Jarvik, Jonathan; Waggoner, Alan S; Sklar, Larry A | Current protocols in cytometry / editorial board, J. Paul Robinson, managing editor ... [et al.] | 24510772 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24510772 |
| Real-Time Detection of Protein Trafficking with High-Throughput Flow Cytometry (HTFC) and Fluorogen-Activating Protein (FAP) Base Biosensor. | Wu, Yang; Tapia, Phillip H; Jarvik, Jonathan; Waggoner, Alan S; Sklar, Larry A | Current protocols in cytometry / editorial board, J. Paul Robinson, managing editor ... [et al.] | 24510772 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24510772 |
| Circadian clocks and feeding time regulate the oscillations and levels of hepatic triglycerides. | Adamovich, Yaarit; Rousso-Noori, Liat; Zwighaft, Ziv; Neufeld-Cohen, Adi; Golik, Marina; Kraut-Cohen, Judith; Wang, Miao; Han, Xianlin; Asher, Gad | Cell metabolism | 24506873 | 2014 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/24506873 |
| Improved spatial resolution of matrix-assisted laser desorption/ionization imaging of lipids in the brain by alkylated derivatives of 2,5-dihydroxybenzoic acid. | Stoyanovsky, D A; Sparvero, L J; Amoscato, A A; He, R R; Watkins, S; Pitt, B R; Bayir, H; Kagan, V E | Rapid communications in mass spectrometry : RCM | 24497278 | 2014 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/24497278 |
| Alterations in Mouse Brain Lipidome after Disruption of CST Gene: A Lipidomics Study. | Wang, Chunyan; Wang, Miao; Zhou, Yunhua; Dupree, Jeffrey L; Han, Xianlin | Molecular neurobiology | 24395133 | 2014 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/24395133 |
| Novel approach in LC-MS/MS using MRM to generate a full profile of acyl-CoAs: discovery of acyl-dephospho-CoAs. | Li, Qingling; Zhang, Shenghui; Berthiaume, Jessica M; Simons, Brigitte; Zhang, Guo-Fang | Journal of lipid research | 24367045 | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24367045 |
| Plasma Proteome Database as a resource for proteomics research: 2014 update. | Nanjappa, Vishalakshi; Thomas, Joji Kurian; Marimuthu, Arivusudar; Muthusamy, Babylakshmi; Radhakrishnan, Aneesha; Sharma, Rakesh; Ahmad Khan, Aafaque; Balakrishnan, Lavanya; Sahasrabuddhe, Nandini A; Kumar, Satwant; Jhaveri, Binit Nitinbhai; Sheth, Kaush | Nucleic acids research | 24304897 | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24304897 |
| Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection. | Grady, Sarah L; Purdy, John G; Rabinowitz, Joshua D; Shenk, Thomas | Proceedings of the National Academy of Sciences of the United States of America | 24297925 | 2013 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/24297925 |
| Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. | Lan, Li; Nakajima, Satoshi; Wei, Leizhen; Sun, Luxi; Hsieh, Ching-Lung; Sobol, Robert W; Bruchez, Marcel; Van Houten, Bennett; Yasui, Akira; Levine, Arthur S | Nucleic acids research | 24293652 | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24293652 |
| Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. | Zhang, Xiaojun; Dantas Machado, Ana Carolina; Ding, Yuan; Chen, Yongheng; Lu, Yan; Duan, Yankun; Tham, Kenneth W; Chen, Lin; Rohs, Remo; Qin, Peter Z | Nucleic acids research | 24293651 | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24293651 |
| Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. | Schoggins, John W; MacDuff, Donna A; Imanaka, Naoko; Gainey, Maria D; Shrestha, Bimmi; Eitson, Jennifer L; Mar, Katrina B; Richardson, R Blake; Ratushny, Alexander V; Litvak, Vladimir; Dabelic, Rea; Manicassamy, Balaji; Aitchison, John D; Aderem, Alan; El | Nature | 24284630 | 2014 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/24284630 |
| Enriching the pore: Splendid complexity from humble origins. | Field, Mark C; Koreny, Ludek; Rout, Michael P | Traffic (Copenhagen, Denmark) | 24279500 | 2013 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/24279500 |
| Pathway Commons at virtual cell: use of pathway data for mathematical modeling. | Blinov, Michael L; Schaff, James C; Ruebenacker, Oliver; Wei, Xintao; Vasilescu, Dan; Gao, Fei; Morgan, Frank; Ye, Li; Lakshminarayana, Anuradha; Moraru, Ion I; Loew, Leslie M | Bioinformatics (Oxford, England) | 24273241 | 2014 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/24273241 |
| The human cap-binding complex is functionally connected to the nuclear RNA exosome. | Andersen, Peter Refsing; Domanski, Michal; Kristiansen, Maiken S; Storvall, Helena; Ntini, Evgenia; Verheggen, Celine; Schein, Aleks; Bunkenborg, Jakob; Poser, Ina; Hallais, Marie; Sandberg, Rickard; Hyman, Anthony; Lacava, John; Rout, Michael P; Andersen | Nature structural & molecular biology | 24270879 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24270879 |
| Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. | Taylor, Martin S; Lacava, John; Mita, Paolo; Molloy, Kelly R; Huang, Cheng Ran Lisa; Li, Donghui; Adney, Emily M; Jiang, Hua; Burns, Kathleen H; Chait, Brian T; Rout, Michael P; Boeke, Jef D; Dai, Lixin | Cell | 24267889 | 2013 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/24267889 |
| Intracellular pH Measurements Using Perfluorocarbon Nanoemulsions. | Patrick, Michael J; Janjic, Jelena M; Teng, Haibing; O'Hear, Meredith R; Brown, Cortlyn W; Stokum, Jesse A; Schmidt, Brigitte F; Ahrens, Eric T; Waggoner, Alan S | Journal of the American Chemical Society | 24266634 | 2013 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/24266634 |
| Peroxisomes take shape. | Smith, Jennifer J; Aitchison, John D | Nature reviews. Molecular cell biology | 24263361 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24263361 |
| A Signaling Network of Thyroid-Stimulating Hormone. | Goel, Renu; Raju, Rajesh; Maharudraiah, Jagadeesha; Sameer Kumar, Ghantasala S; Ghosh, Krishna; Kumar, Amit; Lakshmi, T Pragna; Sharma, Jyoti; Sharma, Rakesh; Balakrishnan, Lavanya; Pan, Archana; Kandasamy, Kumaran; Christopher, Rita; Krishna, V; Mohan, S | Journal of proteomics & bioinformatics | 24255551 | 2011 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/24255551 |
| PhosphoNetworks: a database for human phosphorylation networks. | Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Zhang, Jin; Zhu, Heng; Qian, Jiang | Bioinformatics (Oxford, England) | 24227675 | 2014 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24227675 |
| Genome-wide consequences of deleting any single gene. | Teng, Xinchen; Dayhoff-Brannigan, Margaret; Cheng, Wen-Chih; Gilbert, Catherine E; Sing, Cierra N; Diny, Nicola L; Wheelan, Sarah J; Dunham, Maitreya J; Boeke, Jef D; Pineda, Fernando J; Hardwick, J Marie | Molecular cell | 24211263 | 2013 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/24211263 |
| Modeling of proteins and their assemblies with the Integrative Modeling Platform. | Webb, Benjamin; Lasker, Keren; Velazquez-Muriel, Javier; Schneidman-Duhovny, Dina; Pellarin, Riccardo; Bonomi, Massimiliano; Greenberg, Charles; Raveh, Barak; Tjioe, Elina; Russel, Daniel; Sali, Andrej | Methods in molecular biology (Clifton, N.J.) | 24203340 | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24203340 |
| Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. | NULL | Nature | 24201285 | 2013 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/24201285 |
| High-resolution network biology: connecting sequence with function. | Ryan, Colm J; Cimermancic, Peter; Szpiech, Zachary A; Sali, Andrej; Hernandez, Ryan D; Krogan, Nevan J | Nature reviews. Genetics | 24197012 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24197012 |
| Localization Microscopy using Noncovalent Fluorogen Activation by Genetically Encoded Fluorogen-Activating Proteins. | Yan, Qi; Schwartz, Samantha L; Maji, Suvrajit; Huang, Fang; Szent-Gyorgyi, Chris; Lidke, Diane S; Lidke, Keith A; Bruchez, Marcel P | Chemphyschem : a European journal of chemical physics and physical chemistry | 24194371 | 2013 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/24194371 |
| Loss of TRPML1 promotes production of reactive oxygen species: is oxidative damage a factor in mucolipidosis type IV? | Coblentz, Jessica; St Croix, Claudette; Kiselyov, Kirill | The Biochemical journal | 24192042 | 2014 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/24192042 |
| Molecular mechanisms of system responses to novel stimuli are predictable from public data. | Danziger, Samuel A; Ratushny, Alexander V; Smith, Jennifer J; Saleem, Ramsey A; Wan, Yakun; Arens, Christina E; Armstrong, Abraham M; Sitko, Katherine; Chen, Wei-Ming; Chiang, Jung-Hsien; Reiss, David J; Baliga, Nitin S; Aitchison, John D | Nucleic acids research | 24185701 | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24185701 |
| The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome. | Niepel, Mario; Molloy, Kelly R; Williams, Rosemary; Farr, Julia C; Meinema, Anne C; Vecchietti, Nicholas; Cristea, Ileana M; Chait, Brian T; Rout, Michael P; Strambio-De-Castillia, Caterina | Molecular biology of the cell | 24152732 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24152732 |
| A role for cytosolic isocitrate dehydrogenase as a negative regulator of glucose signaling for insulin secretion in pancreatic ýý-cells. | Guay, Claudiane; Joly, Erik; Pepin, Emilie; Barbeau, Annie; Hentsch, Lisa; Pineda, Marco; Madiraju, S R Murthy; Brunengraber, Henri; Prentki, Marc | PloS one | 24130841 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24130841 |
| Fluorogen-activating-proteins as universal affinity biosensors for immunodetection. | Gallo, Eugenio; Vasilev, Kalin V; Jarvik, Jonathan | Biotechnology and bioengineering | 24122476 | 2013 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/24122476 |
| A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5' terminal sequence of the hepatitis C virus RNA. | Fan, Baochang; Lu, Kuan-Yi; Reymond Sutandy, F X; Chen, Yi-Wen; Konan, Kouacou; Zhu, Heng; Kao, C Cheng; Chen, Chien-Sheng | Molecular & cellular proteomics : MCP | 24113282 | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24113282 |
| Rotenone induces reductive stress and triacylglycerol deposition in C2C12 cells. | He, Quan; Wang, Miao; Petucci, Christopher; Gardell, Stephen J; Han, Xianlin | The international journal of biochemistry & cell biology | 24104397 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24104397 |
| Recycling of kinesin-1 motors by diffusion after transport. | Blasius, T Lynne; Reed, Nathan; Slepchenko, Boris M; Verhey, Kristen J | PloS one | 24098765 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24098765 |
| Recovering a representative conformational ensemble from underdetermined macromolecular structural data. | Berlin, Konstantin; Castaneda, Carlos A; Schneidman-Duhovny, Dina; Sali, Andrej; Nava-Tudela, Alfredo; Fushman, David | Journal of the American Chemical Society | 24093873 | 2013 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/24093873 |
| Supervillin binding to myosin II and synergism with anillin are required for cytokinesis. | Smith, Tara C; Fridy, Peter C; Li, Yinyin; Basil, Shruti; Arjun, Sneha; Friesen, Ryan M; Leszyk, John; Chait, Brian T; Rout, Michael P; Luna, Elizabeth J | Molecular biology of the cell | 24088567 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24088567 |
| Integrated proteomic and metabolic analysis of breast cancer progression. | Shaw, Patrick G; Chaerkady, Raghothama; Wang, Tao; Vasilatos, Shauna; Huang, Yi; Van Houten, Bennett; Pandey, Akhilesh; Davidson, Nancy E | PloS one | 24086712 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24086712 |
| Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase. | Taylor, Martin S; Ruch, Travis R; Hsiao, Po-Yuan; Hwang, Yousang; Zhang, Pingfeng; Dai, Lixin; Huang, Cheng Ran Lisa; Berndsen, Christopher E; Kim, Min-Sik; Pandey, Akhilesh; Wolberger, Cynthia; Marmorstein, Ronen; Machamer, Carolyn; Boeke, Jef D; Cole, P | The Journal of biological chemistry | 24045953 | 2013 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/24045953 |
| Elastic coupling of nascent apCAM adhesions to flowing actin networks. | Mejean, Cecile O; Schaefer, Andrew W; Buck, Kenneth B; Kress, Holger; Shundrovsky, Alla; Merrill, Jason W; Dufresne, Eric R; Forscher, Paul | PloS one | 24039928 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24039928 |
| ATR kinase activation in G1 phase facilitates the repair of ionizing radiation-induced DNA damage. | Gamper, Armin M; Rofougaran, Reza; Watkins, Simon C; Greenberger, Joel S; Beumer, Jan H; Bakkenist, Christopher J | Nucleic acids research | 24038466 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24038466 |
| Kinetochore function and chromosome segregation rely on critical residues in histones h3 and h4 in budding yeast. | Ng, Tessie M; Lenstra, Tineke L; Duggan, Nicole; Jiang, Shuangying; Ceto, Steven; Holstege, Frank C P; Dai, Junbiao; Boeke, Jef D; Biggins, Sue | Genetics | 24037263 | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24037263 |
| Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. | Woodard, Crystal L; Goodwin, C Rory; Wan, Jun; Xia, Shuli; Newman, Robert; Hu, Jianfei; Zhang, Jin; Hayward, S Diane; Qian, Jiang; Laterra, John; Zhu, Heng | PloS one | 24023761 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24023761 |
| SILAC-based quantification of Sirt1-responsive lysine acetylome. | Chen, Yue; Colak, Gozde; Zhao, Yingming | Methods in molecular biology (Clifton, N.J.) | 24014402 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24014402 |
| Single cell metabolic profiling of tumor mimics. | Keithley, Richard B; Weaver, Eric M; Rosado, Andrea M; Metzinger, Mark P; Hummon, Amanda B; Dovichi, Norman J | Analytical chemistry | 24011091 | 2013 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/24011091 |
| Conformational States of macromolecular assemblies explored by integrative structure calculation. | Thalassinos, Konstantinos; Pandurangan, Arun Prasad; Xu, Min; Alber, Frank; Topf, Maya | Structure (London, England : 1993) | 24010709 | 2013 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/24010709 |
| Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces. | Szent-Gyorgyi, Chris; Stanfield, Robyn L; Andreko, Susan; Dempsey, Alison; Ahmed, Mushtaq; Capek, Sarah; Waggoner, Alan S; Wilson, Ian A; Bruchez, Marcel P | Journal of molecular biology | 23978698 | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23978698 |
| Accurate SAXS profile computation and its assessment by contrast variation experiments. | Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A; Sali, Andrej | Biophysical journal | 23972848 | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/23972848 |
| Fatty acidomics: global analysis of lipid species containing a carboxyl group with a charge-remote fragmentation-assisted approach. | Wang, Miao; Han, Rowland H; Han, Xianlin | Analytical chemistry | 23971716 | 2013 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/23971716 |
| Pretreatment with pyridoxamine mitigates isolevuglandin-associated retinal effects in mice exposed to bright light. | Charvet, Casey D; Saadane, Aicha; Wang, Meiyao; Salomon, Robert G; Brunengraber, Henri; Turko, Illarion V; Pikuleva, Irina A | The Journal of biological chemistry | 23970548 | 2013 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/23970548 |
| VirD: a virion display array for profiling functional membrane proteins. | Hu, Shaohui; Feng, Yingzhu; Henson, Brandon; Wang, Bochu; Huang, Xiaofang; Li, Min; Desai, Prashant; Zhu, Heng | Analytical chemistry | 23941274 | 2013 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/23941274 |
| The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress. | Baker, Lindsey A; Ueberheide, Beatrix M; Dewell, Scott; Chait, Brian T; Zheng, Deyou; Allis, C David | Molecular and cellular biology | 23878396 | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23878396 |
| Specific changes of sulfatide levels in individuals with pre-clinical Alzheimer's disease: an early event in disease pathogenesis. | Cheng, Hua; Wang, Miao; Li, Jian-Liang; Cairns, Nigel J; Han, Xianlin | Journal of neurochemistry | 23865640 | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23865640 |
| Molecular crowding shapes gene expression in synthetic cellular nanosystems. | Tan, Cheemeng; Saurabh, Saumya; Bruchez, Marcel P; Schwartz, Russell; Leduc, Philip | Nature nanotechnology | 23851358 | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23851358 |
| PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. | Chen, Wei-Ming; Danziger, Samuel A; Chiang, Jung-Hsien; Aitchison, John D | Bioinformatics (Oxford, England) | 23832245 | 2013 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/23832245 |
| Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms. | Xu, Min; Alber, Frank | Bioinformatics (Oxford, England) | 23812994 | 2013 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/23812994 |
| SIRT5-Mediated Lysine Desuccinylation Impacts Diverse Metabolic Pathways. | Park, Jeongsoon; Chen, Yue; Tishkoff, Daniel X; Peng, Chao; Tan, Minjia; Dai, Lunzhai; Xie, Zhongyu; Zhang, Yi; Zwaans, Bernadette M M; Skinner, Mary E; Lombard, David B; Zhao, Yingming | Molecular cell | 23806337 | 2013 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/23806337 |
| The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence. | Hansen, Anne-Marie; Chaerkady, Raghothama; Sharma, Jyoti; Diaz-Mejia, J Javier; Tyagi, Nidhi; Renuse, Santosh; Jacob, Harrys K C; Pinto, Sneha M; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Delanghe, Bernard; Srinivasan, Narayanaswamy; Emili, Andrew; Kaper, J | PLoS pathogens | 23785281 | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23785281 |
| Superimposed topographic and chemical cues synergistically guide neurite outgrowth. | Kundu, Arnab; Micholt, Liesbeth; Friedrich, Sarah; Rand, Danielle R; Bartic, Carmen; Braeken, Dries; Levchenko, Andre | Lab on a chip | 23752939 | 2013 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/23752939 |
| Population-expression models of immune response. | Stromberg, Sean P; Antia, Rustom; Nemenman, Ilya | Physical biology | 23735782 | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23735782 |
| Cell Adhesion on Micro-Structured Fibronectin Gradients Fabricated by Multiphoton Excited Photochemistry. | Chen, Xiyi; Su, Yuan-Deng; Ajeti, Visar; Chen, Shean-Jen; Campagnola, Paul J | Cellular and molecular bioengineering | 23710258 | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23710258 |
| Detection and correction of interference in SRM analysis. | Bao, Y; Waldemarson, S; Zhang, G; Wahlander, A; Ueberheide, B; Myung, S; Reed, B; Molloy, K; Padovan, J C; Eriksson, J; Neubert, T A; Chait, B T; Fenyo, D | Methods (San Diego, Calif.) | 23707623 | 2013 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/23707623 |
| Selective inhibition of p300 HAT blocks cell cycle progression, induces cellular senescence, and inhibits the DNA damage response in melanoma cells. | Yan, Gai; Eller, Mark S; Elm, Courtney; Larocca, Cecilia A; Ryu, Byungwoo; Panova, Izabela P; Dancy, Beverley M; Bowers, Erin M; Meyers, David; Lareau, Lisa; Cole, Philip A; Taverna, Sean D; Alani, Rhoda M | The Journal of investigative dermatology | 23698071 | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23698071 |
| Saturated very long chain Fatty acids are required for the production of infectious human cytomegalovirus progeny. | Koyuncu, Emre; Purdy, John G; Rabinowitz, Joshua D; Shenk, Thomas | PLoS pathogens | 23696731 | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23696731 |
| Using glycinylation, a chemical derivatization technique, for the quantitation of ubiquitinated proteins. | Fiedler, Katherine L; Cotter, Robert J | Analytical chemistry | 23682733 | 2013 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/23682733 |
| A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants. | Fiedler, Katherine L; Bheda, Poonam; Dai, Junbiao; Boeke, Jef D; Wolberger, Cynthia; Cotter, Robert J | Journal of mass spectrometry : JMS | 23674285 | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23674285 |
| Three-dimensional cultures modeling premalignant progression of human breast epithelial cells: role of cysteine cathepsins. | Mullins, Stefanie R; Sameni, Mansoureth; Blum, Galia; Bogyo, Matthew; Sloane, Bonnie F; Moin, Kamiar | Biological chemistry | 23667900 | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23667900 |
| Proteomic strategies to characterize signaling pathways. | Harsha, H C; Pinto, Sneha M; Pandey, Akhilesh | Methods in molecular biology (Clifton, N.J.) | 23666735 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23666735 |
| Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. | Mitchell, Leslie A; Cai, Yizhi; Taylor, Martin; Noronha, Anne Marie; Chuang, James; Dai, Lixin; Boeke, Jef D | ACS synthetic biology | 23654272 | 2013 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/23654272 |
| Manipulating ionic strength to improve single cell electrophoretic separations. | Keithley, Richard B; Metzinger, Mark P; Rosado, Andrea M; Dovichi, Norman J | Talanta | 23622546 | 2013 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/23622546 |
| Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry. | Nemes, Peter; Rubakhin, Stanislav S; Aerts, Jordan T; Sweedler, Jonathan V | Nature protocols | 23589938 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23589938 |
| In vivo biochemistry: applications for small molecule biosensors in plant biology. | Jones, Alexander M; Grossmann, Guido; Danielson, Jonas Ah; Sosso, Davide; Chen, Li-Qing; Ho, Cheng-Hsun; Frommer, Wolf B | Current opinion in plant biology | 23587939 | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23587939 |
| Postage for the messenger: designating routes for nuclear mRNA export. | Natalizio, Barbara J; Wente, Susan R | Trends in cell biology | 23583578 | 2013 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/23583578 |
| Improved native isolation of endogenous Protein A-tagged protein complexes. | LaCava, John; Chandramouli, Nagarajan; Jiang, Hua; Rout, Michael P | BioTechniques | 23581468 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23581468 |
| Engineering fluorogen activating proteins into self-assembling materials. | Saunders, Matthew J; Liu, Wen; Szent-Gyorgyi, Christopher; Wen, Yi; Drennen, Zachary; Waggoner, Alan S; Meng, Wilson S | Bioconjugate chemistry | 23573960 | 2013 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/23573960 |
| Regulated recycling of mutant CFTR is partially restored by pharmacological treatment. | Holleran, John P; Zeng, Jianxin; Frizzell, Raymond A; Watkins, Simon C | Journal of cell science | 23572510 | 2013 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23572510 |
| Differential principal component analysis of ChIP-seq. | Ji, Hongkai; Li, Xia; Wang, Qian-fei; Ning, Yang | Proceedings of the National Academy of Sciences of the United States of America | 23569280 | 2013 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/23569280 |
| Evolution of modular intraflagellar transport from a coatomer-like progenitor. | van Dam, Teunis J P; Townsend, Matthew J; Turk, Martin; Schlessinger, Avner; Sali, Andrej; Field, Mark C; Huynen, Martijn A | Proceedings of the National Academy of Sciences of the United States of America | 23569277 | 2013 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/23569277 |
| Construction of human activity-based phosphorylation networks. | Newman, Robert H; Hu, Jianfei; Rho, Hee-Sool; Xie, Zhi; Woodard, Crystal; Neiswinger, John; Cooper, Christopher; Shirley, Matthew; Clark, Hillary M; Hu, Shaohui; Hwang, Woochang; Jeong, Jun Seop; Wu, George; Lin, Jimmy; Gao, Xinxin; Ni, Qiang; Goel, Renu; | Molecular systems biology | 23549483 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23549483 |
| Construction of human activity-based phosphorylation networks. | Newman, Robert H; Hu, Jianfei; Rho, Hee-Sool; Xie, Zhi; Woodard, Crystal; Neiswinger, John; Cooper, Christopher; Shirley, Matthew; Clark, Hillary M; Hu, Shaohui; Hwang, Woochang; Jeong, Jun Seop; Wu, George; Lin, Jimmy; Gao, Xinxin; Ni, Qiang; Goel, Renu; Xia, Shuli; Ji, Hongkai; Dalby, Kevin N; Birnbaum, Morris J; Cole, Philip A; Knapp, Stefan; Ryazanov, Alexey G; Zack, Donald J; Blackshaw, Seth; Pawson, Tony; Gingras, Anne-Claude; Desiderio, Stephen; Pandey, Akhilesh; Turk, Benjamin E; Zhang, Jin; Zhu, Heng; Qian, Jiang | Molecular systems biology | 23549483 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23549483 |
| Overview of protein microarrays. | Sutandy, F X Reymond; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng | Current protocols in protein science / editorial board, John E. Coligan ... [et al.] | 23546620 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23546620 |
| Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry. | Nemes, Peter; Rubakhin, Stanislav S; Aerts, Jordan T; Sweedler, Jonathan V | Nature protocols | 23538882 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23538882 |
| Global analysis of phosphorylation networks in humans. | Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Hwang, Woochang; Neiswinger, John; Zhu, Heng; Zhang, Jin; Qian, Jiang | Biochimica et biophysica acta | 23524292 | 2013 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/23524292 |
| Global analysis of phosphorylation networks in humans. | Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Hwang, Woochang; Neiswinger, John; Zhu, Heng; Zhang, Jin; Qian, Jiang | Biochimica et biophysica acta | 23524292 | 2013 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/23524292 |
| Determining target engagement in living systems. | Simon, Gabriel M; Niphakis, Micah J; Cravatt, Benjamin F | Nature chemical biology | 23508173 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23508173 |
| Access guide to human proteinpedia. | Muthusamy, Babylakshmi; Thomas, Joji Kurian; Prasad, T S Keshava; Pandey, Akhilesh | Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] | 23504933 | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23504933 |
| Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. | Sampathkumar, Parthasarathy; Kim, Seung Joong; Upla, Paula; Rice, William J; Phillips, Jeremy; Timney, Benjamin L; Pieper, Ursula; Bonanno, Jeffrey B; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Ketaren, Natalia E; Matsui, Tsutomu; Weiss, Thomas M; S | Structure (London, England : 1993) | 23499021 | 2013 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/23499021 |
| Uncovering nuclear pore complexity with innovation. | Adams, Rebecca L; Wente, Susan R | Cell | 23498931 | 2013 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/23498931 |
| Differential regulation of glucose transport activity in yeast by specific cAMP signatures. | Bermejo, Clara; Haerizadeh, Farzad; Sadoine, Mayuri S C; Chermak, Diane; Frommer, Wolf B | The Biochemical journal | 23495665 | 2013 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23495665 |
| Transcriptomic Profiling of Medial Temporal Lobe Epilepsy. | Venugopal, Abhilash K; Sameer Kumar, Ghantasala S; Mahadevan, Anita; Selvan, Lakshmi Dhevi N; Marimuthu, Arivusudar; Dikshit, Jyoti Bajpai; Tata, Pramila; Ramachandra, Yl; Chaerkady, Raghothama; Sinha, Sanjib; Chandramouli, Ba; Arivazhagan, A; Satishchand | Journal of proteomics & bioinformatics | 23483634 | 2012 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/23483634 |
| Signaling through purinergic receptors for ATP induces human cutaneous innate and adaptive Th17 responses: implications in the pathogenesis of psoriasis. | Killeen, Meaghan E; Ferris, Laura; Kupetsky, Erine A; Falo Jr, Louis; Mathers, Alicia R | Journal of immunology (Baltimore, Md. : 1950) | 23479230 | 2013 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/23479230 |
| A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells. | San Martin, Alejandro; Ceballo, Sebastian; Ruminot, Ivan; Lerchundi, Rodrigo; Frommer, Wolf B; Barros, Luis Felipe | PloS one | 23469056 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23469056 |
| NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. | Ulanovskaya, Olesya A; Zuhl, Andrea M; Cravatt, Benjamin F | Nature chemical biology | 23455543 | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23455543 |
| A role for the nucleoporin Nup170p in chromatin structure and gene silencing. | Van de Vosse, David W; Wan, Yakun; Lapetina, Diego L; Chen, Wei-Ming; Chiang, Jung-Hsien; Aitchison, John D; Wozniak, Richard W | Cell | 23452847 | 2013 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/23452847 |
| Metabolome response to glucose in the ýý-cell line INS-1 832/13. | Lorenz, Matthew A; El Azzouny, Mahmoud A; Kennedy, Robert T; Burant, Charles F | The Journal of biological chemistry | 23426361 | 2013 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/23426361 |
| New centromere autoantigens identified in systemic sclerosis using centromere protein microarrays. | Song, Guang; Hu, Chaojun; Zhu, Heng; Wang, Li; Zhang, Fengchun; Li, Yongzhe; Wu, Lin | The Journal of rheumatology | 23418382 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23418382 |
| Combining small-volume metabolomic and transcriptomic approaches for assessing brain chemistry. | Knolhoff, Ann M; Nautiyal, Katherine M; Nemes, Peter; Kalachikov, Sergey; Morozova, Irina; Silver, Rae; Sweedler, Jonathan V | Analytical chemistry | 23409944 | 2013 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/23409944 |
| Inhibition of ghrelin O-acyltransferase attenuates food deprivation-induced increases in ingestive behavior. | Teubner, Brett J W; Garretson, John T; Hwang, Yousang; Cole, Philip A; Bartness, Timothy J | Hormones and behavior | 23399323 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23399323 |
| Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells. | Hulce, Jonathan J; Cognetta, Armand B; Niphakis, Micah J; Tully, Sarah E; Cravatt, Benjamin F | Nature methods | 23396283 | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23396283 |
| Interactome mapping: using protein microarray technology to reconstruct diverse protein networks. | Uzoma, Ijeoma; Zhu, Heng | Genomics, proteomics & bioinformatics | 23395178 | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23395178 |
| Spatiotemporal resolution of BDNF neuroprotection against glutamate excitotoxicity in cultured hippocampal neurons. | Melo, C V; Okumoto, S; Gomes, J R; Baptista, M S; Bahr, B A; Frommer, W B; Duarte, C B | Neuroscience | 23384605 | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23384605 |
| Using functional proteome microarrays to study protein lysine acetylation. | Lu, Jin-Ying; Lin, Yu-Yi; Boeke, Jef D; Zhu, Heng | Methods in molecular biology (Clifton, N.J.) | 23381860 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23381860 |
| Separation and purification of multiply acetylated proteins using cation-exchange chromatography. | Papazyan, Romeo; Taverna, Sean D | Methods in molecular biology (Clifton, N.J.) | 23381856 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23381856 |
| Simulation of triacylglycerol ion profiles: bioinformatics for interpretation of triacylglycerol biosynthesis. | Han, Rowland H; Wang, Miao; Fang, Xiaoling; Han, Xianlin | Journal of lipid research | 23365150 | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23365150 |
| Metallochaperones regulate intracellular copper levels. | Pang, W Lee; Kaur, Amardeep; Ratushny, Alexander V; Cvetkovic, Aleksandar; Kumar, Sunil; Pan, Min; Arkin, Adam P; Aitchison, John D; Adams, Michael W W; Baliga, Nitin S | PLoS computational biology | 23349626 | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23349626 |
| Global analysis of condition-specific subcellular protein distribution and abundance. | Jung, Sunhee; Smith, Jennifer J; von Haller, Priska D; Dilworth, David J; Sitko, Katherine A; Miller, Leslie R; Saleem, Ramsey A; Goodlett, David R; Aitchison, John D | Molecular & cellular proteomics : MCP | 23349476 | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23349476 |
| 4-Hydroxy-2(E)-nonenal (HNE) catabolism and formation of HNE adducts are modulated by ýý oxidation of fatty acids in the isolated rat heart. | Li, Qingling; Sadhukhan, Sushabhan; Berthiaume, Jessica M; Ibarra, Rafael A; Tang, Hui; Deng, Shuang; Hamilton, Eric; Nagy, Laura E; Tochtrop, Gregory P; Zhang, Guo-Fang | Free radical biology & medicine | 23328733 | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23328733 |
| Neuronal metabolomics by ion mobility mass spectrometry: cocaine effects on glucose and selected biogenic amine metabolites in the frontal cortex, striatum, and thalamus of the rat. | Kaplan, Kimberly A; Chiu, Veronica M; Lukus, Peter A; Zhang, Xing; Siems, William F; Schenk, James O; Hill Jr, Herbert H | Analytical and bioanalytical chemistry | 23314481 | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23314481 |
| Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching. | Di Virgilio, Michela; Callen, Elsa; Yamane, Arito; Zhang, Wenzhu; Jankovic, Mila; Gitlin, Alexander D; Feldhahn, Niklas; Resch, Wolfgang; Oliveira, Thiago Y; Chait, Brian T; Nussenzweig, Andre; Casellas, Rafael; Robbiani, Davide F; Nussenzweig, Michel C | Science (New York, N.Y.) | 23306439 | 2013 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/23306439 |
| High-throughput flow cytometry compatible biosensor based on fluorogen activating protein technology. | Wu, Yang; Tapia, Phillip H; Fisher, Gregory W; Waggoner, Alan S; Jarvik, Jonathan; Sklar, Larry A | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 23303704 | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23303704 |
| Network motifs provide signatures that characterize metabolism. | Shellman, Erin R; Burant, Charles F; Schnell, Santiago | Molecular bioSystems | 23287894 | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23287894 |
| Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach. | Li, Xiang; Foley, Emily A; Kawashima, Shigehiro A; Molloy, Kelly R; Li, Yinyin; Chait, Brian T; Kapoor, Tarun M | Protein science : a publication of the Protein Society | 23281010 | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23281010 |
| Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus. | Lee, Ji Eun; Zamdborg, Leonid; Southey, Bruce R; Atkins Jr, Norman; Mitchell, Jennifer W; Li, Mingxi; Gillette, Martha U; Kelleher, Neil L; Sweedler, Jonathan V | Journal of proteome research | 23256577 | 2013 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/23256577 |
| Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. | Shank, Nathaniel I; Pham, Ha H; Waggoner, Alan S; Armitage, Bruce A | Journal of the American Chemical Society | 23252842 | 2013 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/23252842 |
| Directed evolution of a fluorogen-activating single chain antibody for function and enhanced brightness in the cytoplasm. | Yates, Bradley P; Peck, Michelle A; Berget, Peter B | Molecular biotechnology | 23242633 | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23242633 |
| Automated imaging system for fast quantitation of neurons, cell morphology and neurite morphometry in vivo and in vitro. | Tapias, Victor; Greenamyre, J Timothy; Watkins, Simon C | Neurobiology of disease | 23220621 | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23220621 |
