Building Blocks, Biological Pathways, and Networks (948)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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 TMolecular & cellular proteomics : MCP2014 Aug 26NULL25161197
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; SaMolecular & cellular proteomics : MCP2014 Aug 19NULL25139911
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, SvetlanaMolecular & cellular proteomics : MCP2014 Jul 29NULL25073740
Metabolomics of ApcMin/+ mice genetically susceptible to intestinal cancer.Dazard, Jean-Eudes J; Sandlers, Yana; Doerner, Stephanie K; Berger, Nathan A; Brunengraber, HenriBMC systems biology20147224954394
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 EAnalytical chemistry2014 Jul 16587-9524949523
Enzyme inhibitor discovery by activity-based protein profiling.Niphakis, Micah J; Cravatt, Benjamin FAnnual review of biochemistry2014341-7724905785
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, PraveNature2014 May 29575-8124870542
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 WJournal of biomolecular screening2014 May 12NULL24820110
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, SACS chemical biology2014 Apr 7NULL24707965
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, GuoCell metabolism2014 Apr 1605-1724703693
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 FThe Journal of biological chemistry2014 May 913575-8824675078
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, AkhileshJournal of proteome research2014 Jun 62749-6024669763
The multifunctional nuclear pore complex: a platform for controlling gene expression.Ptak, Christopher; Aitchison, John D; Wozniak, Richard WCurrent opinion in cell biology2014 Mar 2046-5324657998
Human cytomegalovirus pUL37x1-induced calcium flux activates PKC*, inducing altered cell shape and accumulation of cytoplasmic vesicles.Sharon-Friling, Ronit; Shenk, ThomasProceedings of the National Academy of Sciences of the United States of America2014 Mar 25E1140-824616524
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 SMolecular microbiology2014 Apr369-8224612392
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 CMolecular biology of the cell2014 May1421-3624600046
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 JThe Journal of cell biology2014 Mar 3839-5624590176
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, AkhileshDatabase : the journal of biological databases and curation2014bau00724573880
Fluorogen-activating scFv biosensors target surface markers on live cells via streptavidin or single-chain avidin.Gallo, Eugenio; Jarvik, JonathanMolecular biotechnology2014 Jul585-9024562573
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-FangFree radical biology & medicine2014 Feb 1878-8524556413
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 ACurrent protocols in cytometry / editorial board, J. Paul Robinson, managing editor ... [et al.]20149.43.1-9.43.1124510772
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 ACurrent protocols in cytometry / editorial board, J. Paul Robinson, managing editor ... [et al.]20149.43.1-9.43.1124510772
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, GadCell metabolism2014 Feb 4319-3024506873
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 ERapid communications in mass spectrometry : RCM2014 Mar 15403-1224497278
Alterations in Mouse Brain Lipidome after Disruption of CST Gene: A Lipidomics Study.Wang, Chunyan; Wang, Miao; Zhou, Yunhua; Dupree, Jeffrey L; Han, XianlinMolecular neurobiology2014 Jan 7NULL24395133
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-FangJournal of lipid research2014 Mar592-60224367045
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, KaushNucleic acids research2014 JanD959-6524304897
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, ThomasProceedings of the National Academy of Sciences of the United States of America2013 Dec 17E5006-1524297925
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 SNucleic acids research2014 Feb2330-4524293652
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 ZNucleic acids research2014 Feb2789-9724293651
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; ElNature2014 Jan 30691-524284630
Enriching the pore: Splendid complexity from humble origins.Field, Mark C; Koreny, Ludek; Rout, Michael PTraffic (Copenhagen, Denmark)2013 Nov 26NULL24279500
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 MBioinformatics (Oxford, England)2014 Jan 15292-424273241
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; AndersenNature structural & molecular biology2013 Dec1367-7624270879
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, LixinCell2013 Nov 211034-4824267889
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 SJournal of the American Chemical Society2013 Dec 1118445-5724266634
Peroxisomes take shape.Smith, Jennifer J; Aitchison, John DNature reviews. Molecular cell biology2013 Dec803-1724263361
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, SJournal of proteomics & bioinformatics2011 Oct 29NULL24255551
PhosphoNetworks: a database for human phosphorylation networks.Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Zhang, Jin; Zhu, Heng; Qian, JiangBioinformatics (Oxford, England)2014 Jan 1141-224227675
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 MarieMolecular cell2013 Nov 21485-9424211263
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, AndrejMethods in molecular biology (Clifton, N.J.)2014277-9524203340
Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.NULLNature2013 Nov 714624201285
High-resolution network biology: connecting sequence with function.Ryan, Colm J; Cimermancic, Peter; Szpiech, Zachary A; Sali, Andrej; Hernandez, Ryan D; Krogan, Nevan JNature reviews. Genetics2013 Dec865-7924197012
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 PChemphyschem : a European journal of chemical physics and physical chemistry2013 Nov 5NULL24194371
Loss of TRPML1 promotes production of reactive oxygen species: is oxidative damage a factor in mucolipidosis type IV?Coblentz, Jessica; St Croix, Claudette; Kiselyov, KirillThe Biochemical journal2014 Jan 15361-824192042
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 DNucleic acids research2014 Feb1442-6024185701
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, CaterinaMolecular biology of the cell2013 Dec3920-3824152732
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, MarcPloS one2013e7709724130841
Fluorogen-activating-proteins as universal affinity biosensors for immunodetection.Gallo, Eugenio; Vasilev, Kalin V; Jarvik, JonathanBiotechnology and bioengineering2013 Oct 9NULL24122476
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-ShengMolecular & cellular proteomics : MCP2014 Jan84-9224113282
Rotenone induces reductive stress and triacylglycerol deposition in C2C12 cells.He, Quan; Wang, Miao; Petucci, Christopher; Gardell, Stephen J; Han, XianlinThe international journal of biochemistry & cell biology2013 Dec2749-5524104397
Recycling of kinesin-1 motors by diffusion after transport.Blasius, T Lynne; Reed, Nathan; Slepchenko, Boris M; Verhey, Kristen JPloS one2013e7608124098765
Recovering a representative conformational ensemble from underdetermined macromolecular structural data.Berlin, Konstantin; Castaneda, Carlos A; Schneidman-Duhovny, Dina; Sali, Andrej; Nava-Tudela, Alfredo; Fushman, DavidJournal of the American Chemical Society2013 Nov 616595-60924093873
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 JMolecular biology of the cell2013 Dec3603-1924088567
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 EPloS one2013e7622024086712
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, PThe Journal of biological chemistry2013 Nov 832211-2824045953
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, PaulPloS one2013e7338924039928
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 JNucleic acids research2013 Dec10334-4424038466
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, SueGenetics2013 Nov795-80724037263
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, HengPloS one2013e7267124023761
SILAC-based quantification of Sirt1-responsive lysine acetylome.Chen, Yue; Colak, Gozde; Zhao, YingmingMethods in molecular biology (Clifton, N.J.)2013105-2024014402
Single cell metabolic profiling of tumor mimics.Keithley, Richard B; Weaver, Eric M; Rosado, Andrea M; Metzinger, Mark P; Hummon, Amanda B; Dovichi, Norman JAnalytical chemistry2013 Oct 18910-824011091
Conformational States of macromolecular assemblies explored by integrative structure calculation.Thalassinos, Konstantinos; Pandurangan, Arun Prasad; Xu, Min; Alber, Frank; Topf, MayaStructure (London, England : 1993)2013 Sep 31500-824010709
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 PJournal of molecular biology2013 Nov 154595-61323978698
Accurate SAXS profile computation and its assessment by contrast variation experiments.Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A; Sali, AndrejBiophysical journal2013 Aug 20962-7423972848
Fatty acidomics: global analysis of lipid species containing a carboxyl group with a charge-remote fragmentation-assisted approach.Wang, Miao; Han, Rowland H; Han, XianlinAnalytical chemistry2013 Oct 19312-2023971716
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 AThe Journal of biological chemistry2013 Oct 1129267-8023970548
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, HengAnalytical chemistry2013 Sep 38046-5423941274
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 DavidMolecular and cellular biology2013 Oct3735-4823878396
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, XianlinJournal of neurochemistry2013 Dec733-823865640
Molecular crowding shapes gene expression in synthetic cellular nanosystems.Tan, Cheemeng; Saurabh, Saumya; Bruchez, Marcel P; Schwartz, Russell; Leduc, PhilipNature nanotechnology2013 Aug602-823851358
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 DBioinformatics (Oxford, England)2013 Oct 12435-4423832245
Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms.Xu, Min; Alber, FrankBioinformatics (Oxford, England)2013 Jul 1i274-8223812994
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, YingmingMolecular cell2013 Jun 27919-3023806337
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, JPLoS pathogens2013 June100340323785281
Superimposed topographic and chemical cues synergistically guide neurite outgrowth.Kundu, Arnab; Micholt, Liesbeth; Friedrich, Sarah; Rand, Danielle R; Bartic, Carmen; Braeken, Dries; Levchenko, AndreLab on a chip2013 Aug 73070-8123752939
Population-expression models of immune response.Stromberg, Sean P; Antia, Rustom; Nemenman, IlyaPhysical biology2013 Jun3501023735782
Cell Adhesion on Micro-Structured Fibronectin Gradients Fabricated by Multiphoton Excited Photochemistry.Chen, Xiyi; Su, Yuan-Deng; Ajeti, Visar; Chen, Shean-Jen; Campagnola, Paul JCellular and molecular bioengineering2012 Sep307-31923710258
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, DMethods (San Diego, Calif.)2013 May 2323707623
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 MThe Journal of investigative dermatology2013 Oct2444-5223698071
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, ThomasPLoS pathogens2013 Maye100333323696731
Using glycinylation, a chemical derivatization technique, for the quantitation of ubiquitinated proteins.Fiedler, Katherine L; Cotter, Robert JAnalytical chemistry2013 Jun 185827-3423682733
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 JJournal of mass spectrometry : JMS2013 May608-1523674285
