Library of Integrated Network-Based Cellular Signatures (LINCS) (365)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Connecting omics signatures and revealing biological mechanisms with iLINCS.Pilarczyk, Marcin; Fazel-Najafabadi, Mehdi; Kouril, Michal; Shamsaei, Behrouz; Vasiliauskas, Juozas; Niu, Wen; Mahi, Naim; Zhang, Lixia; Clark, Nicholas A; Ren, Yan; White, Shana; Karim, Rashid; Xu, Huan; Biesiada, Jacek; Bennett, Mark F; Davidson, Sarah E; Reichard, John F; Roberts, Kurt; Stathias, Vasileios; Koleti, Amar; Vidovic, Dusica; Clarke, Daniel J B; Schürer, Stephan C; Ma'ayan, Avi; Meller, Jarek; Medvedovic, MarioNature communications2022 08 0935945222
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues.Zatorski, Nicole; Stein, David; Rahman, Rayees; Iyengar, Ravi; Schlessinger, AvnerDatabase : the journal of biological databases and curation2022 Jul 2635881481
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes.Doherty, Laura M; Mills, Caitlin E; Boswell, Sarah A; Liu, Xiaoxi; Hoyt, Charles Tapley; Gyori, Benjamin; Buhrlage, Sara J; Sorger, Peter KeLife2022 06 2335737447
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Erdem, Cemal; Mutsuddy, Arnab; Bensman, Ethan M; Dodd, William B; Saint-Antoine, Michael M; Bouhaddou, Mehdi; Blake, Robert C; Gross, Sean M; Heiser, Laura M; Feltus, F Alex; Birtwistle, Marc RNature communications2022 06 2135729113
A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis.Ternes, Luke; Dane, Mark; Gross, Sean; Labrie, Marilyne; Mills, Gordon; Gray, Joe; Heiser, Laura; Chang, Young HwanCommunications biology2022 03 2335322205
INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer.Liu, Moqing; Smith, Rebecca; Liby, Tiera; Chiotti, Kami; López, Claudia S; Korkola, James EBreast cancer research : BCR2022 Mar 0535248133
Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity.Xiong, Yuguang; Liu, Tong; Chen, Tong; Hansen, Jens; Hu, Bin; Chen, Yibang; Jayaraman, Gomathi; Schürer, Stephan; Vidovic, Dusica; Goldfarb, Joseph; Sobie, Eric A; Birtwistle, Marc R; Iyengar, Ravi; Li, Hong; Azeloglu, Evren UScientific data2022 Jan 2035058449
Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors.Meharena, Hiruy S; Marco, Asaf; Dileep, Vishnu; Lockshin, Elana R; Akatsu, Grace Y; Mullahoo, James; Watson, L Ashley; Ko, Tak; Guerin, Lindsey N; Abdurrob, Fatema; Rengarajan, Shruthi; Papanastasiou, Malvina; Jaffe, Jacob D; Tsai, Li-HueiCell stem cell2022 01 0634995493
A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals.Schaniel, Christoph; Dhanan, Priyanka; Hu, Bin; Xiong, Yuguang; Raghunandan, Teeya; Gonzalez, David M; Dariolli, Rafael; D'Souza, Sunita L; Yadaw, Arjun S; Hansen, Jens; Jayaraman, Gomathi; Mathew, Bino; Machado, Moara; Berger, Seth I; Tripodig, Joseph; Najfeld, Vesna; Garg, Jalaj; Miller, Marc; Surlyn, Colleen S; Michelis, Katherine C; Tangirala, Neelima C; Weerahandi, Himali; Thomas, David C; Beaumont, Kristin G; Sebra, Robert; Mahajan, Milind; Schadt, Eric; Vidovic, Dusica; Schürer, Stephan C; Goldfarb, Joseph; Azeloglu, Evren U; Birtwistle, Marc R; Sobie, Eric A; Kovacic, Jason C; Dubois, Nicole C; Iyengar, RaviStem cell reports2021 Oct 2634739849
Functional Effects of Cardiomyocyte Injury in COVID-19.Siddiq, Mustafa M; Chan, Angel T; Miorin, Lisa; Yadaw, Arjun S; Beaumont, Kristin G; Kehrer, Thomas; Cupic, Anastasija; White, Kris M; Tolentino, Rosa E; Hu, Bin; Stern, Alan D; Tavassoly, Iman; Hansen, Jens; Sebra, Robert; Martinez, Pedro; Prabha, Som; Dubois, Nicole; Schaniel, Christoph; Iyengar-Kapuganti, Rupa; Kukar, Nina; Giustino, Gennaro; Sud, Karan; Nirenberg, Sharon; Kovatch, Patricia; Albrecht, Randy A; Goldfarb, Joseph; Croft, Lori; McLaughlin, Maryann A; Argulian, Edgar; Lerakis, Stamatios; Narula, Jagat; García-Sastre, Adolfo; Iyengar, RaviJournal of virology2022 01 2634669512
Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies.Labrie, Marilyne; Li, Allen; Creason, Allison; Betts, Courtney; Keck, Jamie; Johnson, Brett; Sivagnanam, Shamilene; Boniface, Christopher; Ma, Hongli; Blucher, Aurora; Chang, Young Hwan; Chin, Koei; Vuky, Jacqueline; Guimaraes, Alexander R; Downey, Molly; Lim, Jeong Youn; Gao, Lina; Siex, Kiara; Parmar, Swapnil; Kolodzie, Annette; Spellman, Paul T; Goecks, Jeremy; Coussens, Lisa M; Corless, Christopher L; Bergan, Raymond; Gray, Joe W; Mills, Gordon B; Mitri, Zahi INPJ precision oncology2021 Oct 1934667258
Automatic Transformation and Integration to Improve Visualization and Discovery of Latent Effects in Imaging Data.Hunt, Gregory J; Dane, Mark A; Korkola, James E; Heiser, Laura M; Gagnon-Bartsch, Johann AJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America202034531645
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.Markmiller, Sebastian; Sathe, Shashank; Server, Kari L; Nguyen, Thai B; Fulzele, Amit; Cody, Neal; Javaherian, Ashkan; Broski, Sara; Finkbeiner, Steven; Bennett, Eric J; Lécuyer, Eric; Yeo, Gene WCell reports2021 09 0734496257
Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration.Linsley, Jeremy W; Shah, Kevan; Castello, Nicholas; Chan, Michelle; Haddad, Dominik; Doric, Zak; Wang, Shijie; Leks, Wiktoria; Mancini, Jay; Oza, Viral; Javaherian, Ashkan; Nakamura, Ken; Kokel, David; Finkbeiner, StevenNature communications2021 09 0634489414
Phenotyping Neurodegeneration in Human iPSCs.Li, Jonathan; Fraenkel, ErnestAnnual review of biomedical data science2021 07 2034465166
Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.Dele-Oni, Deborah O; Christianson, Karen E; Egri, Shawn B; Vaca Jacome, Alvaro Sebastian; DeRuff, Katherine C; Mullahoo, James; Sharma, Vagisha; Davison, Desiree; Ko, Tak; Bula, Michael; Blanchard, Joel; Young, Jennie Z; Litichevskiy, Lev; Lu, Xiaodong; Lam, Daniel; Asiedu, Jacob K; Toder, Caidin; Officer, Adam; Peckner, Ryan; MacCoss, Michael J; Tsai, Li-Huei; Carr, Steven A; Papanastasiou, Malvina; Jaffe, Jacob DScientific data2021 08 2534433823
Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA.Garay, Joseph P; Smith, Rebecca; Devlin, Kaylyn; Hollern, Daniel P; Liby, Tiera; Liu, Moqing; Boddapati, Shanta; Watson, Spencer S; Esch, Amanda; Zheng, Ting; Thompson, Wallace; Babcock, Darcie; Kwon, Sunjong; Chin, Koei; Heiser, Laura; Gray, Joe W; Korkola, James EBreast cancer research : BCR2021 08 0334344439
Nuclear accumulation of CHMP7 initiates nuclear pore complex injury and subsequent TDP-43 dysfunction in sporadic and familial ALS.Coyne, Alyssa N; Baskerville, Victoria; Zaepfel, Benjamin L; Dickson, Dennis W; Rigo, Frank; Bennett, Frank; Lusk, C Patrick; Rothstein, Jeffrey DScience translational medicine2021 07 2834321318
Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics.Tognon, Cristina E; Sears, Rosalie C; Mills, Gordon B; Gray, Joe W; Tyner, Jeffrey WAnnual review of cancer biology2021 Mar34222745
Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma.Lue, Hui-Wen; Derrick, Daniel S; Rao, Soumya; Van Gaest, Ahna; Cheng, Larry; Podolak, Jennifer; Lawson, Samantha; Xue, Changhui; Garg, Devin; White 3rd, Ralph; Ryan, Christopher W; Drake, Justin M; Ritz, Anna; Heiser, Laura M; Thomas, George VCell reports. Medicine2021 05 1834095877
Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis.Rossmann, Marlies P; Hoi, Karen; Chan, Victoria; Abraham, Brian J; Yang, Song; Mullahoo, James; Papanastasiou, Malvina; Wang, Ying; Elia, Ilaria; Perlin, Julie R; Hagedorn, Elliott J; Hetzel, Sara; Weigert, Raha; Vyas, Sejal; Nag, Partha P; Sullivan, Lucas B; Warren, Curtis R; Dorjsuren, Bilguujin; Greig, Eugenia Custo; Adatto, Isaac; Cowan, Chad A; Schreiber, Stuart L; Young, Richard A; Meissner, Alexander; Haigis, Marcia C; Hekimi, Siegfried; Carr, Steven A; Zon, Leonard IScience (New York, N.Y.)2021 05 1433986176
Protein structure-based gene expression signatures.Rahman, Rayees; Zatorski, Nicole; Hansen, Jens; Xiong, Yuguang; van Hasselt, J G Coen; Sobie, Eric A; Birtwistle, Marc R; Azeloglu, Evren U; Iyengar, Ravi; Schlessinger, AvnerProceedings of the National Academy of Sciences of the United States of America2021 May 1133941686
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.Uzunangelov, Vladislav; Wong, Christopher K; Stuart, Joshua MPLoS computational biology2021 Apr33861732
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map.Blasco, Andrea; Natoli, Ted; Endres, Michael G; Sergeev, Rinat A; Randazzo, Steven; Paik, Jin H; Macaluso, N J Maximilian; Narayan, Rajiv; Lu, Xiaodong; Peck, David; Lakhani, Karim R; Subramanian, AravindBioinformatics (Oxford, England)2021 Apr 0633824954
Integration of mechanical and ECM microenvironment signals in the determination of cancer stem cell states.Jokela, Tiina A; LaBarge, Mark ACurrent stem cell reports2021 Mar33777660
Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling.Vemulapalli, Vidyasiri; Chylek, Lily A; Erickson, Alison; Pfeiffer, Anamarija; Gabriel, Khal-Hentz; LaRochelle, Jonathan; Subramanian, Kartik; Cao, Ruili; Stegmaier, Kimberley; Mohseni, Morvarid; LaMarche, Matthew J; Acker, Michael G; Sorger, Peter K; Gygi, Steven P; Blacklow, Stephen CeLife2021 Mar 2333755016
Contributions of Yap and Taz dysfunction to breast cancer initiation, progression, and aging-related susceptibility.Fresques, Tara; LaBarge, Mark AAging and cancer2020 Dec33693435
Cell of all trades: oligodendrocyte precursor cells in synaptic, vascular, and immune function.Akay, Leyla Anne; Effenberger, Audrey H; Tsai, Li-HueiGenes & development2021 Feb 0133526585
Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells.Färkkilä, Anniina; Rodríguez, Alfredo; Oikkonen, Jaana; Gulhan, Doga C; Nguyen, Huy; Domínguez, Julieta; Ramos, Sandra; Mills, Caitlin E; Pérez-Villatoro, Fernando; Lazaro, Jean-Bernard; Zhou, Jia; Clairmont, Connor S; Moreau, Lisa A; Park, Peter J; Sorger, Peter K; Hautaniemi, Sampsa; Frias, Sara; D'Andrea, Alan DCancer research2021 Jan 2933514515
PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease.Morozko, Eva L; Smith-Geater, Charlene; Monteys, Alejandro Mas; Pradhan, Subrata; Lim, Ryan G; Langfelder, Peter; Kachemov, Marketta; Hill, Austin; Stocksdale, Jennifer T; Cullis, Pieter R; Wu, Jie; Ochaba, Joseph; Miramontes, Ricardo; Chakraborty, Anirban; Hazra, Tapas K; Lau, Alice; St-Cyr, Sophie; Orellana, Iliana; Kopan, Lexi; Wang, Keona Q; Yeung, Sylvia; Leavitt, Blair R; Reidling, Jack C; Yang, X William; Steffan, Joan S; Davidson, Beverly L; Sarkar, Partha S; Thompson, Leslie MProceedings of the National Academy of Sciences of the United States of America2021 Jan 2633468657
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures.Ho, Ritchie; Workman, Michael J; Mathkar, Pranav; Wu, Kathryn; Kim, Kevin J; O'Rourke, Jacqueline G; Kellogg, Mariko; Montel, Valerie; Banuelos, Maria G; Arogundade, Olubankole Aladesuyi; Diaz-Garcia, Sandra; Oheb, Daniel; Huang, Steven; Khrebtukova, Irina; Watson, Lisa; Ravits, John; Taylor, Kevin; Baloh, Robert H; Svendsen, Clive NCell systems2021 Feb 1733382996
Investigational Treatments for COVID-19 may Increase Ventricular Arrhythmia Risk Through Drug Interactions.Varshneya, Meera; Irurzun-Arana, Itziar; Campana, Chiara; Dariolli, Rafael; Gutierrez, Amy; Pullinger, Taylor K; Sobie, Eric ACPT: pharmacometrics & systems pharmacology2021 0233205613
Physiology of cardiomyocyte injury in COVID-19.Siddiq, Mustafa M; Chan, Angel T; Miorin, Lisa; Yadaw, Arjun S; Beaumont, Kristin G; Kehrer, Thomas; White, Kris M; Cupic, Anastasija; Tolentino, Rosa E; Hu, Bin; Stern, Alan D; Tavassoly, Iman; Hansen, Jens; Martinez, Pedro; Dubois, Nicole; Schaniel, Christoph; Iyengar-Kapuganti, Rupa; Kukar, Nina; Giustino, Gennaro; Sud, Karan; Nirenberg, Sharon; Kovatch, Patricia; Goldfarb, Joseph; Croft, Lori; McLaughlin, Maryann A; Argulian, Edgar; Lerakis, Stamatios; Narula, Jagat; García-Sastre, Adolfo; Iyengar, RavimedRxiv : the preprint server for health sciences.2020 Nov 13;33200140
Avant-garde: an automated data-driven DIA data curation tool.Vaca Jacome, Alvaro Sebastian; Peckner, Ryan; Shulman, Nicholas; Krug, Karsten; DeRuff, Katherine C; Officer, Adam; Christianson, Karen E; MacLean, Brendan; MacCoss, Michael J; Carr, Steven A; Jaffe, Jacob DNature methods.2020 Dec;33199889
Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.Zhao, Wei; Li, Jun; Chen, Mei-Ju M; Luo, Yikai; Ju, Zhenlin; Nesser, Nicole K; Johnson-Camacho, Katie; Boniface, Christopher T; Lawrence, Yancey; Pande, Nupur T; Davies, Michael A; Herlyn, Meenhard; Muranen, Taru; Zervantonakis, Ioannis K; von Euw, Erika; Schultz, Andre; Kumar, Shwetha V; Korkut, Anil; Spellman, Paul T; Akbani, Rehan; Slamon, Dennis J; Gray, Joe W; Brugge, Joan S; Lu, Yiling; Mills, Gordon B; Liang, HanCancer cell2020 Dec 1433157050