| RNF4-dependent hybrid SUMO-ubiquitin chains are signals for RAP80 and thereby mediate the recruitment of BRCA1 to sites of DNA damage. | Guzzo, Catherine M; Berndsen, Christopher E; Zhu, Jianmei; Gupta, Vibhor; Datta, Ajit; Greenberg, Roger A; Wolberger, Cynthia; Matunis, Michael J | Science signaling | 23211528 | 2012 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/23211528 |
| Metabolomics and mass isotopomer analysis as a strategy for pathway discovery: pyrrolyl and cyclopentenyl derivatives of the pro-drug of abuse, levulinate. | Harris, Stephanie R; Zhang, Guo-Fang; Sadhukhan, Sushabhan; Wang, Hua; Shi, Chuan; Puchowicz, Michelle A; Anderson, Vernon E; Salomon, Robert G; Tochtrop, Gregory P; Brunengraber, Henri | Chemical research in toxicology | 23171137 | 2013 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/23171137 |
| Capillary electrophoresis with three-color fluorescence detection for the analysis of glycosphingolipid metabolism. | Keithley, Richard B; Rosenthal, Alison S; Essaka, David C; Tanaka, Hidenori; Yoshimura, Yayoi; Palcic, Monica M; Hindsgaul, Ole; Dovichi, Norman J | The Analyst | 23154386 | 2013 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/23154386 |
| High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome. | Yu, Danni; Danku, John M C; Baxter, Ivan; Kim, Sungjin; Vatamaniuk, Olena K; Vitek, Olga; Ouzzani, Mourad; Salt, David E | BMC genomics | 23151179 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23151179 |
| Proteomics for understanding miRNA biology. | Huang, Tai-Chung; Pinto, Sneha M; Pandey, Akhilesh | Proteomics | 23125164 | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23125164 |
| Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. | Velazquez-Muriel, Javier; Lasker, Keren; Russel, Daniel; Phillips, Jeremy; Webb, Benjamin M; Schneidman-Duhovny, Dina; Sali, Andrej | Proceedings of the National Academy of Sciences of the United States of America | 23112201 | 2012 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/23112201 |
| Phosphorylation of the chromatin binding domain of KSHV LANA. | Woodard, Crystal; Shamay, Meir; Liao, Gangling; Zhu, Jian; Ng, Ai Na; Li, Renfeng; Newman, Rob; Rho, Hee-Sool; Hu, Jianfei; Wan, Jun; Qian, Jiang; Zhu, Heng; Hayward, S Diane | PLoS pathogens | 23093938 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23093938 |
| A method for integrative structure determination of protein-protein complexes. | Schneidman-Duhovny, Dina; Rossi, Andrea; Avila-Sakar, Agustin; Kim, Seung Joong; Velazquez-Muriel, Javier; Strop, Pavel; Liang, Hong; Krukenberg, Kristin A; Liao, Maofu; Kim, Ho Min; Sobhanifar, Solmaz; Dotsch, Volker; Rajpal, Arvind; Pons, Jaume; Agard, | Bioinformatics (Oxford, England) | 23093611 | 2012 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/23093611 |
| Systems biology. How information theory handles cell signaling and uncertainty. | Brennan, Matthew D; Cheong, Raymond; Levchenko, Andre | Science (New York, N.Y.) | 23087235 | 2012 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/23087235 |
| Single-cell metabolomics: changes in the metabolome of freshly isolated and cultured neurons. | Nemes, Peter; Knolhoff, Ann M; Rubakhin, Stanislav S; Sweedler, Jonathan V | ACS chemical neuroscience | 23077722 | 2012 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/23077722 |
| High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization. | Xu, Min; Alber, Frank | BMC systems biology | 23046491 | 2012 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/23046491 |
| Quantitative LC-MS/MS analysis of arachidonoyl amino acids in mouse brain with treatment of FAAH inhibitor. | Han, Bingnan; Wright, Rachel; Kirchhoff, Aaron M; Chester, Julia A; Cooper, Bruce R; Davisson, Vincent Jo; Barker, Eric | Analytical biochemistry | 23044255 | 2013 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/23044255 |
| Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. | Zhu, Heng; Cox, Eric; Qian, Jiang | Proteomics. Clinical applications | 23027439 | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23027439 |
| Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. | Ren, Yunzhao R; Chaerkady, Raghothama; Hu, Shaohui; Wan, Jun; Qian, Jiang; Zhu, Heng; Pandey, Akhilesh; Kern, Scott E | Journal of proteome research | 23025254 | 2012 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/23025254 |
| Zooming in on genome organization. | Zhou, Xianghong Jasmine; Alber, Frank | Nature methods | 23018997 | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23018997 |
| Telomeres, tethers and trypanosomes. | Field, Mark C; Horn, David; Alsford, Sam; Koreny, Ludek; Rout, Michael P | Nucleus (Austin, Tex.) | 22992703 | 2012 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/22992703 |
| Applications of functional protein microarrays in basic and clinical research. | Zhu, Heng; Qian, Jiang | Advances in genetics | 22989767 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22989767 |
| Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). | Kim, Min-Sik; Kuppireddy, Sarada V; Sakamuri, Sruthi; Singal, Mukul; Getnet, Derese; Harsha, H C; Goel, Renu; Balakrishnan, Lavanya; Jacob, Harrys K C; Kashyap, Manoj K; Tankala, Shantal G; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Jaffee, Elizabet | Journal of proteome research | 22985314 | 2012 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/22985314 |
| A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. | Litvak, Vladimir; Ratushny, Alexander V; Lampano, Aaron E; Schmitz, Frank; Huang, Albert C; Raman, Ayush; Rust, Alistair G; Bergthaler, Andreas; Aitchison, John D; Aderem, Alan | Nature | 22982991 | 2012 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/22982991 |
| Ghrelin O-acyltransferase assays and inhibition. | Taylor, Martin S; Hwang, Yousang; Hsiao, Po-Yuan; Boeke, Jef D; Cole, Philip A | Methods in enzymology | 22975055 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22975055 |
| Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition. | Dancy, Beverley M; Crump, Nicholas T; Peterson, Daniel J; Mukherjee, Chandrani; Bowers, Erin M; Ahn, Young-Hoon; Yoshida, Minoru; Zhang, Jin; Mahadevan, Louis C; Meyers, David J; Boeke, Jef D; Cole, Philip A | Chembiochem : a European journal of chemical biology | 22961914 | 2012 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/22961914 |
| High resolution imaging of vascular function in zebrafish. | Watkins, Simon C; Maniar, Salony; Mosher, Mackenzie; Roman, Beth L; Tsang, Michael; St Croix, Claudette M | PloS one | 22952858 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22952858 |
| Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. | van Bodegom, Diederik; Zhong, Jun; Kopp, Nadja; Dutta, Chaitali; Kim, Min-Sik; Bird, Liat; Weigert, Oliver; Tyner, Jeffrey; Pandey, Akhilesh; Yoda, Akinori; Weinstock, David M | Blood | 22915648 | 2012 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/22915648 |
| Constructing the angiome: a global angiogenesis protein interaction network. | Chu, Liang-Hui; Rivera, Corban G; Popel, Aleksander S; Bader, Joel S | Physiological genomics | 22911453 | 2012 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/22911453 |
| Accurate quantification of lipid species by electrospray ionization mass spectrometry - Meet a key challenge in lipidomics. | Yang, Kui; Han, Xianlin | Metabolites | 22905337 | 2011 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/22905337 |
| The application of information theory to biochemical signaling systems. | Rhee, Alex; Cheong, Raymond; Levchenko, Andre | Physical biology | 22872091 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22872091 |
| Latrepirdine stimulates autophagy and reduces accumulation of *-synuclein in cells and in mouse brain. | Steele, J W; Ju, S; Lachenmayer, M L; Liken, J; Stock, A; Kim, S H; Delgado, L M; Alfaro, I E; Bernales, S; Verdile, G; Bharadwaj, P; Gupta, V; Barr, R; Friss, A; Dolios, G; Wang, R; Ringe, D; Protter, A A; Martins, R N; Ehrlich, M E; Yue, Z; Petsko, G A; | Molecular psychiatry | 22869031 | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22869031 |
| Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model. | Steele, J W; Lachenmayer, M L; Ju, S; Stock, A; Liken, J; Kim, S H; Delgado, L M; Alfaro, I E; Bernales, S; Verdile, G; Bharadwaj, P; Gupta, V; Barr, R; Friss, A; Dolios, G; Wang, R; Ringe, D; Fraser, P; Westaway, D; St George-Hyslop, P H; Szabo, P; Relki | Molecular psychiatry | 22850627 | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22850627 |
| Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. | Lu, Kuan-Yi; Tao, Sheng-Ce; Yang, Tzu-Ching; Ho, Yu-Hsuan; Lee, Chia-Hsien; Lin, Chen-Ching; Juan, Hsueh-Fen; Huang, Hsuan-Cheng; Yang, Chin-Yu; Chen, Ming-Shuo; Lin, Yu-Yi; Lu, Jin-Ying; Zhu, Heng; Chen, Chien-Sheng | Molecular & cellular proteomics : MCP | 22843995 | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22843995 |
| ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. | Byrum, Stephanie D; Raman, Ana; Taverna, Sean D; Tackett, Alan J | Cell reports | 22840409 | 2012 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/22840409 |
| Scp160-dependent mRNA trafficking mediates pheromone gradient sensing and chemotropism in yeast. | Gelin-Licht, Rita; Paliwal, Saurabh; Conlon, Patrick; Levchenko, Andre; Gerst, Jeffrey E | Cell reports | 22832273 | 2012 May 31 | https://www.ncbi.nlm.nih.gov/pubmed/22832273 |
| Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. | Chen, Yue; Zhao, Wenhui; Yang, Jeong Soo; Cheng, Zhongyi; Luo, Hao; Lu, Zhike; Tan, Minjia; Gu, Wei; Zhao, Yingming | Molecular & cellular proteomics : MCP | 22826441 | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22826441 |
| Speeding up Evolutionary Search by Small Fitness Fluctuations. | Otwinowski, Jakub; Tanase-Nicola, Sorin; Nemenman, Ilya | Journal of statistical physics | 22822270 | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22822270 |
| Integrative structural modeling with small angle X-ray scattering profiles. | Schneidman-Duhovny, Dina; Kim, Seung Joong; Sali, Andrej | BMC structural biology | 22800408 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22800408 |
| Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics. | Ye, Yu; Stahley, Mary R; Xu, Jianqing; Friedman, Joshua I; Sun, Yan; McKnight, Jeffrey N; Gray, Jeffrey J; Bowman, Gregory D; Stivers, James T | Biochemistry | 22784353 | 2012 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/22784353 |
| Genetically targetable and color-switching fluorescent probe. | Yushchenko, Dmytro A; Zhang, Ming; Yan, Qi; Waggoner, Alan S; Bruchez, Marcel P | Chembiochem : a European journal of chemical biology | 22777954 | 2012 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/22777954 |
| The biochemical anatomy of cortical inhibitory synapses. | Heller, Elizabeth A; Zhang, Wenzhu; Selimi, Fekrije; Earnheart, John C; ýýlimak, Marta A; Santos-Torres, Julio; Ibanez-Tallon, Ines; Aoki, Chiye; Chait, Brian T; Heintz, Nathaniel | PloS one | 22768092 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22768092 |
| Discovery of regulators of receptor internalization with high-throughput flow cytometry. | Wu, Yang; Tapia, Phillip H; Fisher, Gregory W; Simons, Peter C; Strouse, J Jacob; Foutz, Terry; Waggoner, Alan S; Jarvik, Jonathan; Sklar, Larry A | Molecular pharmacology | 22767611 | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22767611 |
| Thiogalactopyranosides are resistant to hydrolysis by ýý-galactosidases. | Adlercreutz, Dietlind; Yoshimura, Yayoi; Mannerstedt, Karin; Wakarchuk, Warren W; Bennett, Eric P; Dovichi, Norman J; Hindsgaul, Ole; Palcic, Monica M | Chembiochem : a European journal of chemical biology | 22740420 | 2012 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/22740420 |
| A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling. | Frazier, Zachary; Alber, Frank | Journal of computational biology : a journal of computational molecular cell biology | 22697237 | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22697237 |
| How networks change with time. | Park, Yongjin; Bader, Joel S | Bioinformatics (Oxford, England) | 22689777 | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22689777 |
| A targeted enzyme approach to sensitization of tyrosine kinase inhibitor-resistant breast cancer cells. | Giordano, Courtney R; Mueller, Kelly L; Terlecky, Laura J; Krentz, Kendra A; Bollig-Fischer, Aliccia; Terlecky, Stanley R; Boerner, Julie L | Experimental cell research | 22687878 | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/22687878 |
| Global tumor protein p53/p63 interactome: making a case for cisplatin chemoresistance. | Huang, Yiping; Jeong, Jun Seop; Okamura, Jun; Sook-Kim, Myoung; Zhu, Heng; Guerrero-Preston, Rafael; Ratovitski, Edward A | Cell cycle (Georgetown, Tex.) | 22672905 | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22672905 |
| Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels. | Domanski, Michal; Molloy, Kelly; Jiang, Hua; Chait, Brian T; Rout, Michael P; Jensen, Torben Heick; LaCava, John | BioTechniques | 22668517 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22668517 |
| Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays. | Hu, Chao-Jun; Song, Guang; Huang, Wei; Liu, Guo-Zhen; Deng, Chui-Wen; Zeng, Hai-Pan; Wang, Li; Zhang, Feng-Chun; Zhang, Xuan; Jeong, Jun Seop; Blackshaw, Seth; Jiang, Li-Zhi; Zhu, Heng; Wu, Lin; Li, Yong-Zhe | Molecular & cellular proteomics : MCP | 22647870 | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22647870 |
| The BECN1 coiled coil domain: an "imperfect" homodimer interface that facilitates ATG14 and UVRAG binding. | Li, Xiaohua; He, Liqiang; Zhang, Mingjie; Yue, Zhenyu; Zhao, Yanxiang | Autophagy | 22647755 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22647755 |
| Serotonin of mast cell origin contributes to hippocampal function. | Nautiyal, Katherine M; Dailey, Christopher A; Jahn, Jaquelyn L; Rodriquez, Elizabeth; Son, Nguyen Hong; Sweedler, Jonathan V; Silver, Rae | The European journal of neuroscience | 22632453 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22632453 |
| Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase. | Grady, Sarah L; Hwang, Jesse; Vastag, Livia; Rabinowitz, Joshua D; Shenk, Thomas | Journal of virology | 22623791 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22623791 |
| Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. | Tjong, Harianto; Gong, Ke; Chen, Lin; Alber, Frank | Genome research | 22619363 | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22619363 |
| Stoichiometry of Nck-dependent actin polymerization in living cells. | Ditlev, Jonathon A; Michalski, Paul J; Huber, Greg; Rivera, Gonzalo M; Mohler, William A; Loew, Leslie M; Mayer, Bruce J | The Journal of cell biology | 22613834 | 2012 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/22613834 |
| Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes. | Oeffinger, Marlene | Proteomics | 22592981 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22592981 |
| Identification of protein SUMOylation sites by mass spectrometry using combined microwave-assisted aspartic acid cleavage and tryptic digestion. | Osula, Omoruyi; Swatkoski, Stephen; Cotter, Robert J | Journal of mass spectrometry : JMS | 22576878 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22576878 |
| Identification of n-hydroxy acid metabolites in electron impact ionization mass spectrometry. | Li, Qingling; Zhang, Guo-Fang | Rapid communications in mass spectrometry : RCM | 22555929 | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22555929 |
| Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. | Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, Dev | Proteins | 22544723 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22544723 |
| A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis. | Cecala, Christine; Rubakhin, Stanislav S; Mitchell, Jennifer W; Gillette, Martha U; Sweedler, Jonathan V | The Analyst | 22543409 | 2012 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/22543409 |
| Asymmetric positive feedback loops reliably control biological responses. | Ratushny, Alexander V; Saleem, Ramsey A; Sitko, Katherine; Ramsey, Stephen A; Aitchison, John D | Molecular systems biology | 22531117 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22531117 |
| Ciliary and nuclear transport: different places, similar routes? | Obado, Samson O; Rout, Michael P | Developmental cell | 22516195 | 2012 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/22516195 |
| Shotgun lipidomics analysis of 4-hydroxyalkenal species directly from lipid extracts after one-step in situ derivatization. | Wang, Miao; Fang, Huafeng; Han, Xianlin | Analytical chemistry | 22500579 | 2012 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/22500579 |
| Principles of model building: an experimentation-aided approach to development of models for signaling networks. | Ganesan, Ambhighainath; Levchenko, Andre | Methods in cell biology | 22482943 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22482943 |
| NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions. | DuBois, Kelly N; Alsford, Sam; Holden, Jennifer M; Buisson, Johanna; Swiderski, Michal; Bart, Jean-Mathieu; Ratushny, Alexander V; Wan, Yakun; Bastin, Philippe; Barry, J David; Navarro, Miguel; Horn, David; Aitchison, John D; Rout, Michael P; Field, Mark | PLoS biology | 22479148 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22479148 |
| Gain control in molecular information processing: lessons from neuroscience. | Nemenman, Ilya | Physical biology | 22475952 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22475952 |
| Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. | Bheda, Poonam; Swatkoski, Stephen; Fiedler, Katherine L; Boeke, Jef D; Cotter, Robert J; Wolberger, Cynthia | Proceedings of the National Academy of Sciences of the United States of America | 22474337 | 2012 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/22474337 |
| Genetically encoded pH sensor for tracking surface proteins through endocytosis. | Grover, Anmol; Schmidt, Brigitte F; Salter, Russell D; Watkins, Simon C; Waggoner, Alan S; Bruchez, Marcel P | Angewandte Chemie (International ed. in English) | 22461279 | 2012 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/22461279 |
| The brain-specific Beta4 subunit downregulates BK channel cell surface expression. | Shruti, Sonal; Urban-Ciecko, Joanna; Fitzpatrick, James A; Brenner, Robert; Bruchez, Marcel P; Barth, Alison L | PloS one | 22438928 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22438928 |
| Metabolism of ýý-hydroxybutyrate in perfused rat livers. | Zhang, Guo-Fang; Sadhukhan, Sushabhan; Ibarra, Rafael A; Lauden, Stephanie M; Chuang, Chia-Ying; Sushailo, Sophia; Chatterjee, Priya; Anderson, Vernon E; Tochtrop, Gregory P; Brunengraber, Henri | The Biochemical journal | 22428548 | 2012 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/22428548 |
| High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. | Xu, Min; Beck, Martin; Alber, Frank | Journal of structural biology | 22420977 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22420977 |
| The yeast nuclear pore complex and transport through it. | Aitchison, John D; Rout, Michael P | Genetics | 22419078 | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22419078 |
| Single cell ganglioside catabolism in primary cerebellar neurons and glia. | Essaka, David C; Prendergast, Jillian; Keithley, Richard B; Hindsgaul, Ole; Palcic, Monica M; Schnaar, Ronald L; Dovichi, Norman J | Neurochemical research | 22407243 | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22407243 |
| Quantitative imaging with fluorescent biosensors. | Okumoto, Sakiko; Jones, Alexander; Frommer, Wolf B | Annual review of plant biology | 22404462 | 2012 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/22404462 |
| Metabolic cytometry: capillary electrophoresis with two-color fluorescence detection for the simultaneous study of two glycosphingolipid metabolic pathways in single primary neurons. | Essaka, David C; Prendergast, Jillian; Keithley, Richard B; Palcic, Monica M; Hindsgaul, Ole; Schnaar, Ronald L; Dovichi, Norman J | Analytical chemistry | 22400492 | 2012 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/22400492 |
| Competitive activity-based protein profiling identifies aza-ýý-lactams as a versatile chemotype for serine hydrolase inhibition. | Zuhl, Andrea M; Mohr, Justin T; Bachovchin, Daniel A; Niessen, Sherry; Hsu, Ku-Lung; Berlin, Jacob M; Dochnahl, Maximilian; Lopez-Alberca, Maria P; Fu, Gregory C; Cravatt, Benjamin F | Journal of the American Chemical Society | 22400490 | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22400490 |
| SUMO binding by the Epstein-Barr virus protein kinase BGLF4 is crucial for BGLF4 function. | Li, Renfeng; Wang, Leyao; Liao, Gangling; Guzzo, Catherine M; Matunis, Michael J; Zhu, Heng; Hayward, S Diane | Journal of virology | 22398289 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22398289 |
| Pharmacological rescue of the mutant cystic fibrosis transmembrane conductance regulator (CFTR) detected by use of a novel fluorescence platform. | Holleran, John P; Glover, Matthew L; Peters, Kathryn W; Bertrand, Carol A; Watkins, Simon C; Jarvik, Jonathan W; Frizzell, Raymond A | Molecular medicine (Cambridge, Mass.) | 22396015 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22396015 |
| A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. | Senutovitch, Nina; Stanfield, Robyn L; Bhattacharyya, Shantanu; Rule, Gordon S; Wilson, Ian A; Armitage, Bruce A; Waggoner, Alan S; Berget, Peter B | Biochemistry | 22390683 | 2012 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/22390683 |
| Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms. | Hersman, Elisabeth; Nelson, Dwella M; Griffith, Wendell P; Jelinek, Christine; Cotter, Robert J | International journal of mass spectrometry | 22389584 | 2012 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/22389584 |
| To the pore and through the pore: a story of mRNA export kinetics. | Oeffinger, Marlene; Zenklusen, Daniel | Biochimica et biophysica acta | 22387213 | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22387213 |
| A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. | Shamay, Meir; Liu, Jianyong; Li, Renfeng; Liao, Gangling; Shen, Li; Greenway, Melanie; Hu, Shaohui; Zhu, Jian; Xie, Zhi; Ambinder, Richard F; Qian, Jiang; Zhu, Heng; Hayward, S Diane | Journal of virology | 22379092 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22379092 |
| Fluorogen activating proteins in flow cytometry for the study of surface molecules and receptors. | Saunders, Matthew J; Szent-Gyorgyi, Christopher; Fisher, Gregory W; Jarvik, Jonathan W; Bruchez, Marcel P; Waggoner, Alan S | Methods (San Diego, Calif.) | 22366230 | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22366230 |
| Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions. | Tetenbaum-Novatt, Jaclyn; Hough, Loren E; Mironska, Roxana; McKenney, Anna Sophia; Rout, Michael P | Molecular & cellular proteomics : MCP | 22357553 | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22357553 |
| Azalysine analogues as probes for protein lysine deacetylation and demethylation. | Dancy, Blair C R; Ming, Shonoi A; Papazyan, Romeo; Jelinek, Christine A; Majumdar, Ananya; Sun, Yan; Dancy, Beverley M; Drury 3rd, William J; Cotter, Robert J; Taverna, Sean D; Cole, Philip A | Journal of the American Chemical Society | 22352831 | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22352831 |
| TSLP signaling network revealed by SILAC-based phosphoproteomics. | Zhong, Jun; Kim, Min-Sik; Chaerkady, Raghothama; Wu, Xinyan; Huang, Tai-Chung; Getnet, Derese; Mitchell, Christopher J; Palapetta, Shyam M; Sharma, Jyoti; O'Meally, Robert N; Cole, Robert N; Yoda, Akinori; Moritz, Albrecht; Loriaux, Marc M; Rush, John; We | Molecular & cellular proteomics : MCP | 22345495 | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22345495 |
| 3D/4D functional imaging of tumor-associated proteolysis: impact of microenvironment. | Moin, Kamiar; Sameni, Mansoureh; Victor, Bernadette C; Rothberg, Jennifer M; Mattingly, Raymond R; Sloane, Bonnie F | Methods in enzymology | 22341225 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22341225 |
| Structure-function mapping of a heptameric module in the nuclear pore complex. | Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D; Williams, Rosemary; Stokes, David L; Chait, Brian T; Sali, Andrej; Rout, Michael P | The Journal of cell biology | 22331846 | 2012 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/22331846 |
| Preparation and electrophoretic separation of Bodipy-Fl-labeled glycosphingolipids. | Sarver, Scott A; Keithley, Richard B; Essaka, David C; Tanaka, Hidenori; Yoshimura, Yayoi; Palcic, Monica M; Hindsgaul, Ole; Dovichi, Norman J | Journal of chromatography. A | 22321948 | 2012 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/22321948 |
| A jumbo problem: mapping the structure and functions of the nuclear pore complex. | Fernandez-Martinez, Javier; Rout, Michael P | Current opinion in cell biology | 22321828 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22321828 |
| Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. | Lin, Yu-yi; Kiihl, Samara; Suhail, Yasir; Liu, Shang-Yun; Chou, Yi-hsuan; Kuang, Zheng; Lu, Jin-ying; Khor, Chin Ni; Lin, Chi-Long; Bader, Joel S; Irizarry, Rafael; Boeke, Jef D | Nature | 22318606 | 2012 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/22318606 |
| Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection. | Terry, Laura J; Vastag, Livia; Rabinowitz, Joshua D; Shenk, Thomas | Proceedings of the National Academy of Sciences of the United States of America | 22315427 | 2012 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/22315427 |
| Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG. | Li, Xiaohua; He, Liqiang; Che, Ka Hing; Funderburk, Sarah F; Pan, Lifeng; Pan, Nina; Zhang, Mingjie; Yue, Zhenyu; Zhao, Yanxiang | Nature communications | 22314358 | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22314358 |
| Regulation of lipid metabolism by Dicer revealed through SILAC mice. | Huang, Tai-Chung; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Getnet, Derese; Yang, Yi; Peterson, Jonathan M; Ghosh, Bidyut; Chaerkady, Raghothama; Leach, Steven D; Marchionni, Luigi; Wong, G William; Pandey, Akhilesh | Journal of proteome research | 22313051 | 2012 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/22313051 |
| Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes. | Field, Mark C; Adung'a, Vincent; Obado, Samson; Chait, Brian T; Rout, Michael P | Parasitology | 22309600 | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22309600 |
| Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. | Lasker, Keren; Forster, Friedrich; Bohn, Stefan; Walzthoeni, Thomas; Villa, Elizabeth; Unverdorben, Pia; Beck, Florian; Aebersold, Ruedi; Sali, Andrej; Baumeister, Wolfgang | Proceedings of the National Academy of Sciences of the United States of America | 22307589 | 2012 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/22307589 |
| Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. | Jeong, Jun Seop; Jiang, Lizhi; Albino, Edisa; Marrero, Josean; Rho, Hee Sool; Hu, Jianfei; Hu, Shaohui; Vera, Carlos; Bayron-Poueymiroy, Diane; Rivera-Pacheco, Zully Ann; Ramos, Leonardo; Torres-Castro, Cecil; Qian, Jiang; Bonaventura, Joseph; Boeke, Jef | Molecular & cellular proteomics : MCP | 22307071 | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22307071 |
| Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. | Sims, Joshua J; Scavone, Francesco; Cooper, Eric M; Kane, Lesley A; Youle, Richard J; Boeke, Jef D; Cohen, Robert E | Nature methods | 22306808 | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22306808 |
| Sampling techniques for single-cell electrophoresis. | Cecala, Christine; Sweedler, Jonathan V | The Analyst | 22288071 | 2012 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/22288071 |
| How chemoproteomics can enable drug discovery and development. | Moellering, Raymond E; Cravatt, Benjamin F | Chemistry & biology | 22284350 | 2012 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/22284350 |
| Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. | Russel, Daniel; Lasker, Keren; Webb, Ben; Velazquez-Muriel, Javier; Tjioe, Elina; Schneidman-Duhovny, Dina; Peterson, Bret; Sali, Andrej | PLoS biology | 22272186 | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22272186 |
| Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. | Tarrant, Mary Katherine; Rho, Hee-Sool; Xie, Zhi; Jiang, Yu Lin; Gross, Christopher; Culhane, Jeffrey C; Yan, Gai; Qian, Jiang; Ichikawa, Yoshitaka; Matsuoka, Tatsuji; Zachara, Natasha; Etzkorn, Felicia A; Hart, Gerald W; Jeong, Jun Seop; Blackshaw, Seth; | Nature chemical biology | 22267120 | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22267120 |
| Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration. | Houk, Andrew R; Jilkine, Alexandra; Mejean, Cecile O; Boltyanskiy, Rostislav; Dufresne, Eric R; Angenent, Sigurd B; Altschuler, Steven J; Wu, Lani F; Weiner, Orion D | Cell | 22265410 | 2012 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/22265410 |
| Electron transfer dissociation mass spectrometry in proteomics. | Kim, Min-Sik; Pandey, Akhilesh | Proteomics | 22246976 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22246976 |
| Dietary regulation of catabolic disposal of 4-hydroxynonenal analogs in rat liver. | Li, Qingling; Tomcik, Kristyen; Zhang, Shenghui; Puchowicz, Michelle A; Zhang, Guo-Fang | Free radical biology & medicine | 22245097 | 2012 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/22245097 |
| Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization. | Donlin, Laura T; Andresen, Christian; Just, Steffen; Rudensky, Eugene; Pappas, Christopher T; Kruger, Martina; Jacobs, Erica Y; Unger, Andreas; Zieseniss, Anke; Dobenecker, Marc-Werner; Voelkel, Tobias; Chait, Brian T; Gregorio, Carol C; Rottbauer, Wolfga | Genes & development | 22241783 | 2012 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/22241783 |
| Single-molecule imaging of translational output from individual RNA granules in neurons. | Tatavarty, Vedakumar; Ifrim, Marius F; Levin, Mikhail; Korza, George; Barbarese, Elisa; Yu, Ji; Carson, John H | Molecular biology of the cell | 22219377 | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22219377 |
| The pharmacological landscape and therapeutic potential of serine hydrolases. | Bachovchin, Daniel A; Cravatt, Benjamin F | Nature reviews. Drug discovery | 22212679 | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22212679 |
| Comparative proteomic analysis of a cytosolic fraction from ýý3 integrin-deficient cells. | Bush, Jason A; Kitaura, Hideki; Ma, Yuliang; Teitelbaum, Steven L; Ross, F Patrick; Smith, Jeffrey W | Cancer genomics & proteomics | 22210044 | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22210044 |
| Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. | Kalhor, Reza; Tjong, Harianto; Jayathilaka, Nimanthi; Alber, Frank; Chen, Lin | Nature biotechnology | 22198700 | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22198700 |
| Vif hijacks CBF-ýý to degrade APOBEC3G and promote HIV-1 infection. | Jager, Stefanie; Kim, Dong Young; Hultquist, Judd F; Shindo, Keisuke; LaRue, Rebecca S; Kwon, Eunju; Li, Ming; Anderson, Brett D; Yen, Linda; Stanley, David; Mahon, Cathal; Kane, Joshua; Franks-Skiba, Kathy; Cimermancic, Peter; Burlingame, Alma; Sali, And | Nature | 22190037 | 2012 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/22190037 |
| Global landscape of HIV-human protein complexes. | Jager, Stefanie; Cimermancic, Peter; Gulbahce, Natali; Johnson, Jeffrey R; McGovern, Kathryn E; Clarke, Starlynn C; Shales, Michael; Mercenne, Gaelle; Pache, Lars; Li, Kathy; Hernandez, Hilda; Jang, Gwendolyn M; Roth, Shoshannah L; Akiva, Eyal; Marlett, J | Nature | 22190034 | 2012 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/22190034 |
| Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography-electrospray ionization-tandem mass spectrometry for samples of intermediate complexity. | Li, Yihan; Champion, Matthew M; Sun, Liangliang; Champion, Patricia A DiGiuseppe; Wojcik, Roza; Dovichi, Norman J | Analytical chemistry | 22182061 | 2012 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/22182061 |
| Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. | Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novere, Nicolas | BMC systems biology | 22172142 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22172142 |
| Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations. | Ewald, Jennifer C; Reich, Sabrina; Baumann, Stephan; Frommer, Wolf B; Zamboni, Nicola | PloS one | 22164251 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22164251 |
| Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. | Lu, Zhike; Cheng, Zhongyi; Zhao, Yingming; Volchenboum, Samuel L | PloS one | 22164248 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22164248 |
| Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. | Goel, Renu; Harsha, H C; Pandey, Akhilesh; Prasad, T S Keshava | Molecular bioSystems | 22159132 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22159132 |
| Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. | Chen, Li-Qing; Qu, Xiao-Qing; Hou, Bi-Huei; Sosso, Davide; Osorio, Sonia; Fernie, Alisdair R; Frommer, Wolf B | Science (New York, N.Y.) | 22157085 | 2012 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/22157085 |
| Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. | Karnovsky, Alla; Weymouth, Terry; Hull, Tim; Tarcea, V Glenn; Scardoni, Giovanni; Laudanna, Carlo; Sartor, Maureen A; Stringer, Kathleen A; Jagadish, H V; Burant, Charles; Athey, Brian; Omenn, Gilbert S | Bioinformatics (Oxford, England) | 22135418 | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22135418 |
| Non-invasive imaging of cysteine cathepsin activity in solid tumors using a 64Cu-labeled activity-based probe. | Ren, Gang; Blum, Galia; Verdoes, Martijn; Liu, Hongguang; Syed, Salahuddin; Edgington, Laura E; Gheysens, Olivier; Miao, Zheng; Jiang, Han; Gambhir, Sanjiv Sam; Bogyo, Matthew; Cheng, Zhen | PloS one | 22132198 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22132198 |
| HSF1-dependent upregulation of Hsp70 by sulfhydryl-reactive inducers of the KEAP1/NRF2/ARE pathway. | Zhang, Ying; Ahn, Young-Hoon; Benjamin, Ivor J; Honda, Tadashi; Hicks, Ronald J; Calabrese, Vittorio; Cole, Philip A; Dinkova-Kostova, Albena T | Chemistry & biology | 22118669 | 2011 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/22118669 |
| Chronic caloric restriction attenuates a loss of sulfatide content in PGC-1ýý-/- mouse cortex: a potential lipidomic role of PGC-1ýý in neurodegeneration. | Kiebish, Michael A; Young, Dee M; Lehman, John J; Han, Xianlin | Journal of lipid research | 22114039 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22114039 |
| Quantum dots find their stride in single molecule tracking. | Bruchez, Marcel P | Current opinion in chemical biology | 22055494 | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22055494 |