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, KamiarBiological chemistry2012 Dec1405-1623667900
Proteomic strategies to characterize signaling pathways.Harsha, H C; Pinto, Sneha M; Pandey, AkhileshMethods in molecular biology (Clifton, N.J.)2013359-7723666735
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 DACS synthetic biology2013 Aug 16473-723654272
Manipulating ionic strength to improve single cell electrophoretic separations.Keithley, Richard B; Metzinger, Mark P; Rosado, Andrea M; Dovichi, Norman JTalanta2013 Jul 15206-1423622546
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 VNature protocols2013 Apr783-9923589938
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 BCurrent opinion in plant biology2013 Jun389-9523587939
Postage for the messenger: designating routes for nuclear mRNA export.Natalizio, Barbara J; Wente, Susan RTrends in cell biology2013 Apr 11NULL23583578
Improved native isolation of endogenous Protein A-tagged protein complexes.LaCava, John; Chandramouli, Nagarajan; Jiang, Hua; Rout, Michael PBioTechniques2013 Apr213-623581468
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 SBioconjugate chemistry2013 May 15803-1023573960
Regulated recycling of mutant CFTR is partially restored by pharmacological treatment.Holleran, John P; Zeng, Jianxin; Frizzell, Raymond A; Watkins, Simon CJournal of cell science2013 Jun 152692-70323572510
Differential principal component analysis of ChIP-seq.Ji, Hongkai; Li, Xia; Wang, Qian-fei; Ning, YangProceedings of the National Academy of Sciences of the United States of America2013 Apr 236789-9423569280
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 AProceedings of the National Academy of Sciences of the United States of America2013 Apr 236943-823569277
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 biology201365523549483
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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 RJournal of immunology (Baltimore, Md. : 1950)2013 Apr 154324-3623479230
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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 VAnalytical chemistry2013 Mar 193136-4323409944
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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-FangFree radical biology & medicine2013 May35-4423328733
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 HAnalytical and bioanalytical chemistry2013 Feb1959-6823314481
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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 MProtein science : a publication of the Protein Society2013 Mar287-9523281010
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 VJournal of proteome research2013 Feb 1585-9323256577
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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 BMolecular biotechnology2013 Jul829-4123242633
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 CNeurobiology of disease2013 Jun158-6823220621
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 JScience signaling2012 Dec 4ra8823211528
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, HenriChemical research in toxicology2013 Feb 18213-2023171137
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 JThe Analyst2013 Jan 7164-7023154386
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 EBMC genomics201262323151179
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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 DianePLoS pathogens2012e100297223093938
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The application of information theory to biochemical signaling systems.Rhee, Alex; Cheong, Raymond; Levchenko, AndrePhysical biology2012 Aug04501122872091
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 psychiatry2013 Aug882-822869031
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; RelkiMolecular psychiatry2013 Aug889-9722850627
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-ShengMolecular & cellular proteomics : MCP2012 Nov1177-9022843995
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 JCell reports2012 Jul 26198-20522840409
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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, YingmingMolecular & cellular proteomics : MCP2012 Oct1048-6222826441
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Integrative structural modeling with small angle X-ray scattering profiles.Schneidman-Duhovny, Dina; Kim, Seung Joong; Sali, AndrejBMC structural biology20121722800408
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 TBiochemistry2012 Jul 316028-3822784353
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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, NathanielPloS one2012e3957222768092
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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 MChembiochem : a European journal of chemical biology2012 Jul 231673-922740420
A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.Frazier, Zachary; Alber, FrankJournal of computational biology : a journal of computational molecular cell biology2012 Jun606-1822697237
How networks change with time.Park, Yongjin; Bader, Joel SBioinformatics (Oxford, England)2012 Jun 15i40-822689777
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 LExperimental cell research2012 Oct 12014-2122687878
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 ACell cycle (Georgetown, Tex.)2012 Jun 152367-7922672905
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, JohnBioTechniques2012 May1-622668517
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-ZheMolecular & cellular proteomics : MCP2012 Sep669-8022647870
The BECN1 coiled coil domain: an "imperfect" homodimer interface that facilitates ATG14 and UVRAG binding.Li, Xiaohua; He, Liqiang; Zhang, Mingjie; Yue, Zhenyu; Zhao, YanxiangAutophagy2012 Aug1258-6022647755
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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, ThomasJournal of virology2012 Aug8259-6822623791
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.Tjong, Harianto; Gong, Ke; Chen, Lin; Alber, FrankGenome research2012 Jul1295-30522619363
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 JThe Journal of cell biology2012 May 28643-5822613834
Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes.Oeffinger, MarleneProteomics2012 May1591-60822592981
Identification of protein SUMOylation sites by mass spectrometry using combined microwave-assisted aspartic acid cleavage and tryptic digestion.Osula, Omoruyi; Swatkoski, Stephen; Cotter, Robert JJournal of mass spectrometry : JMS2012 May644-5422576878
Identification of n-hydroxy acid metabolites in electron impact ionization mass spectrometry.Li, Qingling; Zhang, Guo-FangRapid communications in mass spectrometry : RCM2012 Jun 151355-6222555929
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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 VThe Analyst2012 Jul 72965-7222543409
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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 biology2012e100128722479148
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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, HenriThe Biochemical journal2012 Jun 1333-4122428548
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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 PThe Journal of cell biology2012 Feb 20419-3422331846
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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, NicolasBMC systems biology201119822172142
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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 JScience (New York, N.Y.)2011 Dec 21289-9322033520
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Redundant mechanisms for stable cell locomotion revealed by minimal models.Wolgemuth, Charles W; Stajic, Jelena; Mogilner, AlexBiophysical journal2011 Aug 3545-5321806922
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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 FChemistry & biology2011 Jul 29846-5621802006
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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 AEukaryotic cell2011 Sep1207-1821764909
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.)2011 Sep 161633-721764753
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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 SThe Journal of neuroscience : the official journal of the Society for Neuroscience2011 Jul 69945-5721734286
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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 GChemistry & biology2011 Jun 24752-6521700211
The metabolic serine hydrolases and their functions in mammalian physiology and disease.Long, Jonathan Z; Cravatt, Benjamin FChemical reviews2011 Oct 126022-6321696217
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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 DGenes & development2011 Jun 151306-1921685365
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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 FJournal of neurochemistry2011 Aug499-51121496023
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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 AMolecular endocrinology (Baltimore, Md.)2010 Aug1543-5820573687
A role for 1-acylglycerol-3-phosphate-O-acyltransferase-1 in myoblast differentiation.Subauste, Angela R; Elliott, Brandon; Das, Arun K; Burant, Charles FDifferentiation; research in biological diversity2010 Sep-Oct140-620561744
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, AkhileshMolecular bioSystems2010 Oct1873-8220544124
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, AndreNature nanotechnology2010 Jul545-5120543835
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, RChemistry & biology2010 May 28471-8220534345
Simple haptotactic gradient generation within a triangular microfluidic channel.Park, Jungyul; Kim, Deok-Ho; Kim, Gabriel; Kim, Younghoon; Choi, Eunpyo; Levchenko, AndreLab on a chip2010 Aug 212130-820532357
Time-of-flights and traps: from the Histone Code to Mars.Cotter, Robert J; Swatkoski, Stepehen; Becker, Luann; Evans-Nguyen, TheresaEuropean journal of mass spectrometry (Chichester, England)2010331-4020530839
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 HScience (New York, N.Y.)2010 Jul 9229-3220522742
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, AndrejMolecular & cellular proteomics : MCP2010 Aug1689-70220507923
FoXS: a web server for rapid computation and fitting of SAXS profiles.Schneidman-Duhovny, Dina; Hammel, Michal; Sali, AndrejNucleic acids research2010 JulW540-420507903
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, ThomasJournal of virology2010 Aug7803-1420504932
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, GerdHaematologica2010 Sep1452-6020494937
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 WJournal of biomolecular screening2010 Jul703-920488980
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 FBioinformatics (Oxford, England)2010 Jul 11630-620484328
Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer.Kim, Min-Sik; Kandasamy, Kumaran; Chaerkady, Raghothama; Pandey, AkhileshJournal of the American Society for Mass Spectrometry2010 Sep1606-1120483638
Toward an integrated structural model of the 26S proteasome.Forster, Friedrich; Lasker, Keren; Nickell, Stephan; Sali, Andrej; Baumeister, WolfgangMolecular & cellular proteomics : MCP2010 Aug1666-7720467039