PICALM Rescues Endocytic Defects Caused by the Alzheimer's Disease Risk Factor APOE4.Narayan, Priyanka; Sienski, Grzegorz; Bonner, Julia M; Lin, Yuan-Ta; Seo, Jinsoo; Baru, Valeriya; Haque, Aftabul; Milo, Blerta; Akay, Leyla A; Graziosi, Agnese; Freyzon, Yelena; Landgraf, Dirk; Hesse, William R; Valastyan, Julie; Barrasa, M Inmaculada; Tsai, Li-Huei; Lindquist, SusanCell reports2020 10 0633027662
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model.Yadaw, Arjun S; Li, Yan-Chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, GauravThe Lancet. Digital health.2020 Oct;32984797
Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease.Finkbeiner, StevenNeurobiology of disease2020 1232977020
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity.van Hasselt, J G Coen; Rahman, Rayees; Hansen, Jens; Stern, Alan; Shim, Jaehee V; Xiong, Yuguang; Pickard, Amanda; Jayaraman, Gomathi; Hu, Bin; Mahajan, Milind; Gallo, James M; Goldfarb, Joseph; Sobie, Eric A; Birtwistle, Marc R; Schlessinger, Avner; Azeloglu, Evren U; Iyengar, RaviNature communications.2020 09 23;32968055
Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments.Kimmel, Gregory J; Dane, Mark; Heiser, Laura M; Altrock, Philipp M; Andor, NoemiCancer research.2020 Nov 15;32938640
Systems biology approaches to measure and model phenotypic heterogeneity in cancer.Meyer, Aaron S; Heiser, Laura MCurrent opinion in systems biology.2019 Oct;32864511
Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing.Liu, Yan; Ferguson, Fleur M; Li, Lianbo; Kuljanin, Miljan; Mills, Caitlin E; Subramanian, Kartik; Harshbarger, Wayne; Gondi, Sudershan; Wang, Jinhua; Sorger, Peter K; Mancias, Joseph D; Gray, Nathanael S; Westover, Kenneth DCell chemical biology.2020 Aug 04;32755567
G4C2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD.Coyne, Alyssa N; Zaepfel, Benjamin L; Hayes, Lindsey; Fitchman, Boris; Salzberg, Yuval; Luo, En-Ching; Bowen, Kelly; Trost, Hannah; Aigner, Stefan; Rigo, Frank; Yeo, Gene W; Harel, Amnon; Svendsen, Clive N; Sareen, Dhruv; Rothstein, Jeffrey DNeuron2020 09 2332673563
Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling.Corsello, Steven M; Nagari, Rohith T; Spangler, Ryan D; Rossen, Jordan; Kocak, Mustafa; Bryan, Jordan G; Humeidi, Ranad; Peck, David; Wu, Xiaoyun; Tang, Andrew A; Wang, Vickie M; Bender, Samantha A; Lemire, Evan; Narayan, Rajiv; Montgomery, Philip; Ben-David, Uri; Garvie, Colin W; Chen, Yejia; Rees, Matthew G; Lyons, Nicholas J; McFarland, James M; Wong, Bang T; Wang, Li; Dumont, Nancy; O'Hearn, Patrick J; Stefan, Eric; Doench, John G; Harrington, Caitlin N; Greulich, Heidi; Meyerson, Matthew; Vazquez, Francisca; Subramanian, Aravind; Roth, Jennifer A; Bittker, Joshua A; Boehm, Jesse S; Mader, Christopher C; Tsherniak, Aviad; Golub, Todd RNature cancer.2020 Feb;32613204
Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes.Blanchard, Joel W; Bula, Michael; Davila-Velderrain, Jose; Akay, Leyla Anne; Zhu, Lena; Frank, Alexander; Victor, Matheus B; Bonner, Julia Maeve; Mathys, Hansruedi; Lin, Yuan-Ta; Ko, Tak; Bennett, David A; Cam, Hugh P; Kellis, Manolis; Tsai, Li-HueiNature medicine.2020 06;32514169
Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions.Varshneya, Meera; Irurzun-Arana, Itziar; Campana, Chiara; Dariolli, Rafael; Gutierrez, Amy; Pullinger, Taylor K; Sobie, Eric AmedRxiv : the preprint server for health sciences.2020 May 26;32511528
Clinical predictors of COVID-19 mortality.Yadaw, Arjun S; Li, Yan-Chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, GauravmedRxiv : the preprint server for health sciences.2020 May 22;32511520
Audit logs to enforce document integrity in Skyline and Panorama.Rohde, Tobias; Chupalov, Rita; Shulman, Nicholas; Sharma, Vagisha; Eckels, Josh; Pratt, Brian S; MacCoss, Michael J; MacLean, Brendan XBioinformatics (Oxford, England)2020 08 0132467974
Development of CDK2 and CDK5 Dual Degrader TMX-2172.Teng, Mingxing; Jiang, Jie; He, Zhixiang; Kwiatkowski, Nicholas P; Donovan, Katherine A; Mills, Caitlin E; Victor, Chiara; Hatcher, John M; Fischer, Eric S; Sorger, Peter K; Zhang, Tinghu; Gray, Nathanael SAngewandte Chemie (International ed. in English).2020 May 15;32415712
Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.Lee, Sanghoon; Zhao, Li; Rojas, Christine; Bateman, Nicholas W; Yao, Hui; Lara, Olivia D; Celestino, Joseph; Morgan, Margaret B; Nguyen, Tri V; Conrads, Kelly A; Rangel, Kelly M; Dood, Robert L; Hajek, Richard A; Fawcett, Gloria L; Chu, Randy A; Wilson, Katlin; Loffredo, Jeremy L; Viollet, Coralie; Jazaeri, Amir A; Dalgard, Clifton L; Mao, Xizeng; Song, Xingzhi; Zhou, Ming; Hood, Brian L; Banskota, Nirad; Wilkerson, Matthew D; Te, Jerez; Soltis, Anthony R; Roman, Kristin; Dunn, Andrew; Cordover, David; Eterovic, Agda Karina; Liu, Jinsong; Burks, Jared K; Baggerly, Keith A; Fleming, Nicole D; Lu, Karen H; Westin, Shannon N; Coleman, Robert L; Mills, Gordon B; Casablanca, Yovanni; Zhang, Jianhua; Conrads, Thomas P; Maxwell, George L; Futreal, P Andrew; Sood, Anil KCell reports.2020 Apr 14;32294438
How Machine Learning Will Transform Biomedicine.Goecks, Jeremy; Jalili, Vahid; Heiser, Laura M; Gray, Joe WCell.2020 Apr 02;32243801
Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation.Smith-Geater, Charlene; Hernandez, Sarah J; Lim, Ryan G; Adam, Miriam; Wu, Jie; Stocksdale, Jennifer T; Wassie, Brook T; Gold, Maxwell Philip; Wang, Keona Q; Miramontes, Ricardo; Kopan, Lexi; Orellana, Iliana; Joy, Shona; Kemp, Paul J; Allen, Nicholas D; Fraenkel, Ernest; Thompson, Leslie MStem cell reports.2020 03 10;32109367
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS.Mullahoo, James; Zhang, Terry; Clauser, Karl; Carr, Steven A; Jaffe, Jacob D; Papanastasiou, MalvinaMethods (San Diego, Calif.).2020 Jan 28;32004545
A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.Patel-Murray, Natasha L; Adam, Miriam; Huynh, Nhan; Wassie, Brook T; Milani, Pamela; Fraenkel, ErnestScientific reports.2020 Jan 22;31969612
Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.Lyashenko, Eugenia; Niepel, Mario; Dixit, Purushottam D; Lim, Sang Kyun; Sorger, Peter K; Vitkup, DenniseLife.2020 Jan 21;31961323
Individual Cells Can Resolve Variations in Stimulus Intensity along the IGF-PI3K-AKT Signaling Axis.Gross, Sean M; Dane, Mark A; Bucher, Elmar; Heiser, Laura MCell systems.2019 Dec 18;31838146
Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells.Chopra, Sameer S; Jenney, Anne; Palmer, Adam; Niepel, Mario; Chung, Mirra; Mills, Caitlin; Sivakumaren, Sindhu Carmen; Liu, Qingsong; Chen, Jia-Yun; Yapp, Clarence; Asara, John M; Gray, Nathanael S; Sorger, Peter KCell systems.2020 Jan 22;31812693
Using Transcriptional Signatures to Find Cancer Drivers with LURE.Haan, David; Tao, Ruikang; Friedl, Verena; Anastopoulos, Ioannis N; Wong, Christopher K; Weinstein, Alana S; Stuart, Joshua MPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2020;31797609
Development and Characterization of a Wee1 Kinase Degrader.Li, Zhengnian; Pinch, Benika J; Olson, Calla M; Donovan, Katherine A; Nowak, Rados?aw P; Mills, Caitlin E; Scott, David A; Doctor, Zainab M; Eleuteri, Nicholas A; Chung, Mirra; Sorger, Peter K; Fischer, Eric S; Gray, Nathanael SCell chemical biology.2020 Jan 16;31735695
Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice.Kedaigle, Amanda J; Reidling, Jack C; Lim, Ryan G; Adam, Miriam; Wu, Jie; Wassie, Brook; Stocksdale, Jennifer T; Casale, Malcolm S; Fraenkel, Ernest; Thompson, Leslie MHuman molecular genetics.2020 01 15;31696228
Annot: a Django-based sample, reagent, and experiment metadata tracking system.Bucher, Elmar; Claunch, Cheryl J; Hee, Derrick; Smith, Rebecca L; Devlin, Kaylyn; Thompson, Wallace; Korkola, James E; Heiser, Laura MBMC bioinformatics2019 Nov 0131675914
Building Containerized Workflows Using the BioDepot-Workflow-Builder.Hung, Ling-Hong; Hu, Jiaming; Meiss, Trevor; Ingersoll, Alyssa; Lloyd, Wes; Kristiyanto, Daniel; Xiong, Yuguang; Sobie, Eric; Yeung, Ka YeeCell systems.2019 Sep 06;31521606
Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS.Papanastasiou, Malvina; Mullahoo, James; DeRuff, Katherine C; Bajrami, Besnik; Karageorgos, Ioannis; Johnston, Stephen E; Peckner, Ryan; Myers, Samuel A; Carr, Steven A; Jaffe, Jacob DMolecular & cellular proteomics : MCP.2019 10;31409669
Variational Autoencoding Tissue Response to Microenvironment Perturbation.Schau, Geoffrey F; Thibault, Guillaume; Dane, Mark A; Gray, Joe W; Heiser, Laura M; Chang, Young HwanProceedings of SPIE--the International Society for Optical Engineering.2019 Feb;31379401
Thesaurus: quantifying phosphopeptide positional isomers.Searle, Brian C; Lawrence, Robert T; MacCoss, Michael J; Villén, JuditNature methods.2019 08;31363206
A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines.Niepel, Mario; Hafner, Marc; Mills, Caitlin E; Subramanian, Kartik; Williams, Elizabeth H; Chung, Mirra; Gaudio, Benjamin; Barrette, Anne Marie; Stern, Alan D; Hu, Bin; Korkola, James E; LINCS Consortium; Gray, Joe W; Birtwistle, Marc R; Heiser, Laura M; Sorger, Peter KCell systems.2019 Jul 05;31302153
Multi omics analysis of fibrotic kidneys in two mouse models.Pavkovic, Mira; Pantano, Lorena; Gerlach, Cory V; Brutus, Sergine; Boswell, Sarah A; Everley, Robert A; Shah, Jagesh V; Sui, Shannan H; Vaidya, Vishal SScientific data.2019 06 14;31201317
Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy.Fang, Yong; McGrail, Daniel J; Sun, Chaoyang; Labrie, Marilyne; Chen, Xiaohua; Zhang, Dong; Ju, Zhenlin; Vellano, Christopher P; Lu, Yiling; Li, Yongsheng; Jeong, Kang Jin; Ding, Zhiyong; Liang, Jiyong; Wang, Steven W; Dai, Hui; Lee, Sanghoon; Sahni, Nidhi; Mercado-Uribe, Imelda; Kim, Tae-Beom; Chen, Ken; Lin, Shiaw-Yih; Peng, Guang; Westin, Shannon N; Liu, Jinsong; O'Connor, Mark J; Yap, Timothy A; Mills, Gordon BCancer cell.2019 Jun 10;31185210
Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer.Smith, Rebecca; Devlin, Kaylyn; Kilburn, David; Gross, Sean; Sudar, Damir; Bucher, Elmar; Nederlof, Michel; Dane, Mark; Gray, Joe W; Heiser, Laura; Korkola, James EJournal of visualized experiments : JoVE.2019 May 21;31180341
Cell death assays for neurodegenerative disease drug discovery.Linsley, Jeremy W; Reisine, Terry; Finkbeiner, StevenExpert opinion on drug discovery.2019 Sep;31179783
Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity.Hafner, Marc; Mills, Caitlin E; Subramanian, Kartik; Chen, Chen; Chung, Mirra; Boswell, Sarah A; Everley, Robert A; Liu, Changchang; Walmsley, Charlotte S; Juric, Dejan; Sorger, Peter KCell chemical biology.2019 Jun 06;31178407
IKK? slows Huntington's disease progression in R6/1 mice.Ochaba, Joseph; Fote, Gianna; Kachemov, Marketta; Thein, Soe; Yeung, Sylvia Y; Lau, Alice L; Hernandez, Sarah; Lim, Ryan G; Casale, Malcolm; Neel, Michael J; Monuki, Edwin S; Reidling, Jack; Housman, David E; Thompson, Leslie M; Steffan, Joan SProceedings of the National Academy of Sciences of the United States of America.2019 May 28;31088970
Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming.Wang, Huan; Sheehan, Robert P; Palmer, Adam C; Everley, Robert A; Boswell, Sarah A; Ron-Harel, Noga; Ringel, Alison E; Holton, Kristina M; Jacobson, Connor A; Erickson, Alison R; Maliszewski, Laura; Haigis, Marcia C; Sorger, Peter KCell systems.2019 May 22;31078528
Disruption of podocyte cytoskeletal biomechanics by dasatinib leads to nephrotoxicity.Calizo, Rhodora C; Bhattacharya, Smiti; van Hasselt, J G Coen; Wei, Chengguo; Wong, Jenny S; Wiener, Robert J; Ge, Xuhua; Wong, Nicholas J; Lee, Jia-Jye; Cuttitta, Christina M; Jayaraman, Gomathi; Au, Vivienne H; Janssen, William; Liu, Tong; Li, Hong; Salem, Fadi; Jaimes, Edgar A; Murphy, Barbara; Campbell, Kirk N; Azeloglu, Evren UNature communications.2019 05 03;31053734
Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.Rao, Suman; Gurbani, Deepak; Du, Guangyan; Everley, Robert A; Browne, Christopher M; Chaikuad, Apirat; Tan, Li; Schröder, Martin; Gondi, Sudershan; Ficarro, Scott B; Sim, Taebo; Kim, Nam Doo; Berberich, Matthew J; Knapp, Stefan; Marto, Jarrod A; Westover, Kenneth D; Sorger, Peter K; Gray, Nathanael SCell chemical biology.2019 Apr 11;30982749
The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity.Li, Amy; Lu, Xiaodong; Natoli, Ted; Bittker, Joshua; Sipes, Nisha S; Subramanian, Aravind; Auerbach, Scott; Sherr, David H; Monti, StefanoEnvironmental health perspectives2019 0430964323
Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries.Moret, Nienke; Clark, Nicholas A; Hafner, Marc; Wang, Yuan; Lounkine, Eugen; Medvedovic, Mario; Wang, Jinhua; Gray, Nathanael; Jenkins, Jeremy; Sorger, Peter KCell chemical biology.2019 Mar 12;30956147
Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity.Ferguson, Fleur M; Doctor, Zainab M; Ficarro, Scott B; Browne, Christopher M; Marto, Jarrod A; Johnson, Jared L; Yaron, Tomer M; Cantley, Lewis C; Kim, Nam Doo; Sim, Taebo; Berberich, Matthew J; Kalocsay, Marian; Sorger, Peter K; Gray, Nathanael SCell chemical biology.2019 Mar 11;30930164
Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype.Olson, Calla M; Liang, Yanke; Leggett, Alan; Park, Woojun D; Li, Lianbo; Mills, Caitlin E; Elsarrag, Selma Z; Ficarro, Scott B; Zhang, Tinghu; Düster, Robert; Geyer, Matthias; Sim, Taebo; Marto, Jarrod A; Sorger, Peter K; Westover, Ken D; Lin, Charles Y; Kwiatkowski, Nicholas; Gray, Nathanael SCell chemical biology.2019 Mar 06;30905681
Mitochondrial origins of fractional control in regulated cell death.Santos, Luís C; Vogel, Robert; Chipuk, Jerry E; Birtwistle, Marc R; Stolovitzky, Gustavo; Meyer, PabloNature communications.2019 03 21;30899020
Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers.Heiser, Laura M; Mills, Gordon B; Gray, Joe WCancer cell.2019 Mar 18;30889376
PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.Graim, Kiley; Friedl, Verena; Houlahan, Kathleen E; Stuart, Joshua MPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2019;30864317
Holistic optimization of an RNA-seq workflow for multi-threaded environments.Hung, Ling-Hong; Lloyd, Wes; Agumbe Sridhar, Radhika; Athmalingam Ravishankar, Saranya Devi; Xiong, Yuguang; Sobie, Eric; Yeung, Ka YeeBioinformatics (Oxford, England).2019 10 15;30859176
A multi-targeted probe-based strategy to identify signaling vulnerabilities in cancers.Rao, Suman; Du, Guangyan; Hafner, Marc; Subramanian, Kartik; Sorger, Peter K; Gray, Nathanael SThe Journal of biological chemistry.2019 Mar 11;30858179
Drug Effect Prediction by Integrating L1000 Genomic and Proteomic Big Data.Chen, Wei; Zhou, XiaoboMethods in molecular biology (Clifton, N.J.).2019;30848468
Drug Signature Detection Based on L1000 Genomic and Proteomic Big Data.Chen, Wei; Zhou, XiaoboMethods in molecular biology (Clifton, N.J.).2019;30848467
A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line.Song, Yuyu; Subramanian, Kartik; Berberich, Matthew J; Rodriguez, Steven; Latorre, Isabel J; Luria, Catherine M; Everley, Robert; Albers, Mark W; Mitchison, Timothy J; Sorger, Peter KScientific data.2019 Feb 19;30778261
Dual Inhibition of GSK3? and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo.Reinhardt, Lydia; Kordes, Susanne; Reinhardt, Peter; Glatza, Michael; Baumann, Matthias; Drexler, Hannes C A; Menninger, Sascha; Zischinsky, Gunther; Eickhoff, Jan; Fröb, Claudia; Bhattarai, Prabesh; Arulmozhivarman, Guruchandar; Marrone, Lara; Janosch, Antje; Adachi, Kenjiro; Stehling, Martin; Anderson, Eric N; Abo-Rady, Masin; Bickle, Marc; Pandey, Udai Bhan; Reimer, Michell M; Kizil, Caghan; Schöler, Hans R; Nussbaumer, Peter; Klebl, Bert; Sterneckert, Jared LStem cell reports.2019 Mar 05;30773488
Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites.HD iPSC ConsortiumHuman molecular genetics2020 07 2130768179
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.Hinohara, Kunihiko; Wu, Hua-Jun; Sébastien Vigneau; McDonald, Thomas O; Igarashi, Kyomi J; Yamamoto, Kimiyo N; Madsen, Thomas; Fassl, Anne; Egri, Shawn B; Papanastasiou, Malvina; Ding, Lina; Peluffo, Guillermo; Cohen, Ofir; Kales, Stephen C; Lal-Nag, Madhu; Rai, Ganesha; Maloney, David J; Jadhav, Ajit; Simeonov, Anton; Wagle, Nikhil; Brown, Myles; Meissner, Alexander; Sicinski, Piotr; Jaffe, Jacob D; Jeselsohn, Rinath; Gimelbrant, Alexander A; Michor, Franziska; Polyak, KorneliaCancer cell2019 Feb 1130753830
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.Amodei, Dario; Egertson, Jarrett; MacLean, Brendan X; Johnson, Richard; Merrihew, Gennifer E; Keller, Austin; Marsh, Don; Vitek, Olga; Mallick, Parag; MacCoss, Michael JJournal of the American Society for Mass Spectrometry.2019 Apr;30671891
A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro.Ramm, Susanne; Todorov, Petar; Chandrasekaran, Vidya; Dohlman, Anders; Monteiro, Maria B; Pavkovic, Mira; Muhlich, Jeremy; Shankaran, Harish; Chen, William W; Mettetal, Jerome T; Vaidya, Vishal SToxicological sciences : an official journal of the Society of Toxicology.2019 05 01;30649541
Genomic evolution of cancer models: perils and opportunities.Ben-David, Uri; Beroukhim, Rameen; Golub, Todd RNature reviews. Cancer.2019 02;30578414
Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis.Pereira, Gavin C; Sanchez, Laura; Schaughency, Paul M; Rubio-Roldán, Alejandro; Choi, Jungbin A; Planet, Evarist; Batra, Ranjan; Turelli, Priscilla; Trono, Didier; Ostrow, Lyle W; Ravits, John; Kazazian, Haig H; Wheelan, Sarah J; Heras, Sara R; Mayer, Jens; García-Pérez, Jose Luis; Goodier, John LMobile DNA.2018;30564290
A Curated Resource for Phosphosite-specific Signature Analysis.Krug, Karsten; Mertins, Philipp; Zhang, Bin; Hornbeck, Peter; Raju, Rajesh; Ahmad, Rushdy; Szucs, Matthew; Mundt, Filip; Forestier, Dominique; Jane-Valbuena, Judit; Keshishian, Hasmik; Gillette, Michael A; Tamayo, Pablo; Mesirov, Jill P; Jaffe, Jacob D; Carr, Steven A; Mani, D RMolecular & cellular proteomics : MCP.2019 Mar;30563849
Drug and disease signature integration identifies synergistic combinations in glioblastoma.Stathias, Vasileios; Jermakowicz, Anna M; Maloof, Marie E; Forlin, Michele; Walters, Winston; Suter, Robert K; Durante, Michael A; Williams, Sion L; Harbour, J William; Volmar, Claude-Henry; Lyons, Nicholas J; Wahlestedt, Claes; Graham, Regina M; Ivan, Michael E; Komotar, Ricardo J; Sarkaria, Jann N; Subramanian, Aravind; Golub, Todd R; Schürer, Stephan C; Ayad, Nagi GNature communications.2018 12 14;30552330
A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification.Browne, Christopher M; Jiang, Baishan; Ficarro, Scott B; Doctor, Zainab M; Johnson, Jared L; Card, Joseph D; Sivakumaren, Sindhu Carmen; Alexander, William M; Yaron, Tomer M; Murphy, Charles J; Kwiatkowski, Nicholas P; Zhang, Tinghu; Cantley, Lewis C; Gray, Nathanael S; Marto, Jarrod AJournal of the American Chemical Society.2019 Jan 09;30518210
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.Searle, Brian C; Pino, Lindsay K; Egertson, Jarrett D; Ting, Ying S; Lawrence, Robert T; MacLean, Brendan X; Villén, Judit; MacCoss, Michael JNature communications.2018 12 03;30510204
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.Hinohara, Kunihiko; Wu, Hua-Jun; Vigneau, Sébastien; McDonald, Thomas O; Igarashi, Kyomi J; Yamamoto, Kimiyo N; Madsen, Thomas; Fassl, Anne; Egri, Shawn B; Papanastasiou, Malvina; Ding, Lina; Peluffo, Guillermo; Cohen, Ofir; Kales, Stephen C; Lal-Nag, Madhu; Rai, Ganesha; Maloney, David J; Jadhav, Ajit; Simeonov, Anton; Wagle, Nikhil; Brown, Myles; Meissner, Alexander; Sicinski, Piotr; Jaffe, Jacob D; Jeselsohn, Rinath; Gimelbrant, Alexander A; Michor, Franziska; Polyak, KorneliaCancer cell2018 12 1030472020
Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.Pino, Lindsay K; Searle, Brian C; Huang, Eric L; Noble, William Stafford; Hoofnagle, Andrew N; MacCoss, Michael JAnalytical chemistry.2018 11 06;30350613
Systems biology approach reveals a link between mTORC1 and G2/M DNA damage checkpoint recovery.Hsieh, Hui-Ju; Zhang, Wei; Lin, Shu-Hong; Yang, Wen-Hao; Wang, Jun-Zhong; Shen, Jianfeng; Zhang, Yiran; Lu, Yiling; Wang, Hua; Yu, Jane; Mills, Gordon B; Peng, GuangNature communications.2018 Sep 28;30266942
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.Köksal, Ali Sinan; Beck, Kirsten; Cronin, Dylan R; McKenna, Aaron; Camp, Nathan D; Srivastava, Saurabh; MacGilvray, Matthew E; Bodík, Rastislav; Wolf-Yadlin, Alejandro; Fraenkel, Ernest; Fisher, Jasmin; Gitter, AnthonyCell reports.2018 Sep 25;30257219
A High-Throughput Immune-Oncology Screen Identifies EGFR Inhibitors as Potent Enhancers of Antigen-Specific Cytotoxic T-lymphocyte Tumor Cell Killing.Lizotte, Patrick H; Hong, Ruey-Long; Luster, Troy A; Cavanaugh, Megan E; Taus, Luke J; Wang, Stephen; Dhaneshwar, Abha; Mayman, Naomi; Yang, Aaron; Kulkarni, Meghana; Badalucco, Lauren; Fitzpatrick, Erica; Kao, Hsiang-Fong; Kuraguchi, Mari; Bittinger, Mark; Kirschmeier, Paul T; Gray, Nathanael S; Barbie, David A; Jänne, Pasi ACancer immunology research.2018 12;30242021
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices.Enache, Oana M; Lahr, David L; Natoli, Ted E; Litichevskiy, Lev; Wadden, David; Flynn, Corey; Gould, Joshua; Asiedu, Jacob K; Narayan, Rajiv; Subramanian, AravindBioinformatics (Oxford, England).2018 Sep 10;30203022
Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.Javasky, Elisheva; Shamir, Inbal; Gandhi, Shashi; Egri, Shawn; Sandler, Oded; Rothbart, Scott B; Kaplan, Noam; Jaffe, Jacob D; Goren, Alon; Simon, ItamarGenome research.2018 10;30166406
Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains.Wang, Jinhua; Erazo, Tatiana; Ferguson, Fleur M; Buckley, Dennis L; Gomez, Nestor; Muñoz-Guardiola, Pau; Diéguez-Martínez, Nora; Deng, Xianming; Hao, Mingfeng; Massefski, Walter; Fedorov, Oleg; Offei-Addo, Nana Kwaku; Park, Paul M; Dai, Lingling; DiBona, Amy; Becht, Kelly; Kim, Nam Doo; McKeown, Michael R; Roberts, Justin M; Zhang, Jinwei; Sim, Taebo; Alessi, Dario R; Bradner, James E; Lizcano, Jose M; Blacklow, Stephen C; Qi, Jun; Xu, Xiang; Gray, Nathanael SACS chemical biology.2018 Sep 21;30102854
Genetic and transcriptional evolution alters cancer cell line drug response.Ben-David, Uri; Siranosian, Benjamin; Ha, Gavin; Tang, Helen; Oren, Yaara; Hinohara, Kunihiko; Strathdee, Craig A; Dempster, Joshua; Lyons, Nicholas J; Burns, Robert; Nag, Anwesha; Kugener, Guillaume; Cimini, Beth; Tsvetkov, Peter; Maruvka, Yosef E; O'Rourke, Ryan; Garrity, Anthony; Tubelli, Andrew A; Bandopadhayay, Pratiti; Tsherniak, Aviad; Vazquez, Francisca; Wong, Bang; Birger, Chet; Ghandi, Mahmoud; Thorner, Aaron R; Bittker, Joshua A; Meyerson, Matthew; Getz, Gad; Beroukhim, Rameen; Golub, Todd RNature.2018 08;30089904
Stem cell transplantation for amyotrophic lateral sclerosis.Baloh, Robert H; Glass, Jonathan D; Svendsen, Clive NCurrent opinion in neurology.2018 10;30080719
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array.Koch, Rick J; Barrette, Anne Marie; Stern, Alan D; Hu, Bin; Bouhaddou, Mehdi; Azeloglu, Evren U; Iyengar, Ravi; Birtwistle, Marc RScientific reports.;30054510
A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML.Gopal, Srila; Lu, Qing; Man, Joshua J; Baur, Wendy; Rao, Sitara P; Litichevskiy, Lev; Papanastasiou, Malvina; Creech, Amanda L; DeRuff, Katherine C; Mullahoo, James; Officer, Adam; Egri, Shawn B; Davison, Desiree; Jaffe, Jacob D; Jaffe, Iris ZBlood advances.2018 Jul 24;30021779
AKT isoform-specific expression and activation across cancer lineages.Wang, Jue; Zhao, Wei; Guo, Huifang; Fang, Yong; Stockman, Sarah Elizabeth; Bai, Shanshan; Ng, Patrick Kwok-Shing; Li, Yang; Yu, Qinghua; Lu, Yiling; Jeong, Kang Jin; Chen, Xiaohua; Gao, Meng; Liang, Jiyong; Li, Wentao; Tian, Xingsong; Jonasch, Eric; Mills, Gordon B; Ding, ZhiyongBMC cancer.2018 Jul 16;30012111
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.Lin, Jia-Ren; Izar, Benjamin; Wang, Shu; Yapp, Clarence; Mei, Shaolin; Shah, Parin M; Santagata, Sandro; Sorger, Peter KeLife.2018 Jul 11;29993362
A privileged role for neuronal Na+ channels in regulating ventricular [Ca2+] and arrhythmias.Jones, DeAnalisa C; Gong, Jingqi Q X; Sobie, Eric AThe Journal of general physiology.2018 Jul 02;29899058
Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.Sampattavanich, Somponnat; Steiert, Bernhard; Kramer, Bernhard A; Gyori, Benjamin M; Albeck, John G; Sorger, Peter KCell systems.2018 Jun 27;29886111
Microenvironment-Induced Non-sporadic Expression of the AXL and cKIT Receptors Are Related to Epithelial Plasticity and Drug Resistance.Jokela, Tiina A; Engelsen, Agnete S T; Rybicka, Agata; Pelissier Vatter, Fanny A; Garbe, James C; Miyano, Masaru; Tiron, Crina; Ferariu, Dan; Akslen, Lars A; Stampfer, Martha R; Lorens, James B; LaBarge, Mark AFrontiers in cell and developmental biology.2018;29719832
In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images.Christiansen, Eric M; Yang, Samuel J; Ando, D Michael; Javaherian, Ashkan; Skibinski, Gaia; Lipnick, Scott; Mount, Elliot; O'Neil, Alison; Shah, Kevan; Lee, Alicia K; Goyal, Piyush; Fedus, William; Poplin, Ryan; Esteva, Andre; Berndl, Marc; Rubin, Lee L; Nelson, Philip; Finkbeiner, StevenCell.;29656897
A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.Litichevskiy, Lev; Peckner, Ryan; Abelin, Jennifer G; Asiedu, Jacob K; Creech, Amanda L; Davis, John F; Davison, Desiree; Dunning, Caitlin M; Egertson, Jarrett D; Egri, Shawn; Gould, Joshua; Ko, Tak; Johnson, Sarah A; Lahr, David L; Lam, Daniel; Liu, Zihan; Lyons, Nicholas J; Lu, Xiaodong; MacLean, Brendan X; Mungenast, Alison E; Officer, Adam; Natoli, Ted E; Papanastasiou, Malvina; Patel, Jinal; Sharma, Vagisha; Toder, Courtney; Tubelli, Andrew A; Young, Jennie Z; Carr, Steven A; Golub, Todd R; Subramanian, Aravind; MacCoss, Michael J; Tsai, Li-Huei; Jaffe, Jacob DCell systems.2018 Apr 25;29655704