| Optical sensors for monitoring dynamic changes of intracellular metabolite levels in mammalian cells. | Hou, Bi-Huei; Takanaga, Hitomi; Grossmann, Guido; Chen, Li-Qing; Qu, Xiao-Qing; Jones, Alexander M; Lalonde, Sylvie; Schweissgut, Oliver; Wiechert, Wolfgang; Frommer, Wolf B | Nature protocols | 22036884 | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22036884 |
| Optical sensors for measuring dynamic changes of cytosolic metabolite levels in yeast. | Bermejo, Clara; Haerizadeh, Farzad; Takanaga, Hitomi; Chermak, Diane; Frommer, Wolf B | Nature protocols | 22036883 | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22036883 |
| Increasing the potency and breadth of an HIV antibody by using structure-based rational design. | Diskin, Ron; Scheid, Johannes F; Marcovecchio, Paola M; West Jr, Anthony P; Klein, Florian; Gao, Han; Gnanapragasam, Priyanthi N P; Abadir, Alexander; Seaman, Michael S; Nussenzweig, Michel C; Bjorkman, Pamela J | Science (New York, N.Y.) | 22033520 | 2011 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/22033520 |
| Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. | Li, Renfeng; Zhu, Jian; Xie, Zhi; Liao, Gangling; Liu, Jianyong; Chen, Mei-Ru; Hu, Shaohui; Woodard, Crystal; Lin, Jimmy; Taverna, Sean D; Desai, Prashant; Ambinder, Richard F; Hayward, Gary S; Qian, Jiang; Zhu, Heng; Hayward, S Diane | Cell host & microbe | 22018239 | 2011 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/22018239 |
| UCSF Chimera, MODELLER, and IMP: an integrated modeling system. | Yang, Zheng; Lasker, Keren; Schneidman-Duhovny, Dina; Webb, Ben; Huang, Conrad C; Pettersen, Eric F; Goddard, Thomas D; Meng, Elaine C; Sali, Andrej; Ferrin, Thomas E | Journal of structural biology | 21963794 | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21963794 |
| A practical approach for determination of mass spectral baselines. | Yang, Kui; Fang, Xiaoling; Gross, Richard W; Han, Xianlin | Journal of the American Society for Mass Spectrometry | 21952772 | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21952772 |
| The gain in brain: novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure. | Micheva, Kristina D; Bruchez, Marcel P | Current opinion in neurobiology | 21944260 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21944260 |
| Lectin microarrays: a powerful tool for glycan-based biomarker discovery. | Zhou, Shu-Min; Cheng, Li; Guo, Shu-Juan; Zhu, Heng; Tao, Sheng-Ce | Combinatorial chemistry & high throughput screening | 21933110 | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21933110 |
| Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids. | Long, Jonathan Z; Cisar, Justin S; Milliken, David; Niessen, Sherry; Wang, Chu; Trauger, Sunia A; Siuzdak, Gary; Cravatt, Benjamin F | Nature chemical biology | 21926997 | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21926997 |
| Information transduction capacity of noisy biochemical signaling networks. | Cheong, Raymond; Rhee, Alex; Wang, Chiaochun Joanne; Nemenman, Ilya; Levchenko, Andre | Science (New York, N.Y.) | 21921160 | 2011 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/21921160 |
| Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. | Lu, Jin-Ying; Lin, Yu-Yi; Sheu, Jin-Chuan; Wu, June-Tai; Lee, Fang-Jen; Chen, Yue; Lin, Min-I; Chiang, Fu-Tien; Tai, Tong-Yuan; Berger, Shelley L; Zhao, Yingming; Tsai, Keh-Sung; Zhu, Heng; Chuang, Lee-Ming; Boeke, Jef D | Cell | 21906795 | 2011 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/21906795 |
| Cdk1 uncouples CtIP-dependent resection and Rad51 filament formation during M-phase double-strand break repair. | Peterson, Shaun E; Li, Yinyin; Chait, Brian T; Gottesman, Max E; Baer, Richard; Gautier, Jean | The Journal of cell biology | 21893598 | 2011 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/21893598 |
| Mathematical modeling of biomolecular network dynamics. | Ratushny, Alexander V; Ramsey, Stephen A; Aitchison, John D | Methods in molecular biology (Clifton, N.J.) | 21877294 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21877294 |
| Modeling of proteins and their assemblies with the integrative modeling platform. | Webb, Benjamin; Lasker, Keren; Schneidman-Duhovny, Dina; Tjioe, Elina; Phillips, Jeremy; Kim, Seung Joong; Velazquez-Muriel, Javier; Russel, Daniel; Sali, Andrej | Methods in molecular biology (Clifton, N.J.) | 21877292 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21877292 |
| Statistical analysis of dynamic transcriptional regulatory network structure. | Smith, Jennifer J; Saleem, Ramsey A; Aitchison, John D | Methods in molecular biology (Clifton, N.J.) | 21877289 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21877289 |
| Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity. | Rivera, Corban G; Rosca, Elena V; Pandey, Niranjan B; Koskimaki, Jacob E; Bader, Joel S; Popel, Aleksander S | Journal of medicinal chemistry | 21866962 | 2011 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/21866962 |
| Protein-coat dynamics and cluster phases in intracellular trafficking. | Huber, Greg; Wang, Hui; Mukhopadhyay, Ranjan | Journal of physics. Condensed matter : an Institute of Physics journal | 21862842 | 2011 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/21862842 |
| Live-cell imaging of tumor proteolysis: impact of cellular and non-cellular microenvironment. | Rothberg, Jennifer M; Sameni, Mansoureh; Moin, Kamiar; Sloane, Bonnie F | Biochimica et biophysica acta | 21854877 | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21854877 |
| Dynamic Na+-H+ exchanger regulatory factor-1 association and dissociation regulate parathyroid hormone receptor trafficking at membrane microdomains. | Ardura, Juan A; Wang, Bin; Watkins, Simon C; Vilardaga, Jean-Pierre; Friedman, Peter A | The Journal of biological chemistry | 21832055 | 2011 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/21832055 |
| Metabolic differentiation of neuronal phenotypes by single-cell capillary electrophoresis-electrospray ionization-mass spectrometry. | Nemes, Peter; Knolhoff, Ann M; Rubakhin, Stanislav S; Sweedler, Jonathan V | Analytical chemistry | 21809850 | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21809850 |
| Redundant mechanisms for stable cell locomotion revealed by minimal models. | Wolgemuth, Charles W; Stajic, Jelena; Mogilner, Alex | Biophysical journal | 21806922 | 2011 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/21806922 |
| A novel coatomer-related SEA complex dynamically associates with the vacuole in yeast and is implicated in the response to nitrogen starvation. | Dokudovskaya, Svetlana; Rout, Michael P | Autophagy | 21804352 | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21804352 |
| Monoacylglycerol lipase exerts dual control over endocannabinoid and fatty acid pathways to support prostate cancer. | Nomura, Daniel K; Lombardi, Donald P; Chang, Jae Won; Niessen, Sherry; Ward, Anna M; Long, Jonathan Z; Hoover, Heather H; Cravatt, Benjamin F | Chemistry & biology | 21802006 | 2011 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/21802006 |
| In vivo biochemistry: quantifying ion and metabolite levels in individual cells or cultures of yeast. | Bermejo, Clara; Ewald, Jennifer C; Lanquar, Viviane; Jones, Alexander M; Frommer, Wolf B | The Biochemical journal | 21793803 | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21793803 |
| Metabolomics in early Alzheimer's disease: identification of altered plasma sphingolipidome using shotgun lipidomics. | Han, Xianlin; Rozen, Steve; Boyle, Stephen H; Hellegers, Caroline; Cheng, Hua; Burke, James R; Welsh-Bohmer, Kathleen A; Doraiswamy, P Murali; Kaddurah-Daouk, Rima | PloS one | 21779331 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21779331 |
| Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism. | Vastag, Livia; Koyuncu, Emre; Grady, Sarah L; Shenk, Thomas E; Rabinowitz, Joshua D | PLoS pathogens | 21779165 | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21779165 |
| Nuclear export dynamics of RNA-protein complexes. | Grunwald, David; Singer, Robert H; Rout, Michael | Nature | 21776079 | 2011 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/21776079 |
| Src family kinases mediate epidermal growth factor receptor signaling from lipid rafts in breast cancer cells. | Irwin, Mary E; Bohin, Natacha; Boerner, Julie L | Cancer biology & therapy | 21775822 | 2011 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/21775822 |
| Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. | Chaerkady, Raghothama; Letzen, Brian; Renuse, Santosh; Sahasrabuddhe, Nandini A; Kumar, Praveen; All, Angelo H; Thakor, Nitish V; Delanghe, Bernard; Gearhart, John D; Pandey, Akhilesh; Kerr, Candace L | Proteomics | 21770034 | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21770034 |
| Vacuolar protein sorting protein 13A, TtVPS13A, localizes to the tetrahymena thermophila phagosome membrane and is required for efficient phagocytosis. | Samaranayake, Haresha S; Cowan, Ann E; Klobutcher, Lawrence A | Eukaryotic cell | 21764909 | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21764909 |
| Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. | Scheid, Johannes F; Mouquet, Hugo; Ueberheide, Beatrix; Diskin, Ron; Klein, Florian; Oliveira, Thiago Y K; Pietzsch, John; Fenyo, David; Abadir, Alexander; Velinzon, Klara; Hurley, Arlene; Myung, Sunnie; Boulad, Farid; Poignard, Pascal; Burton, Dennis R; | Science (New York, N.Y.) | 21764753 | 2011 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/21764753 |
| Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. | Han, Xianlin; Yang, Kui; Gross, Richard W | Mass spectrometry reviews | 21755525 | 2012 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/21755525 |
| Bone marrow transplantation augments the effect of brain- and spinal cord-directed adeno-associated virus 2/5 gene therapy by altering inflammation in the murine model of globoid-cell leukodystrophy. | Reddy, Adarsh S; Kim, Joong H; Hawkins-Salsbury, Jacqueline A; Macauley, Shannon L; Tracy, Elisabeth T; Vogler, Carole A; Han, Xialin; Song, Sheng-Kwei; Wozniak, David F; Fowler, Stephen C; Klein, Robyn S; Sands, Mark S | The Journal of neuroscience : the official journal of the Society for Neuroscience | 21734286 | 2011 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/21734286 |
| MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. | Tjioe, Elina; Lasker, Keren; Webb, Ben; Wolfson, Haim J; Sali, Andrej | Nucleic acids research | 21715383 | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21715383 |
| A cell cycle phosphoproteome of the yeast centrosome. | Keck, Jamie M; Jones, Michele H; Wong, Catherine C L; Binkley, Jonathan; Chen, Daici; Jaspersen, Sue L; Holinger, Eric P; Xu, Tao; Niepel, Mario; Rout, Michael P; Vogel, Jackie; Sidow, Arend; Yates 3rd, John R; Winey, Mark | Science (New York, N.Y.) | 21700874 | 2011 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/21700874 |
| Development of Neh2-luciferase reporter and its application for high throughput screening and real-time monitoring of Nrf2 activators. | Smirnova, Natalya A; Haskew-Layton, Renee E; Basso, Manuela; Hushpulian, Dmitry M; Payappilly, Jimmy B; Speer, Rachel E; Ahn, Young-Hoon; Rakhman, Ilay; Cole, Philip A; Pinto, John T; Ratan, Rajiv R; Gazaryan, Irina G | Chemistry & biology | 21700211 | 2011 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/21700211 |
| The metabolic serine hydrolases and their functions in mammalian physiology and disease. | Long, Jonathan Z; Cravatt, Benjamin F | Chemical reviews | 21696217 | 2011 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/21696217 |
| A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. | Lone, Anna Mari; Bachovchin, Daniel A; Westwood, David B; Speers, Anna E; Spicer, Timothy P; Fernandez-Vega, Virneliz; Chase, Peter; Hodder, Peter S; Rosen, Hugh; Cravatt, Benjamin F; Saghatelian, Alan | Journal of the American Chemical Society | 21692504 | 2011 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/21692504 |
| An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. | Hyland, Edel M; Molina, Henrik; Poorey, Kunal; Jie, Chunfa; Xie, Zhi; Dai, Junbiao; Qian, Jiang; Bekiranov, Stefan; Auble, David T; Pandey, Akhilesh; Boeke, Jef D | Genes & development | 21685365 | 2011 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/21685365 |
| Template-free detection of macromolecular complexes in cryo electron tomograms. | Xu, Min; Beck, Martin; Alber, Frank | Bioinformatics (Oxford, England) | 21685103 | 2011 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/21685103 |
| Noise reduction in genome-wide perturbation screens using linear mixed-effect models. | Yu, Danni; Danku, John; Baxter, Ivan; Kim, Sungjin; Vatamaniuk, Olena K; Salt, David E; Vitek, Olga | Bioinformatics (Oxford, England) | 21685046 | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21685046 |
| Structural determinants of limited proteolysis. | Kazanov, Marat D; Igarashi, Yoshinobu; Eroshkin, Alexey M; Cieplak, Piotr; Ratnikov, Boris; Zhang, Ying; Li, Zhanwen; Godzik, Adam; Osterman, Andrei L; Smith, Jeffrey W | Journal of proteome research | 21682278 | 2011 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/21682278 |
| Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. | Field, Mark C; Sali, Andrej; Rout, Michael P | The Journal of cell biology | 21670211 | 2011 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/21670211 |
| Riboneogenesis in yeast. | Clasquin, Michelle F; Melamud, Eugene; Singer, Alexander; Gooding, Jessica R; Xu, Xiaohui; Dong, Aiping; Cui, Hong; Campagna, Shawn R; Savchenko, Alexei; Yakunin, Alexander F; Rabinowitz, Joshua D; Caudy, Amy A | Cell | 21663798 | 2011 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/21663798 |
| Discovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1. | Bachovchin, Daniel A; Zuhl, Andrea M; Speers, Anna E; Wolfe, Monique R; Weerapana, Eranthie; Brown, Steven J; Rosen, Hugh; Cravatt, Benjamin F | Journal of medicinal chemistry | 21639134 | 2011 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/21639134 |
| The modified-bead stretched sample method: development and application to MALDI-MS imaging of protein localization in the spinal cord. | Tucker, Kevin R; Serebryannyy, Leonid A; Zimmerman, Tyler A; Rubakhin, Stanislav S; Sweedler, Jonathan V | Chemical science (Royal Society of Chemistry : 2010) | 21625333 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21625333 |
| A Graphical Model to Determine the Subcellular Protein Location in Artificial Tissues. | Glory-Afshar, Estelle; Osuna-Highley, Elvira; Granger, Brian; Murphy, Robert F | Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging | 21625289 | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21625289 |
| N-terminomics: a high-content screen for protease substrates and their cleavage sites. | Timmer, John C; Salvesen, Guy S | Methods in molecular biology (Clifton, N.J.) | 21604127 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21604127 |
| Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. | Kim, Min-Sik; Zhong, Jun; Kandasamy, Kumaran; Delanghe, Bernard; Pandey, Akhilesh | Proteomics | 21598390 | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21598390 |
| Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. | Agyeman, Abena S; Chaerkady, Raghothama; Shaw, Patrick G; Davidson, Nancy E; Visvanathan, Kala; Pandey, Akhilesh; Kensler, Thomas W | Breast cancer research and treatment | 21597922 | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21597922 |
| Metabolomics, pathway regulation, and pathway discovery. | Zhang, Guo-Fang; Sadhukhan, Sushabhan; Tochtrop, Gregory P; Brunengraber, Henri | The Journal of biological chemistry | 21566142 | 2011 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/21566142 |
| Model building and intelligent acquisition with application to protein subcellular location classification. | Jackson, C; Glory-Afshar, E; Murphy, R F; Kovacevic, J | Bioinformatics (Oxford, England) | 21558154 | 2011 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/21558154 |
| Diffusion amid random overlapping obstacles: similarities, invariants, approximations. | Novak, Igor L; Gao, Fei; Kraikivski, Pavel; Slepchenko, Boris M | The Journal of chemical physics | 21513372 | 2011 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/21513372 |
| Identification and quantitation of unsaturated fatty acid isomers by electrospray ionization tandem mass spectrometry: a shotgun lipidomics approach. | Yang, Kui; Zhao, Zhongdan; Gross, Richard W; Han, Xianlin | Analytical chemistry | 21500847 | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21500847 |
| Small molecule analysis and imaging of fatty acids in the zebra finch song system using time-of-flight-secondary ion mass spectrometry. | Amaya, Kensey R; Sweedler, Jonathan V; Clayton, David F | Journal of neurochemistry | 21496023 | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21496023 |
| Central nervous system dysfunction in a mouse model of FA2H deficiency. | Potter, Kathleen A; Kern, Michael J; Fullbright, George; Bielawski, Jacek; Scherer, Steven S; Yum, Sabrina W; Li, Jian J; Cheng, Hua; Han, Xianlin; Venkata, Jagadish Kummetha; Khan, P Akbar Ali; Rohrer, Barbel; Hama, Hiroko | Glia | 21491498 | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21491498 |
| Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. | Mu, Fangping; Unkefer, Clifford J; Unkefer, Pat J; Hlavacek, William S | Bioinformatics (Oxford, England) | 21478194 | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21478194 |
| MALDI mass spectrometry imaging of neuronal cell cultures. | Zimmerman, Tyler A; Rubakhin, Stanislav S; Sweedler, Jonathan V | Journal of the American Society for Mass Spectrometry | 21472517 | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21472517 |
| Spatial relationships between markers for secretory and endosomal machinery in human cytomegalovirus-infected cells versus those in uninfected cells. | Das, Subhendu; Pellett, Philip E | Journal of virology | 21471245 | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21471245 |
| Monoclonal antibody cocktail as an enrichment tool for acetylome analysis. | Shaw, Patrick G; Chaerkady, Raghothama; Zhang, Zhen; Davidson, Nancy E; Pandey, Akhilesh | Analytical chemistry | 21466224 | 2011 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/21466224 |
| A metabolomic comparison of mouse models of the Neuronal Ceroid Lipofuscinoses. | Salek, Reza M; Pears, Michael R; Cooper, Jonathan D; Mitchison, Hannah M; Pearce, David A; Mortishire-Smith, Russell J; Griffin, Julian L | Journal of biomolecular NMR | 21461951 | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21461951 |
| Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. | Lorenz, Matthew A; Burant, Charles F; Kennedy, Robert T | Analytical chemistry | 21456517 | 2011 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/21456517 |
| A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. | Dokudovskaya, Svetlana; Waharte, Francois; Schlessinger, Avner; Pieper, Ursula; Devos, Damien P; Cristea, Ileana M; Williams, Rosemary; Salamero, Jean; Chait, Brian T; Sali, Andrej; Field, Mark C; Rout, Michael P; Dargemont, Catherine | Molecular & cellular proteomics : MCP | 21454883 | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21454883 |
| Profiling metabolites and peptides in single cells. | Rubakhin, Stanislav S; Romanova, Elena V; Nemes, Peter; Sweedler, Jonathan V | Nature methods | 21451513 | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21451513 |
| The mechanism of nucleocytoplasmic transport through the nuclear pore complex. | Tetenbaum-Novatt, J; Rout, M P | Cold Spring Harbor symposia on quantitative biology | 21447814 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21447814 |
| Differential contributions of histone H3 and H4 residues to heterochromatin structure. | Yu, Qun; Olsen, Lars; Zhang, Xinmin; Boeke, Jef D; Bi, Xin | Genetics | 21441216 | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21441216 |
| Lipidomics at the interface of structure and function in systems biology. | Gross, Richard W; Han, Xianlin | Chemistry & biology | 21439472 | 2011 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/21439472 |
| Measuring deuterium enrichment of glucose hydrogen atoms by gas chromatography/mass spectrometry. | Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory | Analytical chemistry | 21413777 | 2011 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/21413777 |
| Nine orders of magnitude dynamic range: picomolar to millimolar concentration measurement in capillary electrophoresis with laser induced fluorescence detection employing cascaded avalanche photodiode photon counters. | Dada, Oluwatosin O; Essaka, David C; Hindsgaul, Ole; Palcic, Monica M; Prendergast, Jillian; Schnaar, Ronald L; Dovichi, Norman J | Analytical chemistry | 21410138 | 2011 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/21410138 |
| High-throughput lectin microarray-based analysis of live cell surface glycosylation. | Li, Yu; Tao, Sheng-ce; Zhu, Heng; Schneck, Jonathan P | Current protocols in protein science / editorial board, John E. Coligan ... [et al.] | 21400689 | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21400689 |
| Academic cross-fertilization by public screening yields a remarkable class of protein phosphatase methylesterase-1 inhibitors. | Bachovchin, Daniel A; Mohr, Justin T; Speers, Anna E; Wang, Chu; Berlin, Jacob M; Spicer, Timothy P; Fernandez-Vega, Virneliz; Chase, Peter; Hodder, Peter S; Schurer, Stephan C; Nomura, Daniel K; Rosen, Hugh; Fu, Gregory C; Cravatt, Benjamin F | Proceedings of the National Academy of Sciences of the United States of America | 21398589 | 2011 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/21398589 |
| Phosphorylation-dependent 14-3-3 binding to LRRK2 is impaired by common mutations of familial Parkinson's disease. | Li, Xianting; Wang, Qing Jun; Pan, Nina; Lee, Sangkyu; Zhao, Yingming; Chait, Brian T; Yue, Zhenyu | PloS one | 21390248 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21390248 |
| Engineering neuronal growth cones to promote axon regeneration over inhibitory molecules. | Hur, Eun-Mi; Yang, In Hong; Kim, Deok-Ho; Byun, Justin; Saijilafu; Xu, Wen-Lin; Nicovich, Philip R; Cheong, Raymond; Levchenko, Andre; Thakor, Nitish; Zhou, Feng-Quan | Proceedings of the National Academy of Sciences of the United States of America | 21383151 | 2011 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/21383151 |
| A role for zinc in regulating hypoxia-induced contractile events in pulmonary endothelium. | Bernal, Paula J; Bauer, Eileen M; Cao, Rong; Maniar, Salony; Mosher, Mackenzie; Chen, Jun; Wang, Qiming Jane; Glorioso, Joseph C; Pitt, Bruce R; Watkins, Simon C; St Croix, Claudette M | American journal of physiology. Lung cellular and molecular physiology | 21378023 | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21378023 |
| Proteins and an inflammatory network expressed in colon tumors. | Zhu, Wenhong; Fang, Changming; Gramatikoff, Kosi; Niemeyer, Christina C; Smith, Jeffrey W | Journal of proteome research | 21366352 | 2011 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/21366352 |
| Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. | Sampathkumar, Parthasarathy; Gheyi, Tarun; Miller, Stacy A; Bain, Kevin T; Dickey, Mark; Bonanno, Jeffrey B; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D; Martel, Anne; Tsuruta, Hiro; Atwell, Shane; Thomp | Proteins | 21365675 | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21365675 |
| Using a Buffer Gas Modifier to Change Separation Selectivity in Ion Mobility Spectrometry. | Fernandez-Maestre, Roberto; Wu, Ching; Hill, Herbert H | International journal of mass spectrometry | 21344065 | 2010 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21344065 |
| Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. | Brown, Sherry-Ann; Moraru, Ion I; Schaff, James C; Loew, Leslie M | Journal of computational neuroscience | 21340454 | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21340454 |
| Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data. | Bandaru, Pradeep; Bansal, Mukesh; Nemenman, Ilya | Journal of computational biology : a journal of computational molecular cell biology | 21314454 | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21314454 |
| Biotin-4-fluorescein based fluorescence quenching assay for determination of biotin binding capacity of streptavidin conjugated quantum dots. | Mittal, Rowena; Bruchez, Marcel P | Bioconjugate chemistry | 21314110 | 2011 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/21314110 |
| Role of the nuclear envelope in genome organization and gene expression. | Van de Vosse, David W; Wan, Yakun; Wozniak, Richard W; Aitchison, John D | Wiley interdisciplinary reviews. Systems biology and medicine | 21305702 | 2011 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/21305702 |
| Regulation of flagellar motility by the conserved flagellar protein CG34110/Ccdc135/FAP50. | Yang, Yong; Cochran, Deborah A; Gargano, Mary D; King, Iryna; Samhat, Nayef K; Burger, Benjain P; Sabourin, Katherine R; Hou, Yuqing; Awata, Junya; Parry, David A D; Marshall, Wallace F; Witman, George B; Lu, Xiangyi | Molecular biology of the cell | 21289096 | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21289096 |
| MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity. | Blair, Lauren P; Avaritt, Nathan L; Huang, Rong; Cole, Phillip A; Taverna, Sean D; Tackett, Alan J | Epigenetics : official journal of the DNA Methylation Society | 21273814 | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21273814 |
| Characteristics of the earliest cross-neutralizing antibody response to HIV-1. | Mikell, Iliyana; Sather, D Noah; Kalams, Spyros A; Altfeld, Marcus; Alter, Galit; Stamatatos, Leonidas | PLoS pathogens | 21249232 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21249232 |
| Mutant proteins as cancer-specific biomarkers. | Wang, Qing; Chaerkady, Raghothama; Wu, Jian; Hwang, Hee Jung; Papadopoulos, Nick; Kopelovich, Levy; Maitra, Anirban; Matthaei, Hanno; Eshleman, James R; Hruban, Ralph H; Kinzler, Kenneth W; Pandey, Akhilesh; Vogelstein, Bert | Proceedings of the National Academy of Sciences of the United States of America | 21248225 | 2011 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/21248225 |
| The dynamics and mechanism of SUMO chain deconjugation by SUMO-specific proteases. | Bekes, Miklos; Prudden, John; Srikumar, Tharan; Raught, Brian; Boddy, Michael N; Salvesen, Guy S | The Journal of biological chemistry | 21247896 | 2011 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/21247896 |
| Discriminative motif finding for predicting protein subcellular localization. | Lin, Tien-ho; Murphy, Robert F; Bar-Joseph, Ziv | IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM | 21233524 | 2011 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/21233524 |
| Aborted autophagy and nonapoptotic death induced by farnesyl transferase inhibitor and lovastatin. | Wojtkowiak, Jonathan W; Sane, Komal M; Kleinman, Miriam; Sloane, Bonnie F; Reiners Jr, John J; Mattingly, Raymond R | The Journal of pharmacology and experimental therapeutics | 21228063 | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21228063 |
| Nýý-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. | Thao, Sandy; Chen, Chien-Sheng; Zhu, Heng; Escalante-Semerena, Jorge C | PloS one | 21217812 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21217812 |
| Analysis of the citric acid cycle intermediates using gas chromatography-mass spectrometry. | Kombu, Rajan S; Brunengraber, Henri; Puchowicz, Michelle A | Methods in molecular biology (Clifton, N.J.) | 21207288 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21207288 |
| Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. | Smith, Jennifer J; Miller, Leslie R; Kreisberg, Richard; Vazquez, Laura; Wan, Yakun; Aitchison, John D | Molecular systems biology | 21206489 | 2011 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/21206489 |
| Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. | Zanotti, Kimberly J; Silva, Gloria L; Creeger, Yehuda; Robertson, Kelly L; Waggoner, Alan S; Berget, Peter B; Armitage, Bruce A | Organic & biomolecular chemistry | 21180706 | 2011 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/21180706 |
| Neuronal LRP1 knockout in adult mice leads to impaired brain lipid metabolism and progressive, age-dependent synapse loss and neurodegeneration. | Liu, Qiang; Trotter, Justin; Zhang, Juan; Peters, Melinda M; Cheng, Hua; Bao, Jianxin; Han, Xianlin; Weeber, Edwin J; Bu, Guojun | The Journal of neuroscience : the official journal of the Society for Neuroscience | 21159977 | 2010 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/21159977 |
| Metabolism of levulinate in perfused rat livers and live rats: conversion to the drug of abuse 4-hydroxypentanoate. | Harris, Stephanie R; Zhang, Guo-Fang; Sadhukhan, Sushabhan; Murphy, Anne M; Tomcik, Kristyen A; Vazquez, Edwin J; Anderson, Vernon E; Tochtrop, Gregory P; Brunengraber, Henri | The Journal of biological chemistry | 21126961 | 2011 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/21126961 |
| Metabolic Profiling of Human Blood by High Resolution Ion Mobility Mass Spectrometry (IM-MS). | Dwivedi, Prabha; Schultz, Albert J; Hill, Herbert H | International journal of mass spectrometry | 21113320 | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21113320 |
| Isotopomer enrichment assay for very short chain fatty acids and its metabolic applications. | Tomcik, Kristyen; Ibarra, Rafael A; Sadhukhan, Sushabhan; Han, Yong; Tochtrop, Gregory P; Zhang, Guo-Fang | Analytical biochemistry | 21112315 | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21112315 |
| Sugar transporters for intercellular exchange and nutrition of pathogens. | Chen, Li-Qing; Hou, Bi-Huei; Lalonde, Sylvie; Takanaga, Hitomi; Hartung, Mara L; Qu, Xiao-Qing; Guo, Woei-Jiun; Kim, Jung-Gun; Underwood, William; Chaudhuri, Bhavna; Chermak, Diane; Antony, Ginny; White, Frank F; Somerville, Shauna C; Mudgett, Mary Beth; | Nature | 21107422 | 2010 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/21107422 |
| Signaling diversity of PKA achieved via a Ca2+-cAMP-PKA oscillatory circuit. | Ni, Qiang; Ganesan, Ambhighainath; Aye-Han, Nwe-Nwe; Gao, Xinxin; Allen, Michael D; Levchenko, Andre; Zhang, Jin | Nature chemical biology | 21102470 | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21102470 |
| Exploring the spatial and temporal organization of a cell's proteome. | Beck, Martin; Topf, Maya; Frazier, Zachary; Tjong, Harianto; Xu, Min; Zhang, Shihua; Alber, Frank | Journal of structural biology | 21094684 | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21094684 |
| Modeling mass spectrometry-based protein analysis. | Eriksson, Jan; Fenyo, David | Methods in molecular biology (Clifton, N.J.) | 21082431 | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21082431 |
| The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. | Zhong, Jun; Chaerkady, Raghothama; Kandasamy, Kumaran; Gucek, Marjan; Cole, Robert N; Pandey, Akhilesh | Journal of proteomics | 21081186 | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21081186 |
| Structure of Sir2Tm bound to a propionylated peptide. | Bheda, Poonam; Wang, Jennifer T; Escalante-Semerena, Jorge C; Wolberger, Cynthia | Protein science : a publication of the Protein Society | 21080423 | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21080423 |
| Young transplant surgeons and NIH funding. | Englesbe, M J; Sung, R S; Segev, D L | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 21070602 | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21070602 |
| Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45. | Berdygulova, Zhanna; Westblade, Lars F; Florens, Laurence; Koonin, Eugene V; Chait, Brian T; Ramanculov, Erlan; Washburn, Michael P; Darst, Seth A; Severinov, Konstantin; Minakhin, Leonid | Journal of molecular biology | 21050864 | 2011 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/21050864 |
| Quiescent fibroblasts exhibit high metabolic activity. | Lemons, Johanna M S; Feng, Xiao-Jiang; Bennett, Bryson D; Legesse-Miller, Aster; Johnson, Elizabeth L; Raitman, Irene; Pollina, Elizabeth A; Rabitz, Herschel A; Rabinowitz, Joshua D; Coller, Hilary A | PLoS biology | 21049082 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21049082 |
| Monitoring the uptake of glycosphingolipids in Plasmodium falciparum-infected erythrocytes using both fluorescence microscopy and capillary electrophoresis with laser-induced fluorescence detection. | Essaka, David C; White, John; Rathod, Pradip; Whitmore, Colin D; Hindsgaul, Ole; Palcic, Monica M; Dovichi, Norman J | Analytical chemistry | 21043509 | 2010 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21043509 |
| Indium-tin oxide coated microfabricated device for the injection of a single cell into a fused silica capillary for chemical cytometry. | Boardman, Anna; Chang, Tim; Folch, Albert; Dovichi, Norman J | Analytical chemistry | 21033750 | 2010 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21033750 |
| Integrating BioPAX pathway knowledge with SBML models. | Ruebenacker, O; Moraru, I I; Schaff, J C; Blinov, M L | IET systems biology | 21028923 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21028923 |
| The acidic sequence of the NS4A cofactor regulates ATP hydrolysis by the HCV NS3 helicase. | Shiryaev, Sergey A; Chernov, Andrei V; Shiryaeva, Tatiana N; Aleshin, Alexander E; Strongin, Alex Y | Archives of virology | 20978807 | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20978807 |
| STED nanoscopy in living cells using Fluorogen Activating Proteins. | Fitzpatrick, James A J; Yan, Qi; Sieber, Jochen J; Dyba, Marcus; Schwarz, Ulf; Szent-Gyorgyi, Chris; Woolford, Carol A; Berget, Peter B; Waggoner, Alan S; Bruchez, Marcel P | Bioconjugate chemistry | 20976031 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20976031 |
| Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source. | Dwivedi, Prabha; Puzon, Geoffery; Tam, Maggie; Langlais, Denis; Jackson, Shelley; Kaplan, Kimberly; Siems, William F; Schultz, Albert J; Xun, Luying; Woods, Amina; Hill Jr, Herbert H | Journal of mass spectrometry : JMS | 20967735 | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20967735 |
| Resistive glass IM-TOFMS. | Kaplan, Kimberly; Graf, Stephan; Tanner, Christian; Gonin, Marc; Fuhrer, Katrin; Knochenmuss, Richard; Dwivedi, Prabha; Hill Jr, Herbert H | Analytical chemistry | 20964441 | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20964441 |
| Delineation of substrate selection and anaplerosis in tricarboxylic acid cycle of the heart by 13C NMR spectroscopy and mass spectrometry. | Li, Wei; Bian, Fang; Chaudhuri, Priyanjana; Mao, Xian; Brunengraber, Henri; Yu, Xin | NMR in biomedicine | 20960584 | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20960584 |