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 DJournal of the American Society for Mass Spectrometry2010 Aug1417-2220451407
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 AProceedings of the National Academy of Sciences of the United States of America2010 May 259590-520439747
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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 LJournal of pharmaceutical and biomedical analysis2010 Nov 2567-7520417049
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, XianlinJournal of lipid research2010 Aug2153-7020410019
Using isotopic tools to dissect and quantitate parallel metabolic pathways.Sadhukhan, Sushabhan; Han, Yong; Zhang, Guo-Fang; Brunengraber, Henri; Tochtrop, Gregory PJournal of the American Chemical Society2010 May 126309-1120408520
Direct cellular peptidomics of supraoptic magnocellular and hippocampal neurons in low-density co-cultures.Millet, Larry J; Bora, Adriana; Sweedler, Jonathan V; Gillette, Martha UACS chemical neuroscience2010 Jan 2036-4820401326
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 LNeurochemistry international2010 Jul937-4720398713
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 DMolecular & cellular proteomics : MCP2010 Sep2076-8820395639
Chemical standards in ion mobility spectrometry.Fernandez-Maestre, Roberto; Harden, Charles Steve; Ewing, Robert Gordon; Crawford, Christina Lynn; Hill Jr, Herbert HendersonThe Analyst2010 Jun1433-4220369157
Facilitative plasma membrane transporters function during ER transit.Takanaga, Hitomi; Frommer, Wolf BFASEB journal : official publication of the Federation of American Societies for Experimental Biology2010 Aug2849-5820354141
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 DAnalytical chemistry2010 Apr 153212-2120349993
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 JAnalytical and bioanalytical chemistry2010 Aug3305-1020336452
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, HiProteins2010 Jun1992-820310066
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 TMolecular systems biology201035320212525
Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor.Fosbrink, Matthew; Aye-Han, Nwe-Nwe; Cheong, Raymond; Levchenko, Andre; Zhang, JinProceedings of the National Academy of Sciences of the United States of America2010 Mar 235459-6420212108
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,Cell2010 Mar 5678-9120211137
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 FBioorganic & medicinal chemistry letters2010 Apr 12254-820207142
Enzymatic synthesis of Gb3 and iGb3 ceramides.Adlercreutz, Dietlind; Weadge, Joel T; Petersen, Bent O; Duus, Jens O; Dovichi, Norman J; Palcic, Monica MCarbohydrate research2010 Jul 21384-820206917
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 YThe international journal of biochemistry & cell biology2010 Jun987-9520197107
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, PhilipPLoS genetics2010 Febe100085220174551
Comparative analysis of small molecules and histone substrate analogues as LSD1 lysine demethylase inhibitors.Culhane, Jeffrey C; Wang, Dongqing; Yen, Paul M; Cole, Philip AJournal of the American Chemical Society2010 Mar 103164-7620148560
Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study.Simon, Gabriel M; Cravatt, Benjamin FThe Journal of biological chemistry2010 Apr 911051-520147750
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 VBioinformatics (Oxford, England)2010 Apr 1971-320139469
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 FProceedings of the National Academy of Sciences of the United States of America2010 Feb 162944-920133616
Selective desorption/ionization of sulfatides by MALDI-MS facilitated using 9-aminoacridine as matrix.Cheng, Hua; Sun, Gang; Yang, Kui; Gross, Richard W; Han, XianlinJournal of lipid research2010 Jun1599-60920124011
Multi-dimensional mass spectrometry-based shotgun lipidomics and the altered lipids at the mild cognitive impairment stage of Alzheimer's disease.Han, XianlinBiochimica et biophysica acta2010 Aug774-8320117236
Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells.Chaerkady, Raghothama; Kerr, Candace L; Kandasamy, Kumaran; Marimuthu, Arivusudar; Gearhart, John D; Pandey, AkhileshProteomics2010 Apr1359-7320104618
Ribonucleotide and ribonucleoside determination by ambient pressure ion mobility spectrometry.Kanu, Abu B; Hampikian, Greg; Brandt, Simon D; Hill Jr, Herbert HAnalytica chimica acta2010 Jan 1891-720082780
Silent information regulator 3: the Goldilocks of the silencing complex.Norris, Anne; Boeke, Jef DGenes & development2010 Jan 15115-2220080949
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 AProceedings of the National Academy of Sciences of the United States of America2010 Feb 22189-9420080647
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 FCell2010 Jan 849-6120079333
Biochemistry. CO2mmon sense.Frommer, Wolf BScience (New York, N.Y.)2010 Jan 15275-620075235
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 EAnalytical biochemistry2010 Apr 15152-6120074541
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The pathogenic implication of abnormal interaction between apolipoprotein E isoforms, amyloid-beta peptides, and sulfatides in Alzheimer's disease.Han, XianlinMolecular neurobiology2010 Jun97-10620052565
Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap.Zhang, Kai; Chen, Yue; Zhang, Zhihong; Tao, Shengce; Zhu, Heng; Zhao, YingmingProteomics2010 Mar896-90320049863
Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin.Cooper, Eric M; Boeke, Jef D; Cohen, Robert EThe Journal of biological chemistry2010 Apr 210344-5220032457
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 DThe Journal of biological chemistry2010 Feb 266739-4920026609
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 JIntegrative biology : quantitative biosciences from nano to macro2009 Jul469-7620023757
Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain.Lee, Jiyoun; Bogyo, MatthewACS chemical biology2010 Feb 19233-4320017516
pHMA, a pH-sensitive GFP reporter for cell engulfment, in Drosophila embryos, tissues, and cells.Fishilevich, Elane; Fitzpatrick, James A J; Minden, Jonathan SDevelopmental dynamics : an official publication of the American Association of Anatomists2010 Feb559-7320014104
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 DNucleic acids research2010 Mar1431-4020008511
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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 PMolecular cell2009 Dec 11768-8120005841
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 ErecNature structural & molecular biology2010 Jan130-219966800
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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 LMolecular & cellular proteomics : MCP2010 Feb285-9719955084
Aminopeptidase fingerprints, an integrated approach for identification of good substrates and optimal inhibitors.Drag, Marcin; Bogyo, Matthew; Ellman, Jonathan A; Salvesen, Guy SThe Journal of biological chemistry2010 Jan 293310-819948737
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 LThe Journal of biological chemistry2010 Feb 53651-6319940151
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 JMolecular cell2009 Nov 13525-3519917259
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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, HengCell2009 Oct 30610-2219879846
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, MichaelChemistry & biology2009 Oct 301053-6319875079
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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, CharlesThe Journal of biological chemistry2009 Dec 1134861-919846558
Six orders of magnitude dynamic range in capillary electrophoresis with ultrasensitive laser-induced fluorescence detection.Whitmore, Colin D; Essaka, David; Dovichi, Norman JTalanta2009 Dec 15744-819836546
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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 VAnalytical chemistry2009 Nov 159402-919835365
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 MInternational journal of mass spectrometry2008 Oct 1136-14319802328
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 HAnalytical chemistry2009 Oct 17944-5319788315
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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 AJournal of the American Chemical Society2009 Sep 1612960-919737016
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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; SThe Journal of biological chemistry2009 Oct 3030615-2619726693
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 MDevelopmental dynamics : an official publication of the American Association of Anatomists2009 Oct2622-3219718762
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 FThe American journal of pathology2009 Sep1255-6919700761
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Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments.Kandasamy, Kumaran; Pandey, Akhilesh; Molina, HenrikAnalytical chemistry2009 Sep 17170-8019639959
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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 BCell calcium2009 Aug130-519628278
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 ENature structural & molecular biology2009 Aug883-919620964
Using small molecules to dissect mechanisms of microbial pathogenesis.Puri, Aaron W; Bogyo, MatthewACS chemical biology2009 Aug 21603-1619606820
scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms.Falco, Crystal N; Dykstra, Kaitlyn M; Yates, Bradley P; Berget, Peter BBiotechnology journal2009 Sep1328-3619606431
Novel DNA binding properties of the Mcm10 protein from Saccharomyces cerevisiae.Eisenberg, Shlomo; Korza, George; Carson, John; Liachko, Ivan; Tye, Bik-KwoonThe Journal of biological chemistry2009 Sep 1125412-2019605346
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, MatthewNature medicine2009 Aug967-7319597506
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 BThe Journal of biological chemistry2009 Sep 2526839-5019596863
Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics.Niittylae, Totte; Chaudhuri, Bhavna; Sauer, Uwe; Frommer, Wolf BMethods in molecular biology (Clifton, N.J.)2009355-7219588116
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, WolfgangProceedings of the National Academy of Sciences of the United States of America2009 Jul 2111943-719581588
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 JMolecular and cellular biology2009 Sep4604-1119581291
Is there glucose production outside of the liver and kidney?Previs, Stephen F; Brunengraber, Daniel Z; Brunengraber, HenriAnnual review of nutrition200943-5719575601
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 NASN neuro200919570033
NMR-based metabolomics of urine for the atherosclerotic mouse model using apolipoprotein-E deficient mice.Leo, Gregory C; Darrow, Andrew LMagnetic resonance in chemistry : MRC2009 DecS20-519565469
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 YInternational journal of cancer. Journal international du cancer2010 Mar 11067-7819551841
Using a microfluidic device for high-content analysis of cell signaling.Cheong, Raymond; Wang, Chiaochun Joanne; Levchenko, AndreScience signaling2009pl219531802
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Nuclear pore complex biogenesis.Fernandez-Martinez, Javier; Rout, Michael PCurrent opinion in cell biology2009 Aug603-1219524430