Stress Granule Assembly Disrupts Nucleocytoplasmic Transport.Zhang, Ke; Daigle, J Gavin; Cunningham, Kathleen M; Coyne, Alyssa N; Ruan, Kai; Grima, Jonathan C; Bowen, Kelly E; Wadhwa, Harsh; Yang, Peiguo; Rigo, Frank; Taylor, J Paul; Gitler, Aaron D; Rothstein, Jeffrey D; Lloyd, Thomas ECell.2018 05 03;29628143
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.Malta, Tathiane M; Sokolov, Artem; Gentles, Andrew J; Burzykowski, Tomasz; Poisson, Laila; Weinstein, John N; Kami?ska, Bo?ena; Huelsken, Joerg; Omberg, Larsson; Gevaert, Olivier; Colaprico, Antonio; Czerwi?ska, Patrycja; Mazurek, Sylwia; Mishra, Lopa; HeCell.2018 04 05;29625051
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics.Peckner, Ryan; Myers, Samuel A; Jacome, Alvaro Sebastian Vaca; Egertson, Jarrett D; Abelin, Jennifer G; MacCoss, Michael J; Carr, Steven A; Jaffe, Jacob DNature methods.2018 May;29608554
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens.Bouhaddou, Mehdi; Barrette, Anne Marie; Stern, Alan D; Koch, Rick J; DiStefano, Matthew S; Riesel, Eric A; Santos, Luis C; Tan, Annie L; Mertz, Alex E; Birtwistle, Marc RPLoS computational biology.2018 03;29579036
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.Nicolas, Aude (see original citation for additional authors)Neuron.2018 Mar 21;29566793
A High Content Screen in Macrophages Identifies Small Molecule Modulators of STING-IRF3 and NFkB Signaling.Koch, Peter D; Miller, Howard R; Yu, Gary; Tallarico, John A; Sorger, Peter K; Wang, Yuan; Feng, Yan; Thomas, Jason R; Ross, Nathan T; Mitchison, TimothyACS chemical biology.2018 Apr 20;29553248
Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes.Watson, Spencer S; Dane, Mark; Chin, Koei; Tatarova, Zuzana; Liu, Moqing; Liby, Tiera; Thompson, Wallace; Smith, Rebecca; Nederlof, Michel; Bucher, Elmar; Kilburn, David; Whitman, Matthew; Sudar, Damir; Mills, Gordon B; Heiser, Laura M; Jonas, Oliver; Gray, Joe W; Korkola, James ECell systems.2018 Mar 28;29550255
Assessing microscope image focus quality with deep learning.Yang, Samuel J; Berndl, Marc; Michael Ando, D; Barch, Mariya; Narayanaswamy, Arunachalam; Christiansen, Eric; Hoyer, Stephan; Roat, Chris; Hung, Jane; Rueden, Curtis T; Shankar, Asim; Finkbeiner, Steven; Nelson, PhilipBMC bioinformatics.2018 03 15;29540156
Systematic Functional Annotation of Somatic Mutations in Cancer.Ng, Patrick Kwok-Shing; Li, Jun; Jeong, Kang Jin; Shao, Shan; Chen, Hu; Tsang, Yiu Huen; Sengupta, Sohini; Wang, Zixing; Bhavana, Venkata Hemanjani; Tran, Richard; Soewito, Stephanie; Minussi, Darlan Conterno; Moreno, Daniela; Kong, Kathleen; Dogruluk, Turgut; Lu, Hengyu; Gao, Jianjiong; Tokheim, Collin; Zhou, Daniel Cui; Johnson, Amber M; Zeng, Jia; Ip, Carman Ka Man; Ju, Zhenlin; Wester, Matthew; Yu, Shuangxing; Li, Yongsheng; Vellano, Christopher P; Schultz, Nikolaus; Karchin, Rachel; Ding, Li; Lu, Yiling; Cheung, Lydia Wai Ting; Chen, Ken; Shaw, Kenna R; Meric-Bernstam, Funda; Scott, Kenneth L; Yi, Song; Sahni, Nidhi; Liang, Han; Mills, Gordon BCancer cell.2018 Mar 12;29533785
Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition.Jones, Douglas S; Jenney, Anne P; Joughin, Brian A; Sorger, Peter K; Lauffenburger, Douglas AScience signaling.2018 Mar 06;29511118
Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma.Coy, Shannon; Rashid, Rumana; Lin, Jia-Ren; Du, Ziming; Donson, Andrew M; Hankinson, Todd C; Foreman, Nicholas K; Manley, Peter E; Kieran, Mark W; Reardon, David A; Sorger, Peter K; Santagata, SandroNeuro-oncology.2018 Mar 02;29509940
Panorama Public: A public repository for quantitative data sets processed in Skyline.Sharma, Vagisha; Eckels, Josh; Schilling, Birgit; Ludwig, Christina; Jaffe, Jacob D; MacCoss, Michael J; MacLean, BrendanMolecular & cellular proteomics : MCP.2018 Feb 27;29487113
MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments.Berberich, Matthew J; Paulo, Joao A; Everley, Robert AJournal of proteome research.2018 Apr 06;29461835
Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis.Tan, Hua; Zhou, XiaoboMethods in molecular biology (Clifton, N.J.).2018;29344882
A systems biology approach to studying the molecular mechanisms of osteoblastic differentiation under cytokine combination treatment.Tan, Hua; Chen, Ruoying; Li, Wenyang; Zhao, Weiling; Zhang, Yuanyuan; Yang, Yunzhi; Su, Jing; Zhou, XiaoboNPJ Regenerative medicine.2017;29302342
Laser-fabricated cell patterning stencil for single cell analysis.Messner, Jacob J; Glenn, Honor L; Meldrum, Deirdre RBMC biotechnology.2017 Dec 19;29258486
Activity of the PI3K-?,? inhibitor duvelisib in a phase 1 trial and preclinical models of T-cell lymphoma.Horwitz, Steven M; Koch, Raphael; Porcu, Pierluigi; Oki, Yasuhiro; Moskowitz, Alison; Perez, Megan; Myskowski, Patricia; Officer, Adam; Jaffe, Jacob D; Morrow, Sara N; Allen, Kerstin; Douglas, Mark; Stern, Howard; Sweeney, Jennifer; Kelly, Patrick; Kelly, Virginia; Aster, Jon C; Weaver, David; Foss, Francine M; Weinstock, David MBlood.2018 Feb 22;29233821
Prophetic Granger Causality to infer gene regulatory networks.Carlin, Daniel E; Paull, Evan O; Graim, Kiley; Wong, Christopher K; Bivol, Adrian; Ryabinin, Peter; Ellrott, Kyle; Sokolov, Artem; Stuart, Joshua MPloS one.2017;29211761
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.Keenan, Alexandra B; Jenkins, Sherry L; Jagodnik, Kathleen M; Koplev, Simon; He, Edward; Torre, Denis; Wang, Zichen; Dohlman, Anders B; Silverstein, Moshe C; Lachmann, Alexander; Kuleshov, Maxim V; Ma'ayan, Avi; Stathias, Vasileios; Terryn, Raymond; Cooper, Daniel; Forlin, Michele; Koleti, Amar; Vidovic, Dusica; Chung, Caty; Schürer, Stephan C; Vasiliauskas, Jouzas; Pilarczyk, Marcin; Shamsaei, Behrouz; Fazel, Mehdi; Ren, Yan; Niu, Wen; Clark, Nicholas A; White, Shana; Mahi, Naim; Zhang, Lixia; Kouril, Michal; Reichard, John F; Sivaganesan, Siva; Medvedovic, Mario; Meller, Jaroslaw; Koch, Rick J; Birtwistle, Marc R; Iyengar, Ravi; Sobie, Eric A; Azeloglu, Evren U; Kaye, Julia; Osterloh, Jeannette; Haston, Kelly; Kalra, Jaslin; Finkbiener, Steve; Li, Jonathan; Milani, Pamela; Adam, Miriam; Escalante-Chong, Renan; Sachs, Karen; Lenail, Alex; Ramamoorthy, Divya; Fraenkel, Ernest; Daigle, Gavin; Hussain, Uzma; Coye, Alyssa; Rothstein, Jeffrey; Sareen, Dhruv; Ornelas, Loren; Banuelos, Maria; Mandefro, Berhan; Ho, Ritchie; Svendsen, Clive N; Lim, Ryan G; Stocksdale, Jennifer; Casale, Malcolm S; Thompson, Terri G; Wu, Jie; Thompson, Leslie M; Dardov, Victoria; Venkatraman, Vidya; Matlock, Andrea; Van Eyk, Jennifer E; Jaffe, Jacob D; Papanastasiou, Malvina; Subramanian, Aravind; Golub, Todd R; Erickson, Sean D; Fallahi-Sichani, Mohammad; Hafner, Marc; Gray, Nathanael S; Lin, Jia-Ren; Mills, Caitlin E; Muhlich, Jeremy L; Niepel, Mario; Shamu, Caroline E; Williams, Elizabeth H; Wrobel, David; Sorger, Peter K; Heiser, Laura M; Gray, Joe W; Korkola, James E; Mills, Gordon B; LaBarge, Mark; Feiler, Heidi S; Dane, Mark A; Bucher, Elmar; Nederlof, Michel; Sudar, Damir; Gross, Sean; Kilburn, David F; Smith, Rebecca; Devlin, Kaylyn; Margolis, Ron; Derr, Leslie; Lee, Albert; Pillai, AjayCell systems.2017 Nov 24;29199020
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.Subramanian, Aravind; Narayan, Rajiv; Corsello, Steven M; Peck, David D; Natoli, Ted E; Lu, Xiaodong; Gould, Joshua; Davis, John F; Tubelli, Andrew A; Asiedu, Jacob K; Lahr, David L; Hirschman, Jodi E; Liu, Zihan; Donahue, Melanie; Julian, Bina; Khan, Mariya; Wadden, David; Smith, Ian C; Lam, Daniel; Liberzon, Arthur; Toder, Courtney; Bagul, Mukta; Orzechowski, Marek; Enache, Oana M; Piccioni, Federica; Johnson, Sarah A; Lyons, Nicholas J; Berger, Alice H; Shamji, Alykhan F; Brooks, Angela N; Vrcic, Anita; Flynn, Corey; Rosains, Jacqueline; Takeda, David Y; Hu, Roger; Davison, Desiree; Lamb, Justin; Ardlie, Kristin; Hogstrom, Larson; Greenside, Peyton; Gray, Nathanael S; Clemons, Paul A; Silver, Serena; Wu, Xiaoyun; Zhao, Wen-Ning; Read-Button, Willis; Wu, Xiaohua; Haggarty, Stephen J; Ronco, Lucienne V; Boehm, Jesse S; Schreiber, Stuart L; Doench, John G; Bittker, Joshua A; Root, David E; Wong, Bang; Golub, Todd RCell.2017 Nov 30;29195078
Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.Smith, Ian; Greenside, Peyton G; Natoli, Ted; Lahr, David L; Wadden, David; Tirosh, Itay; Narayan, Rajiv; Root, David E; Golub, Todd R; Subramanian, Aravind; Doench, John GPLoS biology.2017 Nov;29190685
A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries.Xiong, Yuguang; Soumillon, Magali; Wu, Jie; Hansen, Jens; Hu, Bin; van Hasselt, Johan G C; Jayaraman, Gomathi; Lim, Ryan; Bouhaddou, Mehdi; Ornelas, Loren; Bochicchio, Jim; Lenaeus, Lindsay; Stocksdale, Jennifer; Shim, Jaehee; Gomez, Emilda; Sareen, DhruvScientific reports.2017 Nov 07;29116112
Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics.Hafner, Marc; Heiser, Laura M; Williams, Elizabeth H; Niepel, Mario; Wang, Nicholas J; Korkola, James E; Gray, Joe W; Sorger, Peter KScientific data.2017 11 07;29112189
TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua MCancer research.2017 Nov 01;29092953
Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas.Li, Jun; Akbani, Rehan; Zhao, Wei; Lu, Yiling; Weinstein, John N; Mills, Gordon B; Liang, HanCancer research.2017 Nov 01;29092939
Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.Niepel, Mario; Hafner, Marc; Duan, Qiaonan; Wang, Zichen; Paull, Evan O; Chung, Mirra; Lu, Xiaodong; Stuart, Joshua M; Golub, Todd R; Subramanian, Aravind; Ma'ayan, Avi; Sorger, Peter KNature communications.2017 Oct 30;29084964
ZEB1-repressed microRNAs inhibit autocrine signaling that promotes vascular mimicry of breast cancer cells.Langer, E M; Kendsersky, N D; Daniel, C J; Kuziel, G M; Pelz, C; Murphy, K M; Capecchi, M R; Sears, R COncogene.2018 Feb 22;29084210
GRcalculator: an online tool for calculating and mining dose-response data.Clark, Nicholas A; Hafner, Marc; Kouril, Michal; Williams, Elizabeth H; Muhlich, Jeremy L; Pilarczyk, Marcin; Niepel, Mario; Sorger, Peter K; Medvedovic, MarioBMC cancer.2017 Oct 24;29065900
Combinatorial Microenvironments Impose a Continuum of Cellular Responses to a Single Pathway-Targeted Anti-cancer Compound.Lin, Chun-Han; Jokela, Tiina; Gray, Joe; LaBarge, Mark ACell reports.2017 Oct 10;29020637
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.Gönen, Mehmet; Weir, Barbara A; Cowley, Glenn S; Vazquez, Francisca; Guan, Yuanfang; Jaiswal, Alok; Karasuyama, Masayuki; Uzunangelov, Vladislav; Wang, Tao; Tsherniak, Aviad; Howell, Sara; Marbach, Daniel; Hoff, Bruce; Norman, Thea C; Airola, Antti; Bivol, Adrian; Bunte, Kerstin; Carlin, Daniel; Chopra, Sahil; Deran, Alden; Ellrott, Kyle; Gopalacharyulu, Peddinti; Graim, Kiley; Kaski, Samuel; Khan, Suleiman A; Newton, Yulia; Ng, Sam; Pahikkala, Tapio; Paull, Evan; Sokolov, Artem; Tang, Hao; Tang, Jing; Wennerberg, Krister; Xie, Yang; Zhan, Xiaowei; Zhu, Fan; Broad-DREAM Community; Aittokallio, Tero; Mamitsuka, Hiroshi; Stuart, Joshua M; Boehm, Jesse S; Root, David E; Xiao, Guanghua; Stolovitzky, Gustavo; Hahn, William C; Margolin, Adam ACell systems.2017 Nov 22;28988802
Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics.Shim, Jaehee V; Chun, Bryan; van Hasselt, Johan G C; Birtwistle, Marc R; Saucerman, Jeffrey J; Sobie, Eric AFrontiers in physiology.;28951721
Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials.Barrette, Anne Marie; Bouhaddou, Mehdi; Birtwistle, Marc RACS chemical neuroscience.2018 01 17;28950062
Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane.Werbin, Jeffrey L; Avendaño, Maier S; Becker, Verena; Jungmann, Ralf; Yin, Peng; Danuser, Gaudenz; Sorger, Peter KScientific reports.2017 Sep 22;28939861
OCIAD2 suppressed tumor growth and invasion via AKT pathway in Hepatocelluar carcinoma.Wu, Dan; Yang, Xufang; Peng, Huiming; Guo, Dongmin; Zhao, Weiling; Zhao, Chen; Zhou, XiaoboCarcinogenesis.2017 09 01;28911005
Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities.Lapek Jr, John D; Greninger, Patricia; Morris, Robert; Amzallag, Arnaud; Pruteanu-Malinici, Iulian; Benes, Cyril H; Haas, WilhelmNature biotechnology.2017 Oct;28892078
Ambiguous interactions between diastolic and SR Ca(2+) in the regulation of cardiac Ca(2+) release.Sobie, Eric A; Williams, George S B; Lederer, W JThe Journal of general physiology.2017 Sep 04;28798276
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.Ting, Ying S; Egertson, Jarrett D; Bollinger, James G; Searle, Brian C; Payne, Samuel H; Noble, William Stafford; MacCoss, Michael JNature methods.2017 Sep;28783153
PCSF: An R-package for network-based interpretation of high-throughput data.Akhmedov, Murodzhon; Kedaigle, Amanda; Chong, Renan Escalante; Montemanni, Roberto; Bertoni, Francesco; Fraenkel, Ernest; Kwee, IvoPLoS computational biology.2017 Jul;28759592