| Proteomic characterization of Her2/neu-overexpressing breast cancer cells. | Chen, Hexin; Pimienta, Genaro; Gu, Yiben; Sun, Xu; Hu, Jianjun; Kim, Min-Sik; Chaerkady, Raghothama; Gucek, Marjan; Cole, Robert N; Sukumar, Saraswati; Pandey, Akhilesh | Proteomics | 20960451 | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20960451 |
| Phosphoproteomics in cancer. | Harsha, H C; Pandey, Akhilesh | Molecular oncology | 20937571 | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20937571 |
| Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction. | Li, Yinyin; Stewart, Nichole K; Berger, Anthony J; Vos, Seychelle; Schoeffler, Allyn J; Berger, James M; Chait, Brian T; Oakley, Martha G | Proceedings of the National Academy of Sciences of the United States of America | 20921377 | 2010 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20921377 |
| Macromolecular docking restrained by a small angle X-ray scattering profile. | Schneidman-Duhovny, Dina; Hammel, Michal; Sali, Andrej | Journal of structural biology | 20920583 | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20920583 |
| Functional protein microarray technology. | Hu, Shaohui; Xie, Zhi; Qian, Jiang; Blackshaw, Seth; Zhu, Heng | Wiley interdisciplinary reviews. Systems biology and medicine | 20872749 | 2011 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/20872749 |
| Kinetic Modeling using BioPAX ontology. | Ruebenacker, Oliver; Moraru, Ion I; Schaff, James C; Blinov, Michael L | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 20862270 | 2007 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20862270 |
| Dynamic analysis of cytosolic glucose and ATP levels in yeast using optical sensors. | Bermejo, Clara; Haerizadeh, Farzad; Takanaga, Hitomi; Chermak, Diane; Frommer, Wolf B | The Biochemical journal | 20854260 | 2010 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/20854260 |
| Integrin-induced PIP5K1C kinase polarization regulates neutrophil polarization, directionality, and in vivo infiltration. | Xu, Wenwen; Wang, Ping; Petri, Bjorn; Zhang, Yong; Tang, Wenwen; Sun, Le; Kress, Holger; Mann, Tom; Shi, Yan; Kubes, Paul; Wu, Dianqing | Immunity | 20850356 | 2010 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/20850356 |
| Evidence for an alternative glycolytic pathway in rapidly proliferating cells. | Vander Heiden, Matthew G; Locasale, Jason W; Swanson, Kenneth D; Sharfi, Hadar; Heffron, Greg J; Amador-Noguez, Daniel; Christofk, Heather R; Wagner, Gerhard; Rabinowitz, Joshua D; Asara, John M; Cantley, Lewis C | Science (New York, N.Y.) | 20847263 | 2010 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/20847263 |
| Modeling experimental design for proteomics. | Eriksson, Jan; Fenyo, David | Methods in molecular biology (Clifton, N.J.) | 20835802 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20835802 |
| Protein quantitation using mass spectrometry. | Zhang, Guoan; Ueberheide, Beatrix M; Waldemarson, Sofia; Myung, Sunnie; Molloy, Kelly; Eriksson, Jan; Chait, Brian T; Neubert, Thomas A; Fenyo, David | Methods in molecular biology (Clifton, N.J.) | 20835801 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20835801 |
| Mass spectrometric protein identification using the global proteome machine. | Fenyo, David; Eriksson, Jan; Beavis, Ronald | Methods in molecular biology (Clifton, N.J.) | 20835799 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20835799 |
| Ion mobility spectrometry for the rapid analysis of over-the-counter drugs and beverages. | Fernandez-Maestre, Roberto; Hill, Herbert H | International journal for ion mobility spectrometry : official publication of the International Society for Ion Mobility Spectrometry | 20835390 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20835390 |
| Circadian integration of glutamatergic signals by little SAAS in novel suprachiasmatic circuits. | Atkins Jr, Norman; Mitchell, Jennifer W; Romanova, Elena V; Morgan, Daniel J; Cominski, Tara P; Ecker, Jennifer L; Pintar, John E; Sweedler, Jonathan V; Gillette, Martha U | PloS one | 20830308 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20830308 |
| Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. | Lasker, Keren; Sali, Andrej; Wolfson, Haim J | Proteins | 20827723 | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20827723 |
| Epidermal growth factor receptor kinase activity is required for gap junction closure and for part of the decrease in ovarian follicle cGMP in response to LH. | Norris, Rachael P; Freudzon, Marina; Nikolaev, Viacheslav O; Jaffe, Laurinda A | Reproduction (Cambridge, England) | 20826538 | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20826538 |
| Emerging principles in protease-based drug discovery. | Drag, Marcin; Salvesen, Guy S | Nature reviews. Drug discovery | 20811381 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20811381 |
| The glycerophospho metabolome and its influence on amino acid homeostasis revealed by brain metabolomics of GDE1(-/-) mice. | Kopp, Florian; Komatsu, Toru; Nomura, Daniel K; Trauger, Sunia A; Thomas, Jason R; Siuzdak, Gary; Simon, Gabriel M; Cravatt, Benjamin F | Chemistry & biology | 20797612 | 2010 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/20797612 |
| A fluopol-ABPP HTS assay to identify PAD inhibitors. | Knuckley, Bryan; Jones, Justin E; Bachovchin, Daniel A; Slack, Jessica; Causey, Corey P; Brown, Steven J; Rosen, Hugh; Cravatt, Benjamin F; Thompson, Paul R | Chemical communications (Cambridge, England) | 20740228 | 2010 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/20740228 |
| A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells. | Nag, Ambarish; Monine, Michael I; Blinov, Michael L; Goldstein, Byron | Journal of immunology (Baltimore, Md. : 1950) | 20733205 | 2010 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/20733205 |
| Using views of Systems Biology Cloud: application for model building. | Ruebenacker, Oliver; Blinov, Michael | Theory in biosciences = Theorie in den Biowissenschaften | 20730508 | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20730508 |
| An integrated micro-electro-fluidic and protein arraying system for parallel analysis of cell responses to controlled microenvironments. | Yin, Zhizhong; Tao, Sheng-Ce; Cheong, Raymond; Zhu, Heng; Levchenko, Andre | Integrative biology : quantitative biosciences from nano to macro | 20714638 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20714638 |
| Temporal profiling of the secretome during adipogenesis in humans. | Zhong, Jun; Krawczyk, Sarah A; Chaerkady, Raghothama; Huang, Hailiang; Goel, Renu; Bader, Joel S; Wong, G William; Corkey, Barbara E; Pandey, Akhilesh | Journal of proteome research | 20707391 | 2010 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/20707391 |
| Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice. | Noguchi, Yasushi; Nishikata, Natsumi; Shikata, Nahoko; Kimura, Yoshiko; Aleman, Jose O; Young, Jamey D; Koyama, Naoto; Kelleher, Joanne K; Takahashi, Michio; Stephanopoulos, Gregory | PloS one | 20706589 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20706589 |
| Activity-based protein profiling for biochemical pathway discovery in cancer. | Nomura, Daniel K; Dix, Melissa M; Cravatt, Benjamin F | Nature reviews. Cancer | 20703252 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20703252 |
| Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction. | Westblade, Lars F; Campbell, Elizabeth A; Pukhrambam, Chirangini; Padovan, Julio C; Nickels, Bryce E; Lamour, Valerie; Darst, Seth A | Nucleic acids research | 20702425 | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20702425 |
| Fluorogenic dendrons with multiple donor chromophores as bright genetically targeted and activated probes. | Szent-Gyorgyi, Christopher; Schmidt, Brigitte F; Fitzpatrick, James A J; Bruchez, Marcel P | Journal of the American Chemical Society | 20698676 | 2010 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/20698676 |
| Genome-wide analysis of effectors of peroxisome biogenesis. | Saleem, Ramsey A; Long-O'Donnell, Rose; Dilworth, David J; Armstrong, Abraham M; Jamakhandi, Arvind P; Wan, Yakun; Knijnenburg, Theo A; Niemisto, Antti; Boyle, John; Rachubinski, Richard A; Shmulevich, Ilya; Aitchison, John D | PloS one | 20694151 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20694151 |
| The Moving Boundary Node Method: A level set-based, finite volume algorithm with applications to cell motility. | Wolgemuth, Charles W; Zajac, Mark | Journal of computational physics | 20689723 | 2010 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/20689723 |
| Branched tricarboxylic acid metabolism in Plasmodium falciparum. | Olszewski, Kellen L; Mather, Michael W; Morrisey, Joanne M; Garcia, Benjamin A; Vaidya, Akhil B; Rabinowitz, Joshua D; Llinas, Manuel | Nature | 20686576 | 2010 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/20686576 |
| Quantifying a pathway: kinetic analysis of actin dendritic nucleation. | Kraikivski, Pavel; Slepchenko, Boris M | Biophysical journal | 20682247 | 2010 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/20682247 |
| Mass spectrometry imaging using the stretched sample approach. | Zimmerman, Tyler A; Rubakhin, Stanislav S; Sweedler, Jonathan V | Methods in molecular biology (Clifton, N.J.) | 20680608 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20680608 |
| The dynamic stress-induced "O-GlcNAc-ome" highlights functions for O-GlcNAc in regulating DNA damage/repair and other cellular pathways. | Zachara, Natasha E; Molina, Henrik; Wong, Ker Yi; Pandey, Akhilesh; Hart, Gerald W | Amino acids | 20676906 | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20676906 |
| Digital analysis and sorting of fluorescence lifetime by flow cytometry. | Houston, Jessica P; Naivar, Mark A; Freyer, James P | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 20662090 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20662090 |
| Trivalent arsenic inhibits the functions of chaperonin complex. | Pan, Xuewen; Reissman, Stefanie; Douglas, Nick R; Huang, Zhiwei; Yuan, Daniel S; Wang, Xiaoling; McCaffery, J Michael; Frydman, Judith; Boeke, Jef D | Genetics | 20660648 | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20660648 |
| Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. | Holleran, John; Brown, Dara; Fuhrman, Margaret H; Adler, Sally A; Fisher, Gregory W; Jarvik, Jonathan W | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 20653017 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20653017 |
| Molecular manipulation and analysis of inositol phosphate and pyrophosphate levels in Mammalian cells. | Otto, James C; York, John D | Methods in molecular biology (Clifton, N.J.) | 20645180 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20645180 |
| Chemical cytometry: fluorescence-based single-cell analysis. | Cohen, Daniella; Dickerson, Jane A; Whitmore, Colin D; Turner, Emily H; Palcic, Monica M; Hindsgaul, Ole; Dovichi, Norman J | Annual review of analytical chemistry (Palo Alto, Calif.) | 20636078 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/20636078 |
| AUTOMATED COMPARISON OF PROTEIN SUBCELLULAR LOCATION PATTERNS BETWEEN IMAGES OF NORMAL AND CANCEROUS TISSUES. | Glory, Estelle; Newberg, Justin; Murphy, Robert F | Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging | 20628549 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/20628549 |
| Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics. | Kapustina, Maryna; Vitriol, Eric; Elston, Timothy C; Loew, Leslie M; Jacobson, Ken | Cytoskeleton (Hoboken, N.J.) | 20623665 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20623665 |
| Site-Specific Introduction of an Acetyl-Lysine Mimic into Peptides and Proteins by Cysteine Alkylation. | Huang, Rong; Holbert, Marc A; Tarrant, Mary Katherine; Curtet, Sandrine; Colquhoun, David R; Dancy, Beverley M; Dancy, Blair C; Hwang, Yousang; Tang, Yong; Meeth, Katrina; Marmorstein, Ronen; Cole, Robert N; Khochbin, Saadi; Cole, Philip A | Journal of the American Chemical Society | 20608637 | 2010 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/20608637 |
| Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA. | Terhune, Scott S; Moorman, Nathaniel J; Cristea, Ileana M; Savaryn, John Paul; Cuevas-Bennett, Christian; Rout, Michael P; Chait, Brian T; Shenk, Thomas | PLoS pathogens | 20585571 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20585571 |
| Signaling from the secretory granule to the nucleus: Uhmk1 and PAM. | Francone, Victor P; Ifrim, Marius F; Rajagopal, Chitra; Leddy, Christopher J; Wang, Yanping; Carson, John H; Mains, Richard E; Eipper, Betty A | Molecular endocrinology (Baltimore, Md.) | 20573687 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20573687 |
| A role for 1-acylglycerol-3-phosphate-O-acyltransferase-1 in myoblast differentiation. | Subauste, Angela R; Elliott, Brandon; Das, Arun K; Burant, Charles F | Differentiation; research in biological diversity | 20561744 | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20561744 |
| Identifying targets of miR-143 using a SILAC-based proteomic approach. | Yang, Yi; Chaerkady, Raghothama; Kandasamy, Kumaran; Huang, Tai-Chung; Selvan, Lakshmi Dhevi N; Dwivedi, Sutopa B; Kent, Oliver A; Mendell, Joshua T; Pandey, Akhilesh | Molecular bioSystems | 20544124 | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20544124 |
| Subcellular-resolution delivery of a cytokine through precisely manipulated nanowires. | Fan, Donglei; Yin, Zhizhong; Cheong, Raymond; Zhu, Frank Q; Cammarata, Robert C; Chien, C L; Levchenko, Andre | Nature nanotechnology | 20543835 | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20543835 |
| Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. | Bowers, Erin M; Yan, Gai; Mukherjee, Chandrani; Orry, Andrew; Wang, Ling; Holbert, Marc A; Crump, Nicholas T; Hazzalin, Catherine A; Liszczak, Glen; Yuan, Hua; Larocca, Cecilia; Saldanha, S Adrian; Abagyan, Ruben; Sun, Yan; Meyers, David J; Marmorstein, R | Chemistry & biology | 20534345 | 2010 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/20534345 |
| Simple haptotactic gradient generation within a triangular microfluidic channel. | Park, Jungyul; Kim, Deok-Ho; Kim, Gabriel; Kim, Younghoon; Choi, Eunpyo; Levchenko, Andre | Lab on a chip | 20532357 | 2010 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/20532357 |
| Time-of-flights and traps: from the Histone Code to Mars. | Cotter, Robert J; Swatkoski, Stepehen; Becker, Luann; Evans-Nguyen, Theresa | European journal of mass spectrometry (Chichester, England) | 20530839 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20530839 |
| An autophagy-enhancing drug promotes degradation of mutant alpha1-antitrypsin Z and reduces hepatic fibrosis. | Hidvegi, Tunda; Ewing, Michael; Hale, Pamela; Dippold, Christine; Beckett, Caroline; Kemp, Carolyn; Maurice, Nicholas; Mukherjee, Amitava; Goldbach, Christina; Watkins, Simon; Michalopoulos, George; Perlmutter, David H | Science (New York, N.Y.) | 20522742 | 2010 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/20522742 |
| Integrative structure modeling of macromolecular assemblies from proteomics data. | Lasker, Keren; Phillips, Jeremy L; Russel, Daniel; Velazquez-Muriel, Javier; Schneidman-Duhovny, Dina; Tjioe, Elina; Webb, Ben; Schlessinger, Avner; Sali, Andrej | Molecular & cellular proteomics : MCP | 20507923 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20507923 |
| FoXS: a web server for rapid computation and fitting of SAXS profiles. | Schneidman-Duhovny, Dina; Hammel, Michal; Sali, Andrej | Nucleic acids research | 20507903 | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20507903 |
| Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein. | Cristea, Ileana M; Moorman, Nathaniel J; Terhune, Scott S; Cuevas, Christian D; O'Keefe, Erin S; Rout, Michael P; Chait, Brian T; Shenk, Thomas | Journal of virology | 20504932 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20504932 |
| Cathepsin X is secreted by human osteoblasts, digests CXCL-12 and impairs adhesion of hematopoietic stem and progenitor cells to osteoblasts. | Staudt, Nicole D; Aicher, Wilhelm K; Kalbacher, Hubert; Stevanovic, Stefan; Carmona, Adriana K; Bogyo, Matthew; Klein, Gerd | Haematologica | 20494937 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20494937 |
| Detection and quantification of beta2AR internalization in living cells using FAP-based biosensor technology. | Fisher, Gregory W; Adler, Sally A; Fuhrman, Margaret H; Waggoner, Alan S; Bruchez, Marcel P; Jarvik, Jonathan W | Journal of biomolecular screening | 20488980 | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20488980 |
| Automated analysis of protein subcellular location in time series images. | Hu, Yanhua; Osuna-Highley, Elvira; Hua, Juchang; Nowicki, Theodore Scott; Stolz, Robert; McKayle, Camille; Murphy, Robert F | Bioinformatics (Oxford, England) | 20484328 | 2010 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20484328 |
| Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. | Kim, Min-Sik; Kandasamy, Kumaran; Chaerkady, Raghothama; Pandey, Akhilesh | Journal of the American Society for Mass Spectrometry | 20483638 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20483638 |
| Toward an integrated structural model of the 26S proteasome. | Forster, Friedrich; Lasker, Keren; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang | Molecular & cellular proteomics : MCP | 20467039 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20467039 |
| QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. | Dilworth, David J; Saleem, Ramsey A; Rogers, Richard S; Mirzaei, Hamid; Boyle, John; Aitchison, John D | Journal of the American Society for Mass Spectrometry | 20451407 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20451407 |
| Electrophilic tuning of the chemoprotective natural product sulforaphane. | Ahn, Young-Hoon; Hwang, Yousang; Liu, Hua; Wang, Xiu Jun; Zhang, Ying; Stephenson, Katherine K; Boronina, Tatiana N; Cole, Robert N; Dinkova-Kostova, Albena T; Talalay, Paul; Cole, Philip A | Proceedings of the National Academy of Sciences of the United States of America | 20439747 | 2010 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/20439747 |
| Model composition for macromolecular regulatory networks. | Randhawa, Ranjit; Shaffer, Clifford A; Tyson, John J | IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM | 20431147 | 2010 Apr-Jun | https://www.ncbi.nlm.nih.gov/pubmed/20431147 |
| Lipidomic metabolism analysis of the endogenous cannabinoid anandamide (N-arachidonylethanolamide). | Placzek, Ekaterina A; Cooper, Bruce R; Placzek, Andrew T; Chester, Julia A; Davisson, V Jo; Barker, Eric L | Journal of pharmaceutical and biomedical analysis | 20417049 | 2010 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20417049 |
| Dynamic simulation of cardiolipin remodeling: greasing the wheels for an interpretative approach to lipidomics. | Kiebish, Michael A; Bell, Rob; Yang, Kui; Phan, Toan; Zhao, Zhongdan; Ames, William; Seyfried, Thomas N; Gross, Richard W; Chuang, Jeffrey H; Han, Xianlin | Journal of lipid research | 20410019 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20410019 |
| Using isotopic tools to dissect and quantitate parallel metabolic pathways. | Sadhukhan, Sushabhan; Han, Yong; Zhang, Guo-Fang; Brunengraber, Henri; Tochtrop, Gregory P | Journal of the American Chemical Society | 20408520 | 2010 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/20408520 |
| Direct cellular peptidomics of supraoptic magnocellular and hippocampal neurons in low-density co-cultures. | Millet, Larry J; Bora, Adriana; Sweedler, Jonathan V; Gillette, Martha U | ACS chemical neuroscience | 20401326 | 2010 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/20401326 |
| A metabolomic study of the CRND8 transgenic mouse model of Alzheimer's disease. | Salek, Reza M; Xia, Jing; Innes, Amy; Sweatman, Brian C; Adalbert, Robert; Randle, Suzanne; McGowan, Eileen; Emson, Piers C; Griffin, Julian L | Neurochemistry international | 20398713 | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20398713 |
| Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. | Saleem, Ramsey A; Rogers, Richard S; Ratushny, Alexander V; Dilworth, David J; Shannon, Paul T; Shteynberg, David; Wan, Yakun; Moritz, Robert L; Nesvizhskii, Alexey I; Rachubinski, Richard A; Aitchison, John D | Molecular & cellular proteomics : MCP | 20395639 | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20395639 |
| Chemical standards in ion mobility spectrometry. | Fernandez-Maestre, Roberto; Harden, Charles Steve; Ewing, Robert Gordon; Crawford, Christina Lynn; Hill Jr, Herbert Henderson | The Analyst | 20369157 | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20369157 |
| Facilitative plasma membrane transporters function during ER transit. | Takanaga, Hitomi; Frommer, Wolf B | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 20354141 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20354141 |
| Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. | Lu, Wenyun; Clasquin, Michelle F; Melamud, Eugene; Amador-Noguez, Daniel; Caudy, Amy A; Rabinowitz, Joshua D | Analytical chemistry | 20349993 | 2010 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/20349993 |
| Capillary array isoelectric focusing with laser-induced fluorescence detection: milli-pH unit resolution and yoctomole mass detection limits in a 32-channel system. | Dada, Oluwatosin O; Ramsay, Lauren M; Dickerson, Jane A; Cermak, Nathan; Jiang, Rong; Zhu, Cuiru; Dovichi, Norman J | Analytical and bioanalytical chemistry | 20336452 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20336452 |
| Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. | Sampathkumar, Parthasarathy; Ozyurt, Sinem A; Do, Johnny; Bain, Kevin T; Dickey, Mark; Rodgers, Logan A; Gheyi, Tarun; Sali, Andrej; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D; Martel, Anne; Tsuruta, Hi | Proteins | 20310066 | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20310066 |
| GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. | Sekedat, Matthew D; Fenyo, David; Rogers, Richard S; Tackett, Alan J; Aitchison, John D; Chait, Brian T | Molecular systems biology | 20212525 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20212525 |
| Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor. | Fosbrink, Matthew; Aye-Han, Nwe-Nwe; Cheong, Raymond; Levchenko, Andre; Zhang, Jin | Proceedings of the National Academy of Sciences of the United States of America | 20212108 | 2010 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/20212108 |
| Distinct factors control histone variant H3.3 localization at specific genomic regions. | Goldberg, Aaron D; Banaszynski, Laura A; Noh, Kyung-Min; Lewis, Peter W; Elsaesser, Simon J; Stadler, Sonja; Dewell, Scott; Law, Martin; Guo, Xingyi; Li, Xuan; Wen, Duancheng; Chapgier, Ariane; DeKelver, Russell C; Miller, Jeffrey C; Lee, Ya-Li; Boydston, | Cell | 20211137 | 2010 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/20211137 |
| Oxime esters as selective, covalent inhibitors of the serine hydrolase retinoblastoma-binding protein 9 (RBBP9). | Bachovchin, Daniel A; Wolfe, Monique R; Masuda, Kim; Brown, Steven J; Spicer, Timothy P; Fernandez-Vega, Virneliz; Chase, Peter; Hodder, Peter S; Rosen, Hugh; Cravatt, Benjamin F | Bioorganic & medicinal chemistry letters | 20207142 | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20207142 |
| Enzymatic synthesis of Gb3 and iGb3 ceramides. | Adlercreutz, Dietlind; Weadge, Joel T; Petersen, Bent O; Duus, Jens O; Dovichi, Norman J; Palcic, Monica M | Carbohydrate research | 20206917 | 2010 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/20206917 |
| Selective and potent furin inhibitors protect cells from anthrax without significant toxicity. | Remacle, Albert G; Gawlik, Katarzyna; Golubkov, Vladislav S; Cadwell, Gregory W; Liddington, Robert C; Cieplak, Piotr; Millis, Sherri Z; Desjardins, Roxane; Routhier, Sophie; Yuan, Xue Wen; Neugebauer, Witold A; Day, Robert; Strongin, Alex Y | The international journal of biochemistry & cell biology | 20197107 | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20197107 |
| Proteasome nuclear activity affects chromosome stability by controlling the turnover of Mms22, a protein important for DNA repair. | Ben-Aroya, Shay; Agmon, Neta; Yuen, Karen; Kwok, Teresa; McManus, Kirk; Kupiec, Martin; Hieter, Philip | PLoS genetics | 20174551 | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20174551 |
| Comparative analysis of small molecules and histone substrate analogues as LSD1 lysine demethylase inhibitors. | Culhane, Jeffrey C; Wang, Dongqing; Yen, Paul M; Cole, Philip A | Journal of the American Chemical Society | 20148560 | 2010 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/20148560 |
| Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. | Simon, Gabriel M; Cravatt, Benjamin F | The Journal of biological chemistry | 20147750 | 2010 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/20147750 |
| Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. | Gao, Jing; Tarcea, V Glenn; Karnovsky, Alla; Mirel, Barbara R; Weymouth, Terry E; Beecher, Christopher W; Cavalcoli, James D; Athey, Brian D; Omenn, Gilbert S; Burant, Charles F; Jagadish, H V | Bioinformatics (Oxford, England) | 20139469 | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20139469 |
| Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns. | Peng, Tao; Bonamy, Ghislain M C; Glory-Afshar, Estelle; Rines, Daniel R; Chanda, Sumit K; Murphy, Robert F | Proceedings of the National Academy of Sciences of the United States of America | 20133616 | 2010 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/20133616 |
| Selective desorption/ionization of sulfatides by MALDI-MS facilitated using 9-aminoacridine as matrix. | Cheng, Hua; Sun, Gang; Yang, Kui; Gross, Richard W; Han, Xianlin | Journal of lipid research | 20124011 | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20124011 |
| Multi-dimensional mass spectrometry-based shotgun lipidomics and the altered lipids at the mild cognitive impairment stage of Alzheimer's disease. | Han, Xianlin | Biochimica et biophysica acta | 20117236 | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20117236 |
| Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. | Chaerkady, Raghothama; Kerr, Candace L; Kandasamy, Kumaran; Marimuthu, Arivusudar; Gearhart, John D; Pandey, Akhilesh | Proteomics | 20104618 | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20104618 |
| Ribonucleotide and ribonucleoside determination by ambient pressure ion mobility spectrometry. | Kanu, Abu B; Hampikian, Greg; Brandt, Simon D; Hill Jr, Herbert H | Analytica chimica acta | 20082780 | 2010 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/20082780 |
| Silent information regulator 3: the Goldilocks of the silencing complex. | Norris, Anne; Boeke, Jef D | Genes & development | 20080949 | 2010 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/20080949 |
| RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia. | Shields, David J; Niessen, Sherry; Murphy, Eric A; Mielgo, Ainhoa; Desgrosellier, Jay S; Lau, Steven K M; Barnes, Leo A; Lesperance, Jacqueline; Bouvet, Michael; Tarin, David; Cravatt, Benjamin F; Cheresh, David A | Proceedings of the National Academy of Sciences of the United States of America | 20080647 | 2010 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/20080647 |
| Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. | Nomura, Daniel K; Long, Jonathan Z; Niessen, Sherry; Hoover, Heather S; Ng, Shu-Wing; Cravatt, Benjamin F | Cell | 20079333 | 2010 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/20079333 |
| Biochemistry. CO2mmon sense. | Frommer, Wolf B | Science (New York, N.Y.) | 20075235 | 2010 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/20075235 |
| Identification of phenylbutyrate-generated metabolites in Huntington disease patients using parallel liquid chromatography/electrochemical array/mass spectrometry and off-line tandem mass spectrometry. | Ebbel, Erika N; Leymarie, Nancy; Schiavo, Susan; Sharma, Swati; Gevorkian, Sona; Hersch, Steven; Matson, Wayne R; Costello, Catherine E | Analytical biochemistry | 20074541 | 2010 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/20074541 |
| NetPath: a public resource of curated signal transduction pathways. | Kandasamy, Kumaran; Mohan, S Sujatha; Raju, Rajesh; Keerthikumar, Shivakumar; Kumar, Ghantasala S Sameer; Venugopal, Abhilash K; Telikicherla, Deepthi; Navarro, J Daniel; Mathivanan, Suresh; Pecquet, Christian; Gollapudi, Sashi Kanth; Tattikota, Sudhir Go | Genome biology | 20067622 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20067622 |
| The pathogenic implication of abnormal interaction between apolipoprotein E isoforms, amyloid-beta peptides, and sulfatides in Alzheimer's disease. | Han, Xianlin | Molecular neurobiology | 20052565 | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20052565 |
| Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. | Zhang, Kai; Chen, Yue; Zhang, Zhihong; Tao, Shengce; Zhu, Heng; Zhao, Yingming | Proteomics | 20049863 | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20049863 |
| Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin. | Cooper, Eric M; Boeke, Jef D; Cohen, Robert E | The Journal of biological chemistry | 20032457 | 2010 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/20032457 |
| Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. | Jung, Sunhee; Marelli, Marcello; Rachubinski, Richard A; Goodlett, David R; Aitchison, John D | The Journal of biological chemistry | 20026609 | 2010 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/20026609 |
| Adhesion and migration of ovarian cancer cells on crosslinked laminin fibers nanofabricated by multiphoton excited photochemistry. | Chen, Xiyi; Brewer, Molly A; Zou, Changping; Campagnola, Paul J | Integrative biology : quantitative biosciences from nano to macro | 20023757 | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20023757 |
| Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain. | Lee, Jiyoun; Bogyo, Matthew | ACS chemical biology | 20017516 | 2010 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/20017516 |
| pHMA, a pH-sensitive GFP reporter for cell engulfment, in Drosophila embryos, tissues, and cells. | Fishilevich, Elane; Fitzpatrick, James A J; Minden, Jonathan S | Developmental dynamics : an official publication of the American Association of Anatomists | 20014104 | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20014104 |
| Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. | Wan, Yakun; Chiang, Jung-Hsien; Lin, Chan-Hsien; Arens, Christina E; Saleem, Ramsey A; Smith, Jennifer J; Aitchison, John D | Nucleic acids research | 20008511 | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20008511 |
| In vitro stable isotope labeling for discovery of novel metabolites by liquid chromatography-mass spectrometry: Confirmation of gamma-tocopherol metabolism in human A549 cell. | Yang, Wen-Chu; Regnier, Fred E; Jiang, Qing; Adamec, Jiri | Journal of chromatography. A | 20006340 | 2010 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/20006340 |
| Rrp17p is a eukaryotic exonuclease required for 5' end processing of Pre-60S ribosomal RNA. | Oeffinger, Marlene; Zenklusen, Daniel; Ferguson, Angelica; Wei, Karen E; El Hage, Aziz; Tollervey, David; Chait, Brian T; Singer, Robert H; Rout, Michael P | Molecular cell | 20005841 | 2009 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/20005841 |
| Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates. | Nesic, Dragana; Miller, Marshall C; Quinkert, Zachary T; Stein, Markus; Chait, Brian T; Stebbins, C Erec | Nature structural & molecular biology | 19966800 | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19966800 |
| CE-MALDI interface based on inkjet technology. | Vannatta, Michael W; Whitmore, Colin D; Dovichi, Norman J | Electrophoresis | 19960472 | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19960472 |
| 4-Bromophenacyl bromide specifically inhibits rhoptry secretion during Toxoplasma invasion. | Ravindran, Sandeep; Lodoen, Melissa B; Verhelst, Steven H L; Bogyo, Matthew; Boothroyd, John C | PloS one | 19956582 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19956582 |
| Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry. | Lee, Ji Eun; Atkins Jr, Norman; Hatcher, Nathan G; Zamdborg, Leonid; Gillette, Martha U; Sweedler, Jonathan V; Kelleher, Neil L | Molecular & cellular proteomics : MCP | 19955084 | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19955084 |
| Aminopeptidase fingerprints, an integrated approach for identification of good substrates and optimal inhibitors. | Drag, Marcin; Bogyo, Matthew; Ellman, Jonathan A; Salvesen, Guy S | The Journal of biological chemistry | 19948737 | 2010 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/19948737 |
| Hsp70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1alpha but Not HIF-2alpha. | Luo, Weibo; Zhong, Jun; Chang, Ryan; Hu, Hongxia; Pandey, Akhilesh; Semenza, Gregg L | The Journal of biological chemistry | 19940151 | 2010 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/19940151 |
| A reciprocal interdependence between Nck and PI(4,5)P(2) promotes localized N-WASp-mediated actin polymerization in living cells. | Rivera, Gonzalo M; Vasilescu, Dan; Papayannopoulos, Venizelos; Lim, Wendell A; Mayer, Bruce J | Molecular cell | 19917259 | 2009 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/19917259 |
| Mass spectrometry-based label-free quantitative proteomics. | Zhu, Wenhong; Smith, Jeffrey W; Huang, Chun-Ming | Journal of biomedicine & biotechnology | 19911078 | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/19911078 |
| Parenteral and enteral metabolism of anaplerotic triheptanoin in normal rats. II. Effects on lipolysis, glucose production, and liver acyl-CoA profile. | Gu, Lei; Zhang, Guo-Fang; Kombu, Rajan S; Allen, Frederick; Kutz, Gerd; Brewer, Wolf-Ulrich; Roe, Charles R; Brunengraber, Henri | American journal of physiology. Endocrinology and metabolism | 19903863 | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19903863 |
| Deterministic and stochastic models of genetic regulatory networks. | Shmulevich, Ilya; Aitchison, John D | Methods in enzymology | 19897099 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19897099 |
| Side chain specificity of ADP-ribosylation by a sirtuin. | Fahie, Kamau; Hu, Po; Swatkoski, Stephen; Cotter, Robert J; Zhang, Yingkai; Wolberger, Cynthia | The FEBS journal | 19895577 | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19895577 |
| Model aggregation: a building-block approach to creating large macromolecular regulatory networks. | Randhawa, Ranjit; Shaffer, Clifford A; Tyson, John J | Bioinformatics (Oxford, England) | 19880372 | 2009 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/19880372 |
| Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. | Hu, Shaohui; Xie, Zhi; Onishi, Akishi; Yu, Xueping; Jiang, Lizhi; Lin, Jimmy; Rho, Hee-sool; Woodard, Crystal; Wang, Hong; Jeong, Jun-Seop; Long, Shunyou; He, Xiaofei; Wade, Herschel; Blackshaw, Seth; Qian, Jiang; Zhu, Heng | Cell | 19879846 | 2009 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/19879846 |