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Capillary electrophoresis with electrospray ionization mass spectrometric detection for single-cell metabolomics.Lapainis, Theodore; Rubakhin, Stanislav S; Sweedler, Jonathan VAnalytical chemistry2009 Jul 155858-6419518091
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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 YMolecular cancer therapeutics2009 Jun1515-2519509255
Expression of a Dianthus flavonoid glucosyltransferase in Saccharomyces cerevisiae for whole-cell biocatalysis.Werner, Sean R; Morgan, John AJournal of biotechnology2009 Jul 15233-4119500622
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 MJournal of the American Society for Mass Spectrometry2009 Sep1617-2519481956
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 YThe Journal of general virology2009 Sep2081-519474250
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, MatthewNature chemical biology2009 Jul469-7819465933
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, DanielPancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]2009410-919451751
c-Myc activates multiple metabolic networks to generate substrates for cell-cycle entry.Morrish, F; Isern, N; Sadilek, M; Jeffrey, M; Hockenbery, D MOncogene2009 Jul 92485-9119448666
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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, DanielNMR in biomedicine2009 Oct826-3319441074
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 FCancer research2009 May 154537-4419435903
An open model of actin dendritic nucleation.Ditlev, Jonathon A; Vacanti, Nathaniel M; Novak, Igor L; Loew, Leslie MBiophysical journal2009 May 63529-4219413959
Automated lipid identification and quantification by multidimensional mass spectrometry-based shotgun lipidomics.Yang, Kui; Cheng, Hua; Gross, Richard W; Han, XianlinAnalytical chemistry2009 Jun 14356-6819408941
Proteolytic and non-proteolytic roles of membrane type-1 matrix metalloproteinase in malignancy.Strongin, Alex YBiochimica et biophysica acta2010 Jan133-4119406172
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, HenriAmerican journal of physiology. Endocrinology and metabolism2009 JulE260-919401458
Model-based global analysis of heterogeneous experimental data using gfit.Levin, Mikhail K; Hingorani, Manju M; Holmes, Raquell M; Patel, Smita S; Carson, John HMethods in molecular biology (Clifton, N.J.)2009335-5919399438
Rule-based modeling of biochemical systems with BioNetGen.Faeder, James R; Blinov, Michael L; Hlavacek, William SMethods in molecular biology (Clifton, N.J.)2009113-6719399430
Structure-based ab initio prediction of transcription factor-binding sites.Liu, L Angela; Bader, Joel SMethods in molecular biology (Clifton, N.J.)200923-4119381536
High throughput substrate phage display for protease profiling.Ratnikov, Boris; Cieplak, Piotr; Smith, Jeffrey WMethods in molecular biology (Clifton, N.J.)200993-11419377968
Multiplexed force measurements on live cells with holographic optical tweezers.Mejean, Cecile O; Schaefer, Andrew W; Millman, Eleanor A; Forscher, Paul; Dufresne, Eric ROptics express2009 Apr 136209-1719365444
ModLink+: improving fold recognition by using protein-protein interactions.Fornes, Oriol; Aragues, Ramon; Espadaler, Jordi; Marti-Renom, Marc A; Sali, Andrej; Oliva, BaldoBioinformatics (Oxford, England)2009 Jun 151506-1219357100
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 : MCP2009 Aug1765-7619357087
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 YPloS one2009e503119352504
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 FExperimental cell research2009 Apr 151234-4619331819
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 FNature biotechnology2009 Apr387-9419329999
Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80.Sims, Joshua J; Cohen, Robert EMolecular cell2009 Mar 27775-8319328070
High-pressure ion mobility spectrometry.Davis, Eric J; Dwivedi, Prabha; Tam, Maggie; Siems, William F; Hill, Herbert HAnalytical chemistry2009 May 13270-519323457
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, HengCell2009 Mar 201073-8419303850
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 YPloS one2009e495219300513
The tethered infinitesimal tori and spheres algorithm: a versatile calculator for axisymmetric problems in equilibrium membrane mechanics.Lim, Gerald H W; Huber, GregBiophysical journal2009 Mar 182064-8119289034
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 YThe Journal of biological chemistry2009 May 812727-3419286653
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 DMolecular and cellular biology2009 May2346-5819273605
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, ZhenyuNature cell biology2009 Apr468-7619270693
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, AkhileshProteomics2009 Mar1374-8419253296
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Fluorescein thiocarbamyl amino acids as internal standards for migration time correction in capillary sieving electrophoresis.Pugsley, Haley R; Swearingen, Kristian E; Dovichi, Norman JJournal of chromatography. A2009 Apr 103418-2019249052
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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 YThe Biochemical journal2009 May 1537-4719232058
The structural dynamics of macromolecular processes.Russel, Daniel; Lasker, Keren; Phillips, Jeremy; Schneidman-Duhovny, Dina; Velazquez-Muriel, Javier A; Sali, AndrejCurrent opinion in cell biology2009 Feb97-10819223165
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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 JunMethods in enzymology2009159-8019216906
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 EThe EMBO journal2009 Mar 18621-3119214193
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, CynthiaJournal of molecular biology2009 Mar 61011-2319211026
Systematic analysis of choline-containing phospholipids using multi-dimensional mass spectrometry-based shotgun lipidomics.Yang, Kui; Zhao, Zhongdan; Gross, Richard W; Han, XianlinJournal of chromatography. B, Analytical technologies in the biomedical and life sciences2009 Sep 152924-3619201264
Metabolic flux correlations, genetic interactions, and disease.Veeramani, Balaji; Bader, Joel SJournal of computational biology : a journal of computational molecular cell biology2009 Feb291-30219193147
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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, AkhileshJournal of proteome research2009 Mar1315-2619173612
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, BorisThe FEBS journal2009 Feb660-819143833
Quantitative imaging for discovery and assembly of the metabo-regulome.Okumoto, Sakiko; Takanaga, Hitomi; Frommer, Wolf BThe New phytologist2008271-9519138219
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 MThe Biochemical journal2009 Apr 15467-7419138167
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, DoraMolecular imaging2008 Sep-Oct199-21319123990
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 FThe Journal of biological chemistry2009 Mar 66101-819114707
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 LBioorganic & medicinal chemistry2009 Jan 15653-919109023
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Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction.Norris, Anne; Bianchet, Mario A; Boeke, Jef DPLoS genetics2008 Dece100030119079580
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, WidmarThe Journal of cell biology2008 Dec 151075-8819064668
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.Blinov, M L; Ruebenacker, O; Moraru, I IIET systems biology2008 Sep363-819045831
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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 JPLoS genetics2008 Nove100027019023413
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, DanielLipids2009 Jan27-3518982376
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High content cell screening in a microfluidic device.Cheong, Raymond; Wang, Chiaochun Joanne; Levchenko, AndreMolecular & cellular proteomics : MCP2009 Mar433-4218953019
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 PMethods in molecular biology (Clifton, N.J.)200877-9218951162
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; PNucleic acids research2009 JanD773-8118948298
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, AkhileshJournal of proteome research2009 Jan48-5818947249
Activity-based probes as a tool for functional proteomic analysis of proteases.Fonovic, Marko; Bogyo, MatthewExpert review of proteomics2008 Oct721-3018937562
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 America2008 Oct 2816653-818931302
End-on imaging: a new perspective on dorsoventral development in Drosophila embryos.Witzberger, Melissa M; Fitzpatrick, James A J; Crowley, Justin C; Minden, Jonathan SDevelopmental dynamics : an official publication of the American Association of Anatomists2008 Nov3252-918855896
Actin bundling: initiation mechanisms and kinetics.Kraikivski, Pavel; Slepchenko, Boris M; Novak, Igor LPhysical review letters2008 Sep 1912810218851415
Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain.Lupardus, Patrick J; Shen, Aimee; Bogyo, Matthew; Garcia, K ChristopherScience (New York, N.Y.)2008 Oct 10265-818845756
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, RonenCurrent opinion in structural biology2008 Dec741-718845255
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 research2009 JanD611-818842634
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How well can the accuracy of comparative protein structure models be predicted?Eramian, David; Eswar, Narayanan; Shen, Min-Yi; Sali, AndrejProtein science : a publication of the Protein Society2008 Nov1881-9318832340
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 DNature biotechnology2008 Oct1179-8618820684
Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723.Huang, Yan; Xun, Randy; Chen, Guanjun; Xun, LuyingJournal of bacteriology2008 Dec7595-60018820023
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Chemical probes for histone-modifying enzymes.Cole, Philip ANature chemical biology2008 Oct590-718800048
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 WThe Journal of biological chemistry2008 Nov 1431378-8418796435
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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 ADevelopment (Cambridge, England)2008 Oct3229-3818776144
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 EProceedings of the National Academy of Sciences of the United States of America2008 Sep 1614112-718776048
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, DanielAnalytical biochemistry2008 Dec 176-8418775407
Reduced-representation methylation mapping.Jeddeloh, Jeffrey A; Greally, John M; Rando, Oliver JGenome biology200823118771577
Apolipoprotein E mediates sulfatide depletion in animal models of Alzheimer's disease.Cheng, Hua; Zhou, Yunhua; Holtzman, David M; Han, XianlinNeurobiology of aging2010 Jul1188-9618762354
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 AJournal of the American Chemical Society2008 Sep 2412620-118761447
Deciphering the unusual acylation pattern of Helicobacter pylori lipid A.Stead, Christopher M; Beasley, Ashley; Cotter, Robert J; Trent, M StephenJournal of bacteriology2008 Nov7012-2118757539
Direct quantitation of psychosine from alkaline-treated lipid extracts with a semi-synthetic internal standard.Jiang, Xuntian; Yang, Kui; Han, XianlinJournal of lipid research2009 Jan162-7218753677