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.Pino, Lindsay K; Searle, Brian C; Bollinger, James G; Nunn, Brook; MacLean, Brendan; MacCoss, Michael JMass spectrometry reviews2020 0528691345
Phosphorylated neurofilament heavy chain: A biomarker of survival for C9ORF72-associated amyotrophic lateral sclerosis.Gendron, Tania F; C9ORF72 Neurofilament Study Group; Daughrity, Lillian M; Heckman, Michael G; Diehl, Nancy N; Wuu, Joanne; Miller, Timothy M; Pastor, Pau; Trojanowski, John Q; Grossman, Murray; Berry, James D; Hu, William T; Ratti, Antonia; Benatar, MichAnnals of neurology.2017 Jul;28628244
Designing Drug-Response Experiments and Quantifying their Results.Hafner, Marc; Niepel, Mario; Subramanian, Kartik; Sorger, Peter KCurrent protocols in chemical biology.2017 Jun 19;28628201
Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells.Niepel, Mario; Hafner, Marc; Chung, Mirra; Sorger, Peter KCurrent protocols in chemical biology.2017 Jun 19;28628199
Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics.Hafner, Marc; Niepel, Mario; Sorger, Peter KNature biotechnology.2017 Jun 07;28591115
AACR Project GENIE: Powering Precision Medicine through an International Consortium.AACR Project GENIE ConsortiumCancer discovery.2017 Aug;28572459
Rational combination therapy with PARP and MEK inhibitors capitalizes on therapeutic liabilities in RAS mutant cancers.Sun, Chaoyang; Fang, Yong; Yin, Jun; Chen, Jian; Ju, Zhenlin; Zhang, Dong; Chen, Xiaohua; Vellano, Christopher P; Jeong, Kang Jin; Ng, Patrick Kwok-Shing; Eterovic, Agda Karina B; Bhola, Neil H; Lu, Yiling; Westin, Shannon N; Grandis, Jennifer R; Lin, Shiaw-Yih; Scott, Kenneth L; Peng, Guang; Brugge, Joan; Mills, Gordon BScience translational medicine.2017 05 31;28566428
Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study.Städler, Nicolas; Dondelinger, Frank; Hill, Steven M; Akbani, Rehan; Lu, Yiling; Mills, Gordon B; Mukherjee, SachBioinformatics (Oxford, England).2017 May 23;28535188
Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits.Lim, Ryan G; Quan, Chris; Reyes-Ortiz, Andrea M; Lutz, Sarah E; Kedaigle, Amanda J; Gipson, Theresa A; Wu, Jie; Vatine, Gad D; Stocksdale, Jennifer; Casale, Malcolm S; Svendsen, Clive N; Fraenkel, Ernest; Housman, David E; Agalliu, Dritan; Thompson, Leslie MCell reports.2017 May 16;28514657
Oncogenic RAS Regulates Long Noncoding RNA Orilnc1 in Human Cancer.Zhang, Dongmei; Zhang, Gao; Hu, Xiaowen; Wu, Lawrence; Feng, Yi; He, Sidan; Zhang, Youyou; Hu, Zhongyi; Yang, Lu; Tian, Tian; Xu, Weiting; Wei, Zhi; Lu, Yiling; Flaherty, Keith T; Zhong, Xiaomin; Mills, Gordon B; Gimotty, Phyllis A; Xu, Xiaowei; Herlyn, Meenhard; Zhang, LinCancer research.2017 Jul 15;28473531
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method.Liu, Keqin; Beck, Dominik; Thoms, Julie A I; Liu, Liang; Zhao, Weiling; Pimanda, John E; Zhou, XiaoboBioinformatics (Oxford, England).2017 Sep 01;28472271
The Drug Repurposing Hub: a next-generation drug library and information resource.Corsello, Steven M; Bittker, Joshua A; Liu, Zihan; Gould, Joshua; McCarren, Patrick; Hirschman, Jodi E; Johnston, Stephen E; Vrcic, Anita; Wong, Bang; Khan, Mariya; Asiedu, Jacob; Narayan, Rajiv; Mader, Christopher C; Subramanian, Aravind; Golub, Todd RNature medicine.2017 Apr 07;28388612
Mutant Huntingtin Disrupts the Nuclear Pore Complex.Grima, Jonathan C; Daigle, J Gavin; Arbez, Nicolas; Cunningham, Kathleen C; Zhang, Ke; Ochaba, Joseph; Geater, Charlene; Morozko, Eva; Stocksdale, Jennifer; Glatzer, Jenna C; Pham, Jacqueline T; Ahmed, Ishrat; Peng, Qi; Wadhwa, Harsh; Pletnikova, Olga; Troncoso, Juan C; Duan, Wenzhen; Snyder, Solomon H; Ranum, Laura P W; Thompson, Leslie M; Lloyd, Thomas E; Ross, Christopher A; Rothstein, Jeffrey DNeuron.2017 Apr 05;28384479
Revealing cancer subtypes with higher-order correlations applied to imaging and omics data.Graim, Kiley; Liu, Tiffany Ting; Achrol, Achal S; Paull, Evan O; Newton, Yulia; Chang, Steven D; Harsh 4th, Griffith R; Cordero, Sergio P; Rubin, Daniel L; Stuart, Joshua MBMC medical genomics.2017 Mar 31;28359308
Poly(GP) proteins are a useful pharmacodynamic marker for C9ORF72-associated amyotrophic lateral sclerosis.Gendron, Tania F; Chew, Jeannie; Stankowski, Jeannette N; Hayes, Lindsey R; Zhang, Yong-Jie; Prudencio, Mercedes; Carlomagno, Yari; Daughrity, Lillian M; Jansen-West, Karen; Perkerson, Emilie A; O'Raw, Aliesha; Cook, Casey; Pregent, Luc; Belzil, Veronique; van Blitterswijk, Marka; Tabassian, Lilia J; Lee, Chris W; Yue, Mei; Tong, Jimei; Song, Yuping; Castanedes-Casey, Monica; Rousseau, Linda; Phillips, Virginia; Dickson, Dennis W; Rademakers, Rosa; Fryer, John D; Rush, Beth K; Pedraza, Otto; Caputo, Ana M; Desaro, Pamela; Palmucci, Carla; Robertson, Amelia; Heckman, Michael G; Diehl, Nancy N; Wiggs, Edythe; Tierney, Michael; Braun, Laura; Farren, Jennifer; Lacomis, David; Ladha, Shafeeq; Fournier, Christina N; McCluskey, Leo F; Elman, Lauren B; Toledo, Jon B; McBride, Jennifer D; Tiloca, Cinzia; Morelli, Claudia; Poletti, Barbara; Solca, Federica; Prelle, Alessandro; Wuu, Joanne; Jockel-Balsarotti, Jennifer; Rigo, Frank; Ambrose, Christine; Datta, Abhishek; Yang, Weixing; Raitcheva, Denitza; Antognetti, Giovanna; McCampbell, Alexander; Van Swieten, John C; Miller, Bruce L; Boxer, Adam L; Brown, Robert H; Bowser, Robert; Miller, Timothy M; Trojanowski, John Q; Grossman, Murray; Berry, James D; Hu, William T; Ratti, Antonia; Traynor, Bryan J; Disney, Matthew D; Benatar, Michael; Silani, Vincenzo; Glass, Jonathan D; Floeter, Mary Kay; Rothstein, Jeffrey D; Boylan, Kevin B; Petrucelli, LeonardScience translational medicine.2017 Mar 29;28356511
A platform for high-throughput bioenergy production phenotype characterization in single cells.Kelbauskas, Laimonas; Glenn, Honor; Anderson, Clifford; Messner, Jacob; Lee, Kristen B; Song, Ganquan; Houkal, Jeff; Su, Fengyu; Zhang, Liqiang; Tian, Yanqing; Wang, Hong; Bussey, Kimberly; Johnson, Roger H; Meldrum, Deirdre RScientific reports.2017 03 28;28349963
Functional variomics and network perturbation: connecting genotype to phenotype in cancer.Yi, Song; Lin, Shengda; Li, Yongsheng; Zhao, Wei; Mills, Gordon B; Sahni, NidhiNature reviews. Genetics.2017 Mar 27;28344341
Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice.HD iPSC ConsortiumNature neuroscience.2017 May;28319609
Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.Farshidfar, Farshad; Zheng, Siyuan; Gingras, Marie-Claude; Newton, Yulia; Shih, Juliann; Robertson, A Gordon; Hinoue, Toshinori; Hoadley, Katherine A; Gibb, Ewan A; Roszik, Jason; Covington, Kyle R; Wu, Chia-Chin; Shinbrot, Eve; Stransky, Nicolas; Hegde, Apurva; Yang, Ju Dong; Reznik, Ed; Sadeghi, Sara; Pedamallu, Chandra Sekhar; Ojesina, Akinyemi I; Hess, Julian M; Auman, J Todd; Rhie, Suhn K; Bowlby, Reanne; Borad, Mitesh J; Cancer Genome Atlas Network; Zhu, Andrew X; Stuart, Josh M; Sander, Chris; Akbani, Rehan; Cherniack, Andrew D; Deshpande, Vikram; Mounajjed, Taofic; Foo, Wai Chin; Torbenson, Michael S; Kleiner, David E; Laird, Peter W; Wheeler, David A; McRee, Autumn J; Bathe, Oliver F; Andersen, Jesper B; Bardeesy, Nabeel; Roberts, Lewis R; Kwong, Lawrence NCell reports.2017 03 14;28297679
Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays.Li, Jun; Zhao, Wei; Akbani, Rehan; Liu, Wenbin; Ju, Zhenlin; Ling, Shiyun; Vellano, Christopher P; Roebuck, Paul; Yu, Qinghua; Eterovic, A Karina; Byers, Lauren A; Davies, Michael A; Deng, Wanleng; Gopal, Y N Vashisht; Chen, Guo; von Euw, Erika M; Slamon, Dennis; Conklin, Dylan; Heymach, John V; Gazdar, Adi F; Minna, John D; Myers, Jeffrey N; Lu, Yiling; Mills, Gordon B; Liang, HanCancer cell.2017 Feb 13;28196595
Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy.Woo, Caroline J; Maier, Verena K; Davey, Roshni; Brennan, James; Li, Guangde; Brothers 2nd, John; Schwartz, Brian; Gordo, Susana; Kasper, Anne; Okamoto, Trevor R; Johansson, Hans E; Mandefro, Berhan; Sareen, Dhruv; Bialek, Peter; Chau, B Nelson; Bhat, Balkrishen; Bullough, David; Barsoum, JamesProceedings of the National Academy of Sciences of the United States of America.2017 Feb 21;28193854
Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells.Stillitano, Francesca; Hansen, Jens; Kong, Chi-Wing; Karakikes, Ioannis; Funck-Brentano, Christian; Geng, Lin; Scott, Stuart; Reynier, Stephan; Wu, Ma; Valogne, Yannick; Desseaux, Carole; Salem, Joe-Elie; Jeziorowska, Dorota; Zahr, Noël; Li, Ronald; Iyengar, Ravi; Hajjar, Roger J; Hulot, Jean-SébastieneLife.2017 01 30;28134617
Differentiation of Human Induced Pluripotent Stem Cells to Mammary-like Organoids.Qu, Ying; Han, Bingchen; Gao, Bowen; Bose, Shikha; Gong, Yiping; Wawrowsky, Kolja; Giuliano, Armando E; Sareen, Dhruv; Cui, XiaojiangStem cell reports.2017 Feb 14;28132888
Genome-Scale Networks Link Neurodegenerative Disease Genes to ?-Synuclein through Specific Molecular Pathways.Khurana, Vikram; Peng, Jian; Chung, Chee Yeun; Auluck, Pavan K; Fanning, Saranna; Tardiff, Daniel F; Bartels, Theresa; Koeva, Martina; Eichhorn, Stephen W; Benyamini, Hadar; Lou, Yali; Nutter-Upham, Andy; Baru, Valeriya; Freyzon, Yelena; Tuncbag, Nurcan; Cell systems.2017 02 22;28131822
Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state.Fallahi-Sichani, Mohammad; Becker, Verena; Izar, Benjamin; Baker, Gregory J; Lin, Jia-Ren; Boswell, Sarah A; Shah, Parin; Rotem, Asaf; Garraway, Levi A; Sorger, Peter KMolecular systems biology.2017 Jan 09;28069687
A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization.Erickson, Brian K; Rose, Christopher M; Braun, Craig R; Erickson, Alison R; Knott, Jeffrey; McAlister, Graeme C; Wühr, Martin; Paulo, Joao A; Everley, Robert A; Gygi, Steven PMolecular cell.2017 Jan 19;28065596
Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors.Tan, Li; Gurbani, Deepak; Weisberg, Ellen L; Jones, Douglas S; Rao, Suman; Singer, William D; Bernard, Faviola M; Mowafy, Samar; Jenney, Annie; Du, Guangyan; Nonami, Atsushi; Griffin, James D; Lauffenburger, Douglas A; Westover, Kenneth D; Sorger, Peter K; Gray, Nathanael SBioorganic & medicinal chemistry.2017 Feb 15;28038940
Structure-guided development of covalent TAK1 inhibitors.Tan, Li; Gurbani, Deepak; Weisberg, Ellen L; Hunter, John C; Li, Lianbo; Jones, Douglas S; Ficarro, Scott B; Mowafy, Samar; Tam, Chun-Pong; Rao, Suman; Du, Guangyan; Griffin, James D; Sorger, Peter K; Marto, Jarrod A; Westover, Kenneth D; Gray, Nathanael SBioorganic & medicinal chemistry.2017 Feb 01;28011204
Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment.Liu, Tiffany T; Achrol, Achal S; Mitchell, Lex A; Rodriguez, Scott A; Feroze, Abdullah; Iv, Michael; Kim, Christine; Chaudhary, Navjot; Gevaert, Olivier; Stuart, Josh M; Harsh, Griffith R; Chang, Steven D; Rubin, Daniel LNeuro-oncology.2017 Jul 01;28007759
Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags.Everley, Robert A; Huttlin, Edward L; Erickson, Alison R; Beausoleil, Sean A; Gygi, Steven PJournal of proteome research.2017 Feb 03;27978624
Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging.Lin, Jia-Ren; Fallahi-Sichani, Mohammad; Chen, Jia-Yun; Sorger, Peter KCurrent protocols in chemical biology.2016 Dec 07;27925668
I love it when a plan comes together: Insight gained through convergence of competing mathematical models.Gong, Jingqi Q X; Shim, Jaehee V; Núñez-Acosta, Elisa; Sobie, Eric AJournal of molecular and cellular cardiology.2017 01;27913283
Drug response consistency in CCLE and CGP.Bouhaddou, Mehdi; DiStefano, Matthew S; Riesel, Eric A; Carrasco, Emilce; Holzapfel, Hadassa Y; Jones, DeAnalisa C; Smith, Gregory R; Stern, Alan D; Somani, Sulaiman S; Thompson, T Victoria; Birtwistle, Marc RNature2016 11 3027905419
A Roadmap to Successful Clinical Proteomics.Wright, Ian; Van Eyk, Jennifer EClinical chemistry.2017 01;27864386
Neomorphic mutations create therapeutic challenges in cancer.Takiar, V; Ip, C K M; Gao, M; Mills, G B; Cheung, L W TOncogene.2017 Mar 23;27841866
Suppression of the metastatic spread of breast cancer by DN10764 (AZD7762)-mediated inhibition of AXL signaling.Park, Joon-Suk; Lee, ChuHee; Kim, Hyun-Kyoung; Kim, Dayea; Son, Jung Beom; Ko, Eunhwa; Cho, Joong-Heui; Kim, Nam-Doo; Nan, Hong-Yan; Kim, Choong-Yong; Yoon, Sukkyoon; Lee, Sun-Hwa; Choi, Hwan GeunOncotarget.2016 Dec 13;27829217
Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation.Jones, Douglas S; Jenney, Anne P; Swantek, Jennifer L; Burke, John M; Lauffenburger, Douglas A; Sorger, Peter KNature chemical biology.2016 Oct 31;27820799
Functional kinomics establishes a critical node of volume-sensitive cation-Cl(-) cotransporter regulation in the mammalian brain.Zhang, Jinwei; Gao, Geng; Begum, Gulnaz; Wang, Jinhua; Khanna, Arjun R; Shmukler, Boris E; Daubner, Gerrit M; de Los Heros, Paola; Davies, Paul; Varghese, Joby; Bhuiyan, Mohammad Iqbal H; Duan, Jinjing; Zhang, Jin; Duran, Daniel; Alper, Seth L; Sun, Dandan; Elledge, Stephen J; Alessi, Dario R; Kahle, Kristopher TScientific reports.2016 Oct 26;27782176