| Hemoglobin digestion in blood-feeding ticks: mapping a multipeptidase pathway by functional proteomics. | Horn, Martin; Nussbaumerova, Martina; Sanda, Miloslav; Kovarova, Zuzana; Srba, Jindrich; Franta, Zdenek; Sojka, Daniel; Bogyo, Matthew; Caffrey, Conor R; Kopacek, Petr; Mares, Michael | Chemistry & biology | 19875079 | 2009 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/19875079 |
| Role of band 3 in regulating metabolic flux of red blood cells. | Lewis, Ian A; Campanella, M Estela; Markley, John L; Low, Philip S | Proceedings of the National Academy of Sciences of the United States of America | 19846781 | 2009 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/19846781 |
| Identification of Isn1 and Sdt1 as glucose- and vitamin-regulated nicotinamide mononucleotide and nicotinic acid mononucleotide [corrected] 5'-nucleotidases responsible for production of nicotinamide riboside and nicotinic acid riboside. | Bogan, Katrina L; Evans, Charles; Belenky, Peter; Song, Peng; Burant, Charles F; Kennedy, Robert; Brenner, Charles | The Journal of biological chemistry | 19846558 | 2009 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/19846558 |
| Six orders of magnitude dynamic range in capillary electrophoresis with ultrasensitive laser-induced fluorescence detection. | Whitmore, Colin D; Essaka, David; Dovichi, Norman J | Talanta | 19836546 | 2009 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/19836546 |
| Molecular machines or pleiomorphic ensembles: signaling complexes revisited. | Mayer, Bruce J; Blinov, Michael L; Loew, Leslie M | Journal of biology | 19835637 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19835637 |
| MALDI mass spectrometric imaging using the stretched sample method to reveal neuropeptide distributions in aplysia nervous tissue. | Zimmerman, Tyler A; Rubakhin, Stanislav S; Romanova, Elena V; Tucker, Kevin R; Sweedler, Jonathan V | Analytical chemistry | 19835365 | 2009 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/19835365 |
| Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State. | Frey, Brian L; Krusemark, Casey J; Ledvina, Aaron R; Coon, Joshua J; Belshaw, Peter J; Smith, Lloyd M | International journal of mass spectrometry | 19802328 | 2008 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/19802328 |
| Monitoring dynamic changes in lymph metabolome of fasting and fed rats by electrospray ionization-ion mobility mass spectrometry (ESI-IMMS). | Kaplan, Kimberly; Dwivedi, Prabha; Davidson, Sean; Yang, Qing; Tso, Patrick; Siems, William; Hill Jr, Herbert H | Analytical chemistry | 19788315 | 2009 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/19788315 |
| Genetically encoded biosensors based on engineered fluorescent proteins. | Frommer, Wolf B; Davidson, Michael W; Campbell, Robert E | Chemical Society reviews | 19771330 | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19771330 |
| Structural and kinetic determinants of protease substrates. | Timmer, John C; Zhu, Wenhong; Pop, Cristina; Regan, Tim; Snipas, Scott J; Eroshkin, Alexey M; Riedl, Stefan J; Salvesen, Guy S | Nature structural & molecular biology | 19767749 | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19767749 |
| Examination of the brain mitochondrial lipidome using shotgun lipidomics. | Kiebish, Michael A; Han, Xianlin; Seyfried, Thomas N | Methods in molecular biology (Clifton, N.J.) | 19763468 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19763468 |
| Catabolism of 4-hydroxyacids and 4-hydroxynonenal via 4-hydroxy-4-phosphoacyl-CoAs. | Zhang, Guo-Fang; Kombu, Rajan S; Kasumov, Takhar; Han, Yong; Sadhukhan, Sushabhan; Zhang, Jianye; Sayre, Lawrence M; Ray, Dale; Gibson, K Michael; Anderson, Vernon A; Tochtrop, Gregory P; Brunengraber, Henri | The Journal of biological chemistry | 19759021 | 2009 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/19759021 |
| Efficient framework for automated classification of subcellular patterns in budding yeast. | Huh, Seungil; Lee, Donghun; Murphy, Robert F | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 19753630 | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19753630 |
| Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. | Zhao, Yingming; Jensen, Ole N | Proteomics | 19743430 | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19743430 |
| Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. | Shank, Nathaniel I; Zanotti, Kimberly J; Lanni, Frederick; Berget, Peter B; Armitage, Bruce A | Journal of the American Chemical Society | 19737016 | 2009 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/19737016 |
| Global motions of the nuclear pore complex: insights from elastic network models. | Lezon, Timothy R; Sali, Andrej; Bahar, Ivet | PLoS computational biology | 19730674 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19730674 |
| Rab35 controls actin bundling by recruiting fascin as an effector protein. | Zhang, Jun; Fonovic, Marko; Suyama, Kaye; Bogyo, Matthew; Scott, Matthew P | Science (New York, N.Y.) | 19729655 | 2009 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/19729655 |
| Inflammatory proprotein convertase-matrix metalloproteinase proteolytic pathway in antigen-presenting cells as a step to autoimmune multiple sclerosis. | Shiryaev, Sergey A; Remacle, Albert G; Savinov, Alexei Y; Chernov, Andrei V; Cieplak, Piotr; Radichev, Ilian A; Williams, Roy; Shiryaeva, Tatiana N; Gawlik, Katarzyna; Postnova, Tatiana I; Ratnikov, Boris I; Eroshkin, Alexei M; Motamedchaboki, Khatereh; S | The Journal of biological chemistry | 19726693 | 2009 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/19726693 |
| Using total internal reflection fluorescence (TIRF) microscopy to visualize cortical actin and microtubules in the Drosophila syncytial embryo. | Webb, Rebecca L; Rozov, Orr; Watkins, Simon C; McCartney, Brooke M | Developmental dynamics : an official publication of the American Association of Anatomists | 19718762 | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19718762 |
| Bone marrow-derived cathepsin K cleaves SPARC in bone metastasis. | Podgorski, Izabela; Linebaugh, Bruce E; Koblinski, Jennifer E; Rudy, Deborah L; Herroon, Mackenzie K; Olive, Mary B; Sloane, Bonnie F | The American journal of pathology | 19700761 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19700761 |
| Interrelations between C4 ketogenesis, C5 ketogenesis, and anaplerosis in the perfused rat liver. | Deng, Shuang; Zhang, Guo-Fang; Kasumov, Takhar; Roe, Charles R; Brunengraber, Henri | The Journal of biological chemistry | 19666922 | 2009 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/19666922 |
| New connections, new components, real dynamics. | Bader, Joel S | Science signaling | 19654414 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19654414 |
| An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. | Forster, Friedrich; Lasker, Keren; Beck, Florian; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang | Biochemical and biophysical research communications | 19653995 | 2009 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/19653995 |
| Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures. | Novak, Igor L; Kraikivski, Pavel; Slepchenko, Boris M | Biophysical journal | 19651034 | 2009 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/19651034 |
| Biochemical mechanisms for regulating protrusion by nematode major sperm protein. | Stajic, Jelena; Wolgemuth, Charles W | Biophysical journal | 19651033 | 2009 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/19651033 |
| Lipidomics: developments and applications. | Han, Xianlin | Journal of chromatography. B, Analytical technologies in the biomedical and life sciences | 19640809 | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/19640809 |
| Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. | Kandasamy, Kumaran; Pandey, Akhilesh; Molina, Henrik | Analytical chemistry | 19639959 | 2009 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/19639959 |
| Comparative assessment of substrates and activity based probes as tools for non-invasive optical imaging of cysteine protease activity. | Blum, Galia; Weimer, Robby M; Edgington, Laura E; Adams, Walter; Bogyo, Matthew | PloS one | 19636372 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19636372 |
| Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. | Amanchy, Ramars; Zhong, Jun; Hong, Rosa; Kim, James H; Gucek, Marjan; Cole, Robert N; Molina, Henrik; Pandey, Akhilesh | Molecular oncology | 19632164 | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19632164 |
| Design, syntheses, and evaluation of Taspase1 inhibitors. | Lee, Jeong Tae; Chen, David Y; Yang, Zhimou; Ramos, Alexander D; Hsieh, James J-D; Bogyo, Matthew | Bioorganic & medicinal chemistry letters | 19631530 | 2009 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/19631530 |
| PathBuilder--open source software for annotating and developing pathway resources. | Kandasamy, Kumaran; Keerthikumar, Shivakumar; Raju, Rajesh; Keshava Prasad, T S; Ramachandra, Y L; Mohan, Sujatha; Pandey, Akhilesh | Bioinformatics (Oxford, England) | 19628504 | 2009 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/19628504 |
| Osmotic induction of calcium accumulation in human embryonic kidney cells detected with a high sensitivity FRET calcium sensor. | Hou, Bi-Huei; Takanaga, Hitomi; Griesbeck, Oliver; Frommer, Wolf B | Cell calcium | 19628278 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19628278 |
| Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains. | Sims, Joshua J; Haririnia, Aydin; Dickinson, Bryan C; Fushman, David; Cohen, Robert E | Nature structural & molecular biology | 19620964 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19620964 |
| Using small molecules to dissect mechanisms of microbial pathogenesis. | Puri, Aaron W; Bogyo, Matthew | ACS chemical biology | 19606820 | 2009 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/19606820 |
| scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms. | Falco, Crystal N; Dykstra, Kaitlyn M; Yates, Bradley P; Berget, Peter B | Biotechnology journal | 19606431 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19606431 |
| Novel DNA binding properties of the Mcm10 protein from Saccharomyces cerevisiae. | Eisenberg, Shlomo; Korza, George; Carson, John; Liachko, Ivan; Tye, Bik-Kwoon | The Journal of biological chemistry | 19605346 | 2009 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/19605346 |
| Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes. | Edgington, Laura E; Berger, Alicia B; Blum, Galia; Albrow, Victoria E; Paulick, Margot G; Lineberry, Neil; Bogyo, Matthew | Nature medicine | 19597506 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19597506 |
| Toxoplasma gondii cathepsin L is the primary target of the invasion-inhibitory compound morpholinurea-leucyl-homophenyl-vinyl sulfone phenyl. | Larson, Eric T; Parussini, Fabiola; Huynh, My-Hang; Giebel, Jonathan D; Kelley, Angela M; Zhang, Li; Bogyo, Matthew; Merritt, Ethan A; Carruthers, Vern B | The Journal of biological chemistry | 19596863 | 2009 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/19596863 |
| Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics. | Niittylae, Totte; Chaudhuri, Bhavna; Sauer, Uwe; Frommer, Wolf B | Methods in molecular biology (Clifton, N.J.) | 19588116 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19588116 |
| Insights into the molecular architecture of the 26S proteasome. | Nickell, Stephan; Beck, Florian; Scheres, Sjors H W; Korinek, Andreas; Forster, Friedrich; Lasker, Keren; Mihalache, Oana; Sun, Na; Nagy, Istvan; Sali, Andrej; Plitzko, Jurgen M; Carazo, Jose-Maria; Mann, Matthias; Baumeister, Wolfgang | Proceedings of the National Academy of Sciences of the United States of America | 19581588 | 2009 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/19581588 |
| A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. | Gradolatto, Angeline; Smart, Sherri K; Byrum, Stephanie; Blair, Lauren P; Rogers, Richard S; Kolar, Elizabeth A; Lavender, Heather; Larson, Signe K; Aitchison, John D; Taverna, Sean D; Tackett, Alan J | Molecular and cellular biology | 19581291 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19581291 |
| Is there glucose production outside of the liver and kidney? | Previs, Stephen F; Brunengraber, Daniel Z; Brunengraber, Henri | Annual review of nutrition | 19575601 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19575601 |
| In vitro growth environment produces lipidomic and electron transport chain abnormalities in mitochondria from non-tumorigenic astrocytes and brain tumours. | Kiebish, Michael A; Han, Xianlin; Cheng, Hua; Seyfried, Thomas N | ASN neuro | 19570033 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19570033 |
| NMR-based metabolomics of urine for the atherosclerotic mouse model using apolipoprotein-E deficient mice. | Leo, Gregory C; Darrow, Andrew L | Magnetic resonance in chemistry : MRC | 19565469 | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19565469 |
| Timp-2 binding with cellular MT1-MMP stimulates invasion-promoting MEK/ERK signaling in cancer cells. | Sounni, Nor Eddine; Rozanov, Dmitri V; Remacle, Albert G; Golubkov, Vladislav S; Noel, Agnes; Strongin, Alex Y | International journal of cancer. Journal international du cancer | 19551841 | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/19551841 |
| Using a microfluidic device for high-content analysis of cell signaling. | Cheong, Raymond; Wang, Chiaochun Joanne; Levchenko, Andre | Science signaling | 19531802 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19531802 |
| Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. | DeGrasse, Jeffrey A; DuBois, Kelly N; Devos, Damien; Siegel, T Nicolai; Sali, Andrej; Field, Mark C; Rout, Michael P; Chait, Brian T | Molecular & cellular proteomics : MCP | 19525551 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19525551 |
| Nuclear pore complex biogenesis. | Fernandez-Martinez, Javier; Rout, Michael P | Current opinion in cell biology | 19524430 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19524430 |
| Kinematics of the swimming of Spiroplasma. | Yang, Jing; Wolgemuth, Charles W; Huber, Greg | Physical review letters | 19519138 | 2009 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/19519138 |
| Capillary electrophoresis with electrospray ionization mass spectrometric detection for single-cell metabolomics. | Lapainis, Theodore; Rubakhin, Stanislav S; Sweedler, Jonathan V | Analytical chemistry | 19518091 | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19518091 |
| Long-term persistence and spectral blue shifting of quantum dots in vivo. | Fitzpatrick, James A J; Andreko, Susan K; Ernst, Lauren A; Waggoner, Alan S; Ballou, Byron; Bruchez, Marcel P | Nano letters | 19518087 | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19518087 |
| Engineering a leucine zipper-TRAIL homotrimer with improved cytotoxicity in tumor cells. | Rozanov, Dmitri V; Savinov, Alexei Y; Golubkov, Vladislav S; Rozanova, Olga L; Postnova, Tatiana I; Sergienko, Eduard A; Vasile, Stefan; Aleshin, Alexander E; Rega, Michele F; Pellecchia, Maurizio; Strongin, Alex Y | Molecular cancer therapeutics | 19509255 | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19509255 |
| Expression of a Dianthus flavonoid glucosyltransferase in Saccharomyces cerevisiae for whole-cell biocatalysis. | Werner, Sean R; Morgan, John A | Journal of biotechnology | 19500622 | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19500622 |
| Modifying the charge state distribution of proteins in electrospray ionization mass spectrometry by chemical derivatization. | Krusemark, Casey J; Frey, Brian L; Belshaw, Peter J; Smith, Lloyd M | Journal of the American Society for Mass Spectrometry | 19481956 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19481956 |
| NS4A regulates the ATPase activity of the NS3 helicase: a novel cofactor role of the non-structural protein NS4A from West Nile virus. | Shiryaev, Sergey A; Chernov, Andrei V; Aleshin, Alexander E; Shiryaeva, Tatiana N; Strongin, Alex Y | The Journal of general virology | 19474250 | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19474250 |
| Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin. | Shen, Aimee; Lupardus, Patrick J; Albrow, Victoria E; Guzzetta, Andrew; Powers, James C; Garcia, K Christopher; Bogyo, Matthew | Nature chemical biology | 19465933 | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19465933 |
| Nuclear magnetic resonance spectroscopy-based metabolomics of the fatty pancreas: implicating fat in pancreatic pathology. | Zyromski, Nicholas J; Mathur, Abhishek; Gowda, G A Nagana; Murphy, Carl; Swartz-Basile, Deborah A; Wade, Terence E; Pitt, Henry A; Raftery, Daniel | Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] | 19451751 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19451751 |
| c-Myc activates multiple metabolic networks to generate substrates for cell-cycle entry. | Morrish, F; Isern, N; Sadilek, M; Jeffrey, M; Hockenbery, D M | Oncogene | 19448666 | 2009 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/19448666 |
| A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. | Bell, Alexander W; Deutsch, Eric W; Au, Catherine E; Kearney, Robert E; Beavis, Ron; Sechi, Salvatore; Nilsson, Tommy; Bergeron, John J M; HUPO Test Sample Working Group | Nature methods | 19448641 | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19448641 |
| 1H NMR metabolomics study of age profiling in children. | Gu, Haiwei; Pan, Zhengzheng; Xi, Bowei; Hainline, Bryan E; Shanaiah, Narasimhamurthy; Asiago, Vincent; Gowda, G A Nagana; Raftery, Daniel | NMR in biomedicine | 19441074 | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19441074 |
| VEGF-A induces angiogenesis by perturbing the cathepsin-cysteine protease inhibitor balance in venules, causing basement membrane degradation and mother vessel formation. | Chang, Sung-Hee; Kanasaki, Keizo; Gocheva, Vasilena; Blum, Galia; Harper, Jay; Moses, Marsha A; Shih, Shou-Ching; Nagy, Janice A; Joyce, Johanna; Bogyo, Matthew; Kalluri, Raghu; Dvorak, Harold F | Cancer research | 19435903 | 2009 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/19435903 |
| An open model of actin dendritic nucleation. | Ditlev, Jonathon A; Vacanti, Nathaniel M; Novak, Igor L; Loew, Leslie M | Biophysical journal | 19413959 | 2009 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/19413959 |
| Automated lipid identification and quantification by multidimensional mass spectrometry-based shotgun lipidomics. | Yang, Kui; Cheng, Hua; Gross, Richard W; Han, Xianlin | Analytical chemistry | 19408941 | 2009 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/19408941 |
| Proteolytic and non-proteolytic roles of membrane type-1 matrix metalloproteinase in malignancy. | Strongin, Alex Y | Biochimica et biophysica acta | 19406172 | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19406172 |
| Dynamics of glutathione and ophthalmate traced with 2H-enriched body water in rats and humans. | Kombu, Rajan S; Zhang, Guo-Fang; Abbas, Rime; Mieyal, John J; Anderson, Vernon E; Kelleher, Joanne K; Sanabria, Juan R; Brunengraber, Henri | American journal of physiology. Endocrinology and metabolism | 19401458 | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19401458 |
| Model-based global analysis of heterogeneous experimental data using gfit. | Levin, Mikhail K; Hingorani, Manju M; Holmes, Raquell M; Patel, Smita S; Carson, John H | Methods in molecular biology (Clifton, N.J.) | 19399438 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19399438 |
| Rule-based modeling of biochemical systems with BioNetGen. | Faeder, James R; Blinov, Michael L; Hlavacek, William S | Methods in molecular biology (Clifton, N.J.) | 19399430 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19399430 |
| Structure-based ab initio prediction of transcription factor-binding sites. | Liu, L Angela; Bader, Joel S | Methods in molecular biology (Clifton, N.J.) | 19381536 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19381536 |
| High throughput substrate phage display for protease profiling. | Ratnikov, Boris; Cieplak, Piotr; Smith, Jeffrey W | Methods in molecular biology (Clifton, N.J.) | 19377968 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19377968 |
| Multiplexed force measurements on live cells with holographic optical tweezers. | Mejean, Cecile O; Schaefer, Andrew W; Millman, Eleanor A; Forscher, Paul; Dufresne, Eric R | Optics express | 19365444 | 2009 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/19365444 |
| ModLink+: improving fold recognition by using protein-protein interactions. | Fornes, Oriol; Aragues, Ramon; Espadaler, Jordi; Marti-Renom, Marc A; Sali, Andrej; Oliva, Baldo | Bioinformatics (Oxford, England) | 19357100 | 2009 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/19357100 |
| Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. | Chen, Chien-Sheng; Sullivan, Sean; Anderson, Troy; Tan, Aik Choon; Alex, Philip J; Brant, Steven R; Cuffari, Carmen; Bayless, Theodore M; Talor, Monica V; Burek, C Lynne; Wang, Huan; Li, Richard; Datta, Lisa Wu; Wu, Yuqiong; Winslow, Raimond L; Zhu, Heng; | Molecular & cellular proteomics : MCP | 19357087 | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19357087 |
| Autocatalytic activation of the furin zymogen requires removal of the emerging enzyme's N-terminus from the active site. | Gawlik, Katarzyna; Shiryaev, Sergey A; Zhu, Wenhong; Motamedchaboki, Khatereh; Desjardins, Roxane; Day, Robert; Remacle, Albert G; Stec, Boguslaw; Strongin, Alex Y | PloS one | 19352504 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19352504 |
| Live-cell imaging demonstrates extracellular matrix degradation in association with active cathepsin B in caveolae of endothelial cells during tube formation. | Cavallo-Medved, Dora; Rudy, Deborah; Blum, Galia; Bogyo, Matthew; Caglic, Dejan; Sloane, Bonnie F | Experimental cell research | 19331819 | 2009 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/19331819 |
| Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. | Bachovchin, Daniel A; Brown, Steven J; Rosen, Hugh; Cravatt, Benjamin F | Nature biotechnology | 19329999 | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19329999 |
| Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80. | Sims, Joshua J; Cohen, Robert E | Molecular cell | 19328070 | 2009 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/19328070 |
| High-pressure ion mobility spectrometry. | Davis, Eric J; Dwivedi, Prabha; Tam, Maggie; Siems, William F; Hill, Herbert H | Analytical chemistry | 19323457 | 2009 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/19323457 |
| Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. | Lin, Yu-yi; Lu, Jin-ying; Zhang, Junmei; Walter, Wendy; Dang, Weiwei; Wan, Jun; Tao, Sheng-Ce; Qian, Jiang; Zhao, Yingming; Boeke, Jef D; Berger, Shelley L; Zhu, Heng | Cell | 19303850 | 2009 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/19303850 |
| Matrix metalloproteinase proteolysis of the myelin basic protein isoforms is a source of immunogenic peptides in autoimmune multiple sclerosis. | Shiryaev, Sergey A; Savinov, Alexei Y; Cieplak, Piotr; Ratnikov, Boris I; Motamedchaboki, Khatereh; Smith, Jeffrey W; Strongin, Alex Y | PloS one | 19300513 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19300513 |
| The tethered infinitesimal tori and spheres algorithm: a versatile calculator for axisymmetric problems in equilibrium membrane mechanics. | Lim, Gerald H W; Huber, Greg | Biophysical journal | 19289034 | 2009 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/19289034 |
| Epigenetic control of the invasion-promoting MT1-MMP/MMP-2/TIMP-2 axis in cancer cells. | Chernov, Andrei V; Sounni, Nor Eddine; Remacle, Albert G; Strongin, Alex Y | The Journal of biological chemistry | 19286653 | 2009 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/19286653 |
| Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. | Wan, Yakun; Saleem, Ramsey A; Ratushny, Alexander V; Roda, Oriol; Smith, Jennifer J; Lin, Chan-Hsien; Chiang, Jung-Hsien; Aitchison, John D | Molecular and cellular biology | 19273605 | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19273605 |
| Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex. | Zhong, Yun; Wang, Qing Jun; Li, Xianting; Yan, Ying; Backer, Jonathan M; Chait, Brian T; Heintz, Nathaniel; Yue, Zhenyu | Nature cell biology | 19270693 | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19270693 |
| Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. | Yang, Yi; Chaerkady, Raghothama; Beer, Michael A; Mendell, Joshua T; Pandey, Akhilesh | Proteomics | 19253296 | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19253296 |
| Levels and localization of mechanosensitive channel proteins in Bacillus subtilis. | Wahome, Paul G; Cowan, Ann E; Setlow, Barbara; Setlow, Peter | Archives of microbiology | 19252899 | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19252899 |
| Fluorescein thiocarbamyl amino acids as internal standards for migration time correction in capillary sieving electrophoresis. | Pugsley, Haley R; Swearingen, Kristian E; Dovichi, Norman J | Journal of chromatography. A | 19249052 | 2009 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/19249052 |
| Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. | Lasker, Keren; Topf, Maya; Sali, Andrej; Wolfson, Haim J | Journal of molecular biology | 19233204 | 2009 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/19233204 |
| Biochemical evidence of the interactions of membrane type-1 matrix metalloproteinase (MT1-MMP) with adenine nucleotide translocator (ANT): potential implications linking proteolysis with energy metabolism in cancer cells. | Radichev, Ilian A; Remacle, Albert G; Sounni, Nor Eddine; Shiryaev, Sergey A; Rozanov, Dmitri V; Zhu, Wenhong; Golubkova, Natalya V; Postnova, Tatiana I; Golubkov, Vladislav S; Strongin, Alex Y | The Biochemical journal | 19232058 | 2009 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/19232058 |
| The structural dynamics of macromolecular processes. | Russel, Daniel; Lasker, Keren; Phillips, Jeremy; Schneidman-Duhovny, Dina; Velazquez-Muriel, Javier A; Sali, Andrej | Current opinion in cell biology | 19223165 | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19223165 |
| HistoneHits: a database for histone mutations and their phenotypes. | Huang, Hailiang; Maertens, Alexandra M; Hyland, Edel M; Dai, Junbiao; Norris, Anne; Boeke, Jef D; Bader, Joel S | Genome research | 19218532 | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19218532 |
| Using genetic mouse models to study the biology and pathology of autophagy in the central nervous system. | Yue, Zhenyu; Holstein, Gay R; Chait, Brian T; Wang, Qing Jun | Methods in enzymology | 19216906 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19216906 |
| K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. | Cooper, Eric M; Cutcliffe, Colleen; Kristiansen, Troels Z; Pandey, Akhilesh; Pickart, Cecile M; Cohen, Robert E | The EMBO journal | 19214193 | 2009 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/19214193 |
| Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1. | Wang, Tao; Yin, Luming; Cooper, Eric M; Lai, Ming-Yih; Dickey, Seth; Pickart, Cecile M; Fushman, David; Wilkinson, Keith D; Cohen, Robert E; Wolberger, Cynthia | Journal of molecular biology | 19211026 | 2009 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/19211026 |
| Systematic analysis of choline-containing phospholipids using multi-dimensional mass spectrometry-based shotgun lipidomics. | Yang, Kui; Zhao, Zhongdan; Gross, Richard W; Han, Xianlin | Journal of chromatography. B, Analytical technologies in the biomedical and life sciences | 19201264 | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/19201264 |
| Metabolic flux correlations, genetic interactions, and disease. | Veeramani, Balaji; Bader, Joel S | Journal of computational biology : a journal of computational molecular cell biology | 19193147 | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19193147 |
| Regulation of peroxisome dynamics. | Smith, Jennifer J; Aitchison, John D | Current opinion in cell biology | 19188056 | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19188056 |
| Analysis of dye binding by and membrane potential in spores of Bacillus species. | Magge, A; Setlow, B; Cowan, A E; Setlow, P | Journal of applied microbiology | 19187156 | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19187156 |
| Temporal analysis of neural differentiation using quantitative proteomics. | Chaerkady, Raghothama; Kerr, Candace L; Marimuthu, Arivusudar; Kelkar, Dhanashree S; Kashyap, Manoj Kumar; Gucek, Marjan; Gearhart, John D; Pandey, Akhilesh | Journal of proteome research | 19173612 | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19173612 |
| Autocatalytic processing of procathepsin B is triggered by proenzyme activity. | Pungercar, Jerica Rozman; Caglic, Dejan; Sajid, Mohammed; Dolinar, Marko; Vasiljeva, Olga; Pozgan, Urska; Turk, Dusan; Bogyo, Matthew; Turk, Vito; Turk, Boris | The FEBS journal | 19143833 | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19143833 |
| Quantitative imaging for discovery and assembly of the metabo-regulome. | Okumoto, Sakiko; Takanaga, Hitomi; Frommer, Wolf B | The New phytologist | 19138219 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/19138219 |
| Substrate specificity of transthyretin: identification of natural substrates in the nervous system. | Liz, Marcia A; Fleming, Carolina E; Nunes, Ana F; Almeida, Maria R; Mar, Fernando M; Choe, Youngchool; Craik, Charles S; Powers, James C; Bogyo, Matthew; Sousa, Monica M | The Biochemical journal | 19138167 | 2009 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/19138167 |
| Functional live-cell imaging demonstrates that beta1-integrin promotes type IV collagen degradation by breast and prostate cancer cells. | Sameni, Mansoureh; Dosescu, Julie; Yamada, Kenneth M; Sloane, Bonnie F; Cavallo-Medved, Dora | Molecular imaging | 19123990 | 2008 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/19123990 |
| Triglyceride synthesis in epididymal adipose tissue: contribution of glucose and non-glucose carbon sources. | Bederman, Ilya R; Foy, Steven; Chandramouli, Visvanathan; Alexander, James C; Previs, Stephen F | The Journal of biological chemistry | 19114707 | 2009 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/19114707 |
| Development of an optimized activatable MMP-14 targeted SPECT imaging probe. | Watkins, Gregory A; Jones, Ella Fung; Scott Shell, M; VanBrocklin, Henry F; Pan, Mei-Hsiu; Hanrahan, Stephen M; Feng, Jin Jin; He, Jiang; Sounni, Nor Eddine; Dill, Ken A; Contag, Christopher H; Coussens, Lisa M; Franc, Benjamin L | Bioorganic & medicinal chemistry | 19109023 | 2009 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/19109023 |
| Automated trapping, assembly, and sorting with holographic optical tweezers. | Chapin, Stephen C; Germain, Vincent; Dufresne, Eric R | Optics express | 19096726 | 2006 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/19096726 |
| Precision and recall estimates for two-hybrid screens. | Huang, Hailiang; Bader, Joel S | Bioinformatics (Oxford, England) | 19091773 | 2009 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/19091773 |
| Imaging and quantifying the dynamics of tumor-associated proteolysis. | Sameni, Mansoureh; Cavallo-Medved, Dora; Dosescu, Julie; Jedeszko, Christopher; Moin, Kamiar; Mullins, Stefanie R; Olive, Mary B; Rudy, Deborah; Sloane, Bonnie F | Clinical & experimental metastasis | 19082919 | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19082919 |
| Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction. | Norris, Anne; Bianchet, Mario A; Boeke, Jef D | PLoS genetics | 19079580 | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19079580 |
| Plasma membrane microdomains regulate turnover of transport proteins in yeast. | Grossmann, Guido; Malinsky, Jan; Stahlschmidt, Wiebke; Loibl, Martin; Weig-Meckl, Ina; Frommer, Wolf B; Opekarova, Miroslava; Tanner, Widmar | The Journal of cell biology | 19064668 | 2008 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/19064668 |
| Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. | Blinov, M L; Ruebenacker, O; Moraru, I I | IET systems biology | 19045831 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19045831 |
| Virtual Cell modelling and simulation software environment. | Moraru, I I; Schaff, J C; Slepchenko, B M; Blinov, M L; Morgan, F; Lakshminarayana, A; Gao, F; Li, Y; Loew, L M | IET systems biology | 19045830 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19045830 |
| Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast. | Kaplan, Tommy; Liu, Chih Long; Erkmann, Judith A; Holik, John; Grunstein, Michael; Kaufman, Paul D; Friedman, Nir; Rando, Oliver J | PLoS genetics | 19023413 | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19023413 |
| Visualization of bile homeostasis using (1)H-NMR spectroscopy as a route for assessing liver cancer. | Nagana Gowda, G A; Shanaiah, Narasimhamurthy; Cooper, Amanda; Maluccio, Mary; Raftery, Daniel | Lipids | 18982376 | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18982376 |
| Oscillatory phosphorylation of yeast Fus3 MAP kinase controls periodic gene expression and morphogenesis. | Hilioti, Zoe; Sabbagh Jr, Walid; Paliwal, Saurabh; Bergmann, Adriel; Goncalves, Marcus D; Bardwell, Lee; Levchenko, Andre | Current biology : CB | 18976914 | 2008 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/18976914 |
| High content cell screening in a microfluidic device. | Cheong, Raymond; Wang, Chiaochun Joanne; Levchenko, Andre | Molecular & cellular proteomics : MCP | 18953019 | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18953019 |
| High-yield isolation and subcellular proteomic characterization of nuclear and subnuclear structures from trypanosomes. | DeGrasse, Jeffrey A; Chait, Brian T; Field, Mark C; Rout, Michael P | Methods in molecular biology (Clifton, N.J.) | 18951162 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18951162 |
| Human Proteinpedia: a unified discovery resource for proteomics research. | Kandasamy, Kumaran; Keerthikumar, Shivakumar; Goel, Renu; Mathivanan, Suresh; Patankar, Nandini; Shafreen, Beema; Renuse, Santosh; Pawar, Harsh; Ramachandra, Y L; Acharya, Pradip Kumar; Ranganathan, Prathibha; Chaerkady, Raghothama; Keshava Prasad, T S; P | Nucleic acids research | 18948298 | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18948298 |
| Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. | Molina, Henrik; Yang, Yi; Ruch, Travis; Kim, Jae-Woo; Mortensen, Peter; Otto, Tamara; Nalli, Anuradha; Tang, Qi-Qun; Lane, M Daniel; Chaerkady, Raghothama; Pandey, Akhilesh | Journal of proteome research | 18947249 | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18947249 |
| Activity-based probes as a tool for functional proteomic analysis of proteases. | Fonovic, Marko; Bogyo, Matthew | Expert review of proteomics | 18937562 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18937562 |
| Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. | Dixon, Scott J; Fedyshyn, Yaroslav; Koh, Judice L Y; Prasad, T S Keshava; Chahwan, Charly; Chua, Gordon; Toufighi, Kiana; Baryshnikova, Anastasija; Hayles, Jacqueline; Hoe, Kwang-Lae; Kim, Dong-Uk; Park, Han-Oh; Myers, Chad L; Pandey, Akhilesh; Durocher, | Proceedings of the National Academy of Sciences of the United States of America | 18931302 | 2008 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/18931302 |
| End-on imaging: a new perspective on dorsoventral development in Drosophila embryos. | Witzberger, Melissa M; Fitzpatrick, James A J; Crowley, Justin C; Minden, Jonathan S | Developmental dynamics : an official publication of the American Association of Anatomists | 18855896 | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18855896 |
| Actin bundling: initiation mechanisms and kinetics. | Kraikivski, Pavel; Slepchenko, Boris M; Novak, Igor L | Physical review letters | 18851415 | 2008 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/18851415 |
| Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain. | Lupardus, Patrick J; Shen, Aimee; Bogyo, Matthew; Garcia, K Christopher | Science (New York, N.Y.) | 18845756 | 2008 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/18845756 |
| Structure and chemistry of the p300/CBP and Rtt109 histone acetyltransferases: implications for histone acetyltransferase evolution and function. | Wang, Ling; Tang, Yong; Cole, Philip A; Marmorstein, Ronen | Current opinion in structural biology | 18845255 | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18845255 |
| PMAP: databases for analyzing proteolytic events and pathways. | Igarashi, Yoshinobu; Heureux, Emily; Doctor, Kutbuddin S; Talwar, Priti; Gramatikova, Svetlana; Gramatikoff, Kosi; Zhang, Ying; Blinov, Michael; Ibragimova, Salmaz S; Boyd, Sarah; Ratnikov, Boris; Cieplak, Piotr; Godzik, Adam; Smith, Jeffrey W; Osterman, | Nucleic acids research | 18842634 | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18842634 |
| Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. | Qi, Yan; Suhail, Yasir; Lin, Yu-yi; Boeke, Jef D; Bader, Joel S | Genome research | 18832443 | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18832443 |
| How well can the accuracy of comparative protein structure models be predicted? | Eramian, David; Eswar, Narayanan; Shen, Min-Yi; Sali, Andrej | Protein science : a publication of the Protein Society | 18832340 | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18832340 |
| Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy. | Munger, Joshua; Bennett, Bryson D; Parikh, Anuraag; Feng, Xiao-Jiang; McArdle, Jessica; Rabitz, Herschel A; Shenk, Thomas; Rabinowitz, Joshua D | Nature biotechnology | 18820684 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18820684 |
| Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723. | Huang, Yan; Xun, Randy; Chen, Guanjun; Xun, Luying | Journal of bacteriology | 18820023 | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18820023 |
| Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. | Dai, Junbiao; Hyland, Edel M; Yuan, Daniel S; Huang, Hailiang; Bader, Joel S; Boeke, Jef D | Cell | 18805098 | 2008 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/18805098 |
| Chemical probes for histone-modifying enzymes. | Cole, Philip A | Nature chemical biology | 18800048 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18800048 |
| Inhibition of fatty-acid synthase induces caspase-8-mediated tumor cell apoptosis by up-regulating DDIT4. | Knowles, Lynn M; Yang, Chen; Osterman, Andrei; Smith, Jeffrey W | The Journal of biological chemistry | 18796435 | 2008 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/18796435 |
| Metabolomics-based methods for early disease diagnostics. | Gowda, G A Nagana; Zhang, Shucha; Gu, Haiwei; Asiago, Vincent; Shanaiah, Narasimhamurthy; Raftery, Daniel | Expert review of molecular diagnostics | 18785810 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18785810 |
| Luteinizing hormone causes MAP kinase-dependent phosphorylation and closure of connexin 43 gap junctions in mouse ovarian follicles: one of two paths to meiotic resumption. | Norris, Rachael P; Freudzon, Marina; Mehlmann, Lisa M; Cowan, Ann E; Simon, Alexander M; Paul, David L; Lampe, Paul D; Jaffe, Laurinda A | Development (Cambridge, England) | 18776144 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18776144 |
| Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. | Guha, Udayan; Chaerkady, Raghothama; Marimuthu, Arivusudar; Patterson, A Scott; Kashyap, Manoj K; Harsha, H C; Sato, Mitsuo; Bader, Joel S; Lash, Alex E; Minna, John D; Pandey, Akhilesh; Varmus, Harold E | Proceedings of the National Academy of Sciences of the United States of America | 18776048 | 2008 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/18776048 |
| Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats. | Zhang, Shucha; Nagana Gowda, G A; Asiago, Vincent; Shanaiah, Narasimhamurthy; Barbas, Coral; Raftery, Daniel | Analytical biochemistry | 18775407 | 2008 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/18775407 |
| Reduced-representation methylation mapping. | Jeddeloh, Jeffrey A; Greally, John M; Rando, Oliver J | Genome biology | 18771577 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18771577 |
| Apolipoprotein E mediates sulfatide depletion in animal models of Alzheimer's disease. | Cheng, Hua; Zhou, Yunhua; Holtzman, David M; Han, Xianlin | Neurobiology of aging | 18762354 | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18762354 |
| A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. | Ozhalici-Unal, Hayriye; Pow, Crystal Lee; Marks, Sarah A; Jesper, Lawrence D; Silva, Gloria L; Shank, Nathaniel I; Jones, Elizabeth W; Burnette 3rd, James M; Berget, Peter B; Armitage, Bruce A | Journal of the American Chemical Society | 18761447 | 2008 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/18761447 |
| Deciphering the unusual acylation pattern of Helicobacter pylori lipid A. | Stead, Christopher M; Beasley, Ashley; Cotter, Robert J; Trent, M Stephen | Journal of bacteriology | 18757539 | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18757539 |
| Direct quantitation of psychosine from alkaline-treated lipid extracts with a semi-synthetic internal standard. | Jiang, Xuntian; Yang, Kui; Han, Xianlin | Journal of lipid research | 18753677 | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18753677 |
| A domino effect in antifolate drug action in Escherichia coli. | Kwon, Yun Kyung; Lu, Wenyun; Melamud, Eugene; Khanam, Nurussaba; Bognar, Andrew; Rabinowitz, Joshua D | Nature chemical biology | 18724364 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18724364 |
| Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. | Zhang, Junmei; Sprung, Robert; Pei, Jimin; Tan, Xiaohong; Kim, Sungchan; Zhu, Heng; Liu, Chuan-Fa; Grishin, Nick V; Zhao, Yingming | Molecular & cellular proteomics : MCP | 18723842 | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18723842 |
| Characterization of spores of Bacillus subtilis that lack most coat layers. | Ghosh, Sonali; Setlow, Barbara; Wahome, Paul G; Cowan, Ann E; Plomp, Marco; Malkin, Alexander J; Setlow, Peter | Journal of bacteriology | 18723620 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18723620 |
| Interface of an array of five capillaries with an array of one-nanoliter wells for high-resolution electrophoretic analysis as an approach to high-throughput chemical cytometry. | Boardman, Anna K; McQuaide, Sarah C; Zhu, Cuiru; Whitmore, Colin D; Lidstrom, Mary E; Dovichi, Norman J | Analytical chemistry | 18717573 | 2008 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/18717573 |
| A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. | Chaerkady, Raghothama; Harsha, H C; Nalli, Anuradha; Gucek, Marjan; Vivekanandan, Perumal; Akhtar, Javed; Cole, Robert N; Simmers, Jessica; Schulick, Richard D; Singh, Sujay; Torbenson, Michael; Pandey, Akhilesh; Thuluvath, Paul J | Journal of proteome research | 18715028 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18715028 |
| Kinetic flux profiling for quantitation of cellular metabolic fluxes. | Yuan, Jie; Bennett, Bryson D; Rabinowitz, Joshua D | Nature protocols | 18714301 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18714301 |
| Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. | Bennett, Bryson D; Yuan, Jie; Kimball, Elizabeth H; Rabinowitz, Joshua D | Nature protocols | 18714298 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18714298 |
| SIMS and MALDI MS imaging of the spinal cord. | Monroe, Eric B; Annangudi, Suresh P; Hatcher, Nathan G; Gutstein, Howard B; Rubakhin, Stanislav S; Sweedler, Jonathan V | Proteomics | 18712768 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18712768 |
| Adapting the stretched sample method from tissue profiling to imaging. | Zimmerman, Tyler A; Monroe, Eric B; Sweedler, Jonathan V | Proteomics | 18712762 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18712762 |
| Human monocytes augment invasiveness and proteolytic activity of inflammatory breast cancer. | Mohamed, Mona Mostafa; Cavallo-Medved, Dora; Sloane, Bonnie F | Biological chemistry | 18710343 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18710343 |
| Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification. | Zhu, Jianmei; Zhu, Shanshan; Guzzo, Catherine M; Ellis, Nathan A; Sung, Ki Sa; Choi, Cheol Yong; Matunis, Michael J | The Journal of biological chemistry | 18708356 | 2008 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/18708356 |
| Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. | Chaudhuri, Bhavna; Hormann, Friederike; Lalonde, Sylvie; Brady, Siobhan M; Orlando, David A; Benfey, Philip; Frommer, Wolf B | The Plant journal : for cell and molecular biology | 18702670 | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18702670 |
| Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. | Amanchy, Ramars; Zhong, Jun; Molina, Henrik; Chaerkady, Raghothama; Iwahori, Akiko; Kalume, Dario Eluan; Gronborg, Mads; Joore, Jos; Cope, Leslie; Pandey, Akhilesh | Journal of proteome research | 18698806 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18698806 |
| Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. | Forster, Friedrich; Webb, Benjamin; Krukenberg, Kristin A; Tsuruta, Hiro; Agard, David A; Sali, Andrej | Journal of molecular biology | 18694757 | 2008 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/18694757 |
| Predicting optimal resolving power for ambient pressure ion mobility spectrometry. | Kanu, Abu B; Gribb, Molly M; Hill Jr, Herbert H | Analytical chemistry | 18683951 | 2008 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/18683951 |
| Quantification of carnitine and acylcarnitines in biological matrices by HPLC electrospray ionization-mass spectrometry. | Minkler, Paul E; Stoll, Maria S K; Ingalls, Stephen T; Yang, Shuming; Kerner, Janos; Hoppel, Charles L | Clinical chemistry | 18678604 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18678604 |
| A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. | Lin, Yu-yi; Qi, Yan; Lu, Jin-ying; Pan, Xuewen; Yuan, Daniel S; Zhao, Yingming; Bader, Joel S; Boeke, Jef D | Genes & development | 18676811 | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/18676811 |
| Amino(oligo)thiophene-based environmentally sensitive biomembrane chromophores. | Yan, Ping; Xie, Aifang; Wei, Meide; Loew, Leslie M | The Journal of organic chemistry | 18665648 | 2008 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/18665648 |
| The role of cathepsin X in the migration and invasiveness of T lymphocytes. | Jevnikar, Zala; Obermajer, Natasa; Bogyo, Matthew; Kos, Janko | Journal of cell science | 18664495 | 2008 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/18664495 |
| On sensitivity amplification in intracellular signaling cascades. | Racz, Eva; Slepchenko, Boris M | Physical biology | 18663279 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18663279 |
| Bioengineering a humanized acne microenvironment model: proteomics analysis of host responses to Propionibacterium acnes infection in vivo. | Nakatsuji, Teruaki; Shi, Yang; Zhu, Wenhong; Huang, Cheng-Po; Chen, Yun-Ru; Lee, Dong-Youn; Smith, Jeffery W; Zouboulis, Christos C; Gallo, Richard L; Huang, Chun-Ming | Proteomics | 18651708 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18651708 |
| The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency. | Sallee, Nathan A; Rivera, Gonzalo M; Dueber, John E; Vasilescu, Dan; Mullins, R Dyche; Mayer, Bruce J; Lim, Wendell A | Nature | 18650806 | 2008 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/18650806 |
| Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. | Tao, Sheng-Ce; Li, Yu; Zhou, Jiangbing; Qian, Jiang; Schnaar, Ronald L; Zhang, Ying; Goldstein, Irwin J; Zhu, Heng; Schneck, Jonathan P | Glycobiology | 18625848 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18625848 |
| Control of transcriptional variability by overlapping feed-forward regulatory motifs. | Ratushny, Alexander V; Ramsey, Stephen A; Roda, Oriol; Wan, Yakun; Smith, Jennifer J; Aitchison, John D | Biophysical journal | 18621837 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18621837 |
| Casein kinase 2 binds to the C terminus of Na+/H+ exchanger 3 (NHE3) and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. | Sarker, Rafiquel; Gronborg, Mads; Cha, Boyoung; Mohan, Sachin; Chen, Yueping; Pandey, Akhilesh; Litchfield, David; Donowitz, Mark; Li, Xuhang | Molecular biology of the cell | 18614797 | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18614797 |
| Carbon-on-metal films for surface plasmon resonance detection of DNA arrays. | Lockett, Matthew R; Weibel, Stephen C; Phillips, Margaret F; Shortreed, Michael R; Sun, Bin; Corn, Robert M; Hamers, Robert J; Cerrina, Franco; Smith, Lloyd M | Journal of the American Chemical Society | 18597426 | 2008 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/18597426 |
| Stable isotope-coded quaternization for comparative quantification of estrogen metabolites by high-performance liquid chromatography-electrospray ionization mass spectrometry. | Yang, Wen-Chu; Regnier, Fred E; Sliva, Dan; Adamec, Jiri | Journal of chromatography. B, Analytical technologies in the biomedical and life sciences | 18595786 | 2008 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/18595786 |
| Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. | Shachaf, Catherine M; Gentles, Andrew J; Elchuri, Sailaja; Sahoo, Debashis; Soen, Yoav; Sharpe, Orr; Perez, Omar D; Chang, Maria; Mitchel, Dennis; Robinson, William H; Dill, David; Nolan, Garry P; Plevritis, Sylvia K; Felsher, Dean W | Cancer research | 18593912 | 2008 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/18593912 |
| Mass spectrometry of acoustically levitated droplets. | Westphall, Michael S; Jorabchi, Kaveh; Smith, Lloyd M | Analytical chemistry | 18582090 | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/18582090 |
| Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage. | Celic, Ivana; Verreault, Alain; Boeke, Jef D | Genetics | 18579506 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18579506 |
| Metabolite identification using a nanoelectrospray LC-EC-array-MS integrated system. | Schiavo, Susan; Ebbel, Erika; Sharma, Swati; Matson, Wayne; Kristal, Bruce S; Hersch, Steven; Vouros, Paul | Analytical chemistry | 18576668 | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/18576668 |
| Human Proteinpedia as a resource for clinical proteomics. | Mathivanan, Suresh; Pandey, Akhilesh | Molecular & cellular proteomics : MCP | 18573810 | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18573810 |
| Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. | Tang, Yong; Holbert, Marc A; Wurtele, Hugo; Meeth, Katrina; Rocha, Walter; Gharib, Marlene; Jiang, Eva; Thibault, Pierre; Verreault, Alain; Verrault, Alain; Cole, Philip A; Marmorstein, Ronen | Nature structural & molecular biology | 18568037 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18568037 |
| Global impact of oncogenic Src on a phosphotyrosine proteome. | Luo, Weifeng; Slebos, Robbert J; Hill, Salisha; Li, Ming; Brabek, Jan; Amanchy, Ramars; Chaerkady, Raghothama; Pandey, Akhilesh; Ham, Amy-Joan L; Hanks, Steven K | Journal of proteome research | 18563927 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18563927 |
| The incredible shrinking world of DNA microarrays. | Wheelan, Sarah J; Martinez Murillo, Francisco; Boeke, Jef D | Molecular bioSystems | 18563246 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18563246 |
| Visualizing protease activity in living cells: from two dimensions to four dimensions. | Jedeszko, Christopher; Sameni, Mansoureh; Olive, Mary B; Moin, Kamiar; Sloane, Bonnie F | Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.] | 18551423 | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18551423 |
| High-sugar diets increase cardiac dysfunction and mortality in hypertension compared to low-carbohydrate or high-starch diets. | Sharma, Naveen; Okere, Isidore C; Barrows, Brian R; Lei, Biao; Duda, Monika K; Yuan, Celvie L; Previs, Stephen F; Sharov, Victor G; Azimzadeh, Agnes M; Ernsberger, Paul; Hoit, Brian D; Sabbah, Hani; Stanley, William C | Journal of hypertension | 18551017 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18551017 |
| Metabolomic and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle. I. Interrelation between gluconeogenesis and cataplerosis; formation of methoxamates from aminooxyacetate and ketoacids. | Yang, Lili; Kombu, Rajan S; Kasumov, Takhar; Zhu, Shu-Han; Cendrowski, Andrea V; David, France; Anderson, Vernon E; Kelleher, Joanne K; Brunengraber, Henri | The Journal of biological chemistry | 18544527 | 2008 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/18544527 |
| Metabolomic and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle: II. Heterogeneity of metabolite labeling pattern. | Yang, Lili; Kasumov, Takhar; Kombu, Rajan S; Zhu, Shu-Han; Cendrowski, Andrea V; David, France; Anderson, Vernon E; Kelleher, Joanne K; Brunengraber, Henri | The Journal of biological chemistry | 18544526 | 2008 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/18544526 |
| Data management in structural genomics: an overview. | Haquin, Sabrina; Oeuillet, Eric; Pajon, Anne; Harris, Mark; Jones, Alwyn T; van Tilbeurgh, Herman; Markley, John L; Zolnai, Zolt; Poupon, Anne | Methods in molecular biology (Clifton, N.J.) | 18542857 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18542857 |
| Comprehensive comparison of collision induced dissociation and electron transfer dissociation. | Molina, Henrik; Matthiesen, Rune; Kandasamy, Kumaran; Pandey, Akhilesh | Analytical chemistry | 18540640 | 2008 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/18540640 |
| Microfluidics-based electrospray ionization enhances the intrasource separation of lipid classes and extends identification of individual molecular species through multi-dimensional mass spectrometry: development of an automated high-throughput platform f | Han, Xianlin; Yang, Kui; Gross, Richard W | Rapid communications in mass spectrometry : RCM | 18523984 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18523984 |
| Fluorescence resonance energy transfer sensors for quantitative monitoring of pentose and disaccharide accumulation in bacteria. | Kaper, Thijs; Lager, Ida; Looger, Loren L; Chermak, Diane; Frommer, Wolf B | Biotechnology for biofuels | 18522753 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18522753 |
| Molecular signature of MT1-MMP: transactivation of the downstream universal gene network in cancer. | Rozanov, Dmitri V; Savinov, Alexei Y; Williams, Roy; Liu, Kang; Golubkov, Vladislav S; Krajewski, Stan; Strongin, Alex Y | Cancer research | 18519667 | 2008 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/18519667 |
| Improved residual water suppression: WET180. | Mo, Huaping; Raftery, Daniel | Journal of biomolecular NMR | 18506578 | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18506578 |
| Substrate cleavage analysis of furin and related proprotein convertases. A comparative study. | Remacle, Albert G; Shiryaev, Sergey A; Oh, Eok-Soo; Cieplak, Piotr; Srinivasan, Anupama; Wei, Ge; Liddington, Robert C; Ratnikov, Boris I; Parent, Amelie; Desjardins, Roxane; Day, Robert; Smith, Jeffrey W; Lebl, Michal; Strongin, Alex Y | The Journal of biological chemistry | 18505722 | 2008 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/18505722 |
| Analytical strategies for LC-MS-based targeted metabolomics. | Lu, Wenyun; Bennett, Bryson D; Rabinowitz, Joshua D | Journal of chromatography. B, Analytical technologies in the biomedical and life sciences | 18502704 | 2008 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/18502704 |
| Saccharomyces cerevisiae Yta7 regulates histone gene expression. | Gradolatto, Angeline; Rogers, Richard S; Lavender, Heather; Taverna, Sean D; Allis, C David; Aitchison, John D; Tackett, Alan J | Genetics | 18493054 | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18493054 |
| Detection of protein modifications and counterfeit protein pharmaceuticals using isotope tags for relative and absolute quantification and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry: studies of insulins. | Ye, Hongping; Hill, John; Kauffman, John; Gryniewicz, Connie; Han, Xianlin | Analytical biochemistry | 18489896 | 2008 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/18489896 |
| Sulfatides facilitate apolipoprotein E-mediated amyloid-beta peptide clearance through an endocytotic pathway. | Zeng, Youchun; Han, Xianlin | Journal of neurochemistry | 18485101 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18485101 |
| Nitric-oxide-mediated zinc release contributes to hypoxic regulation of pulmonary vascular tone. | Bernal, Paula J; Leelavanichkul, Karanee; Bauer, Eileen; Cao, Rong; Wilson, Annette; Wasserloos, Karla J; Watkins, Simon C; Pitt, Bruce R; St Croix, Claudette M | Circulation research | 18483408 | 2008 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/18483408 |
| Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. | Li, Fuyang; Dong, Junchao; Pan, Xuewen; Oum, Ji-Hyun; Boeke, Jef D; Lee, Sang Eun | Molecular cell | 18471978 | 2008 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/18471978 |
| Caspase-8 cleaves histone deacetylase 7 and abolishes its transcription repressor function. | Scott, Fiona L; Fuchs, Greg J; Boyd, Sarah E; Denault, Jean-Bernard; Hawkins, Christine J; Dequiedt, Franck; Salvesen, Guy S | The Journal of biological chemistry | 18458084 | 2008 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/18458084 |
| Shotgun lipidomics reveals the temporally dependent, highly diversified cardiolipin profile in the mammalian brain: temporally coordinated postnatal diversification of cardiolipin molecular species with neuronal remodeling. | Cheng, Hua; Mancuso, David J; Jiang, Xuntian; Guan, Shaoping; Yang, Jingyue; Yang, Kui; Sun, Gang; Gross, Richard W; Han, Xianlin | Biochemistry | 18454555 | 2008 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/18454555 |
| Preserved protein synthesis in the heart in response to acute fasting and chronic food restriction despite reductions in liver and skeletal muscle. | Yuan, Celvie L; Sharma, Naveen; Gilge, Danielle A; Stanley, William C; Li, Yi; Hatzoglou, Maria; Previs, Stephen F | American journal of physiology. Endocrinology and metabolism | 18445754 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18445754 |
| Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. | Wang, Joy Xin; Breaker, Ronald R | Biochemistry and cell biology = Biochimie et biologie cellulaire | 18443629 | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18443629 |
| The two-component NS2B-NS3 proteinase represses DNA unwinding activity of the West Nile virus NS3 helicase. | Chernov, Andrei V; Shiryaev, Sergey A; Aleshin, Alexander E; Ratnikov, Boris I; Smith, Jeffrey W; Liddington, Robert C; Strongin, Alex Y | The Journal of biological chemistry | 18442976 | 2008 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/18442976 |
| Multiplexed RNA trafficking in oligodendrocytes and neurons. | Carson, John H; Gao, Yuanzheng; Tatavarty, Vedakumar; Levin, Mikhail K; Korza, George; Francone, Victor P; Kosturko, Linda D; Maggipinto, Michael J; Barbarese, Elisa | Biochimica et biophysica acta | 18442491 | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18442491 |
| Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. | Ben-Aroya, Shay; Coombes, Candice; Kwok, Teresa; O'Donnell, Kathryn A; Boeke, Jef D; Hieter, Philip | Molecular cell | 18439903 | 2008 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/18439903 |
| Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. | Saleem, Ramsey A; Knoblach, Barbara; Mast, Fred D; Smith, Jennifer J; Boyle, John; Dobson, C Melissa; Long-O'Donnell, Rose; Rachubinski, Richard A; Aitchison, John D | The Journal of cell biology | 18426976 | 2008 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/18426976 |
| Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. | Moorman, Nathaniel J; Cristea, Ileana M; Terhune, Scott S; Rout, Michael P; Chait, Brian T; Shenk, Thomas | Cell host & microbe | 18407068 | 2008 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/18407068 |
| Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. | Meluh, Pamela B; Pan, Xuewen; Yuan, Daniel S; Tiffany, Carol; Chen, Ou; Sookhai-Mahadeo, Sharon; Wang, Xiaoling; Peyser, Brian D; Irizarry, Rafael; Spencer, Forrest A; Boeke, Jef D | Methods in molecular biology (Clifton, N.J.) | 18392971 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18392971 |
| p21-Activated kinase 1 coordinates aberrant cell survival and pericellular proteolysis in a three-dimensional culture model for premalignant progression of human breast cancer. | Li, Quanwen; Mullins, Stefanie Roshy; Sloane, Bonnie F; Mattingly, Raymond R | Neoplasia (New York, N.Y.) | 18392133 | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18392133 |
| Chemokine and cytokine mediated loss of regulatory T cells in lymph nodes during pathogenic simian immunodeficiency virus infection. | Qin, Shulin; Sui, Yongjun; Soloff, Adam C; Junecko, Beth A Fallert; Kirschner, Denise E; Murphey-Corb, Michael A; Watkins, Simon C; Tarwater, Patrick M; Pease, James E; Barratt-Boyes, Simon M; Reinhart, Todd A | Journal of immunology (Baltimore, Md. : 1950) | 18390737 | 2008 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/18390737 |
| Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. | Wang, Joy Xin; Lee, Elaine R; Morales, Dianali Rivera; Lim, Jinsoo; Breaker, Ronald R | Molecular cell | 18374645 | 2008 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/18374645 |
| Detection of nitric oxide in single cells. | Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan V | The Analyst | 18365109 | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18365109 |
| Polarized immune responses differentially regulate cancer development. | Johansson, Magnus; Denardo, David G; Coussens, Lisa M | Immunological reviews | 18363999 | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18363999 |
| Novel isolation procedure for short-, medium-, and long-chain acyl-coenzyme A esters from tissue. | Minkler, Paul E; Kerner, Janos; Ingalls, Stephen T; Hoppel, Charles L | Analytical biochemistry | 18355435 | 2008 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/18355435 |
| Evaluation of alpha,beta-unsaturated ketone-based probes for papain-family cysteine proteases. | Yang, Zhimou; Fonovic, Marko; Verhelst, Steven H L; Blum, Galia; Bogyo, Matthew | Bioorganic & medicinal chemistry | 18343672 | 2009 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18343672 |
| Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. | Constantin, Tudor P; Silva, Gloria L; Robertson, Kelly L; Hamilton, Tamara P; Fague, Kaitlin; Waggoner, Alan S; Armitage, Bruce A | Organic letters | 18338898 | 2008 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/18338898 |
| Quantitative proteomics using stable isotope labeling with amino acids in cell culture. | Harsha, H C; Molina, Henrik; Pandey, Akhilesh | Nature protocols | 18323819 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18323819 |
| Integrating diverse data for structure determination of macromolecular assemblies. | Alber, Frank; Forster, Friedrich; Korkin, Dmitry; Topf, Maya; Sali, Andrej | Annual review of biochemistry | 18318657 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18318657 |
| Multiplexed dendritic targeting of alpha calcium calmodulin-dependent protein kinase II, neurogranin, and activity-regulated cytoskeleton-associated protein RNAs by the A2 pathway. | Gao, Yuanzheng; Tatavarty, Vedakumar; Korza, George; Levin, Mikhail K; Carson, John H | Molecular biology of the cell | 18305102 | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18305102 |
| Application of activity-based probes to the study of enzymes involved in cancer progression. | Paulick, Margot G; Bogyo, Matthew | Current opinion in genetics & development | 18294838 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18294838 |
| Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. | Savalia, Dhruti; Westblade, Lars F; Goel, Manisha; Florens, Laurence; Kemp, Priscilla; Akulenko, Natalja; Pavlova, Olga; Padovan, Julio C; Chait, Brian T; Washburn, Michael P; Ackermann, Hans-W; Mushegian, Arcady; Gabisonia, Tarasii; Molineux, Ian; Severi | Journal of molecular biology | 18294652 | 2008 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/18294652 |
| Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile virus two-component NS2B-NS3 proteinase. | Radichev, Ilian; Shiryaev, Sergey A; Aleshin, Alexander E; Ratnikov, Boris I; Smith, Jeffrey W; Liddington, Robert C; Strongin, Alex Y | The Journal of general virology | 18272753 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18272753 |
| Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions. | Westblade, Lars F; Minakhin, Leonid; Kuznedelov, Konstantin; Tackett, Alan J; Chang, Emmanuel J; Mooney, Rachel A; Vvedenskaya, Irina; Wang, Qing Jun; Fenyo, David; Rout, Michael P; Landick, Robert; Chait, Brian T; Severinov, Konstantin; Darst, Seth A | Journal of proteome research | 18271525 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18271525 |
| Human Proteinpedia enables sharing of human protein data. | Mathivanan, Suresh; Ahmed, Mukhtar; Ahn, Natalie G; Alexandre, Hainard; Amanchy, Ramars; Andrews, Philip C; Bader, Joel S; Balgley, Brian M; Bantscheff, Marcus; Bennett, Keiryn L; Bjorling, Erik; Blagoev, Blagoy; Bose, Ron; Brahmachari, Samir K; Burlingam | Nature biotechnology | 18259167 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18259167 |
| Metabolite identification via the Madison Metabolomics Consortium Database. | Cui, Qiu; Lewis, Ian A; Hegeman, Adrian D; Anderson, Mark E; Li, Jing; Schulte, Christopher F; Westler, William M; Eghbalnia, Hamid R; Sussman, Michael R; Markley, John L | Nature biotechnology | 18259166 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18259166 |
| Protein arrays on patterned porous gold substrates interrogated with mass spectrometry: detection of peptides in plasma. | Evans-Nguyen, Kenyon M; Tao, Sheng-Ce; Zhu, Heng; Cotter, Robert J | Analytical chemistry | 18254611 | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/18254611 |
| Ionomics and the study of the plant ionome. | Salt, David E; Baxter, Ivan; Lahner, Brett | Annual review of plant biology | 18251712 | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18251712 |
| Diet-induced obesity alters protein synthesis: tissue-specific effects in fasted versus fed mice. | Anderson, Stephanie R; Gilge, Danielle A; Steiber, Alison L; Previs, Stephen F | Metabolism: clinical and experimental | 18249206 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18249206 |
| Identification of proteases that regulate erythrocyte rupture by the malaria parasite Plasmodium falciparum. | Arastu-Kapur, Shirin; Ponder, Elizabeth L; Fonovic, Ursa Pecar; Yeoh, Sharon; Yuan, Fang; Fonovic, Marko; Grainger, Munira; Phillips, Carolyn I; Powers, James C; Bogyo, Matthew | Nature chemical biology | 18246061 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18246061 |
| Targeted metabolomic analysis of Escherichia coli by desorption electrospray ionization and extractive electrospray ionization mass spectrometry. | Jackson, Ayanna U; Werner, Sean R; Talaty, Nari; Song, Yishu; Campbell, Karinna; Cooks, R Graham; Morgan, John A | Analytical biochemistry | 18243123 | 2008 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/18243123 |
| Depolymerization-driven flow in nematode spermatozoa relates crawling speed to size and shape. | Zajac, Mark; Dacanay, Brian; Mohler, William A; Wolgemuth, Charles W | Biophysical journal | 18227129 | 2008 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/18227129 |
| Ion mobility-mass spectrometry. | Kanu, Abu B; Dwivedi, Prabha; Tam, Maggie; Matz, Laura; Hill Jr, Herbert H | Journal of mass spectrometry : JMS | 18200615 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18200615 |
| Plasmid-chromosome shuffling for non-deletion alleles in yeast. | Huang, Zhiwei; Sucgang, Richard S; Lin, Yu-yi; Shi, Xiaomin; Boeke, Jef D; Pan, Xuewen | Nature methods | 18193055 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18193055 |
| HTS identifies novel and specific uncompetitive inhibitors of the two-component NS2B-NS3 proteinase of West Nile virus. | Johnston, Paul A; Phillips, Jennifer; Shun, Tong Ying; Shinde, Sunita; Lazo, John S; Huryn, Donna M; Myers, Michael C; Ratnikov, Boris I; Smith, Jeffrey W; Su, Ying; Dahl, Russell; Cosford, Nicholas D P; Shiryaev, Sergey A; Strongin, Alex Y | Assay and drug development technologies | 18181690 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18181690 |
| GLUT1 and GLUT9 as major contributors to glucose influx in HepG2 cells identified by a high sensitivity intramolecular FRET glucose sensor. | Takanaga, Hitomi; Chaudhuri, Bhavna; Frommer, Wolf B | Biochimica et biophysica acta | 18177733 | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18177733 |
| Imaging of glutamate in brain slices using FRET sensors. | Dulla, Chris; Tani, Hiroaki; Okumoto, Sakiko; Frommer, Wolf B; Reimer, Rich J; Huguenard, John R | Journal of neuroscience methods | 18160134 | 2008 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/18160134 |
| Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. | Choi, Hyungwon; Nesvizhskii, Alexey I | Journal of proteome research | 18159924 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18159924 |
| Shotgun lipidomics identifies a paired rule for the presence of isomeric ether phospholipid molecular species. | Yang, Kui; Zhao, Zhongdan; Gross, Richard W; Han, Xianlin | PloS one | 18159251 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18159251 |
| Fluorogen-activating single-chain antibodies for imaging cell surface proteins. | Szent-Gyorgyi, Christopher; Schmidt, Brigitte F; Schmidt, Brigitte A; Creeger, Yehuda; Fisher, Gregory W; Zakel, Kelly L; Adler, Sally; Fitzpatrick, James A J; Woolford, Carol A; Yan, Qi; Vasilev, Kalin V; Berget, Peter B; Bruchez, Marcel P; Jarvik, Jonat | Nature biotechnology | 18157118 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18157118 |
| Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm. | Oh, Cheolhwan; Huang, Xiaodong; Regnier, Fred E; Buck, Charles; Zhang, Xiang | Journal of chromatography. A | 18093607 | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18093607 |
| A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. | Chen, Chien-Sheng; Korobkova, Ekaterina; Chen, Hao; Zhu, Jian; Jian, Xing; Tao, Sheng-Ce; He, Chuan; Zhu, Heng | Nature methods | 18084297 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18084297 |
| Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex. | Lee, David J; Busby, Stephen J W; Westblade, Lars F; Chait, Brian T | Journal of bacteriology | 18083804 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18083804 |
| Simultaneous nitric oxide and dehydroascorbic acid imaging by combining diaminofluoresceins and diaminorhodamines. | Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan V | Journal of neuroscience methods | 18083236 | 2008 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/18083236 |
| Expression of murine leukemia virus envelope protein is sufficient for the induction of apoptosis. | Zhao, Xiaoqing; Yoshimura, Fayth K | Journal of virology | 18077710 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18077710 |
| Electrostatic interactions of colloidal particles in nonpolar solvents: role of surface chemistry and charge control agents. | Sainis, Sunil K; Germain, Vincent; Mejean, Cecile O; Dufresne, Eric R | Langmuir : the ACS journal of surfaces and colloids | 18062711 | 2008 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/18062711 |
| Enrichment tags for enhanced-resolution profiling of the polar metabolome. | Carlson, Erin E; Cravatt, Benjamin F | Journal of the American Chemical Society | 18052286 | 2007 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/18052286 |
| The molecular architecture of the nuclear pore complex. | Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M; Zhang, Wenzhu; Kipper, Julia; Devos, Damien; Suprapto, Adisetyantari; Karni-Schmidt, Orit; Williams, Rosemary; Chait, Brian T; Sali, Andrej; Rout, Michael P | Nature | 18046406 | 2007 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/18046406 |
| Applications of protein microarray technology. | Tao, Sheng-Ce; Chen, Chien-Sheng; Zhu, Heng | Combinatorial chemistry & high throughput screening | 18045082 | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18045082 |
| An update on lipidomics: progress and application in biomarker and drug development. | Han, Xianlin | Current opinion in molecular therapeutics | 18041669 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18041669 |
| A metabolomic study of brain tissues from aged mice with low expression of the vesicular monoamine transporter 2 (VMAT2) gene. | Salek, Reza M; Colebrooke, Rebecca E; Macintosh, Robin; Lynch, Patrick J; Sweatman, Brian C; Emson, Piers C; Griffin, Julian L | Neurochemical research | 18041582 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18041582 |
| Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. | Huang, Hailiang; Jedynak, Bruno M; Bader, Joel S | PLoS computational biology | 18039026 | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18039026 |
| 5-HT and 5-HT-SO4, but not tryptophan or 5-HIAA levels in single feeding neurons track animal hunger state. | Hatcher, N G; Zhang, X; Stuart, J N; Moroz, L L; Sweedler, J V; Gillette, R | Journal of neurochemistry | 18036151 | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18036151 |
| Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. | Qian, Yuntao; Murphy, Robert F | Bioinformatics (Oxford, England) | 18033795 | 2008 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/18033795 |
| Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells. | Sriram, Ganesh; Rahib, Lola; He, Jian-Sen; Campos, Allison E; Parr, Lilly S; Liao, James C; Dipple, Katrina M | Molecular genetics and metabolism | 18029214 | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18029214 |
| Quantitative proteomes and in vivo secretomes of progressive and regressive UV-induced fibrosarcoma tumor cells: mimicking tumor microenvironment using a dermis-based cell-trapped system linked to tissue chamber. | Shi, Yang; Elmets, Craig A; Smith, Jeffery W; Liu, Yu-Tsueng; Chen, Yun-Ru; Huang, Cheng-Po; Zhu, Wenhong; Ananthaswamy, Honnavara N; Gallo, Richard L; Huang, Chun-Ming | Proteomics | 18022937 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18022937 |
| Tissue inhibitor of metalloproteinases-2 binding to membrane-type 1 matrix metalloproteinase induces MAPK activation and cell growth by a non-proteolytic mechanism. | D'Alessio, Silvia; Ferrari, Giovanni; Cinnante, Karma; Scheerer, William; Galloway, Aubrey C; Roses, Daniel F; Rozanov, Dmitri V; Remacle, Albert G; Oh, Eok-Soo; Shiryaev, Sergey A; Strongin, Alex Y; Pintucci, Giuseppe; Mignatti, Paolo | The Journal of biological chemistry | 17991754 | 2008 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/17991754 |
| Atherogenic diet causes lethal ileo-ceco-colitis in cyclooxygenase-2 deficient mice. | Lin, James A; Watanabe, Junji; Rozengurt, Nora; Narasimha, Ajay; Martin, Martin G; Wang, Jenny; Braun, Jonathan; Langenbach, Robert; Reddy, Srinivasa T | Prostaglandins & other lipid mediators | 17991612 | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17991612 |
| Ab initio prediction of transcription factor binding sites. | Liu, L Angela; Bader, Joel S | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 17990512 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17990512 |
| New bioinformatics resources for metabolomics. | Markley, John L; Anderson, Mark E; Cui, Qiu; Eghbalnia, Hamid R; Lewis, Ian A; Hegeman, Adrian D; Li, Jing; Schulte, Christopher F; Sussman, Michael R; Westler, William M; Ulrich, Eldon L; Zolnai, Zsolt | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 17990489 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17990489 |
| Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra. | Lewis, Ian A; Schommer, Seth C; Hodis, Brendan; Robb, Kate A; Tonelli, Marco; Westler, William M; Sussman, Michael R; Markley, John L | Analytical chemistry | 17985927 | 2007 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/17985927 |
| Salt tolerance of desorption electrospray ionization (DESI). | Jackson, Ayanna U; Talaty, Nari; Cooks, R Graham; Van Berkel, Gary J | Journal of the American Society for Mass Spectrometry | 17977744 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17977744 |
| Cysteine cathepsin non-inhibitory binding partners: modulating intracellular trafficking and function. | Victor, Bernadette C; Sloane, Bonnie F | Biological chemistry | 17976005 | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17976005 |
| Automated learning of generative models for subcellular location: building blocks for systems biology. | Zhao, Ting; Murphy, Robert F | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 17972315 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17972315 |
| Host pathogen protein interactions predicted by comparative modeling. | Davis, Fred P; Barkan, David T; Eswar, Narayanan; McKerrow, James H; Sali, Andrej | Protein science : a publication of the Protein Society | 17965183 | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17965183 |
| Chemical cytometry: the chemical analysis of single cells. | Turner, Emily H; Cohen, Daniella; Pugsley, Haley R; Gonzalez Gomez, David; Whitmore, Colin D; Zhu, Cuiru; Dovichi, Norman J | Analytical and bioanalytical chemistry | 17955216 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17955216 |
| Biochemical analysis of inositol phosphate kinases. | Otto, James C; Mulugu, Sashidhar; Fridy, Peter C; Chiou, Shean-Tai; Armbruster, Blaine N; Ribeiro, Anthony A; York, John D | Methods in enzymology | 17954248 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17954248 |
| Functional dissection of a HECT ubiquitin E3 ligase. | Lu, Jin-Ying; Lin, Yu-Yi; Qian, Jiang; Tao, Sheng-Ce; Zhu, Jian; Pickart, Cecile; Zhu, Heng | Molecular & cellular proteomics : MCP | 17951556 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17951556 |
| Pre-SAT180, a simple and effective method for residual water suppression. | Mo, Huaping; Raftery, Daniel | Journal of magnetic resonance (San Diego, Calif. : 1997) | 17945521 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17945521 |
| Characterization of protein hubs by inferring interacting motifs from protein interactions. | Aragues, Ramon; Sali, Andrej; Bonet, Jaume; Marti-Renom, Marc A; Oliva, Baldo | PLoS computational biology | 17941705 | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17941705 |
| Endosomes and lysosomes play distinct roles in sulfatide-induced neuroblastoma apoptosis: potential mechanisms contributing to abnormal sulfatide metabolism in related neuronal diseases. | Zeng, Youchun; Cheng, Hua; Jiang, Xuntian; Han, Xianlin | The Biochemical journal | 17939778 | 2008 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/17939778 |
| Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. | Zhang, Jingyu; Harnpicharnchai, Piyanun; Jakovljevic, Jelena; Tang, Lan; Guo, Yurong; Oeffinger, Marlene; Rout, Michael P; Hiley, Shawna L; Hughes, Timothy; Woolford Jr, John L | Genes & development | 17938242 | 2007 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/17938242 |
| Proteolysis of the membrane type-1 matrix metalloproteinase prodomain: implications for a two-step proteolytic processing and activation. | Golubkov, Vladislav S; Chekanov, Alexei V; Shiryaev, Sergey A; Aleshin, Alexander E; Ratnikov, Boris I; Gawlik, Katarzyna; Radichev, Ilian; Motamedchaboki, Khatereh; Smith, Jeffrey W; Strongin, Alex Y | The Journal of biological chemistry | 17938169 | 2007 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/17938169 |
| Potential solutions for confocal imaging of living animals. | Croix, Claudette St; Zipfel, Warren R; Watkins, Simon C | BioTechniques | 17933097 | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17933097 |
| Vesicle shape, molecular tilt, and the suppression of necks. | Jiang, Hongyuan; Huber, Greg; Pelcovits, Robert A; Powers, Thomas R | Physical review. E, Statistical, nonlinear, and soft matter physics | 17930272 | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17930272 |
| Comprehensive analysis of diverse ribonucleoprotein complexes. | Oeffinger, Marlene; Wei, Karen E; Rogers, Richard; DeGrasse, Jeffrey A; Chait, Brian T; Aitchison, John D; Rout, Michael P | Nature methods | 17922018 | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17922018 |
| Alkaline methanolysis of lipid extracts extends shotgun lipidomics analyses to the low-abundance regime of cellular sphingolipids. | Jiang, Xuntian; Cheng, Hua; Yang, Kui; Gross, Richard W; Han, Xianlin | Analytical biochemistry | 17920553 | 2007 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/17920553 |
| Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations. | Phillippi, Julie A; Miller, Eric; Weiss, Lee; Huard, Johnny; Waggoner, Alan; Campbell, Phil | Stem cells (Dayton, Ohio) | 17901398 | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17901398 |
| Nanosensor detection of an immunoregulatory tryptophan influx/kynurenine efflux cycle. | Kaper, Thijs; Looger, Loren L; Takanaga, Hitomi; Platten, Michael; Steinman, Lawrence; Frommer, Wolf B | PLoS biology | 17896864 | 2007 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/17896864 |
| Negative autoregulation by FAS mediates robust fetal erythropoiesis. | Socolovsky, Merav; Murrell, Michael; Liu, Ying; Pop, Ramona; Porpiglia, Ermelinda; Levchenko, Andre | PLoS biology | 17896863 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17896863 |
| Vesicle-like biomechanics governs important aspects of nuclear geometry in fission yeast. | Lim H W, Gerald; Huber, Greg; Torii, Yoshihiro; Hirata, Aiko; Miller, Jonathan; Sazer, Shelley | PloS one | 17895989 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17895989 |
| Alterations in an inositol phosphate code through synergistic activation of a G protein and inositol phosphate kinases. | Otto, James C; Kelly, Patrick; Chiou, Shean-Tai; York, John D | Proceedings of the National Academy of Sciences of the United States of America | 17895383 | 2007 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/17895383 |
| Aplysia temptin - the 'glue' in the water-borne attractin pheromone complex. | Cummins, Scott F; Xie, Fang; de Vries, Melissa R; Annangudi, Suresh P; Misra, Milind; Degnan, Bernard M; Sweedler, Jonathan V; Nagle, Gregg T; Schein, Catherine H | The FEBS journal | 17894821 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17894821 |
| Central carbon metabolism in the progression of mammary carcinoma. | Richardson, Adam D; Yang, Chen; Osterman, Andrei; Smith, Jeffrey W | Breast cancer research and treatment | 17879159 | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17879159 |
| LSD1 and the chemistry of histone demethylation. | Culhane, Jeffrey C; Cole, Philip A | Current opinion in chemical biology | 17851108 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17851108 |
| A G(s)-linked receptor maintains meiotic arrest in mouse oocytes, but luteinizing hormone does not cause meiotic resumption by terminating receptor-G(s) signaling. | Norris, Rachael P; Freudzon, Leon; Freudzon, Marina; Hand, Arthur R; Mehlmann, Lisa M; Jaffe, Laurinda A | Developmental biology | 17850783 | 2007 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/17850783 |
| Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. | Blum, Galia; von Degenfeld, Georges; Merchant, Milton J; Blau, Helen M; Bogyo, Matthew | Nature chemical biology | 17828252 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17828252 |
| Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. | Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory | Analytical chemistry | 17822305 | 2007 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/17822305 |
| Specific inhibition of autoimmune T cell transmigration contributes to beta cell functionality and insulin synthesis in non-obese diabetic (NOD) mice. | Savinov, Alexei Y; Rozanov, Dmitri V; Strongin, Alex Y | The Journal of biological chemistry | 17761671 | 2007 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/17761671 |
| Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. | Komatsu, Masaaki; Wang, Qing Jun; Holstein, Gay R; Friedrich Jr, Victor L; Iwata, Jun-ichi; Kominami, Eiki; Chait, Brian T; Tanaka, Keiji; Yue, Zhenyu | Proceedings of the National Academy of Sciences of the United States of America | 17726112 | 2007 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/17726112 |
| Rapid analysis of metabolites and drugs of abuse from urine samples by desorption electrospray ionization-mass spectrometry. | Kauppila, Tiina J; Talaty, Nari; Kuuranne, Tiia; Kotiaho, Tapio; Kostiainen, Risto; Cooks, R Graham | The Analyst | 17710261 | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17710261 |
| Stable isotope assisted assignment of elemental compositions for metabolomics. | Hegeman, Adrian D; Schulte, Christopher F; Cui, Qiu; Lewis, Ian A; Huttlin, Edward L; Eghbalnia, Hamid; Harms, Amy C; Ulrich, Eldon L; Markley, John L; Sussman, Michael R | Analytical chemistry | 17708672 | 2007 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/17708672 |
| 1H NMR study of the effects of sample contamination in the metabolomic analysis of mouse urine. | Gu, Haiwei; Pan, Zhengzheng; Duda, Chester; Mann, Doug; Kissinger, Candice; Rohde, Candace; Raftery, Daniel | Journal of pharmaceutical and biomedical analysis | 17707608 | 2007 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/17707608 |
| Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases. | Fridy, Peter C; Otto, James C; Dollins, D Eric; York, John D | The Journal of biological chemistry | 17690096 | 2007 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/17690096 |
| beta-Cell mitochondria exhibit membrane potential heterogeneity that can be altered by stimulatory or toxic fuel levels. | Wikstrom, Jakob D; Katzman, Shana M; Mohamed, Hibo; Twig, Gilad; Graf, Solomon A; Heart, Emma; Molina, Anthony J A; Corkey, Barbara E; de Vargas, Lina Moitoso; Danial, Nika N; Collins, Sheila; Shirihai, Orian S | Diabetes | 17686943 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17686943 |
| N-lysine propionylation controls the activity of propionyl-CoA synthetase. | Garrity, Jane; Gardner, Jeffrey G; Hawse, William; Wolberger, Cynthia; Escalante-Semerena, Jorge C | The Journal of biological chemistry | 17684016 | 2007 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/17684016 |
| Inhibition of cysteine cathepsin protease activity enhances chemotherapy regimens by decreasing tumor growth and invasiveness in a mouse model of multistage cancer. | Bell-McGuinn, Katherine M; Garfall, Alfred L; Bogyo, Matthew; Hanahan, Douglas; Joyce, Johanna A | Cancer research | 17671208 | 2007 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/17671208 |
| Yoctomole analysis of ganglioside metabolism in PC12 cellular homogenates. | Whitmore, Colin D; Olsson, Ulf; Larsson, E Andreas; Hindsgaul, Ole; Palcic, Monica M; Dovichi, Norman J | Electrophoresis | 17668449 | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17668449 |
| Profiling constitutive proteolytic events in vivo. | Timmer, John C; Enoksson, Mari; Wildfang, Eric; Zhu, Wenhong; Igarashi, Yoshinobu; Denault, Jean-Benard; Ma, Yuliang; Dummitt, Benjamin; Chang, Yie-Hwa; Mast, Alan E; Eroshkin, Alexey; Smith, Jeffrey W; Tao, W Andy; Salvesen, Guy S | The Biochemical journal | 17650073 | 2007 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/17650073 |
| Automated image analysis of protein localization in budding yeast. | Chen, Shann-Ching; Zhao, Ting; Gordon, Geoffrey J; Murphy, Robert F | Bioinformatics (Oxford, England) | 17646347 | 2007 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/17646347 |
| A novel anti-atherogenic role for COX-2--potential mechanism for the cardiovascular side effects of COX-2 inhibitors. | Narasimha, Ajay; Watanabe, Junji; Lin, James A; Hama, Susan; Langenbach, Robert; Navab, Mohamad; Fogelman, Alan M; Reddy, Srinivasa T | Prostaglandins & other lipid mediators | 17643885 | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17643885 |
| Efficiency, selectivity, and robustness of nucleocytoplasmic transport. | Zilman, Anton; Di Talia, Stefano; Chait, Brian T; Rout, Michael P; Magnasco, Marcelo O | PLoS computational biology | 17630825 | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17630825 |
| Proteomics evaluation of chemically cleavable activity-based probes. | Fonovic, Marko; Verhelst, Steven H L; Sorum, Mark T; Bogyo, Matthew | Molecular & cellular proteomics : MCP | 17615255 | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17615255 |
| Class selection of amino acid metabolites in body fluids using chemical derivatization and their enhanced 13C NMR. | Shanaiah, Narasimhamurthy; Desilva, M Aruni; Nagana Gowda, G A; Raftery, Michael A; Hainline, Bryan E; Raftery, Daniel | Proceedings of the National Academy of Sciences of the United States of America | 17606902 | 2007 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/17606902 |
| Multiple roles for acetylation in the interaction of p300 HAT with ATF-2. | Karanam, Balasubramanyam; Wang, Ling; Wang, Dongxia; Liu, Xin; Marmorstein, Ronen; Cotter, Robert; Cole, Philip A | Biochemistry | 17590016 | 2007 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/17590016 |
| Controlling charge on levitating drops. | Hilger, Ryan T; Westphall, Michael S; Smith, Lloyd M | Analytical chemistry | 17580951 | 2007 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/17580951 |
| Metabolic cytometry. Glycosphingolipid metabolism in single cells. | Whitmore, Colin D; Hindsgaul, Ole; Palcic, Monica M; Schnaar, Ronald L; Dovichi, Norman J | Analytical chemistry | 17567107 | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17567107 |
| Relative quantification of carboxylic acid metabolites by liquid chromatography-mass spectrometry using isotopic variants of cholamine. | Lamos, Shane M; Shortreed, Michael R; Frey, Brian L; Belshaw, Peter J; Smith, Lloyd M | Analytical chemistry | 17563114 | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17563114 |
| Inaccuracies in selected ion monitoring determination of isotope ratios obviated by profile acquisition: nucleotide 18O/16O measurements. | Cassano, Adam G; Wang, Benlian; Anderson, David R; Previs, Stephen; Harris, Michael E; Anderson, Vernon E | Analytical biochemistry | 17560863 | 2007 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/17560863 |
| Isotopologue distributions of peptide product ions by tandem mass spectrometry: quantitation of low levels of deuterium incorporation. | Wang, Benlian; Sun, Gang; Anderson, David R; Jia, Minghong; Previs, Stephen; Anderson, Vernon E | Analytical biochemistry | 17559791 | 2007 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/17559791 |
| The adapter importin-alpha provides flexible control of nuclear import at the expense of efficiency. | Riddick, Greg; Macara, Ian G | Molecular systems biology | 17551513 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17551513 |
| Transcriptional responses to fatty acid are coordinated by combinatorial control. | Smith, Jennifer J; Ramsey, Stephen A; Marelli, Marcello; Marzolf, Bruz; Hwang, Daehee; Saleem, Ramsey A; Rachubinski, Richard A; Aitchison, John D | Molecular systems biology | 17551510 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17551510 |
| Identification of proteolytic cleavage sites by quantitative proteomics. | Enoksson, Mari; Li, Jingwei; Ivancic, Melanie M; Timmer, John C; Wildfang, Eric; Eroshkin, Alexey; Salvesen, Guy S; Tao, W Andy | Journal of proteome research | 17547438 | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17547438 |
| Distinctive features of angiogenesis and lymphangiogenesis determine their functionality during de novo tumor development. | Eichten, Alexandra; Hyun, William C; Coussens, Lisa M | Cancer research | 17545601 | 2007 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/17545601 |
| Targeting host cell furin proprotein convertases as a therapeutic strategy against bacterial toxins and viral pathogens. | Shiryaev, Sergey A; Remacle, Albert G; Ratnikov, Boris I; Nelson, Nicholas A; Savinov, Alexei Y; Wei, Ge; Bottini, Massimo; Rega, Michele F; Parent, Amelie; Desjardins, Roxane; Fugere, Martin; Day, Robert; Sabet, Mojgan; Pellecchia, Maurizio; Liddington, | The Journal of biological chemistry | 17537721 | 2007 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/17537721 |
| Rapid resolution of carbohydrate isomers by electrospray ionization ambient pressure ion mobility spectrometry-time-of-flight mass spectrometry (ESI-APIMS-TOFMS). | Dwivedi, Prabha; Bendiak, Brad; Clowers, Brian H; Hill Jr, Herbert H | Journal of the American Society for Mass Spectrometry | 17532226 | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17532226 |
| Design, synthesis, and evaluation of in vivo potency and selectivity of epoxysuccinyl-based inhibitors of papain-family cysteine proteases. | Sadaghiani, Amir Masoud; Verhelst, Steven H L; Gocheva, Vasilena; Hill, Kimberly; Majerova, Eva; Stinson, Sherman; Joyce, Johanna A; Bogyo, Matthew | Chemistry & biology | 17524981 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17524981 |
| A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms. | Shastri, Avantika A; Morgan, John A | Phytochemistry | 17524438 | 2007 Aug-Sep | https://www.ncbi.nlm.nih.gov/pubmed/17524438 |
| Mechanistic analysis of a suicide inactivator of histone demethylase LSD1. | Szewczuk, Lawrence M; Culhane, Jeffrey C; Yang, Maojun; Majumdar, Ananya; Yu, Hongtao; Cole, Philip A | Biochemistry | 17511474 | 2007 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/17511474 |
| Metabolomic investigation of CLN6 neuronal ceroid lipofuscinosis in affected South Hampshire sheep. | Pears, Michael R; Salek, Reza M; Palmer, David N; Kay, Graham W; Mortishire-Smith, Russell J; Griffin, Julian L | Journal of neuroscience research | 17510975 | 2007 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/17510975 |
| Insulin-like growth factor II receptor-mediated intracellular retention of cathepsin B is essential for transformation of endothelial cells by Kaposi's sarcoma-associated herpesvirus. | Rose, Patrick P; Bogyo, Matthew; Moses, Ashlee V; Fruh, Klaus | Journal of virology | 17507477 | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17507477 |
| Fluxomics: mass spectrometry versus quantitative imaging. | Wiechert, Wolfgang; Schweissgut, Oliver; Takanaga, Hitomi; Frommer, Wolf B | Current opinion in plant biology | 17481942 | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17481942 |
| Roles for inositol polyphosphate kinases in the regulation of nuclear processes and developmental biology. | Seeds, Andrew M; Frederick, Joshua P; Tsui, Marco M K; York, John D | Advances in enzyme regulation | 17467778 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17467778 |
| Influenza A virus elevates active cathepsin B in primary murine DC. | Burster, Timo; Giffon, Thierry; Dahl, Martin E; Bjorck, Pia; Bogyo, Matthew; Weber, Ekkehard; Mahmood, Kutubuddin; Lewis, David B; Mellins, Elizabeth D | International immunology | 17446210 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17446210 |
| Type I collagen is a genetic modifier of matrix metalloproteinase 2 in murine skeletal development. | Egeblad, Mikala; Shen, H-C Jennifer; Behonick, Danielle J; Wilmes, Lisa; Eichten, Alexandra; Korets, Lidiya V; Kheradmand, Farrah; Werb, Zena; Coussens, Lisa M | Developmental dynamics : an official publication of the American Association of Anatomists | 17440987 | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17440987 |
| Regulation of a cyclin-CDK-CDK inhibitor complex by inositol pyrophosphates. | Lee, Young-Sam; Mulugu, Sashidhar; York, John D; O'Shea, Erin K | Science (New York, N.Y.) | 17412959 | 2007 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/17412959 |
| A conserved family of enzymes that phosphorylate inositol hexakisphosphate. | Mulugu, Sashidhar; Bai, Wenli; Fridy, Peter C; Bastidas, Robert J; Otto, James C; Dollins, D Eric; Haystead, Timothy A; Ribeiro, Anthony A; York, John D | Science (New York, N.Y.) | 17412958 | 2007 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/17412958 |
| Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. | Aleshin, Alexander E; Shiryaev, Sergey A; Strongin, Alex Y; Liddington, Robert C | Protein science : a publication of the Protein Society | 17400917 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17400917 |
| Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. | Antoniewicz, Maciek R; Kraynie, David F; Laffend, Lisa A; Gonzalez-Lergier, Joanna; Kelleher, Joanne K; Stephanopoulos, Gregory | Metabolic engineering | 17400499 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17400499 |
| Where does all the PIP2 come from? | Loew, Leslie M | The Journal of physiology | 17395623 | 2007 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/17395623 |
| Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. | Hyberts, Sven G; Heffron, Gregory J; Tarragona, Nestor G; Solanky, Kirty; Edmonds, Katherine A; Luithardt, Harry; Fejzo, Jasna; Chorev, Michael; Aktas, Huseyin; Colson, Kimberly; Falchuk, Kenneth H; Halperin, Jose A; Wagner, Gerhard | Journal of the American Chemical Society | 17388596 | 2007 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/17388596 |
| Decoding transcriptional regulatory interactions. | Liu, L Angela; Bader, Joel S | Physica D. Nonlinear phenomena | 17364011 | 2006 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17364011 |
| RNA-binding proteins that inhibit RNA virus infection. | Zhu, Jian; Gopinath, Kodetham; Murali, Ayaluru; Yi, Guanghui; Hayward, S Diane; Zhu, Heng; Kao, Cheng | Proceedings of the National Academy of Sciences of the United States of America | 17360619 | 2007 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/17360619 |
| Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. | Rodionov, Dmitry A; Kurnasov, Oleg V; Stec, Boguslaw; Wang, Yan; Roberts, Mary F; Osterman, Andrei L | Proceedings of the National Academy of Sciences of the United States of America | 17360515 | 2007 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/17360515 |
| The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. | Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B; Halpern, Aaron L; Williamson, Shannon J; Remington, Karin; Eisen, Jonathan A; Heidelberg, Karla B; Manning, Gerard; Li, Weizhong; Jaroszewski, Lukasz; Cieplak, Piotr; Miller, Christopher S; Li, Huiying; M | PLoS biology | 17355171 | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17355171 |
| A curated compendium of phosphorylation motifs. | Amanchy, Ramars; Periaswamy, Balamurugan; Mathivanan, Suresh; Reddy, Raghunath; Tattikota, Sudhir Gopal; Pandey, Akhilesh | Nature biotechnology | 17344875 | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17344875 |
| Design and performance of an atmospheric pressure ion mobility Fourier transform ion cyclotron resonance mass spectrometer. | Tang, Xiaoting; Bruce, James E; Hill Jr, Herbert H | Rapid communications in mass spectrometry : RCM | 17318922 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17318922 |
| Activity based probes for proteases: applications to biomarker discovery, molecular imaging and drug screening. | Fonovic, Marko; Bogyo, Matthew | Current pharmaceutical design | 17313359 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17313359 |
| Switching the substrate specificity of the two-component NS2B-NS3 flavivirus proteinase by structure-based mutagenesis. | Shiryaev, Sergey A; Ratnikov, Boris I; Aleshin, Alexander E; Kozlov, Igor A; Nelson, Nicholas A; Lebl, Michal; Smith, Jeffrey W; Liddington, Robert C; Strongin, Alex Y | Journal of virology | 17301157 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17301157 |
| Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana. | Huttlin, Edward L; Hegeman, Adrian D; Harms, Amy C; Sussman, Michael R | Molecular & cellular proteomics : MCP | 17293592 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17293592 |
| Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. | Molina, Henrik; Horn, David M; Tang, Ning; Mathivanan, Suresh; Pandey, Akhilesh | Proceedings of the National Academy of Sciences of the United States of America | 17287340 | 2007 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/17287340 |
| Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. | Taverna, Sean D; Ueberheide, Beatrix M; Liu, Yifan; Tackett, Alan J; Diaz, Robert L; Shabanowitz, Jeffrey; Chait, Brian T; Hunt, Donald F; Allis, C David | Proceedings of the National Academy of Sciences of the United States of America | 17284592 | 2007 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/17284592 |
| Humoral immunity, inflammation and cancer. | Tan, Ting-Ting; Coussens, Lisa M | Current opinion in immunology | 17276050 | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17276050 |
| Immune cells as anti-cancer therapeutic targets and tools. | Johansson, Magnus; Tan, Tingting; de Visser, Karin E; Coussens, Lisa M | Journal of cellular biochemistry | 17265430 | 2007 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/17265430 |
| Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. | Styczynski, Mark P; Moxley, Joel F; Tong, Lily V; Walther, Jason L; Jensen, Kyle L; Stephanopoulos, Gregory N | Analytical chemistry | 17263323 | 2007 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/17263323 |
| Tandem time-of-flight (TOF/TOF) mass spectrometry and the curved-field reflectron. | Cotter, Robert J; Griffith, Wendell; Jelinek, Christine | Journal of chromatography. B, Analytical technologies in the biomedical and life sciences | 17258517 | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17258517 |
| Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. | Benvin, Andrea L; Creeger, Yehuda; Fisher, Gregory W; Ballou, Byron; Waggoner, Alan S; Armitage, Bruce A | Journal of the American Chemical Society | 17256855 | 2007 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/17256855 |
| An evaluation of human protein-protein interaction data in the public domain. | Mathivanan, Suresh; Periaswamy, Balamurugan; Gandhi, T K B; Kandasamy, Kumaran; Suresh, Shubha; Mohmood, Riaz; Ramachandra, Y L; Pandey, Akhilesh | BMC bioinformatics | 17254303 | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17254303 |
| The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses. | Furmonaviciene, R; Ghaemmaghami, A M; Boyd, S E; Jones, N S; Bailey, K; Willis, A C; Sewell, H F; Mitchell, D A; Shakib, F | Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology | 17250696 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17250696 |
| Ubiquitous presence of argininosuccinate at millimolar levels in the central nervous system of Aplysia californica. | Ye, Xiaoying; Kim, Won-Suk; Rubakhin, Stanislav S; Sweedler, Jonathan V | Journal of neurochemistry | 17250653 | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17250653 |
| Inositol polyphosphate kinases: regulators of nuclear function. | Seeds, Andrew M; York, John D | Biochemical Society symposium | 17233590 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17233590 |
| Development of calpain-specific inactivators by screening of positional scanning epoxide libraries. | Cuerrier, Dominic; Moldoveanu, Tudor; Campbell, Robert L; Kelly, Jacqueline; Yoruk, Bilge; Verhelst, Steven H L; Greenbaum, Doron; Bogyo, Matthew; Davies, Peter L | The Journal of biological chemistry | 17218315 | 2007 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/17218315 |
| A mild chemically cleavable linker system for functional proteomic applications. | Verhelst, Steven H L; Fonovic, Marko; Bogyo, Matthew | Angewandte Chemie (International ed. in English) | 17205587 | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17205587 |
| Modeling the cholesteatoma microenvironment: coculture of HaCaT keratinocytes with WS1 fibroblasts induces MMP-2 activation, invasive phenotype, and proteolysis of the extracellular matrix. | Laeeq, Sabahat; Faust, Russell | The Laryngoscope | 17204986 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17204986 |
| Monitoring diet effects via biofluids and their implications for metabolomics studies. | Gu, Haiwei; Chen, Huanwen; Pan, Zhengzheng; Jackson, Ayanna U; Talaty, Nari; Xi, Bowei; Kissinger, Candice; Duda, Chester; Mann, Doug; Raftery, Daniel; Cooks, R Graham | Analytical chemistry | 17194125 | 2007 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/17194125 |
| dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. | Pan, Xuewen; Yuan, Daniel S; Ooi, Siew-Loon; Wang, Xiaoling; Sookhai-Mahadeo, Sharon; Meluh, Pamela; Boeke, Jef D | Methods (San Diego, Calif.) | 17189863 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17189863 |