A domino effect in antifolate drug action in Escherichia coli.Kwon, Yun Kyung; Lu, Wenyun; Melamud, Eugene; Khanam, Nurussaba; Bognar, Andrew; Rabinowitz, Joshua DNature chemical biology2008 Oct602-818724364
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, YingmingMolecular & cellular proteomics : MCP2009 Feb215-2518723842
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, PeterJournal of bacteriology2008 Oct6741-818723620
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 JAnalytical chemistry2008 Oct 17631-418717573
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 JJournal of proteome research2008 Oct4289-9818715028
Kinetic flux profiling for quantitation of cellular metabolic fluxes.Yuan, Jie; Bennett, Bryson D; Rabinowitz, Joshua DNature protocols20081328-4018714301
Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach.Bennett, Bryson D; Yuan, Jie; Kimball, Elizabeth H; Rabinowitz, Joshua DNature protocols20081299-31118714298
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 VProteomics2008 Sep3746-5418712768
Adapting the stretched sample method from tissue profiling to imaging.Zimmerman, Tyler A; Monroe, Eric B; Sweedler, Jonathan VProteomics2008 Sep3809-1518712762
Human monocytes augment invasiveness and proteolytic activity of inflammatory breast cancer.Mohamed, Mona Mostafa; Cavallo-Medved, Dora; Sloane, Bonnie FBiological chemistry2008 Aug1117-2118710343
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 JThe Journal of biological chemistry2008 Oct 2429405-1518708356
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 BThe Plant journal : for cell and molecular biology2008 Dec948-6218702670
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, AkhileshJournal of proteome research2008 Sep3900-1018698806
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, AndrejJournal of molecular biology2008 Oct 171089-10618694757
Predicting optimal resolving power for ambient pressure ion mobility spectrometry.Kanu, Abu B; Gribb, Molly M; Hill Jr, Herbert HAnalytical chemistry2008 Sep 16610-918683951
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 LClinical chemistry2008 Sep1451-6218678604
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 DGenes & development2008 Aug 12062-7418676811
Amino(oligo)thiophene-based environmentally sensitive biomembrane chromophores.Yan, Ping; Xie, Aifang; Wei, Meide; Loew, Leslie MThe Journal of organic chemistry2008 Sep 56587-9418665648
The role of cathepsin X in the migration and invasiveness of T lymphocytes.Jevnikar, Zala; Obermajer, Natasa; Bogyo, Matthew; Kos, JankoJournal of cell science2008 Aug 152652-6118664495
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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-MingProteomics2008 Aug3406-1518651708
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 ANature2008 Aug 211005-818650806
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 PGlycobiology2008 Oct761-918625848
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 DBiophysical journal2008 Oct3715-2318621837
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, XuhangMolecular biology of the cell2008 Sep3859-7018614797
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 MJournal of the American Chemical Society2008 Jul 98611-318597426
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, JiriJournal of chromatography. B, Analytical technologies in the biomedical and life sciences2008 Jul 15233-4018595786
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 WCancer research2008 Jul 15132-4218593912
Mass spectrometry of acoustically levitated droplets.Westphall, Michael S; Jorabchi, Kaveh; Smith, Lloyd MAnalytical chemistry2008 Aug 15847-5318582090
Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage.Celic, Ivana; Verreault, Alain; Boeke, Jef DGenetics2008 Aug1769-8418579506
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, PaulAnalytical chemistry2008 Aug 15912-2318576668
Human Proteinpedia as a resource for clinical proteomics.Mathivanan, Suresh; Pandey, AkhileshMolecular & cellular proteomics : MCP2008 Oct2038-4718573810
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, RonenNature structural & molecular biology2008 Jul738-4518568037
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 KJournal of proteome research2008 Aug3447-6018563927
The incredible shrinking world of DNA microarrays.Wheelan, Sarah J; Martinez Murillo, Francisco; Boeke, Jef DMolecular bioSystems2008 Jul726-3218563246
Visualizing protease activity in living cells: from two dimensions to four dimensions.Jedeszko, Christopher; Sameni, Mansoureh; Olive, Mary B; Moin, Kamiar; Sloane, Bonnie FCurrent protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]2008 JunUnit 4.2018551423
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 CJournal of hypertension2008 Jul1402-1018551017
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, HenriThe Journal of biological chemistry2008 Aug 821978-8718544527
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, HenriThe Journal of biological chemistry2008 Aug 821988-9618544526
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, AnneMethods in molecular biology (Clifton, N.J.)200849-7918542857
Comprehensive comparison of collision induced dissociation and electron transfer dissociation.Molina, Henrik; Matthiesen, Rune; Kandasamy, Kumaran; Pandey, AkhileshAnalytical chemistry2008 Jul 14825-3518540640
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 fHan, Xianlin; Yang, Kui; Gross, Richard WRapid communications in mass spectrometry : RCM2008 Jul2115-2418523984
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 BBiotechnology for biofuels20081118522753
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 YCancer research2008 Jun 14086-9618519667
Improved residual water suppression: WET180.Mo, Huaping; Raftery, DanielJournal of biomolecular NMR2008 Jun105-1118506578
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 YThe Journal of biological chemistry2008 Jul 2520897-90618505722
Analytical strategies for LC-MS-based targeted metabolomics.Lu, Wenyun; Bennett, Bryson D; Rabinowitz, Joshua DJournal of chromatography. B, Analytical technologies in the biomedical and life sciences2008 Aug 15236-4218502704
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 JGenetics2008 May291-30418493054
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, XianlinAnalytical biochemistry2008 Aug 15182-9118489896
Sulfatides facilitate apolipoprotein E-mediated amyloid-beta peptide clearance through an endocytotic pathway.Zeng, Youchun; Han, XianlinJournal of neurochemistry2008 Aug1275-8618485101
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 MCirculation research2008 Jun 201575-8318483408
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 EunMolecular cell2008 May 9325-3518471978
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 SThe Journal of biological chemistry2008 Jul 1119499-51018458084
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, XianlinBiochemistry2008 May 275869-8018454555
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 FAmerican journal of physiology. Endocrinology and metabolism2008 JulE216-2218445754
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.Wang, Joy Xin; Breaker, Ronald RBiochemistry and cell biology = Biochimie et biologie cellulaire2008 Apr157-6818443629
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 YThe Journal of biological chemistry2008 Jun 2017270-818442976
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, ElisaBiochimica et biophysica acta2008 Aug453-818442491
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, PhilipMolecular cell2008 Apr 25248-5818439903
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 DThe Journal of cell biology2008 Apr 21281-9218426976
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, ThomasCell host & microbe2008 Apr 17253-6218407068
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 DMethods in molecular biology (Clifton, N.J.)2008221-4718392971
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 RNeoplasia (New York, N.Y.)2008 Apr314-2918392133
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 AJournal of immunology (Baltimore, Md. : 1950)2008 Apr 155530-618390737
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 RMolecular cell2008 Mar 28691-70218374645
Detection of nitric oxide in single cells.Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan VThe Analyst2008 Apr423-3318365109
Polarized immune responses differentially regulate cancer development.Johansson, Magnus; Denardo, David G; Coussens, Lisa MImmunological reviews2008 Apr145-5418363999
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 LAnalytical biochemistry2008 May 15275-618355435
Evaluation of alpha,beta-unsaturated ketone-based probes for papain-family cysteine proteases.Yang, Zhimou; Fonovic, Marko; Verhelst, Steven H L; Blum, Galia; Bogyo, MatthewBioorganic & medicinal chemistry2009 Feb 11071-818343672
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 AOrganic letters2008 Apr 171561-418338898
Quantitative proteomics using stable isotope labeling with amino acids in cell culture.Harsha, H C; Molina, Henrik; Pandey, AkhileshNature protocols2008505-1618323819
Integrating diverse data for structure determination of macromolecular assemblies.Alber, Frank; Forster, Friedrich; Korkin, Dmitry; Topf, Maya; Sali, AndrejAnnual review of biochemistry2008443-7718318657
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 HMolecular biology of the cell2008 May2311-2718305102
Application of activity-based probes to the study of enzymes involved in cancer progression.Paulick, Margot G; Bogyo, MatthewCurrent opinion in genetics & development2008 Feb97-10618294838
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; SeveriJournal of molecular biology2008 Mar 28774-8918294652
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 YThe Journal of general virology2008 Mar636-4118272753
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 AJournal of proteome research2008 Mar1244-5018271525
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; BurlingamNature biotechnology2008 Feb164-718259167
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 LNature biotechnology2008 Feb162-418259166
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 JAnalytical chemistry2008 Mar 11448-5818254611
Ionomics and the study of the plant ionome.Salt, David E; Baxter, Ivan; Lahner, BrettAnnual review of plant biology2008709-3318251712
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 FMetabolism: clinical and experimental2008 Mar347-5418249206
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, MatthewNature chemical biology2008 Mar203-1318246061
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 AAnalytical biochemistry2008 Apr 15272-8118243123
Depolymerization-driven flow in nematode spermatozoa relates crawling speed to size and shape.Zajac, Mark; Dacanay, Brian; Mohler, William A; Wolgemuth, Charles WBiophysical journal2008 May 153810-2318227129
Ion mobility-mass spectrometry.Kanu, Abu B; Dwivedi, Prabha; Tam, Maggie; Matz, Laura; Hill Jr, Herbert HJournal of mass spectrometry : JMS2008 Jan1-2218200615
Plasmid-chromosome shuffling for non-deletion alleles in yeast.Huang, Zhiwei; Sucgang, Richard S; Lin, Yu-yi; Shi, Xiaomin; Boeke, Jef D; Pan, XuewenNature methods2008 Feb167-918193055
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 YAssay and drug development technologies2007 Dec737-5018181690