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.Martinez, Fernando J; Pratt, Gabriel A; Van Nostrand, Eric L; Batra, Ranjan; Huelga, Stephanie C; Kapeli, Katannya; Freese, Peter; Chun, Seung J; Ling, Karen; Gelboin-Burkhart, Chelsea; Fijany, Layla; Wang, Harrison C; Nussbacher, Julia K; Broski, Sara M; Kim, Hong Joo; Lardelli, Rea; Sundararaman, Balaji; Donohue, John P; Javaherian, Ashkan; Lykke-Andersen, Jens; Finkbeiner, Steven; Bennett, C Frank; Ares Jr, Manuel; Burge, Christopher B; Taylor, J Paul; Rigo, Frank; Yeo, Gene WNeuron.2016 Nov 23;27773581
Cell size assays for mass cytometry.Stern, Alan D; Rahman, Adeeb H; Birtwistle, Marc RCytometry. Part A : the journal of the International Society for Analytical Cytology.2016 Oct 21;27768827
Ratiometric fluorescent pH-sensitive polymers for high-throughput monitoring of extracellular pH.Zhang, Liqiang; Su, Fengyu; Kong, Xiangxing; Lee, Fred; Day, Kevin; Gao, Weimin; Vecera, Mary E; Sohr, Jeremy M; Buizer, Sean; Tian, Yanqing; Meldrum, Deirdre RRSC advances.2016;27721974
Matrix factorization reveals aging-specific co-expression gene modules in the fat and muscle tissues in nonhuman primates.Wang, Yongcui; Zhao, Weiling; Zhou, XiaoboScientific reports.2016 Oct 05;27703186
Intraglomerular crosstalk elaborately regulates podocyte injury and repair in diabetic patients: insights from a 3D multiscale modeling study.Tan, Hua; Yi, Hualin; Zhao, Weiling; Ma, Jian-Xing; Zhang, Yuanyuan; Zhou, XiaoboOncotarget.2016 Nov 08;27683034
Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.Lu, Yiling; Ling, Shiyun; Hegde, Apurva M; Byers, Lauren A; Coombes, Kevin; Mills, Gordon B; Akbani, RehanSeminars in oncology.2016 Aug;27663479
Reverse Phase Protein Arrays for Compound Profiling.Moerke, Nathan; Fallahi-Sichani, MohammadCurrent protocols in chemical biology.2016 Sep 13;27622568
Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms.Jaffe, Jacob D; Feeney, Caitlin M; Patel, Jinal; Lu, Xiaodong; Mani, D RJournal of the American Society for Mass Spectrometry.2016 Aug 25;27562500
Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease.Vazquez-Arango, Pilar; Vowles, Jane; Browne, Cathy; Hartfield, Elizabeth; Fernandes, Hugo J R; Mandefro, Berhan; Sareen, Dhruv; James, William; Wade-Martins, Richard; Cowley, Sally A; Murphy, Shona; O'Reilly, DawnNucleic acids research.2016 12 15;27536002
Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.Drake, Justin M; Paull, Evan O; Graham, Nicholas A; Lee, John K; Smith, Bryan A; Titz, Bjoern; Stoyanova, Tanya; Faltermeier, Claire M; Uzunangelov, Vladislav; Carlin, Daniel E; Fleming, Daniel Teo; Wong, Christopher K; Newton, Yulia; Sudha, Sud; Vashisht, Ajay A; Huang, Jiaoti; Wohlschlegel, James A; Graeber, Thomas G; Witte, Owen N; Stuart, Joshua MCell.2016 Aug 11;27499020
Revealing disease-associated pathways by network integration of untargeted metabolomics.Pirhaji, Leila; Milani, Pamela; Leidl, Mathias; Curran, Timothy; Avila-Pacheco, Julian; Clish, Clary B; White, Forest M; Saghatelian, Alan; Fraenkel, ErnestNature methods.2016 Sep;27479327
ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks.Ho, Ritchie; Sances, Samuel; Gowing, Genevieve; Amoroso, Mackenzie Weygandt; O'Rourke, Jacqueline G; Sahabian, Anais; Wichterle, Hynek; Baloh, Robert H; Sareen, Dhruv; Svendsen, Clive NNature neuroscience.2016 Sep;27428653
Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features.Chen, Huaidong; Chen, Wei; Liu, Chenglin; Zhang, Le; Su, Jing; Zhou, XiaoboScientific reports.2016 Jul 18;27427091
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.Shi, Tujin; Niepel, Mario; McDermott, Jason E; Gao, Yuqian; Nicora, Carrie D; Chrisler, William B; Markillie, Lye M; Petyuk, Vladislav A; Smith, Richard D; Rodland, Karin D; Sorger, Peter K; Qian, Wei-Jun; Wiley, H StevenScience signaling.2016;27405981
Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer.Chong, Curtis R; Bahcall, Magda; Capelletti, Marzia; Kosaka, Takayuki; Ercan, Dalia; Sim, Taebo; Sholl, Lynette M; Nishino, Mizuki; Johnson, Bruce E; Gray, Nathanael S; Jänne, Pasi AClinical cancer research : an official journal of the American Association for Cancer Research.2017 Jan 01;27370605
Network Modeling Identifies Patient-specific Pathways in Glioblastoma.Tuncbag, Nurcan; Milani, Pamela; Pokorny, Jenny L; Johnson, Hannah; Sio, Terence T; Dalin, Simona; Iyekegbe, Dennis O; White, Forest M; Sarkaria, Jann N; Fraenkel, ErnestScientific reports.2016 06 29;27354287
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.Smith, Gregory R; Birtwistle, Marc RPloS one.2016;27326762
Targeting MTHFD2 in acute myeloid leukemia.Pikman, Yana; Puissant, Alexandre; Alexe, Gabriela; Furman, Andrew; Chen, Liying M; Frumm, Stacey M; Ross, Linda; Fenouille, Nina; Bassil, Christopher F; Lewis, Caroline A; Ramos, Azucena; Gould, Joshua; Stone, Richard M; DeAngelo, Daniel J; Galinsky, Ilene; Clish, Clary B; Kung, Andrew L; Hemann, Michael T; Vander Heiden, Matthew G; Banerji, Versha; Stegmaier, KimberlyThe Journal of experimental medicine.2016 Jun 27;27325891
Functional characterization of somatic mutations in cancer using network-based inference of protein activity.Alvarez, Mariano J; Shen, Yao; Giorgi, Federico M; Lachmann, Alexander; Ding, B Belinda; Ye, B Hilda; Califano, AndreaNature genetics.2016 08;27322546
Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis.Lee, Sebum; Shang, Yulei; Redmond, Stephanie A; Urisman, Anatoly; Tang, Amy A; Li, Kathy H; Burlingame, Alma L; Pak, Ryan A; Jovi?i?, Ana; Gitler, Aaron D; Wang, Jinhua; Gray, Nathanael S; Seeley, William W; Siddique, Teepu; Bigio, Eileen H; Lee, Virginia M-Y; Trojanowski, John Q; Chan, Jonah R; Huang, Eric JNeuron.2016 07 06;27321923
1,8-Naphthalimide Derivative Dyes with Large Stokes Shifts for Targeting Live-Cell Mitochondria.Zhang, Liqiang; Su, Fengyu; Kong, Xiangxing; Lee, Fred; Sher, Steven; Day, Kevin; Tian, Yanqing; Meldrum, Deirdre RChembiochem : a European journal of chemical biology.2016 09 15;27319799
Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells.Milani, Pamela; Escalante-Chong, Renan; Shelley, Brandon C; Patel-Murray, Natasha L; Xin, Xiaofeng; Adam, Miriam; Mandefro, Berhan; Sareen, Dhruv; Svendsen, Clive N; Fraenkel, ErnestScientific reports.2016;27146274
Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs.Hafner, Marc; Niepel, Mario; Chung, Mirra; Sorger, Peter KNature methods.2016 Jun;27135972
TNF-? modulates genome-wide redistribution of ?Np63?/TAp73 and NF-?B cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer.Si, H; Lu, H; Yang, X; Mattox, A; Jang, M; Bian, Y; Sano, E; Viadiu, H; Yan, B; Yau, C; Ng, S; Lee, S K; Romano, R-A; Davis, S; Walker, R L; Xiao, W; Sun, H; Wei, L; Sinha, S; Benz, C C; Stuart, J M; Meltzer, P S; Van Waes, C; Chen, ZOncogene.2016 Nov 03;27132513
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.Tuncbag, Nurcan; Gosline, Sara J C; Kedaigle, Amanda; Soltis, Anthony R; Gitter, Anthony; Fraenkel, ErnestPLoS computational biology.2016 Apr;27096930
N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells.Lee, John K; Phillips, John W; Smith, Bryan A; Park, Jung Wook; Stoyanova, Tanya; McCaffrey, Erin F; Baertsch, Robert; Sokolov, Artem; Meyerowitz, Justin G; Mathis, Colleen; Cheng, Donghui; Stuart, Joshua M; Shokat, Kevan M; Gustafson, W Clay; Huang, Jiaoti; Witte, Owen NCancer cell.2016 Apr 11;27050099
C9ORF72 poly(GA) aggregates sequester and impair HR23 and nucleocytoplasmic transport proteins.Zhang, Yong-Jie; Gendron, Tania F; Grima, Jonathan C; Sasaguri, Hiroki; Jansen-West, Karen; Xu, Ya-Fei; Katzman, Rebecca B; Gass, Jennifer; Murray, Melissa E; Shinohara, Mitsuru; Lin, Wen-Lang; Garrett, Aliesha; Stankowski, Jeannette N; Daughrity, Lillian; Tong, Jimei; Perkerson, Emilie A; Yue, Mei; Chew, Jeannie; Castanedes-Casey, Monica; Kurti, Aishe; Wang, Zizhao S; Liesinger, Amanda M; Baker, Jeremy D; Jiang, Jie; Lagier-Tourenne, Clotilde; Edbauer, Dieter; Cleveland, Don W; Rademakers, Rosa; Boylan, Kevin B; Bu, Guojun; Link, Christopher D; Dickey, Chad A; Rothstein, Jeffrey D; Dickson, Dennis W; Fryer, John D; Petrucelli, LeonardNature neuroscience.;26998601
The oxindole Syk inhibitor OXSI-2 blocks nigericin-induced inflammasome signaling and pyroptosis independent of potassium efflux.Yaron, Jordan R; Rao, Mounica Y; Gangaraju, Sandhya; Zhang, Liqiang; Kong, Xiangxing; Su, Fengyu; Tian, Yanqing; Glenn, Honor L; Meldrum, Deirdre RBiochemical and biophysical research communications.2016 Apr 8;26970308
Pathway-Based Genomics Prediction using Generalized Elastic Net.Sokolov, Artem; Carlin, Daniel E; Paull, Evan O; Baertsch, Robert; Stuart, Joshua MPLoS computational biology.2016 Mar;26960204
Improved Prediction of Drug-Induced Torsades de Pointes Through Simulations of Dynamics and Machine Learning Algorithms.Lancaster, M Cummins; Sobie, E AClinical pharmacology and therapeutics.2016 10;26950176
''Pop-slide'' patterning: Rapid fabrication of microstructured PDMS gasket slides for biological applications.Ramji, Ramesh; Khan, Nafeesa T; Muñoz-Rojas, Andrés; Miller-Jensen, KathrynRSC advances.2015;26949529
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.Abelin, Jennifer G; Patel, Jinal; Lu, Xiaodong; Feeney, Caitlin M; Fagbami, Lola; Creech, Amanda L; Hu, Roger; Lam, Daniel; Davison, Desiree; Pino, Lindsay; Qiao, Jana W; Kuhn, Eric; Officer, Adam; Li, Jianxue; Abbatiello, Susan; Subramanian, Aravind; Sidman, Richard; Snyder, Evan; Carr, Steven A; Jaffe, Jacob DMolecular & cellular proteomics : MCP.2016 May;26912667
In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands.Govindarajah, Vinothini; Leung, Yuet-Kin; Ying, Jun; Gear, Robin; Bornschein, Robert L; Medvedovic, Mario; Ho, Shuk-MeiThe Journal of nutritional biochemistry.2016 Mar;73-8226895667
Prediction of treatment efficacy for prostate cancer using a mathematical model.Peng, Huiming; Zhao, Weiling; Tan, Hua; Ji, Zhiwei; Li, Jingsong; Li, King; Zhou, XiaoboScientific reports.2016 Feb 12;26868634
Methods for SWATH?: Data Independent Acquisition on TripleTOF Mass Spectrometers.Holewinski, Ronald J; Parker, Sarah J; Matlock, Andrea D; Venkatraman, Vidya; Van Eyk, Jennifer EMethods in molecular biology (Clifton, N.J.).2016;26867750
Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.Whiteaker, Jeffrey R; Halusa, Goran N; Hoofnagle, Andrew N; Sharma, Vagisha; MacLean, Brendan; Yan, Ping; Wrobel, John A; Kennedy, Jacob; Mani, D R; Zimmerman, Lisa J; Meyer, Matthew R; Mesri, Mehdi; Boja, Emily; Carr, Steven A; Chan, Daniel W; Chen, Xian; Chen, Jing; Davies, Sherri R; Ellis, Matthew J C; Fenyö, David; Hiltke, Tara; Ketchum, Karen A; Kinsinger, Chris; Kuhn, Eric; Liebler, Daniel C; Liu, Tao; Loss, Michael; MacCoss, Michael J; Qian, Wei-Jun; Rivers, Robert; Rodland, Karin D; Ruggles, Kelly V; Scott, Mitchell G; Smith, Richard D; Thomas, Stefani; Townsend, R Reid; Whiteley, Gordon; Wu, Chaochao; Zhang, Hui; Zhang, Zhen; Rodriguez, Henry; Paulovich, Amanda GMethods in molecular biology (Clifton, N.J.).2016;26867747
A three-groups model for high-throughput survival screens.Shaby, Benjamin A; Skibinski, Gaia; Ando, Michael; LaDow, Eva S; Finkbeiner, StevenBiometrics.2016 Jan 28;26821783
Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Have Reduced Expression of Proteins Important in Neuronal Development.Fuller, Heidi R; Mandefro, Berhan; Shirran, Sally L; Gross, Andrew R; Kaus, Anjoscha S; Botting, Catherine H; Morris, Glenn E; Sareen, DhruvFrontiers in cellular neuroscience.2015;26793058
ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.Sokolov, Artem; Paull, Evan O; Stuart, Joshua MPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2016;26776204
Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas.Liu, T T; Achrol, A S; Mitchell, L A; Du, W A; Loya, J J; Rodriguez, S A; Feroze, A; Westbroek, E M; Yeom, K W; Stuart, J M; Chang, S D; Harsh 4th, G R; Rubin, D LAJNR. American journal of neuroradiology.2016 Apr;26744442
Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation.Zhu, Xiaodong; Girardo, David; Govek, Eve-Ellen; John, Keisha; Mellén, Marian; Tamayo, Pablo; Mesirov, Jill P; Hatten, Mary ENeuron.2016 Jan 06;26711116
Computational systems biology in cancer brain metastasis.Peng, Huiming; Tan, Hua; Zhao, Weiling; Jin, Guangxu; Sharma, Sambad; Xing, Fei; Watabe, Kounosuke; Zhou, XiaoboFrontiers in bioscience (Scholar edition).2016;26709906
Pharmacogenomic agreement between two cancer cell line data sets.Cancer Cell Line Encyclopedia Consortium; Genomics of Drug Sensitivity in Cancer ConsortiumNature.2015 Dec 3;84-726570998