| Expression and purification of a two-component flaviviral proteinase resistant to autocleavage at the NS2B-NS3 junction region. | Shiryaev, Sergey A; Aleshin, Alexander E; Ratnikov, Boris I; Smith, Jeffrey W; Liddington, Robert C; Strongin, Alex Y | Protein expression and purification | 17189703 | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17189703 |
| Design of cell-permeable, fluorescent activity-based probes for the lysosomal cysteine protease asparaginyl endopeptidase (AEP)/legumain. | Sexton, Kelly B; Witte, Martin D; Blum, Galia; Bogyo, Matthew | Bioorganic & medicinal chemistry letters | 17189693 | 2007 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/17189693 |
| Purdue ionomics information management system. An integrated functional genomics platform. | Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S; Salt, David E | Plant physiology | 17189337 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17189337 |
| Tagging and detection strategies for activity-based proteomics. | Sadaghiani, Amir M; Verhelst, Steven Hl; Bogyo, Matthew | Current opinion in chemical biology | 17174138 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17174138 |
| Specificity of aza-peptide electrophile activity-based probes of caspases. | Sexton, K B; Kato, D; Berger, A B; Fonovic, M; Verhelst, S H L; Bogyo, M | Cell death and differentiation | 17170749 | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17170749 |
| Gas-phase chiral separations by ion mobility spectrometry. | Dwivedi, Prabha; Wu, Ching; Matz, Laura M; Clowers, Brian H; Siems, William F; Hill Jr, Herbert H | Analytical chemistry | 17165808 | 2006 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/17165808 |
| Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. | Taverna, Sean D; Ilin, Serge; Rogers, Richard S; Tanny, Jason C; Lavender, Heather; Li, Haitao; Baker, Lindsey; Boyle, John; Blair, Lauren P; Chait, Brian T; Patel, Dinshaw J; Aitchison, John D; Tackett, Alan J; Allis, C David | Molecular cell | 17157260 | 2006 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/17157260 |
| Cysteine protease inhibitors block Toxoplasma gondii microneme secretion and cell invasion. | Teo, Chin Fen; Zhou, Xing Wang; Bogyo, Matthew; Carruthers, Vern B | Antimicrobial agents and chemotherapy | 17145790 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17145790 |
| CutDB: a proteolytic event database. | Igarashi, Yoshinobu; Eroshkin, Alexey; Gramatikova, Svetlana; Gramatikoff, Kosi; Zhang, Ying; Smith, Jeffrey W; Osterman, Andrei L; Godzik, Adam | Nucleic acids research | 17142225 | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17142225 |
| Recombinant production and structural studies of the Aplysia water-borne protein pheromone enticin indicates it has a novel disulfide stabilized fold. | Cummins, Scott F; Xie, Fang; Misra, Milind; Amare, Andinet; Jakubowski, Jennifer A; de Vries, Melissa R; Sweedler, Jonathan V; Nagle, Gregg T; Schein, Catherine H | Peptides | 17141371 | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17141371 |
| Exposure to azide markedly decreases the abundance of mRNAs encoding cholesterol synthetic enzymes and inhibits cholesterol synthesis. | Kasturi, Sriram; Bederman, Ilya R; Christopher, Bridgette; Previs, Stephen F; Ismail-Beigi, Faramarz | Journal of cellular biochemistry | 17131385 | 2007 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/17131385 |
| Fatty acid-specific fluorescent probes and their use in resolving mixtures of unbound free fatty acids in equilibrium with albumin. | Huber, Andrew H; Kampf, J Patrick; Kwan, Thomas; Zhu, Baolong; Kleinfeld, Alan M | Biochemistry | 17128966 | 2006 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/17128966 |
| Commonly used caspase inhibitors designed based on substrate specificity profiles lack selectivity. | Berger, Alicia B; Sexton, Kelly B; Bogyo, Matthew | Cell research | 17117159 | 2006 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17117159 |
| Characterizing electrospray ionization using atmospheric pressure ion mobility spectrometry. | Tang, Xiaoting; Bruce, James E; Hill Jr, Herbert H | Analytical chemistry | 17105168 | 2006 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/17105168 |
| Structural modeling of protein interactions by analogy: application to PSD-95. | Korkin, Dmitry; Davis, Fred P; Alber, Frank; Luong, Tinh; Shen, Min-Yi; Lucic, Vladan; Kennedy, Mary B; Sali, Andrej | PLoS computational biology | 17096593 | 2006 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/17096593 |
| Solid-phase methods for the preparation of epoxysuccinate-based inhibitors of cysteine proteases. | Sadaghiani, Amir M; Verhelst, Steven H L; Bogyo, Matthew | Journal of combinatorial chemistry | 17096566 | 2006 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/17096566 |
| Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. | Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory | Metabolic engineering | 17088092 | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17088092 |
| Altered cholesterol homeostasis in cultured and in vivo models of cystic fibrosis. | White, Nicole M; Jiang, Dechen; Burgess, James D; Bederman, Ilya R; Previs, Stephen F; Kelley, Thomas J | American journal of physiology. Lung cellular and molecular physiology | 17085523 | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17085523 |
| Membrane type-1 matrix metalloproteinase confers aneuploidy and tumorigenicity on mammary epithelial cells. | Golubkov, Vladislav S; Chekanov, Alexey V; Savinov, Alexey Y; Rozanov, Dmitri V; Golubkova, Natalya V; Strongin, Alex Y | Cancer research | 17079467 | 2006 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/17079467 |
| Synthesis of reference standards to enable single cell metabolomic studies of tetramethylrhodamine-labeled ganglioside GM1. | Larsson, E Andreas; Olsson, Ulf; Whitmore, Colin D; Martins, Rita; Tettamanti, Guido; Schnaar, Ronald L; Dovichi, Norman J; Palcic, Monica M; Hindsgaul, Ole | Carbohydrate research | 17069778 | 2007 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/17069778 |
| Analysis of immune cell infiltrates during squamous carcinoma development. | Junankar, Simon R; Eichten, Alexandra; Kramer, Annegret; de Visser, Karin E; Coussens, Lisa M | The journal of investigative dermatology. Symposium proceedings / the Society for Investigative Dermatology, Inc. [and] European Society for Dermatological Research | 17069009 | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17069009 |
| Cleavage preference distinguishes the two-component NS2B-NS3 serine proteinases of Dengue and West Nile viruses. | Shiryaev, Sergey A; Kozlov, Igor A; Ratnikov, Boris I; Smith, Jeffrey W; Lebl, Michal; Strongin, Alex Y | The Biochemical journal | 17067286 | 2007 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/17067286 |
| Significant proportions of nuclear transport proteins with reduced intracellular mobilities resolved by fluorescence correlation spectroscopy. | Paradise, Allison; Levin, Mikhail K; Korza, George; Carson, John H | Journal of molecular biology | 17056062 | 2007 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/17056062 |
| Proteomics of the peroxisome. | Saleem, R A; Smith, J J; Aitchison, J D | Biochimica et biophysica acta | 17050007 | 2006 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17050007 |
| A multichannel native fluorescence detection system for capillary electrophoretic analysis of neurotransmitters in single neurons. | Lapainis, T; Scanlan, C; Rubakhin, S S; Sweedler, J V | Analytical and bioanalytical chemistry | 17047942 | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17047942 |
| Signal enhancement in HPLC/microcoil NMR using automated column trapping. | Djukovic, Danijel; Liu, Shuhui; Henry, Ian; Tobias, Brian; Raftery, Daniel | Analytical chemistry | 17037915 | 2006 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/17037915 |
| A novel analytical method for in vivo phosphate tracking. | Gu, Hong; Lalonde, Sylvie; Okumoto, Sakiko; Looger, Loren L; Scharff-Poulsen, Anne Marie; Grossman, Arthur R; Kossmann, Jens; Jakobsen, Iver; Frommer, Wolf B | FEBS letters | 17034793 | 2006 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/17034793 |
| Protein chip fabrication by capture of nascent polypeptides. | Tao, Sheng-Ce; Zhu, Heng | Nature biotechnology | 17013375 | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17013375 |
| Inhibition of endothelial cell proliferation and angiogenesis by orlistat, a fatty acid synthase inhibitor. | Browne, Cecille D; Hindmarsh, Elizabeth J; Smith, Jeffrey W | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 17012255 | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17012255 |
| Intravital fluorescence microscopy in pulmonary research. | St Croix, Claudette M; Leelavanichkul, Karanee; Watkins, Simon C | Advanced drug delivery reviews | 16996641 | 2006 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/16996641 |
| Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. | Shortreed, Michael R; Lamos, Shane M; Frey, Brian L; Phillips, Margaret F; Patel, Madhusudan; Belshaw, Peter J; Smith, Lloyd M | Analytical chemistry | 16970314 | 2006 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/16970314 |
| Mechanistic insights into targeting T cell membrane proteinase to promote islet beta-cell rejuvenation in type 1 diabetes. | Savinov, Alexei Y; Rozanov, Dmitri V; Strongin, Alex Y | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 16940151 | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16940151 |
| Unique contrast patterns from resonance-enhanced chiral SHG of cell membranes. | Yan, Ping; Millard, Andrew C; Wei, Meide; Loew, Leslie M | Journal of the American Chemical Society | 16925413 | 2006 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/16925413 |
| Engineered hybrid dimers: tracking the activation pathway of caspase-7. | Denault, Jean-Bernard; Bekes, Miklos; Scott, Fiona L; Sexton, Kelly M B; Bogyo, Matthew; Salvesen, Guy S | Molecular cell. | 16916640 | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16916640 |
| Identification of early intermediates of caspase activation using selective inhibitors and activity-based probes. | Berger, Alicia B; Witte, Martin D; Denault, Jean-Bernard; Sadaghiani, Amir Masoud; Sexton, Kelly M B; Salvesen, Guy S; Bogyo, Matthew | Molecular cell. | 16916639 | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16916639 |
| HiRes--a tool for comprehensive assessment and interpretation of metabolomic data. | Zhao, Qi; Stoyanova, Radka; Du, Shuyan; Sajda, Paul; Brown, Truman R | Bioinformatics (Oxford, England) | 16895927 | 2006 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/16895927 |
| Tracking and elucidating alphavirus-host protein interactions. | Cristea, Ileana M; Carroll, John-William N; Rout, Michael P; Rice, Charles M; Chait, Brian T; MacDonald, Margaret R | The Journal of biological chemistry | 16895903 | 2006 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/16895903 |
| Induction of autophagy in axonal dystrophy and degeneration. | Wang, Qing Jun; Ding, Yaomei; Kohtz, D Stave; Kohtz, Stave; Mizushima, Noboru; Cristea, Ileana M; Rout, Michael P; Chait, Brian T; Zhong, Yun; Heintz, Nathaniel; Yue, Zhenyu | The Journal of neuroscience : the official journal of the Society for Neuroscience. | 16885219 | 2006 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/16885219 |
| Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. | Takahashi, Hidekazu; McCaffery, J Michael; Irizarry, Rafael A; Boeke, Jef D | Molecular cell | 16857587 | 2006 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/16857587 |
| Control of acetyl-coenzyme A synthetase (AcsA) activity by acetylation/deacetylation without NAD(+) involvement in Bacillus subtilis. | Gardner, Jeffrey G; Grundy, Frank J; Henkin, Tina M; Escalante-Semerena, Jorge C | Journal of bacteriology. | 16855235 | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16855235 |
| Inositol phosphate metabolomics: merging genetic perturbation with modernized radiolabeling methods. | Stevenson-Paulik, Jill; Chiou, Shean-Tai; Frederick, Josh P; dela Cruz, June; Seeds, Andrew M; Otto, James C; York, John D | Methods (San Diego, Calif.) | 16829132 | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16829132 |
| Principal component analysis of urine metabolites detected by NMR and DESI-MS in patients with inborn errors of metabolism. | Pan, Zhengzheng; Gu, Haiwei; Talaty, Nari; Chen, Huanwen; Shanaiah, Narasimhamurthy; Hainline, Bryan E; Cooks, R Graham; Raftery, Daniel | Analytical and bioanalytical chemistry | 16821030 | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/16821030 |
| The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. | Celic, Ivana; Masumoto, Hiroshi; Griffith, Wendell P; Meluh, Pamela; Cotter, Robert J; Boeke, Jef D; Verreault, Alain | Current biology : CB. | 16815704 | 2006 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/16815704 |
| Phosphoproteomic analysis of Her2/neu signaling and inhibition. | Bose, Ron; Molina, Henrik; Patterson, A Scott; Bitok, John K; Periaswamy, Balamurugan; Bader, Joel S; Pandey, Akhilesh; Cole, Philip A | Proceedings of the National Academy of Sciences of the United States of America. | 16785428 | 2006 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/16785428 |
| Regulation of nuclear processes by inositol polyphosphates. | York, John D | Biochimica et biophysica acta. | 16781889 | 2006 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/16781889 |
| Interference with the complement system by tumor cell membrane type-1 matrix metalloproteinase plays a significant role in promoting metastasis in mice. | Rozanov, Dmitri V; Savinov, Alexei Y; Golubkov, Vladislav S; Tomlinson, Stephen; Strongin, Alex Y | Cancer research. | 16778201 | 2006 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/16778201 |
| New surfaces for desorption electrospray ionization mass spectrometry: porous silicon and ultra-thin layer chromatography plates. | Kauppila, Tiina J; Talaty, Nari; Salo, Piia K; Kotiaho, Tapio; Kostiainen, Risto; Cooks, R Graham | Rapid communications in mass spectrometry : RCM | 16773669 | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16773669 |
| Practical, catalytic, asymmetric synthesis of beta-lactones via a sequential ketene dimerization/hydrogenation process: inhibitors of the thioesterase domain of fatty acid synthase. | Purohit, Vikram C; Richardson, Robyn D; Smith, Jeffrey W; Romo, Daniel | The Journal of organic chemistry | 16749788 | 2006 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/16749788 |
| Multiple signaling pathways regulate yeast cell death during the response to mating pheromones. | Zhang, Nan-Nan; Dudgeon, Drew D; Paliwal, Saurabh; Levchenko, Andre; Grote, Eric; Cunningham, Kyle W | Molecular biology of the cell. | 16738305 | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16738305 |
| Protein complex compositions predicted by structural similarity. | Davis, Fred P; Braberg, Hannes; Shen, Min-Yi; Pieper, Ursula; Sali, Andrej; Madhusudhan, M S | Nucleic acids research. | 16738133 | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16738133 |
| Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. | Wang, Dongxia; Kalume, Dario; Pickart, Cecile; Pandey, Akhilesh; Cotter, Robert J | Analytical chemistry | 16737224 | 2006 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/16737224 |
| Gene function prediction from congruent synthetic lethal interactions in yeast. | Ye, Ping; Peyser, Brian D; Pan, Xuewen; Boeke, Jef D; Spencer, Forrest A; Bader, Joel S | Molecular systems biology | 16729061 | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16729061 |
| Mislocalization and unconventional functions of cellular MMPs in cancer. | Strongin, Alex Y | Cancer metastasis reviews. | 16680575 | 2006 Mar | https://www.ncbi.nlm.nih.gov/pubmed/16680575 |
| A selective activity-based probe for the papain family cysteine protease dipeptidyl peptidase I/cathepsin C. | Yuan, Fang; Verhelst, Steven H L; Blum, Galia; Coussens, Lisa M; Bogyo, Matthew | Journal of the American Chemical Society | 16637611 | 2006 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/16637611 |
| Furin regulates the intracellular activation and the uptake rate of cell surface-associated MT1-MMP. | Remacle, A G; Rozanov, D V; Fugere, M; Day, R; Strongin, A Y | Oncogene. | 16636666 | 2006 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/16636666 |
| Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. | Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory | Metabolic engineering. | 16631402 | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16631402 |
| Protein microarrays. | Chen, Chien-Sheng; Zhu, Heng | BioTechniques. | 16629388 | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16629388 |
| Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation. | Chen, Huanwen; Pan, Zhengzheng; Talaty, Nari; Raftery, Daniel; Cooks, R Graham | Rapid communications in mass spectrometry : RCM | 16628593 | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16628593 |
| O-glycosylation regulates autolysis of cellular membrane type-1 matrix metalloproteinase (MT1-MMP). | Remacle, Albert G; Chekanov, Alexei V; Golubkov, Vladislav S; Savinov, Alexei Y; Rozanov, Dmitri V; Strongin, Alex Y | The Journal of biological chemistry. | 16627478 | 2006 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/16627478 |
| Protease accessibility laddering: a proteomic tool for probing protein structure. | Dokudovskaya, Svetlana; Williams, Rosemary; Devos, Damien; Sali, Andrej; Chait, Brian T; Rout, Michael P | Structure (London, England : 1993) | 16615907 | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16615907 |
| Novel aza peptide inhibitors and active-site probes of papain-family cysteine proteases. | Verhelst, Steven H L; Witte, Martin D; Arastu-Kapur, Shirin; Fonovic, Marko; Bogyo, Matthew | Chembiochem : a European journal of chemical biology | 16607671 | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16607671 |
| Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. | Nathan, Dafna; Ingvarsdottir, Kristin; Sterner, David E; Bylebyl, Gwendolyn R; Dokmanovic, Milos; Dorsey, Jean A; Whelan, Kelly A; Krsmanovic, Mihajlo; Lane, William S; Meluh, Pamela B; Johnson, Erica S; Berger, Shelley L | Genes & development. | 16598039 | 2006 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/16598039 |
| A mechanism-based inactivator for histone demethylase LSD1. | Culhane, Jeffrey C; Szewczuk, Lawrence M; Liu, Xin; Da, Guoping; Marmorstein, Ronen; Cole, Philip A | Journal of the American Chemical Society | 16594666 | 2006 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/16594666 |
| Quantification of malonyl-coenzyme A in tissue specimens by high-performance liquid chromatography/mass spectrometry. | Minkler, Paul E; Kerner, Janos; Kasumov, Takhar; Parland, William; Hoppel, Charles L | Analytical biochemistry. | 16545769 | 2006 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/16545769 |
| D-Aspartate as a putative cell-cell signaling molecule in the Aplysia californica central nervous system. | Miao, Hai; Rubakhin, Stanislav S; Scanlan, Cory R; Wang, Liping; Sweedler, Jonathan V | Journal of neurochemistry | 16539650 | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16539650 |
| Serotonin catabolism and the formation and fate of 5-hydroxyindole thiazolidine carboxylic acid. | Squires, Leah N; Jakubowski, Jennifer A; Stuart, Jeffrey N; Rubakhin, Stanislav S; Hatcher, Nathan G; Kim, Won-Suk; Chen, Kevin; Shih, Jean C; Seif, Isabelle; Sweedler, Jonathan V | The Journal of biological chemistry. | 16537538 | 2006 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/16537538 |
| Measuring nitric oxide in single neurons by capillary electrophoresis with laser-induced fluorescence: use of ascorbate oxidase in diaminofluorescein measurements. | Kim, Won-Suk; Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan V | Analytical chemistry | 16536421 | 2006 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/16536421 |
| Inflammation, proteases and cancer. | van Kempen, Leon C L; de Visser, Karin E; Coussens, Lisa M | European journal of cancer (Oxford, England : 1990) | 16524717 | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16524717 |
| Matrix metalloproteinase 26 proteolysis of the NH2-terminal domain of the estrogen receptor beta correlates with the survival of breast cancer patients. | Savinov, Alexei Y; Remacle, Albert G; Golubkov, Vladislav S; Krajewska, Maryla; Kennedy, Susan; Duffy, Michael J; Rozanov, Dmitri V; Krajewski, Stan; Strongin, Alex Y | Cancer research. | 16510592 | 2006 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/16510592 |
| Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. | Gandhi, T K B; Zhong, Jun; Mathivanan, Suresh; Karthick, L; Chandrika, K N; Mohan, S Sujatha; Sharma, Salil; Pinkert, Stefan; Nagaraju, Shilpa; Periaswamy, Balamurugan; Mishra, Goparani; Nandakumar, Kannabiran; Shen, Beiyi; Deshpande, Nandan; Nayak, Rashm | Nature genetics. | 16501559 | 2006 Mar | https://www.ncbi.nlm.nih.gov/pubmed/16501559 |
| A DNA integrity network in the yeast Saccharomyces cerevisiae. | Pan, Xuewen; Ye, Ping; Yuan, Daniel S; Wang, Xiaoling; Bader, Joel S; Boeke, Jef D | Cell. | 16487579 | 2006 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/16487579 |
| GeneDesign: rapid, automated design of multikilobase synthetic genes. | Richardson, Sarah M; Wheelan, Sarah J; Yarrington, Robert M; Boeke, Jef D | Genome research. | 16481661 | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16481661 |
| Tagging and tracking individual networks within a complex mitochondrial web with photoactivatable GFP. | Twig, Gilad; Graf, Solomon A; Wikstrom, Jakob D; Mohamed, Hibo; Haigh, Sarah E; Elorza, Alvaro; Deutsch, Motti; Zurgil, Naomi; Reynolds, Nicole; Shirihai, Orian S | American journal of physiology. Cell physiology. | 16481372 | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16481372 |
| Simple fold composition and modular architecture of the nuclear pore complex. | Devos, Damien; Dokudovskaya, Svetlana; Williams, Rosemary; Alber, Frank; Eswar, Narayanan; Chait, Brian T; Rout, Michael P; Sali, Andrej | Proceedings of the National Academy of Sciences of the United States of America. | 16461911 | 2006 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/16461911 |
| Rectilinear ion trap mass spectrometer with atmospheric pressure interface and electrospray ionization source. | Song, Qingyu; Kothari, Sameer; Senko, Michael A; Schwartz, Jae C; Amy, Jonathan W; Stafford, George C; Cooks, R Graham; Ouyang, Zheng | Analytical chemistry | 16448044 | 2006 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/16448044 |
| Characterization and application of a new optical probe for membrane lipid domains. | Jin, Lei; Millard, Andrew C; Wuskell, Joseph P; Dong, Xuemei; Wu, Dianqing; Clark, Heather A; Loew, Leslie M | Biophysical journal | 16415047 | 2006 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/16415047 |
| Dynamic imaging of protease activity with fluorescently quenched activity-based probes. | Blum, Galia; Mullins, Stefanie R; Keren, Kinneret; Fonovic, Marko; Jedeszko, Christopher; Rice, Mark J; Sloane, Bonnie F; Bogyo, Matthew | Nature chemical biology | 16408036 | 2005 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16408036 |
| Activity-based probes that target diverse cysteine protease families. | Kato, Daisuke; Boatright, Kelly M; Berger, Alicia B; Nazif, Tamim; Blum, Galia; Ryan, Ciara; Chehade, Kareem A H; Salvesen, Guy S; Bogyo, Matthew | Nature chemical biology | 16407991 | 2005 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16407991 |
| Functional imaging of tumor proteolysis. | Sloane, Bonnie F; Sameni, Mansoureh; Podgorski, Izabela; Cavallo-Medved, Dora; Moin, Kamiar | Annual review of pharmacology and toxicology. | 16402907 | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16402907 |
| Human protein reference database--2006 update. | Mishra, Gopa R; Suresh, M; Kumaran, K; Kannabiran, N; Suresh, Shubha; Bala, P; Shivakumar, K; Anuradha, N; Reddy, Raghunath; Raghavan, T Madhan; Menon, Shalini; Hanumanthu, G; Gupta, Malvika; Upendran, Sapna; Gupta, Shweta; Mahesh, M; Jacob, Bincy; Mathew | Nucleic acids research. | 16381900 | 2006 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/16381900 |
| Novel application of the "doubly labeled" water method: measuring CO2 production and the tissue-specific dynamics of lipid and protein in vivo. | Bederman, Ilya R; Dufner, Danielle A; Alexander, James C; Previs, Stephen F | American journal of physiology. Endocrinology and metabolism. | 16368786 | 2006 May | https://www.ncbi.nlm.nih.gov/pubmed/16368786 |
| The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. | Dilworth, David J; Tackett, Alan J; Rogers, Richard S; Yi, Eugene C; Christmas, Rowan H; Smith, Jennifer J; Siegel, Andrew F; Chait, Brian T; Wozniak, Richard W; Aitchison, John D | The Journal of cell biology | 16365162 | 2005 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/16365162 |
| Bioinformatics and proteomics approaches for aging research. | Raghothama, Chaerkady; Harsha, H C; Prasad, C K; Pandey, Akhilesh | Biogerontology. | 16333756 | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16333756 |
| A general solid phase method for the preparation of diverse azapeptide probes directed against cysteine proteases. | Kato, Daisuke; Verhelst, Steven H L; Sexton, Kelly B; Bogyo, Matthew | Organic letters. | 16321013 | 2005 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/16321013 |
| Use of semiselective TOCSY and the pearson correlation for the metabonomic analysis of biofluid mixtures: application to urine. | Sandusky, Peter; Raftery, Daniel | Analytical chemistry | 16316181 | 2005 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/16316181 |
| Evidence for high-capacity bidirectional glucose transport across the endoplasmic reticulum membrane by genetically encoded fluorescence resonance energy transfer nanosensors. | Fehr, Marcus; Takanaga, Hitomi; Ehrhardt, David W; Frommer, Wolf B | Molecular and cellular biology | 16314530 | 2005 Dec | https://www.ncbi.nlm.nih.gov/pubmed/16314530 |
| Subcellular analysis of D-aspartate. | Miao, Hai; Rubakhin, Stanislav S; Sweedler, Jonathan V | Analytical chemistry | 16285665 | 2005 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/16285665 |
| Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. | Hyland, Edel M; Cosgrove, Michael S; Molina, Henrik; Wang, Dongxia; Pandey, Akhilesh; Cottee, Robert J; Boeke, Jef D | Molecular and cellular biology. | 16260619 | 2005 Nov | https://www.ncbi.nlm.nih.gov/pubmed/16260619 |
| High resolution 1H NMR-based metabolomics indicates a neurotransmitter cycling deficit in cerebral tissue from a mouse model of Batten disease. | Pears, Michael R; Cooper, Jonathan D; Mitchison, Hannah M; Mortishire-Smith, Russell J; Pearce, David A; Griffin, Julian L | The Journal of biological chemistry. | 16239221 | 2005 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/16239221 |
| The transmembrane domain is essential for the microtubular trafficking of membrane type-1 matrix metalloproteinase (MT1-MMP). | Remacle, Albert G; Rozanov, Dmitri V; Baciu, Peter C; Chekanov, Alexei V; Golubkov, Vladislav S; Strongin, Alex Y | Journal of cell science. | 16219679 | 2005 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/16219679 |
| Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. | Gronborg, Mads; Kristiansen, Troels Zakarias; Iwahori, Akiko; Chang, Rubens; Reddy, Raghunath; Sato, Norihiro; Molina, Henrik; Jensen, Ole Norregaard; Hruban, Ralph H; Goggins, Michael G; Maitra, Anirban; Pandey, Akhilesh | Molecular & cellular proteomics : MCP. | 16215274 | 2006 Jan | https://www.ncbi.nlm.nih.gov/pubmed/16215274 |
| Direct identification of ubiquitination sites on ubiquitin-conjugated CHIP using MALDI mass spectrometry. | Wang, Dongxia; Xu, Wanping; McGrath, Sara C; Patterson, Cam; Neckers, Len; Cotter, Robert J | Journal of proteome research. | 16212406 | 2005 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/16212406 |
| Proteomic resources: integrating biomedical information in humans. | Suresh, Shubha; Sujatha Mohan, S; Mishra, Goparani; Hanumanthu, G R; Suresh, M; Reddy, Raghunath; Pandey, Akhilesh | Gene. | 16202541 | 2005 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/16202541 |
| Shining light on signaling and metabolic networks by genetically encoded biosensors. | Lalonde, Sylvie; Ehrhardt, David W; Frommer, Wolf B | Current opinion in plant biology | 16188489 | 2005 Dec | https://www.ncbi.nlm.nih.gov/pubmed/16188489 |
| Dynamic properties of network motifs contribute to biological network organization. | Prill, Robert J; Iglesias, Pablo A; Levchenko, Andre | PLoS biology | 16187794 | 2005 Nov | https://www.ncbi.nlm.nih.gov/pubmed/16187794 |
| Fluorescent proteins as proteomic probes. | Cristea, Ileana M; Williams, Rosemary; Chait, Brian T; Rout, Michael P | Molecular & cellular proteomics : MCP | 16155292 | 2005 Dec | https://www.ncbi.nlm.nih.gov/pubmed/16155292 |
| Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering. | Deuschle, Karen; Okumoto, Sakiko; Fehr, Marcus; Looger, Loren L; Kozhukh, Leonid; Frommer, Wolf B | Protein science : a publication of the Protein Society | 16131659 | 2005 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16131659 |
| Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. | Stevenson-Paulik, Jill; Bastidas, Robert J; Chiou, Shean-Tai; Frye, Roy A; York, John D | Proceedings of the National Academy of Sciences of the United States of America | 16107538 | 2005 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/16107538 |
| Measuring D-amino acid-containing neuropeptides with capillary electrophoresis. | Sheeley, Sarah A; Miao, Hai; Ewing, Michael A; Rubakhin, Stanislav S; Sweedler, Jonathan V | The Analyst | 16021220 | 2005 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16021220 |
| Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. | Phillips, Carolyn I; Bogyo, Matthew | Cellular microbiology. | 16008574 | 2005 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16008574 |
| Diverse polyubiquitin interaction properties of ubiquitin-associated domains. | Raasi, Shahri; Varadan, Ranjani; Fushman, David; Pickart, Cecile M | Nature structural & molecular biology. | 16007098 | 2005 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16007098 |
| Imaging mass spectrometry: fundamentals and applications to drug discovery. | Rubakhin, Stanislav S; Jurchen, John C; Monroe, Eric B; Sweedler, Jonathan V | Drug discovery today | 15970265 | 2005 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/15970265 |
| Automatic detection of subsystem/pathway variants in genome analysis. | Ye, Yuzhen; Osterman, Andrei; Overbeek, Ross; Godzik, Adam | Bioinformatics (Oxford, England) | 15961494 | 2005 Jun | https://www.ncbi.nlm.nih.gov/pubmed/15961494 |
| Genetically encoded FRET sensors for visualizing metabolites with subcellular resolution in living cells. | Looger, Loren L; Lalonde, Sylvie; Frommer, Wolf B | Plant physiology. | 15955913 | 2005 Jun | https://www.ncbi.nlm.nih.gov/pubmed/15955913 |
| Inhibition of membrane type-1 matrix metalloproteinase by cancer drugs interferes with the homing of diabetogenic T cells into the pancreas. | Savinov, Alexei Y; Rozanov, Dmitri V; Golubkov, Vladislav S; Wong, F Susan; Strongin, Alex Y | The Journal of biological chemistry. | 15944163 | 2005 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/15944163 |
| Molecular definition of a novel inositol polyphosphate metabolic pathway initiated by inositol 1,4,5-trisphosphate 3-kinase activity in Saccharomyces cerevisiae. | Seeds, Andrew M; Bastidas, Robert J; York, John D | The Journal of biological chemistry | 15944147 | 2005 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/15944147 |
| Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors. | Okumoto, Sakiko; Looger, Loren L; Micheva, Kristina D; Reimer, Richard J; Smith, Stephen J; Frommer, Wolf B | Proceedings of the National Academy of Sciences of the United States of America | 15939876 | 2005 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/15939876 |
| Online microdialysis-dynamic nanoelectrospray ionization-mass spectrometry for monitoring neuropeptide secretion. | Jakubowski, Jennifer A; Hatcher, Nathan G; Sweedler, Jonathan V | Journal of mass spectrometry : JMS. | 15934039 | 2005 Jul | https://www.ncbi.nlm.nih.gov/pubmed/15934039 |
| Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability. | Golubkov, Vladislav S; Boyd, Sarah; Savinov, Alexei Y; Chekanov, Alexei V; Osterman, Andrei L; Remacle, Albert; Rozanov, Dmitri V; Doxsey, Stephen J; Strongin, Alex Y | The Journal of biological chemistry. | 15878869 | 2005 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/15878869 |
| Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. | Molina, Henrik; Parmigiani, Giovanni; Pandey, Akhilesh | Analytical chemistry | 15859588 | 2005 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/15859588 |
| Maspin alters the carcinoma proteome. | Chen, Emily I; Florens, Laurence; Axelrod, Fumiko T; Monosov, Edward; Barbas 3rd, Carlos F; Yates 3rd, John R; Felding-Habermann, Brunhilde; Smith, Jeffrey W | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 15857880 | 2005 Jul | https://www.ncbi.nlm.nih.gov/pubmed/15857880 |
| Solid-phase synthesis of double-headed epoxysuccinyl activity-based probes for selective targeting of papain family cysteine proteases. | Verhelst, Steven H L; Bogyo, Matthew | Chembiochem : a European journal of chemical biology. | 15776409 | 2005 May | https://www.ncbi.nlm.nih.gov/pubmed/15776409 |
| Approach for determining protein ubiquitination sites by MALDI-TOF mass spectrometry. | Wang, Dongxia; Cotter, Robert J | Analytical chemistry | 15732931 | 2005 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/15732931 |
| Strategy for the isolation, derivatization, chromatographic separation, and detection of carnitine and acylcarnitines. | Minkler, Paul E; Ingalls, Stephen T; Hoppel, Charles L | Analytical chemistry | 15732930 | 2005 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/15732930 |
| Chemical proteomics applied to target identification and drug discovery. | Verhelst, Steven H L; Bogyo, Matthew | BioTechniques. | 15727120 | 2005 Feb | https://www.ncbi.nlm.nih.gov/pubmed/15727120 |
| Genetically encoded sensors for metabolites. | Deuschle, Karen; Fehr, Marcus; Hilpert, Melanie; Lager, Ida; Lalonde, Sylvie; Looger, Loren L; Okumoto, Sakiko; Persson, Jorgen; Schmidt, Anja; Frommer, Wolf B | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 15688353 | 2005 Mar | https://www.ncbi.nlm.nih.gov/pubmed/15688353 |
| Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. | Berger, Alicia B; Vitorino, Phillip M; Bogyo, Matthew | American journal of pharmacogenomics : genomics-related research in drug development and clinical practice. | 15651898 | 2004 | https://www.ncbi.nlm.nih.gov/pubmed/15651898 |
| Cyclic nucleotide-gated cation channels mediate sodium absorption by IMCD (mIMCD-K2) cells. | Vandorpe, D H; Ciampolillo, F; Green, R B; Stanton, B A | The American journal of physiology. | 9124526 | 1997 Mar | https://www.ncbi.nlm.nih.gov/pubmed/9124526 |