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 BBiochimica et biophysica acta2008 Apr1091-918177733
Imaging of glutamate in brain slices using FRET sensors.Dulla, Chris; Tani, Hiroaki; Okumoto, Sakiko; Frommer, Wolf B; Reimer, Rich J; Huguenard, John RJournal of neuroscience methods2008 Mar 15306-1918160134
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.Choi, Hyungwon; Nesvizhskii, Alexey IJournal of proteome research2008 Jan254-6518159924
Shotgun lipidomics identifies a paired rule for the presence of isomeric ether phospholipid molecular species.Yang, Kui; Zhao, Zhongdan; Gross, Richard W; Han, XianlinPloS one2007e136818159251
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, JonatNature biotechnology2008 Feb235-4018157118
Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm.Oh, Cheolhwan; Huang, Xiaodong; Regnier, Fred E; Buck, Charles; Zhang, XiangJournal of chromatography. A2008 Feb 1205-1518093607
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, HengNature methods2008 Jan69-7418084297
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 TJournal of bacteriology2008 Feb1284-918083804
Simultaneous nitric oxide and dehydroascorbic acid imaging by combining diaminofluoresceins and diaminorhodamines.Ye, Xiaoying; Rubakhin, Stanislav S; Sweedler, Jonathan VJournal of neuroscience methods2008 Mar 15373-8218083236
Expression of murine leukemia virus envelope protein is sufficient for the induction of apoptosis.Zhao, Xiaoqing; Yoshimura, Fayth KJournal of virology2008 Mar2586-918077710
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 RLangmuir : the ACS journal of surfaces and colloids2008 Feb 191160-418062711
Enrichment tags for enhanced-resolution profiling of the polar metabolome.Carlson, Erin E; Cravatt, Benjamin FJournal of the American Chemical Society2007 Dec 2615780-218052286
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 PNature2007 Nov 29695-70118046406
Applications of protein microarray technology.Tao, Sheng-Ce; Chen, Chien-Sheng; Zhu, HengCombinatorial chemistry & high throughput screening2007 Sep706-1818045082
An update on lipidomics: progress and application in biomarker and drug development.Han, XianlinCurrent opinion in molecular therapeutics2007 Dec586-9118041669
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 LNeurochemical research2008 Feb292-30018041582
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.Huang, Hailiang; Jedynak, Bruno M; Bader, Joel SPLoS computational biology2007 Nove21418039026
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, RJournal of neurochemistry2008 Mar1358-6318036151
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.Qian, Yuntao; Murphy, Robert FBioinformatics (Oxford, England)2008 Feb 15569-7618033795
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 MMolecular genetics and metabolism2008 Feb145-5918029214
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-MingProteomics2007 Dec4589-60018022937
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, PaoloThe Journal of biological chemistry2008 Jan 487-9917991754
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 TProstaglandins & other lipid mediators2007 Nov98-10717991612
Ab initio prediction of transcription factor binding sites.Liu, L Angela; Bader, Joel SPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2007484-9517990512
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, ZsoltPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2007157-6817990489
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 LAnalytical chemistry2007 Dec 159385-9017985927
Salt tolerance of desorption electrospray ionization (DESI).Jackson, Ayanna U; Talaty, Nari; Cooks, R Graham; Van Berkel, Gary JJournal of the American Society for Mass Spectrometry2007 Dec2218-2517977744
Cysteine cathepsin non-inhibitory binding partners: modulating intracellular trafficking and function.Victor, Bernadette C; Sloane, Bonnie FBiological chemistry2007 Nov1131-4017976005
Automated learning of generative models for subcellular location: building blocks for systems biology.Zhao, Ting; Murphy, Robert FCytometry. Part A : the journal of the International Society for Analytical Cytology2007 Dec978-9017972315
Host pathogen protein interactions predicted by comparative modeling.Davis, Fred P; Barkan, David T; Eswar, Narayanan; McKerrow, James H; Sali, AndrejProtein science : a publication of the Protein Society2007 Dec2585-9617965183
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 JAnalytical and bioanalytical chemistry2008 Jan223-617955216
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 DMethods in enzymology2007171-8517954248
Functional dissection of a HECT ubiquitin E3 ligase.Lu, Jin-Ying; Lin, Yu-Yi; Qian, Jiang; Tao, Sheng-Ce; Zhu, Jian; Pickart, Cecile; Zhu, HengMolecular & cellular proteomics : MCP2008 Jan35-4517951556
Pre-SAT180, a simple and effective method for residual water suppression.Mo, Huaping; Raftery, DanielJournal of magnetic resonance (San Diego, Calif. : 1997)2008 Jan1-617945521
Characterization of protein hubs by inferring interacting motifs from protein interactions.Aragues, Ramon; Sali, Andrej; Bonet, Jaume; Marti-Renom, Marc A; Oliva, BaldoPLoS computational biology2007 Sep1761-7117941705
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, XianlinThe Biochemical journal2008 Feb 1581-9217939778
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 LGenes & development2007 Oct 152580-9217938242
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 YThe Journal of biological chemistry2007 Dec 1436283-9117938169
Potential solutions for confocal imaging of living animals.Croix, Claudette St; Zipfel, Warren R; Watkins, Simon CBioTechniques2007 Jul14-917933097
Vesicle shape, molecular tilt, and the suppression of necks.Jiang, Hongyuan; Huber, Greg; Pelcovits, Robert A; Powers, Thomas RPhysical review. E, Statistical, nonlinear, and soft matter physics2007 Sep03190817930272
Comprehensive analysis of diverse ribonucleoprotein complexes.Oeffinger, Marlene; Wei, Karen E; Rogers, Richard; DeGrasse, Jeffrey A; Chait, Brian T; Aitchison, John D; Rout, Michael PNature methods2007 Nov951-617922018
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, XianlinAnalytical biochemistry2007 Dec 15135-4517920553
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, PhilStem cells (Dayton, Ohio)2008 Jan127-3417901398
Nanosensor detection of an immunoregulatory tryptophan influx/kynurenine efflux cycle.Kaper, Thijs; Looger, Loren L; Takanaga, Hitomi; Platten, Michael; Steinman, Lawrence; Frommer, Wolf BPLoS biology2007 Sep 25e25717896864
Negative autoregulation by FAS mediates robust fetal erythropoiesis.Socolovsky, Merav; Murrell, Michael; Liu, Ying; Pop, Ramona; Porpiglia, Ermelinda; Levchenko, AndrePLoS biology2007 Octe25217896863
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, ShelleyPloS one2007e94817895989
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 DProceedings of the National Academy of Sciences of the United States of America2007 Oct 215653-817895383
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 HThe FEBS journal2007 Oct5425-3717894821
Central carbon metabolism in the progression of mammary carcinoma.Richardson, Adam D; Yang, Chen; Osterman, Andrei; Smith, Jeffrey WBreast cancer research and treatment2008 Jul297-30717879159
LSD1 and the chemistry of histone demethylation.Culhane, Jeffrey C; Cole, Philip ACurrent opinion in chemical biology2007 Oct561-817851108
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 ADevelopmental biology2007 Oct 15240-917850783
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, MatthewNature chemical biology2007 Oct668-7717828252
Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis.Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, GregoryAnalytical chemistry2007 Oct 17554-917822305
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 YThe Journal of biological chemistry2007 Nov 232106-1117761671
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, ZhenyuProceedings of the National Academy of Sciences of the United States of America2007 Sep 414489-9417726112
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 GrahamThe Analyst2007 Sep868-7517710261
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 RAnalytical chemistry2007 Sep 156912-2117708672
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, DanielJournal of pharmaceutical and biomedical analysis2007 Sep 21134-4017707608
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 DThe Journal of biological chemistry2007 Oct 1930754-6217690096
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 SDiabetes2007 Oct2569-7817686943
N-lysine propionylation controls the activity of propionyl-CoA synthetase.Garrity, Jane; Gardner, Jeffrey G; Hawse, William; Wolberger, Cynthia; Escalante-Semerena, Jorge CThe Journal of biological chemistry2007 Oct 1230239-4517684016
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 ACancer research2007 Aug 17378-8517671208
Yoctomole analysis of ganglioside metabolism in PC12 cellular homogenates.Whitmore, Colin D; Olsson, Ulf; Larsson, E Andreas; Hindsgaul, Ole; Palcic, Monica M; Dovichi, Norman JElectrophoresis2007 Aug3100-417668449
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 SThe Biochemical journal2007 Oct 141-817650073
Automated image analysis of protein localization in budding yeast.Chen, Shann-Ching; Zhao, Ting; Gordon, Geoffrey J; Murphy, Robert FBioinformatics (Oxford, England)2007 Jul 1i66-7117646347
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 TProstaglandins & other lipid mediators2007 Aug24-3317643885
Efficiency, selectivity, and robustness of nucleocytoplasmic transport.Zilman, Anton; Di Talia, Stefano; Chait, Brian T; Rout, Michael P; Magnasco, Marcelo OPLoS computational biology2007 Jule12517630825
Proteomics evaluation of chemically cleavable activity-based probes.Fonovic, Marko; Verhelst, Steven H L; Sorum, Mark T; Bogyo, MatthewMolecular & cellular proteomics : MCP2007 Oct1761-7017615255
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, DanielProceedings of the National Academy of Sciences of the United States of America2007 Jul 1011540-417606902
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 ABiochemistry2007 Jul 178207-1617590016
Controlling charge on levitating drops.Hilger, Ryan T; Westphall, Michael S; Smith, Lloyd MAnalytical chemistry2007 Aug 16027-3017580951
Metabolic cytometry. Glycosphingolipid metabolism in single cells.Whitmore, Colin D; Hindsgaul, Ole; Palcic, Monica M; Schnaar, Ronald L; Dovichi, Norman JAnalytical chemistry2007 Jul 155139-4217567107
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 MAnalytical chemistry2007 Jul 155143-917563114
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 EAnalytical biochemistry2007 Aug 128-3917560863
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 EAnalytical biochemistry2007 Aug 140-817559791
The adapter importin-alpha provides flexible control of nuclear import at the expense of efficiency.Riddick, Greg; Macara, Ian GMolecular systems biology200711817551513
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 DMolecular systems biology200711517551510
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 AndyJournal of proteome research2007 Jul2850-817547438
Distinctive features of angiogenesis and lymphangiogenesis determine their functionality during de novo tumor development.Eichten, Alexandra; Hyun, William C; Coussens, Lisa MCancer research2007 Jun 15211-2017545601
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 chemistry2007 Jul 2020847-5317537721