Large-Scale Drug Screens Support Precision Medicine.Gray, Joe W; Mills, Gordon BCancer discovery.2015 Nov;1130-226526695
Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases.Haston, Kelly M; Finkbeiner, StevenAnnual review of pharmacology and toxicology.2016;26514199
K(+) regulates Ca(2+) to drive inflammasome signaling: dynamic visualization of ion flux in live cells.Yaron, J R; Gangaraju, S; Rao, M Y; Kong, X; Zhang, L; Su, F; Tian, Y; Glenn, H L; Meldrum, D RCell death & disease.2015;e195426512962
Landscape of Targeted Anti-Cancer Drug Synergies in Melanoma Identifies a Novel BRAF-VEGFR/PDGFR Combination Treatment.Friedman, Adam A; Amzallag, Arnaud; Pruteanu-Malinici, Iulian; Baniya, Subash; Cooper, Zachary A; Piris, Adriano; Hargreaves, Leeza; Igras, Vivien; Frederick, Dennie T; Lawrence, Donald P; Haber, Daniel A; Flaherty, Keith T; Wargo, Jennifer A; Ramaswamy, Sridhar; Benes, Cyril H; Fisher, David EPloS one.2015;e014031026461489
Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method.Lin, Jia-Ren; Fallahi-Sichani, Mohammad; Sorger, Peter KNature communications.2015;26399630
Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models.Mitrofanova, Antonina; Aytes, Alvaro; Zou, Min; Shen, Michael M; Abate-Shen, Cory; Califano, AndreaCell reports.2015 Sep 29;2060-7126387954
In silico model-based inference: an emerging approach for inverse problems in engineering better medicines.Klinke 2nd, David J; Birtwistle, Marc RCurrent opinion in chemical engineering.2015 Nov 1;14-2426309811
The C9orf72 repeat expansion disrupts nucleocytoplasmic transport.Zhang, Ke; Donnelly, Christopher J; Haeusler, Aaron R; Grima, Jonathan C; Machamer, James B; Steinwald, Peter; Daley, Elizabeth L; Miller, Sean J; Cunningham, Kathleen M; Vidensky, Svetlana; Gupta, Saksham; Thomas, Michael A; Hong, Ingie; Chiu, Shu-Ling; Huganir, Richard L; Ostrow, Lyle W; Matunis, Michael J; Wang, Jiou; Sattler, Rita; Lloyd, Thomas E; Rothstein, Jeffrey DNature.2015 Sep 3;56-6126308891
A highly selective mitochondria-targeting fluorescent K(+) sensor.Kong, Xiangxing; Su, Fengyu; Zhang, Liqiang; Yaron, Jordan; Lee, Fred; Shi, Zhengwei; Tian, Yanqing; Meldrum, Deirdre RAngewandte Chemie (International ed. in English).2015 Oct 5;12053-726302172
Systemic modeling myeloma-osteoclast interactions under normoxic/hypoxic condition using a novel computational approach.Ji, Zhiwei; Wu, Dan; Zhao, Weiling; Peng, Huiming; Zhao, Shengjie; Huang, Deshuang; Zhou, XiaoboScientific reports.2015;26282073
A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro.Adler, Melanie; Ramm, Susanne; Hafner, Marc; Muhlich, Jeremy L; Gottwald, Esther Maria; Weber, Elijah; Jaklic, Alenka; Ajay, Amrendra Kumar; Svoboda, Daniel; Auerbach, Scott; Kelly, Edward J; Himmelfarb, Jonathan; Vaidya, Vishal SJournal of the American Society of Nephrology : JASN.2016 Apr;26260164
Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics.Goodspeed, Andrew; Heiser, Laura M; Gray, Joe W; Costello, James CMolecular cancer research : MCR.2016 Jan;26248648
Genome-wide mutational spectra analysis reveals significant cancer-specific heterogeneity.Tan, Hua; Bao, Jiguang; Zhou, XiaoboScientific reports.2015;26212640
Elucidating Compound Mechanism of Action by Network Perturbation Analysis.Woo, Jung Hoon; Shimoni, Yishai; Yang, Wan Seok; Subramaniam, Prem; Iyer, Archana; Nicoletti, Paola; Rodríguez Martínez, María; López, Gonzalo; Mattioli, Michela; Realubit, Ronald; Karan, Charles; Stockwell, Brent R; Bansal, Mukesh; Califano, AndreaCell.2015 Jul 16;441-5126186195
Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation.Xue, Qiong; Lu, Yao; Eisele, Markus R; Sulistijo, Endah S; Khan, Nafeesa; Fan, Rong; Miller-Jensen, KathrynScience signaling.2015 Jun 16;ra5926082435
Multiplexed peptide analysis using data-independent acquisition and Skyline.Egertson, Jarrett D; MacLean, Brendan; Johnson, Richard; Xuan, Yue; MacCoss, Michael JNature protocols.2015 Jun;887-90325996789
Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold.Roux, Jérémie; Hafner, Marc; Bandara, Samuel; Sims, Joshua J; Hudson, Hannah; Chai, Diana; Sorger, Peter KMolecular systems biology.2015 May;25953765
Network pharmacodynamic models for customized cancer therapy.Gallo, James M; Birtwistle, Marc RWiley interdisciplinary reviews. Systems biology and medicine.2015 Jul-Aug;243-5125914386
Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.Repunte-Canonigo, Vez; Shin, William; Vendruscolo, Leandro F; Lefebvre, Celine; van der Stap, Lena; Kawamura, Tomoya; Schlosburg, Joel E; Alvarez, Mariano; Koob, George F; Califano, Andrea; Sanna, Pietro PaoloGenome biology.2015;25886852
Cell-Based Screening: Extracting Meaning from Complex DataFinkbeiner S., Frumkin M., Kassner PDNeuron 2015 Apr 886(1):160-17425856492
Modeling the relationship of epigenetic modifications to transcription factor binding.Liu, Liang; Jin, Guangxu; Zhou, XiaoboNucleic acids research.2015 Apr 30;3873-8525820421
Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis.Fallahi-Sichani, Mohammad; Moerke, Nathan J; Niepel, Mario; Zhang, Tinghu; Gray, Nathanael S; Sorger, Peter KMolecular systems biology.2015 Mar;25814555
A functional landscape of resistance to ALK inhibition in lung cancer.Wilson, Frederick H; Johannessen, Cory M; Piccioni, Federica; Tamayo, Pablo; Kim, Jong Wook; Van Allen, Eliezer M; Corsello, Steven M; Capelletti, Marzia; Calles, Antonio; Butaney, Mohit; Sharifnia, Tanaz; Gabriel, Stacey B; Mesirov, Jill P; Hahn, William C; Engelman, Jeffrey A; Meyerson, Matthew; Root, David E; Jänne, Pasi A; Garraway, Levi ACancer cell.2015 Mar 9;397-40825759024
Multi-scale modeling for the transmission of influenza and the evaluation of interventions toward it.Guo, Dongmin; Li, King C; Peters, Timothy R; Snively, Beverly M; Poehling, Katherine A; Zhou, XiaoboScientific reports.2015;25757402
Assessment of ABT-263 activity across a cancer cell line collection leads to a potent combination therapy for small-cell lung cancer.Faber, Anthony C; Farago, Anna F; Costa, Carlotta; Dastur, Anahita; Gomez-Caraballo, Maria; Robbins, Rebecca; Wagner, Bethany L; Rideout 3rd, William M; Jakubik, Charles T; Ham, Jungoh; Edelman, Elena J; Ebi, Hiromichi; Yeo, Alan T; Hata, Aaron N; Song, Youngchul; Patel, Neha U; March, Ryan J; Tam, Ah Ting; Milano, Randy J; Boisvert, Jessica L; Hicks, Mark A; Elmiligy, Sarah; Malstrom, Scott E; Rivera, Miguel N; Harada, Hisashi; Windle, Brad E; Ramaswamy, Sridhar; Benes, Cyril H; Jacks, Tyler; Engelman, Jeffrey AProceedings of the National Academy of Sciences of the United States of America.2015 Mar 17;E1288-9625737542
Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands.Lu, Yao; Xue, Qiong; Eisele, Markus R; Sulistijo, Endah S; Brower, Kara; Han, Lin; Amir, El-Ad David; Pe'er, Dana; Miller-Jensen, Kathryn; Fan, RongProceedings of the National Academy of Sciences of the United States of America.2015 Feb 17;E607-1525646488
RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.Suresh, V; Liu, Liang; Adjeroh, Donald; Zhou, XiaoboNucleic acids research.2015 Feb 18;1370-925609700
Compound signature detection on LINCS L1000 big data.Liu, Chenglin; Su, Jing; Yang, Fei; Wei, Kun; Ma, Jinwen; Zhou, XiaoboMolecular bioSystems.2015 Mar;714-2225609570
A coding single-nucleotide polymorphism in lysine demethylase KDM4A associates with increased sensitivity to mTOR inhibitors.Van Rechem, Capucine; Black, Joshua C; Greninger, Patricia; Zhao, Yang; Donado, Carlos; Burrowes, Paul D; Ladd, Brendon; Christiani, David C; Benes, Cyril H; Whetstine, Johnathan RCancer discovery.2015 Mar;245-5425564517
Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis.Van Rechem, Capucine; Black, Joshua C; Boukhali, Myriam; Aryee, Martin J; Graslund, Susanne; Haas, Wilhelm; Benes, Cyril H; Whetstine, Johnathan RCancer discovery.2015 Mar;255-6325564516
Analytical reduction of combinatorial complexity arising from multiple protein modification sites.Birtwistle, Marc RJournal of the Royal Society, Interface / the Royal Society.2015 Feb 6;25519995
Genetic modifiers of EGFR dependence in non-small cell lung cancer.Sharifnia, Tanaz; Rusu, Victor; Piccioni, Federica; Bagul, Mukta; Imielinski, Marcin; Cherniack, Andrew D; Pedamallu, Chandra Sekhar; Wong, Bang; Wilson, Frederick H; Garraway, Levi A; Altshuler, David; Golub, Todd R; Root, David E; Subramanian, Aravind; Meyerson, MatthewProceedings of the National Academy of Sciences of the United States of America.2014 Dec 30;18661-625512530
Using the BioAssay Ontology for analyzing high-throughput screening data.Zander Balderud, Linda; Murray, David; Larsson, Niklas; Vempati, Uma; Schurer, Stephan C; Bjareland, Marcus; Engkvist, OlaJournal of biomolecular screening.2015 Mar;402-1525512330
Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.Creech, Amanda L; Taylor, Jordan E; Maier, Verena K; Wu, Xiaoyun; Feeney, Caitlin M; Udeshi, Namrata D; Peach, Sally E; Boehm, Jesse S; Lee, Jeannie T; Carr, Steven A; Jaffe, Jacob DMethods (San Diego, Calif.).2015 Jan 15;57-6425448295
A community computational challenge to predict the activity of pairs of compounds.Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P; Costello, James C; Tang, Hao; Xiao, Guanghua; Li, Yajuan; Allen, Jeffrey; Zhong, Rui; Chen, Beibei; Kim, Minsoo; Wang, Tao; Heiser, Laura M; Realubit, Ronald; Mattioli, Michela; Alvarez, MarNature biotechnology.2014 Dec;1213-2225419740
A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis.Gujral, Taranjit S; Chan, Marina; Peshkin, Leonid; Sorger, Peter K; Kirschner, Marc W; MacBeath, GavinCell.2014 Nov 6;844-5625417160
Patient-derived models of acquired resistance can identify effective drug combinations for cancer.Crystal, Adam S; Shaw, Alice T; Sequist, Lecia V; Friboulet, Luc; Niederst, Matthew J; Lockerman, Elizabeth L; Frias, Rosa L; Gainor, Justin F; Amzallag, Arnaud; Greninger, Patricia; Lee, Dana; Kalsy, Anuj; Gomez-Caraballo, Maria; Elamine, Leila; Howe, Emily; Hur, Wooyoung; Lifshits, Eugene; Robinson, Hayley E; Katayama, Ryohei; Faber, Anthony C; Awad, Mark M; Ramaswamy, Sridhar; Mino-Kenudson, Mari; Iafrate, A John; Benes, Cyril H; Engelman, Jeffrey AScience (New York, N.Y.).2014 Dec 19;1480-625394791
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.Chiu, Hua-Sheng; Llobet-Navas, David; Yang, Xuerui; Chung, Wei-Jen; Ambesi-Impiombato, Alberto; Iyer, Archana; Kim, Hyunjae Ryan; Seviour, Elena G; Luo, Zijun; Sehgal, Vasudha; Moss, Tyler; Lu, Yiling; Ram, Prahlad; Silva, José; Mills, Gordon B; Califano,Genome research.2015 Feb;257-6725378249
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action.Vidovi?, Du?ica; Koleti, Amar; Schürer, Stephan CFrontiers in genetics.2014;25324859
Epigenetic pathways and glioblastoma treatment: insights from signaling cascades.Allen, Bryce K; Stathias, Vasileios; Maloof, Marie E; Vidovic, Dusica; Winterbottom, Emily F; Capobianco, Anthony J; Clarke, Jennifer; Schurer, Stephan; Robbins, David J; Ayad, Nagi GJournal of cellular biochemistry.2015 Mar;351-6325290986
A-770041 reverses paclitaxel and doxorubicin resistance in osteosarcoma cells.Duan, Zhenfeng; Zhang, Jianming; Ye, Shunan; Shen, Jacson; Choy, Edwin; Cote, Gregory; Harmon, David; Mankin, Henry; Hua, Yingqi; Zhang, Yu; Gray, Nathanael S; Hornicek, Francis JBMC cancer.2014;25236161
Upregulation of IGF1R by mutant RAS in leukemia and potentiation of RAS signaling inhibitors by small-molecule inhibition of IGF1R.Weisberg, Ellen; Nonami, Atsushi; Chen, Zhao; Nelson, Erik; Chen, Yongfei; Liu, Feiyang; Cho, HaeYeon; Zhang, Jianming; Sattler, Martin; Mitsiades, Constantine; Wong, Kwok-Kin; Liu, Qingsong; Gray, Nathanael S; Griffin, James DClinical cancer research : an official journal of the American Association for Cancer Research.2014 Nov 1;5483-9525186968
Drugging MYCN through an allosteric transition in Aurora kinase A.Gustafson, William Clay; Meyerowitz, Justin Gabriel; Nekritz, Erin A; Chen, Justin; Benes, Cyril; Charron, Elise; Simonds, Erin F; Seeger, Robert; Matthay, Katherine K; Hertz, Nicholas T; Eilers, Martin; Shokat, Kevan M; Weiss, William ACancer cell.2014 Sep 8;414-2725175806
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation.Clark, Alex M; Bunin, Barry A; Litterman, Nadia K; Schürer, Stephan C; Visser, UbboPeerJ.2014;25165633
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Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, AviBioinformatics (Oxford, England).2014 Nov 15;3289-9025100688
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Discovery of type II inhibitors of TGF*-activated kinase 1 (TAK1) and mitogen-activated protein kinase kinase kinase kinase 2 (MAP4K2).Tan, Li; Nomanbhoy, Tyzoon; Gurbani, Deepak; Patricelli, Matthew; Hunter, John; Geng, Jiefei; Herhaus, Lina; Zhang, Jianming; Pauls, Eduardo; Ham, Youngjin; Choi, Hwan Geun; Xie, Ting; Deng, Xianming; Buhrlage, Sara J; Sim, Taebo; Cohen, Philip; Sapkota, Gopal; Westover, Kenneth D; Gray, Nathanael SJournal of medicinal chemistry.2015 Jan 8;183-9625075558
