Building Blocks, Biological Pathways, and Networks (BBPN)
Building Blocks, Biological Pathways, and Networks (BBPN)
Program Publications
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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 |
|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Enzyme inhibitor discovery by activity-based protein profiling. | Niphakis, Micah J; Cravatt, Benjamin F | Annual review of biochemistry | 24905785 | 2014 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Enriching the pore: Splendid complexity from humble origins. | Field, Mark C; Koreny, Ludek; Rout, Michael P | Traffic (Copenhagen, Denmark) | 24279500 | 2013 Nov 26 |
| 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 |
| 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 |
| 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 |
| 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 |
| Peroxisomes take shape. | Smith, Jennifer J; Aitchison, John D | Nature reviews. Molecular cell biology | 24263361 | 2013 Dec |
| 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 |
| 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 |
| 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 |
| 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 |
| Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. | NULL | Nature | 24201285 | 2013 Nov 7 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Fluorogen-activating-proteins as universal affinity biosensors for immunodetection. | Gallo, Eugenio; Vasilev, Kalin V; Jarvik, Jonathan | Biotechnology and bioengineering | 24122476 | 2013 Oct 9 |
| 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 |
| 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 |
| Recycling of kinesin-1 motors by diffusion after transport. | Blasius, T Lynne; Reed, Nathan; Slepchenko, Boris M; Verhey, Kristen J | PloS one | 24098765 | 2013 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| SILAC-based quantification of Sirt1-responsive lysine acetylome. | Chen, Yue; Colak, Gozde; Zhao, Yingming | Methods in molecular biology (Clifton, N.J.) | 24014402 | 2013 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Population-expression models of immune response. | Stromberg, Sean P; Antia, Rustom; Nemenman, Ilya | Physical biology | 23735782 | 2013 Jun |
| 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 |
| 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 |
| 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 |
| 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 |
| Using glycinylation, a chemical derivatization technique, for the quantitation of ubiquitinated proteins. | Fiedler, Katherine L; Cotter, Robert J | Analytical chemistry | 23682733 | 2013 Jun 18 |
| 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 |
| 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 |
| Proteomic strategies to characterize signaling pathways. | Harsha, H C; Pinto, Sneha M; Pandey, Akhilesh | Methods in molecular biology (Clifton, N.J.) | 23666735 | 2013 |
| 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 |
| 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 |
| 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 |
| 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 |
| Postage for the messenger: designating routes for nuclear mRNA export. | Natalizio, Barbara J; Wente, Susan R | Trends in cell biology | 23583578 | 2013 Apr 11 |
| Improved native isolation of endogenous Protein A-tagged protein complexes. | LaCava, John; Chandramouli, Nagarajan; Jiang, Hua; Rout, Michael P | BioTechniques | 23581468 | 2013 Apr |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Chemical probes for histone-modifying enzymes. | Cole, Philip A | Nature chemical biology | 18800048 | 2008 Oct |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Reduced-representation methylation mapping. | Jeddeloh, Jeffrey A; Greally, John M; Rando, Oliver J | Genome biology | 18771577 | 2008 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Kinetic flux profiling for quantitation of cellular metabolic fluxes. | Yuan, Jie; Bennett, Bryson D; Rabinowitz, Joshua D | Nature protocols | 18714301 | 2008 |
| 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 |
| 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 |
| Adapting the stretched sample method from tissue profiling to imaging. | Zimmerman, Tyler A; Monroe, Eric B; Sweedler, Jonathan V | Proteomics | 18712762 | 2008 Sep |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| On sensitivity amplification in intracellular signaling cascades. | Racz, Eva; Slepchenko, Boris M | Physical biology | 18663279 | 2008 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mass spectrometry of acoustically levitated droplets. | Westphall, Michael S; Jorabchi, Kaveh; Smith, Lloyd M | Analytical chemistry | 18582090 | 2008 Aug 1 |
| Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage. | Celic, Ivana; Verreault, Alain; Boeke, Jef D | Genetics | 18579506 | 2008 Aug |
| 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 |
| Human Proteinpedia as a resource for clinical proteomics. | Mathivanan, Suresh; Pandey, Akhilesh | Molecular & cellular proteomics : MCP | 18573810 | 2008 Oct |
| 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 |
| 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 |
| The incredible shrinking world of DNA microarrays. | Wheelan, Sarah J; Martinez Murillo, Francisco; Boeke, Jef D | Molecular bioSystems | 18563246 | 2008 Jul |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Comprehensive comparison of collision induced dissociation and electron transfer dissociation. | Molina, Henrik; Matthiesen, Rune; Kandasamy, Kumaran; Pandey, Akhilesh | Analytical chemistry | 18540640 | 2008 Jul 1 |
| 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 |
| 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 |
| 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 |