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 HJournal of the American Society for Mass Spectrometry2007 Jul1163-7517532226
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, MatthewChemistry & biology2007 May499-51117524981
A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms.Shastri, Avantika A; Morgan, John APhytochemistry2007 Aug-Sep2302-1217524438
Mechanistic analysis of a suicide inactivator of histone demethylase LSD1.Szewczuk, Lawrence M; Culhane, Jeffrey C; Yang, Maojun; Majumdar, Ananya; Yu, Hongtao; Cole, Philip ABiochemistry2007 Jun 126892-90217511474
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 LJournal of neuroscience research2007 Nov 153494-50417510975
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, KlausJournal of virology2007 Aug8050-6217507477
Fluxomics: mass spectrometry versus quantitative imaging.Wiechert, Wolfgang; Schweissgut, Oliver; Takanaga, Hitomi; Frommer, Wolf BCurrent opinion in plant biology2007 Jun323-3017481942
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 DAdvances in enzyme regulation200710-2517467778
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 DInternational immunology2007 May645-5517446210
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 MDevelopmental dynamics : an official publication of the American Association of Anatomists2007 Jun1683-9317440987
Regulation of a cyclin-CDK-CDK inhibitor complex by inositol pyrophosphates.Lee, Young-Sam; Mulugu, Sashidhar; York, John D; O'Shea, Erin KScience (New York, N.Y.)2007 Apr 6109-1217412959
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 DScience (New York, N.Y.)2007 Apr 6106-917412958
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 CProtein science : a publication of the Protein Society2007 May795-80617400917
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, GregoryMetabolic engineering2007 May277-9217400499
Where does all the PIP2 come from?Loew, Leslie MThe Journal of physiology2007 Aug 1945-5117395623
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, GerhardJournal of the American Chemical Society2007 Apr 255108-1617388596
Decoding transcriptional regulatory interactions.Liu, L Angela; Bader, Joel SPhysica D. Nonlinear phenomena2006 Dec174-18117364011
RNA-binding proteins that inhibit RNA virus infection.Zhu, Jian; Gopinath, Kodetham; Murali, Ayaluru; Yi, Guanghui; Hayward, S Diane; Zhu, Heng; Kao, ChengProceedings of the National Academy of Sciences of the United States of America2007 Feb 273129-3417360619
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 LProceedings of the National Academy of Sciences of the United States of America2007 Mar 134279-8417360515
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; MPLoS biology2007 Mare1617355171
A curated compendium of phosphorylation motifs.Amanchy, Ramars; Periaswamy, Balamurugan; Mathivanan, Suresh; Reddy, Raghunath; Tattikota, Sudhir Gopal; Pandey, AkhileshNature biotechnology2007 Mar285-617344875
Design and performance of an atmospheric pressure ion mobility Fourier transform ion cyclotron resonance mass spectrometer.Tang, Xiaoting; Bruce, James E; Hill Jr, Herbert HRapid communications in mass spectrometry : RCM20071115-2217318922
Activity based probes for proteases: applications to biomarker discovery, molecular imaging and drug screening.Fonovic, Marko; Bogyo, MatthewCurrent pharmaceutical design2007253-6117313359
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 YJournal of virology2007 May4501-917301157
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 RMolecular & cellular proteomics : MCP2007 May860-8117293592
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.Molina, Henrik; Horn, David M; Tang, Ning; Mathivanan, Suresh; Pandey, AkhileshProceedings of the National Academy of Sciences of the United States of America2007 Feb 132199-20417287340
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 DavidProceedings of the National Academy of Sciences of the United States of America2007 Feb 132086-9117284592
Humoral immunity, inflammation and cancer.Tan, Ting-Ting; Coussens, Lisa MCurrent opinion in immunology2007 Apr209-1617276050
Immune cells as anti-cancer therapeutic targets and tools.Johansson, Magnus; Tan, Tingting; de Visser, Karin E; Coussens, Lisa MJournal of cellular biochemistry2007 Jul 1918-2617265430
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 NAnalytical chemistry2007 Feb 1966-7317263323
Tandem time-of-flight (TOF/TOF) mass spectrometry and the curved-field reflectron.Cotter, Robert J; Griffith, Wendell; Jelinek, ChristineJournal of chromatography. B, Analytical technologies in the biomedical and life sciences2007 Aug2-1317258517
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 AJournal of the American Chemical Society2007 Feb 212025-3417256855
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, AkhileshBMC bioinformatics2006S1917254303
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, FClinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology2007 Feb231-4217250696
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 VJournal of neurochemistry2007 May632-4017250653
Inositol polyphosphate kinases: regulators of nuclear function.Seeds, Andrew M; York, John DBiochemical Society symposium2007183-9717233590
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 LThe Journal of biological chemistry2007 Mar 309600-1117218315
A mild chemically cleavable linker system for functional proteomic applications.Verhelst, Steven H L; Fonovic, Marko; Bogyo, MatthewAngewandte Chemie (International ed. in English)20071284-617205587
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, RussellThe Laryngoscope2007 Feb313-817204986
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 GrahamAnalytical chemistry2007 Jan 189-9717194125
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 DMethods (San Diego, Calif.)2007 Feb206-2117189863
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 YProtein expression and purification2007 Apr334-917189703
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, MatthewBioorganic & medicinal chemistry letters2007 Feb 1649-5317189693
Purdue ionomics information management system. An integrated functional genomics platform.Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S; Salt, David EPlant physiology2007 Feb600-1117189337
Tagging and detection strategies for activity-based proteomics.Sadaghiani, Amir M; Verhelst, Steven Hl; Bogyo, MatthewCurrent opinion in chemical biology2007 Feb20-817174138
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, MCell death and differentiation2007 Apr727-3217170749
Gas-phase chiral separations by ion mobility spectrometry.Dwivedi, Prabha; Wu, Ching; Matz, Laura M; Clowers, Brian H; Siems, William F; Hill Jr, Herbert HAnalytical chemistry2006 Dec 158200-617165808
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 DavidMolecular cell2006 Dec 8785-9617157260
Cysteine protease inhibitors block Toxoplasma gondii microneme secretion and cell invasion.Teo, Chin Fen; Zhou, Xing Wang; Bogyo, Matthew; Carruthers, Vern BAntimicrobial agents and chemotherapy2007 Feb679-8817145790
CutDB: a proteolytic event database.Igarashi, Yoshinobu; Eroshkin, Alexey; Gramatikova, Svetlana; Gramatikoff, Kosi; Zhang, Ying; Smith, Jeffrey W; Osterman, Andrei L; Godzik, AdamNucleic acids research2007 JanD546-917142225
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 HPeptides2007 Jan94-10217141371
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, FaramarzJournal of cellular biochemistry2007 Mar 11034-4417131385
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 MBiochemistry2006 Dec 514263-7417128966
Commonly used caspase inhibitors designed based on substrate specificity profiles lack selectivity.Berger, Alicia B; Sexton, Kelly B; Bogyo, MatthewCell research2006 Dec961-317117159
Characterizing electrospray ionization using atmospheric pressure ion mobility spectrometry.Tang, Xiaoting; Bruce, James E; Hill Jr, Herbert HAnalytical chemistry2006 Nov 157751-6017105168
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, AndrejPLoS computational biology2006 Nov 10e15317096593
Solid-phase methods for the preparation of epoxysuccinate-based inhibitors of cysteine proteases.Sadaghiani, Amir M; Verhelst, Steven H L; Bogyo, MatthewJournal of combinatorial chemistry2006 Nov-Dec802-417096566
Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions.Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, GregoryMetabolic engineering2007 Jan68-8617088092
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 JAmerican journal of physiology. Lung cellular and molecular physiology2007 FebL476-8617085523
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 YCancer research2006 Nov 110460-517079467
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, OleCarbohydrate research2007 Feb 26482-917069778
Analysis of immune cell infiltrates during squamous carcinoma development.Junankar, Simon R; Eichten, Alexandra; Kramer, Annegret; de Visser, Karin E; Coussens, Lisa MThe journal of investigative dermatology. Symposium proceedings / the Society for Investigative Dermatology, Inc. [and] European Society for Dermatological Research2006 Sep36-4317069009
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 YThe Biochemical journal2007 Feb 1743-5217067286
Significant proportions of nuclear transport proteins with reduced intracellular mobilities resolved by fluorescence correlation spectroscopy.Paradise, Allison; Levin, Mikhail K; Korza, George; Carson, John HJournal of molecular biology2007 Jan 550-6517056062
Proteomics of the peroxisome.Saleem, R A; Smith, J J; Aitchison, J DBiochimica et biophysica acta2006 Dec1541-5117050007
A multichannel native fluorescence detection system for capillary electrophoretic analysis of neurotransmitters in single neurons.Lapainis, T; Scanlan, C; Rubakhin, S S; Sweedler, J VAnalytical and bioanalytical chemistry2007 Jan97-10517047942
Signal enhancement in HPLC/microcoil NMR using automated column trapping.Djukovic, Danijel; Liu, Shuhui; Henry, Ian; Tobias, Brian; Raftery, DanielAnalytical chemistry2006 Oct 157154-6017037915
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 BFEBS letters2006 Oct 305885-9317034793
Protein chip fabrication by capture of nascent polypeptides.Tao, Sheng-Ce; Zhu, HengNature biotechnology2006 Oct1253-417013375
Inhibition of endothelial cell proliferation and angiogenesis by orlistat, a fatty acid synthase inhibitor.Browne, Cecille D; Hindmarsh, Elizabeth J; Smith, Jeffrey WFASEB journal : official publication of the Federation of American Societies for Experimental Biology2006 Oct2027-3517012255
Intravital fluorescence microscopy in pulmonary research.St Croix, Claudette M; Leelavanichkul, Karanee; Watkins, Simon CAdvanced drug delivery reviews2006 Sep 15834-4016996641
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 MAnalytical chemistry2006 Sep 156398-40316970314
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 YFASEB journal : official publication of the Federation of American Societies for Experimental Biology2006 Sep1793-80116940151
Unique contrast patterns from resonance-enhanced chiral SHG of cell membranes.Yan, Ping; Millard, Andrew C; Wei, Meide; Loew, Leslie MJournal of the American Chemical Society2006 Aug 3011030-116925413
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 SMolecular cell.2006 Aug523-3316916640
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, MatthewMolecular cell.2006 Aug509-2116916639
HiRes--a tool for comprehensive assessment and interpretation of metabolomic data.Zhao, Qi; Stoyanova, Radka; Du, Shuyan; Sajda, Paul; Brown, Truman RBioinformatics (Oxford, England)2006 Oct 152562-416895927
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 RThe Journal of biological chemistry2006 Oct 630269-7816895903
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, ZhenyuThe Journal of neuroscience : the official journal of the Society for Neuroscience.2006 Aug 28057-6816885219
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.Takahashi, Hidekazu; McCaffery, J Michael; Irizarry, Rafael A; Boeke, Jef DMolecular cell2006 Jul 21207-1716857587
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 CJournal of bacteriology.2006 Aug5460-816855235
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 DMethods (San Diego, Calif.) 2006 Jun112-2116829132
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, DanielAnalytical and bioanalytical chemistry2007 Jan539-4916821030
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, AlainCurrent biology : CB.2006 Jul 111280-916815704
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 AProceedings of the National Academy of Sciences of the United States of America.2006 Jun 279773-816785428
Regulation of nuclear processes by inositol polyphosphates.York, John DBiochimica et biophysica acta.2006 May-Jun552-916781889
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 YCancer research.2006 Jun 156258-6316778201
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 GrahamRapid communications in mass spectrometry : RCM20062143-5016773669
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, DanielThe Journal of organic chemistry2006 Jun 94549-5816749788
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 WMolecular biology of the cell.2006 Aug3409-2216738305
Protein complex compositions predicted by structural similarity.Davis, Fred P; Braberg, Hannes; Shen, Min-Yi; Pieper, Ursula; Sali, Andrej; Madhusudhan, M SNucleic acids research.20062943-5216738133
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 JAnalytical chemistry2006 Jun 13681-716737224
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 SMolecular systems biology20052005.002616729061
Mislocalization and unconventional functions of cellular MMPs in cancer.Strongin, Alex YCancer metastasis reviews.2006 Mar87-9816680575
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, MatthewJournal of the American Chemical Society2006 May 35616-716637611
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 YOncogene.2006 Sep 145648-5516636666
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements.Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, GregoryMetabolic engineering.2006 Jul324-3716631402
Protein microarrays.Chen, Chien-Sheng; Zhu, HengBioTechniques.2006 Apr423, 425, 427 passim16629388
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 GrahamRapid communications in mass spectrometry : RCM20061577-8416628593
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 YThe Journal of biological chemistry.2006 Jun 2316897-90516627478
Protease accessibility laddering: a proteomic tool for probing protein structure.Dokudovskaya, Svetlana; Williams, Rosemary; Devos, Damien; Sali, Andrej; Chait, Brian T; Rout, Michael PStructure (London, England : 1993) 2006 Apr653-6016615907
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, MatthewChembiochem : a European journal of chemical biology2006 Jun943-5016607671
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 LGenes & development.2006 Apr 15966-7616598039
A mechanism-based inactivator for histone demethylase LSD1.Culhane, Jeffrey C; Szewczuk, Lawrence M; Liu, Xin; Da, Guoping; Marmorstein, Ronen; Cole, Philip AJournal of the American Chemical Society2006 Apr 124536-716594666
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 LAnalytical biochemistry.2006 May 124-3216545769
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 VJournal of neurochemistry2006 Apr595-60616539650
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 VThe Journal of biological chemistry.2006 May 1213463-7016537538
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 VAnalytical chemistry2006 Mar 151859-6516536421
Inflammation, proteases and cancer.van Kempen, Leon C L; de Visser, Karin E; Coussens, Lisa MEuropean journal of cancer (Oxford, England : 1990) 2006 Apr728-3416524717
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 YCancer research.2006 Mar 12716-2416510592
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, RashmNature genetics.2006 Mar285-9316501559
A DNA integrity network in the yeast Saccharomyces cerevisiae.Pan, Xuewen; Ye, Ping; Yuan, Daniel S; Wang, Xiaoling; Bader, Joel S; Boeke, Jef DCell.2006 Mar 101069-8116487579
GeneDesign: rapid, automated design of multikilobase synthetic genes.Richardson, Sarah M; Wheelan, Sarah J; Yarrington, Robert M; Boeke, Jef DGenome research.2006 Apr550-616481661
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 SAmerican journal of physiology. Cell physiology.2006 JulC176-8416481372
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, AndrejProceedings of the National Academy of Sciences of the United States of America.2006 Feb 142172-716461911
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, ZhengAnalytical chemistry2006 Feb 1718-2516448044
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 MBiophysical journal2006 Apr 12563-7516415047
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, MatthewNature chemical biology2005 Sep203-916408036
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, MatthewNature chemical biology2005 Jun33-816407991
Functional imaging of tumor proteolysis.Sloane, Bonnie F; Sameni, Mansoureh; Podgorski, Izabela; Cavallo-Medved, Dora; Moin, KamiarAnnual review of pharmacology and toxicology.2006301-1516402907
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; MathewNucleic acids research.2006 Jan 1D411-416381900
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 FAmerican journal of physiology. Endocrinology and metabolism.2006 MayE1048-5616368786
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 DThe Journal of cell biology2005 Dec 19955-6516365162
Bioinformatics and proteomics approaches for aging research.Raghothama, Chaerkady; Harsha, H C; Prasad, C K; Pandey, AkhileshBiogerontology.2005227-3216333756
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, MatthewOrganic letters.2005 Dec 85649-5216321013
Use of semiselective TOCSY and the pearson correlation for the metabonomic analysis of biofluid mixtures: application to urine.Sandusky, Peter; Raftery, DanielAnalytical chemistry2005 Dec 17717-2316316181
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 BMolecular and cellular biology2005 Dec11102-1216314530
Subcellular analysis of D-aspartate.Miao, Hai; Rubakhin, Stanislav S; Sweedler, Jonathan VAnalytical chemistry2005 Nov 157190-416285665
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 DMolecular and cellular biology.2005 Nov10060-7016260619
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 LThe Journal of biological chemistry.2005 Dec 3042508-1416239221
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 YJournal of cell science. 2005 Nov 14975-8416219679
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, AkhileshMolecular & cellular proteomics : MCP.2006 Jan157-7116215274
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 JJournal of proteome research.2005 Sep-Oct1554-6016212406
Proteomic resources: integrating biomedical information in humans.Suresh, Shubha; Sujatha Mohan, S; Mishra, Goparani; Hanumanthu, G R; Suresh, M; Reddy, Raghunath; Pandey, AkhileshGene.2005 Dec 3013-816202541
Shining light on signaling and metabolic networks by genetically encoded biosensors.Lalonde, Sylvie; Ehrhardt, David W; Frommer, Wolf BCurrent opinion in plant biology2005 Dec574-8116188489
Dynamic properties of network motifs contribute to biological network organization.Prill, Robert J; Iglesias, Pablo A; Levchenko, AndrePLoS biology2005 Nove34316187794
Fluorescent proteins as proteomic probes.Cristea, Ileana M; Williams, Rosemary; Chait, Brian T; Rout, Michael PMolecular & cellular proteomics : MCP2005 Dec1933-4116155292
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 BProtein science : a publication of the Protein Society2005 Sep2304-1416131659
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 DProceedings of the National Academy of Sciences of the United States of America2005 Aug 3012612-716107538
Measuring D-amino acid-containing neuropeptides with capillary electrophoresis.Sheeley, Sarah A; Miao, Hai; Ewing, Michael A; Rubakhin, Stanislav S; Sweedler, Jonathan VThe Analyst2005 Aug1198-20316021220
Proteomics meets microbiology: technical advances in the global mapping of protein expression and function.Phillips, Carolyn I; Bogyo, MatthewCellular microbiology.2005 Aug1061-7616008574
Diverse polyubiquitin interaction properties of ubiquitin-associated domains.Raasi, Shahri; Varadan, Ranjani; Fushman, David; Pickart, Cecile MNature structural & molecular biology. 2005 Aug708-1416007098
Imaging mass spectrometry: fundamentals and applications to drug discovery.Rubakhin, Stanislav S; Jurchen, John C; Monroe, Eric B; Sweedler, Jonathan VDrug discovery today2005 Jun 15823-3715970265
Automatic detection of subsystem/pathway variants in genome analysis.Ye, Yuzhen; Osterman, Andrei; Overbeek, Ross; Godzik, AdamBioinformatics (Oxford, England) 2005 Juni478-8615961494
Genetically encoded FRET sensors for visualizing metabolites with subcellular resolution in living cells.Looger, Loren L; Lalonde, Sylvie; Frommer, Wolf BPlant physiology. 2005 Jun555-715955913
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 YThe Journal of biological chemistry. 2005 Jul 2927755-815944163
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 DThe Journal of biological chemistry2005 Jul 2927654-6115944147
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 BProceedings of the National Academy of Sciences of the United States of America2005 Jun 148740-515939876
Online microdialysis-dynamic nanoelectrospray ionization-mass spectrometry for monitoring neuropeptide secretion.Jakubowski, Jennifer A; Hatcher, Nathan G; Sweedler, Jonathan VJournal of mass spectrometry : JMS. 2005 Jul924-3115934039
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 YThe Journal of biological chemistry. 2005 Jul 125079-8615878869
Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry.Molina, Henrik; Parmigiani, Giovanni; Pandey, AkhileshAnalytical chemistry2005 May 12739-4415859588
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 WFASEB journal : official publication of the Federation of American Societies for Experimental Biology2005 Jul1123-415857880
Solid-phase synthesis of double-headed epoxysuccinyl activity-based probes for selective targeting of papain family cysteine proteases.Verhelst, Steven H L; Bogyo, MatthewChembiochem : a European journal of chemical biology.2005 May824-715776409
Approach for determining protein ubiquitination sites by MALDI-TOF mass spectrometry.Wang, Dongxia; Cotter, Robert JAnalytical chemistry2005 Mar 11458-6615732931
Strategy for the isolation, derivatization, chromatographic separation, and detection of carnitine and acylcarnitines.Minkler, Paul E; Ingalls, Stephen T; Hoppel, Charles LAnalytical chemistry2005 Mar 11448-5715732930
Chemical proteomics applied to target identification and drug discovery.Verhelst, Steven H L; Bogyo, MatthewBioTechniques. 2005 Feb175-715727120
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