| Improved residual water suppression: WET180. | Mo, Huaping; Raftery, Daniel | Journal of biomolecular NMR | 18506578 | 2008 Jun |
| 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 |
| 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 |
| 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 |
| 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 |
| Sulfatides facilitate apolipoprotein E-mediated amyloid-beta peptide clearance through an endocytotic pathway. | Zeng, Youchun; Han, Xianlin | Journal of neurochemistry | 18485101 | 2008 Aug |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Detection of nitric oxide in single cells. | Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan V | The Analyst | 18365109 | 2008 Apr |
| Polarized immune responses differentially regulate cancer development. | Johansson, Magnus; Denardo, David G; Coussens, Lisa M | Immunological reviews | 18363999 | 2008 Apr |
| 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 |
| 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 |
| 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 |
| Quantitative proteomics using stable isotope labeling with amino acids in cell culture. | Harsha, H C; Molina, Henrik; Pandey, Akhilesh | Nature protocols | 18323819 | 2008 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Ionomics and the study of the plant ionome. | Salt, David E; Baxter, Ivan; Lahner, Brett | Annual review of plant biology | 18251712 | 2008 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms. | Shastri, Avantika A; Morgan, John A | Phytochemistry | 17524438 | 2007 Aug-Sep |
| 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 |
| 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 |
| 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 |
| Fluxomics: mass spectrometry versus quantitative imaging. | Wiechert, Wolfgang; Schweissgut, Oliver; Takanaga, Hitomi; Frommer, Wolf B | Current opinion in plant biology | 17481942 | 2007 Jun |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Where does all the PIP2 come from? | Loew, Leslie M | The Journal of physiology | 17395623 | 2007 Aug 1 |
| 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 |
| Decoding transcriptional regulatory interactions. | Liu, L Angela; Bader, Joel S | Physica D. Nonlinear phenomena | 17364011 | 2006 Dec |
| 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 |
| 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 |
| 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 |
| A curated compendium of phosphorylation motifs. | Amanchy, Ramars; Periaswamy, Balamurugan; Mathivanan, Suresh; Reddy, Raghunath; Tattikota, Sudhir Gopal; Pandey, Akhilesh | Nature biotechnology | 17344875 | 2007 Mar |
| 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 |
| Activity based probes for proteases: applications to biomarker discovery, molecular imaging and drug screening. | Fonovic, Marko; Bogyo, Matthew | Current pharmaceutical design | 17313359 | 2007 |
| 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 |
| 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 |
| 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 |
| 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 |
| Humoral immunity, inflammation and cancer. | Tan, Ting-Ting; Coussens, Lisa M | Current opinion in immunology | 17276050 | 2007 Apr |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Inositol polyphosphate kinases: regulators of nuclear function. | Seeds, Andrew M; York, John D | Biochemical Society symposium | 17233590 | 2007 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Tagging and detection strategies for activity-based proteomics. | Sadaghiani, Amir M; Verhelst, Steven Hl; Bogyo, Matthew | Current opinion in chemical biology | 17174138 | 2007 Feb |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Characterizing electrospray ionization using atmospheric pressure ion mobility spectrometry. | Tang, Xiaoting; Bruce, James E; Hill Jr, Herbert H | Analytical chemistry | 17105168 | 2006 Nov 15 |
| 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 |
| 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 |
| Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. | Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory | Metabolic engineering | 17088092 | 2007 Jan |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Proteomics of the peroxisome. | Saleem, R A; Smith, J J; Aitchison, J D | Biochimica et biophysica acta | 17050007 | 2006 Dec |
| 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 |
| 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 |
| 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 |
| Protein chip fabrication by capture of nascent polypeptides. | Tao, Sheng-Ce; Zhu, Heng | Nature biotechnology | 17013375 | 2006 Oct |
| 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 |
| Intravital fluorescence microscopy in pulmonary research. | St Croix, Claudette M; Leelavanichkul, Karanee; Watkins, Simon C | Advanced drug delivery reviews | 16996641 | 2006 Sep 15 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Regulation of nuclear processes by inositol polyphosphates. | York, John D | Biochimica et biophysica acta. | 16781889 | 2006 May-Jun |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mislocalization and unconventional functions of cellular MMPs in cancer. | Strongin, Alex Y | Cancer metastasis reviews. | 16680575 | 2006 Mar |
| 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 |
| 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 |
| 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 |
| Protein microarrays. | Chen, Chien-Sheng; Zhu, Heng | BioTechniques. | 16629388 | 2006 Apr |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bioinformatics and proteomics approaches for aging research. | Raghothama, Chaerkady; Harsha, H C; Prasad, C K; Pandey, Akhilesh | Biogerontology. | 16333756 | 2005 |
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