A microchip platform for interrogating tumor-macrophage paracrine signaling at the single-cell level.Elitas, Meltem; Brower, Kara; Lu, Yao; Chen, Jonathan J; Fan, RongLab on a chip2014 Sep 213582-825057779
Targeting transcription regulation in cancer with a covalent CDK7 inhibitor.Kwiatkowski, Nicholas; Zhang, Tinghu; Rahl, Peter B; Abraham, Brian J; Reddy, Jessica; Ficarro, Scott B; Dastur, Anahita; Amzallag, Arnaud; Ramaswamy, Sridhar; Tesar, Bethany; Jenkins, Catherine E; Hannett, Nancy M; McMillin, Douglas; Sanda, Takaomi; Sim,Nature2014 Jul 31616-2025043025
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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.Wawer, Mathias J; Li, Kejie; Gustafsdottir, Sigrun M; Ljosa, Vebjorn; Bodycombe, Nicole E; Marton, Melissa A; Sokolnicki, Katherine L; Bray, Mark-Anthony; Kemp, Melissa M; Winchester, Ellen; Taylor, Bradley; Grant, George B; Hon, C Suk-Yee; Duvall, Jeremy R; Wilson, J Anthony; Bittker, Joshua A; Dancik, Vlado; Narayan, Rajiv; Subramanian, Aravind; Winckler, Wendy; Golub, Todd R; Carpenter, Anne E; Shamji, Alykhan F; Schreiber, Stuart L; Clemons, Paul AProceedings of the National Academy of Sciences of the United States of America.2014 Jul 29;10911-625024206
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Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte.Hays, Thomas; Ma'ayan, Avi; Clark, Neil R; Tan, Christopher M; Teixeira, Avelino; Teixeira, Angela; Choi, Jae W; Burdis, Nora; Jung, Sung Yun; Bajaj, Amol O; O'Malley, Bert W; He, John C; Hyink, Deborah P; Klotman, Paul EPloS one2014e10066024949636
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Identification of Wee1 as a novel therapeutic target for mutant RAS-driven acute leukemia and other malignancies.Weisberg, E; Nonami, A; Chen, Z; Liu, F; Zhang, J; Sattler, M; Nelson, E; Cowens, K; Christie, A L; Mitsiades, C; Wong, K-K; Liu, Q; Gray, N; Griffin, J DLeukemia.2015 Jan;27-3724791855
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A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells.Tang, YangzhongCurrent protocols in chemical biology2014 Mar5-Jan24652619
The characteristic direction: a geometrical approach to identify differentially expressed genes.Clark, Neil R; Hu, Kevin S; Feldmann, Axel S; Kou, Yan; Chen, Edward Y; Duan, Qiaonan; Ma'ayan, AviBMC bioinformatics20147924650281
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Discovery of a potent, covalent BTK inhibitor for B-cell lymphoma.Wu, Hong; Wang, Wenchao; Liu, Feiyang; Weisberg, Ellen L; Tian, Bei; Chen, Yongfei; Li, Binhua; Wang, Aoli; Wang, Beilei; Zhao, Zheng; McMillin, Douglas W; Hu, Chen; Li, Hong; Wang, Jinhua; Liang, Yanke; Buhrlage, Sara J; Liang, Junting; Liu, Jing; Yang, ACS chemical biology2014 May 161086-9124556163
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).Vempati, Uma D; Chung, Caty; Mader, Chris; Koleti, Amar; Datar, Nakul; Vidovi?, Du?ica; Wrobel, David; Erickson, Sean; Muhlich, Jeremy L; Berriz, Gabriel; Benes, Cyril H; Subramanian, Aravind; Pillai, Ajay; Shamu, Caroline E; Schürer, Stephan CJournal of biomolecular screening.2014 Jun;24518066
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Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents.Ficarro, Scott B; Biagi, Jessica M; Wang, Jinhua; Scotcher, Jenna; Koleva, Rositsa I; Card, Joseph D; Adelmant, Guillaume; He, Huan; Askenazi, Manor; Marshall, Alan G; Young, Nicolas L; Gray, Nathanael S; Marto, Jarrod AJournal of the American Society for Mass Spectrometry2014 Apr636-5024496597
Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects.Shao, Hongwei; Peng, Tao; Ji, Zhiwei; Su, Jing; Zhou, XiaoboPloS one2013e8083224339888
Systems modeling of anti-apoptotic pathways in prostate cancer: psychological stress triggers a synergism pattern switch in drug combination therapy.Sun, Xiaoqiang; Bao, Jiguang; Nelson, Kyle C; Li, King Chuen; Kulik, George; Zhou, XiaoboPLoS computational biology2013 Dece100335824339759
Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones.Deng, Xianming; Elkins, Jonathan M; Zhang, Jinwei; Yang, Qingkai; Erazo, Tatiana; Gomez, Nestor; Choi, Hwan Geun; Wang, Jinhua; Dzamko, Nicolas; Lee, Jiing-Dwan; Sim, Taebo; Kim, Namdoo; Alessi, Dario R; Lizcano, Jose M; Knapp, Stefan; Gray, Nathanael SEuropean journal of medicinal chemistry2013 Dec758-6724239623
Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones.Deng, Xianming; Elkins, Jonathan M; Zhang, Jinwei; Yang, Qingkai; Erazo, Tatiana; Gomez, Nestor; Choi, Hwan Geun; Wang, Jinhua; Dzamko, Nicolas; Lee, Jiing-Dwan; Sim, Taebo; Kim, NamDoo; Alessi, Dario R; Lizcano, Jose M; Knapp, Stefan; Gray, Nathanael SEuropean journal of medicinal chemistry2013 Dec758-6724239623
A melanocyte lineage program confers resistance to MAP kinase pathway inhibition.Johannessen, Cory M; Johnson, Laura A; Piccioni, Federica; Townes, Aisha; Frederick, Dennie T; Donahue, Melanie K; Narayan, Rajiv; Flaherty, Keith T; Wargo, Jennifer A; Root, David E; Garraway, Levi ANature2013 Dec 5138-4224185007
mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to BCL-2/BCL-XL inhibition by suppressing MCL-1.Faber, Anthony C; Coffee, Erin M; Costa, Carlotta; Dastur, Anahita; Ebi, Hiromichi; Hata, Aaron N; Yeo, Alan T; Edelman, Elena J; Song, Youngchul; Tam, Ah Ting; Boisvert, Jessica L; Milano, Randy J; Roper, Jatin; Kodack, David P; Jain, Rakesh K; Corcoran,Cancer discovery2014 Jan42-5224163374
A dual sensor for real-time monitoring of glucose and oxygen.Zhang, Liqiang; Su, Fengyu; Buizer, Sean; Lu, Hongguang; Gao, Weimin; Tian, Yanqing; Meldrum, DeirdreBiomaterials2013 Dec9779-8824090834
A fluorescent colorimetric pH sensor and the influences of matrices on sensing performances.Tian, Yanqing; Fuller, Emily; Klug, Summer; Lee, Fred; Su, Fengyu; Zhang, Liqiang; Chao, Shih-Hui; Meldrum, Deirdre RSensors and actuators. B, Chemical2013 Oct10-Jan24078772
Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines.Niepel, Mario; Hafner, Marc; Pace, Emily A; Chung, Mirra; Chai, Diana H; Zhou, Lili; Schoeberl, Birgit; Sorger, Peter KScience signaling2013ra8424065145
Red blood cell tracking using optical flow methods.Guo, Dongmin; van de Ven, Anne L; Zhou, XiaoboIEEE journal of biomedical and health informatics.2014 May;24058034
Modeling cell-cell interactions in regulating multiple myeloma initiating cell fate.Peng, Tao; Peng, Huiming; Choi, Dong Soon; Su, Jing; Chang, Chung-Che Jeff; Zhou, XiaoboIEEE journal of biomedical and health informatics2014 Mar484-9124058033
In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase.Tan, Hua; Wei, Kun; Bao, Jiguang; Zhou, XiaoboMolecular bioSystems2013 Nov2764-7424056678
Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules.Chen, Jing; Hu, Zhen; Phatak, Mukta; Reichard, John; Freudenberg, Johannes M; Sivaganesan, Siva; Medvedovic, MarioPLoS computational biology2013 Sepe100319824039560
Metrics other than potency reveal systematic variation in responses to cancer drugs.Fallahi-Sichani, Mohammad; Honarnejad, Saman; Heiser, Laura M; Gray, Joe W; Sorger, Peter KNature chemical biology2013 Nov708-1424013279
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).Paull, Evan O; Carlin, Daniel E; Niepel, Mario; Sorger, Peter K; Haussler, David; Stuart, Joshua MBioinformatics (Oxford, England)2013 Nov 12757-6423986566
Effects of the selective MPS1 inhibitor MPS1-IN-3 on glioblastoma sensitivity to antimitotic drugs.Tannous, Bakhos A; Kerami, Mariam; Van der Stoop, Petra M; Kwiatkowski, Nicholas; Wang, Jinhua; Zhou, Wenjun; Kessler, Almuth F; Lewandrowski, Grant; Hiddingh, Lotte; Sol, Nik; Lagerweij, Tonny; Wedekind, Laurine; Niers, Johanna M; Barazas, Marco; NilssonJournal of the National Cancer Institute2013 Sep 41322-3123940287
Discovery of a Potent and Selective DDR1 Receptor Tyrosine Kinase Inhibitor.Kim, Hyung-Gu; Tan, Li; Weisberg, Ellen L; Liu, Feiyang; Canning, Peter; Choi, Hwan Geun; Ezell, Scott A; Wu, Hong; Zhao, Zheng; Wang, Jinhua; Mandinova, Anna; Griffin, James D; Bullock, Alex N; Liu, Qingsong; Lee, Sam W; Gray, Nathanael SACS chemical biology2013 Oct 182145-5023899692
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SNVHMM: predicting single nucleotide variants from next generation sequencing.Bian, Jiawen; Liu, Chenglin; Wang, Hongyan; Xing, Jing; Kachroo, Priyanka; Zhou, XiaoboBMC bioinformatics201322523855743
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Differential Determinants of Cancer Cell Insensitivity to Antimitotic Drugs Discriminated by a One-Step Cell Imaging Assay.Tang, Yangzhong; Xie, Tiao; Florian, Stefan; Moerke, Nathan; Shamu, Caroline; Benes, Cyril; Mitchison, Timothy JJournal of biomolecular screening2013 Jun 20NULL23788527
Single cell functional proteomics for assessing immune response in cancer therapy: technology, methods, and applications.Ma, Chao; Fan, Rong; Elitas, MeltemFrontiers in oncology.2013;23755371
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Selective Akt inhibitors synergize with tyrosine kinase inhibitors and effectively override stroma-associated cytoprotection of mutant FLT3-positive AML cells.Weisberg, Ellen; Liu, Qingsong; Zhang, Xin; Nelson, Erik; Sattler, Martin; Liu, Feiyang; Nicolais, Maria; Zhang, Jianming; Mitsiades, Constantine; Smith, Robert W; Stone, Richard; Galinsky, Ilene; Nonami, Atsushi; Griffin, James D; Gray, NathanaelPloS one2013e5647323437141
Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR.Liu, Qingsong; Xu, Chunxiao; Kirubakaran, Sivapriya; Zhang, Xin; Hur, Wooyoung; Liu, Yan; Kwiatkowski, Nicholas P; Wang, Jinhua; Westover, Kenneth D; Gao, Peng; Ercan, Dalia; Niepel, Mario; Thoreen, Carson C; Kang, Seong A; Patricelli, Matthew P; Wang, Yuchuan; Tupper, Tanya; Altabef, Abigail; Kawamura, Hidemasa; Held, Kathryn D; Chou, Danny M; Elledge, Stephen J; Janne, Pasi A; Wong, Kwok-Kin; Sabatini, David M; Gray, Nathanael SCancer research2013 Apr 152574-8623436801
High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity.Lu, Yao; Chen, Jonathan J; Mu, Luye; Xue, Qiong; Wu, Yu; Wu, Pei-Hsun; Li, Jie; Vortmeyer, Alexander O; Miller-Jensen, Kathryn; Wirtz, Denis; Fan, RongAnalytical chemistry2013 Feb 192548-5623339603
Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays.Fan, Jing; Dy, Jennifer G; Chang, Chung-Che; Zhou, XiaoboChinese journal of cancer2013 Apr170-8523327800
Systems pharmacology meets predictive, preventive, personalized and participatory medicine.Jenkins, Sherry L; Ma'ayan, AviPharmacogenomics2013 Jan119-2223327571
Functionalizing genomic data for personalization of medicine.Benes, C HClinical pharmacology and therapeutics2013 Apr309-1123321554
A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosis.Shao, Hongwei; He, Ying; Li, King C P; Zhou, XiaoboMolecular bioSystems2013 Mar398-40623287963
Kinome-wide activity modeling from diverse public high-quality data sets.Schurer, Stephan C; Muskal, Steven MJournal of chemical information and modeling2013 Jan 2827-3823259810
Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models.Corcoran, Ryan B; Cheng, Katherine A; Hata, Aaron N; Faber, Anthony C; Ebi, Hiromichi; Coffee, Erin M; Greninger, Patricia; Brown, Ronald D; Godfrey, Jason T; Cohoon, Travis J; Song, Youngchul; Lifshits, Eugene; Hung, Kenneth E; Shioda, Toshi; Dias-Santagata, Dora; Singh, Anurag; Settleman, Jeffrey; Benes, Cyril H; Mino-Kenudson, Mari; Wong, Kwok-Kin; Engelman, Jeffrey ACancer cell2013 Jan 14121-823245996
Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models.Wang, Hongyan; Zhou, XiaoboChinese journal of cancer2013 Apr186-9423237214
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).Vempati, Uma D; Przydzial, Magdalena J; Chung, Caty; Abeyruwan, Saminda; Mir, Ahsan; Sakurai, Kunie; Visser, Ubbo; Lemmon, Vance P; Schurer, Stephan CPloS one2012e4919823155465
Brain Penetrant LRRK2 Inhibitor.Choi, Hwan Geun; Zhang, Jinwei; Deng, Xianming; Hatcher, John M; Patricelli, Matthew P; Zhao, Zheng; Alessi, Dario R; Gray, Nathanael SACS medicinal chemistry letters2012 Aug 9658-66223066449
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.Ng, Sam; Collisson, Eric A; Sokolov, Artem; Goldstein, Theodore; Gonzalez-Perez, Abel; Lopez-Bigas, Nuria; Benz, Christopher; Haussler, David; Stuart, Joshua MBioinformatics (Oxford, England)2012 Sep 15i640-i64622962493
Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis.Sun, Xiaoqiang; Zhang, Le; Tan, Hua; Bao, Jiguang; Strouthos, Costas; Zhou, XiaoboBMC bioinformatics201221822935054
Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway.Sun, Xiaoqiang; Su, Jing; Bao, Jiguang; Peng, Tao; Zhang, Le; Zhang, Yuanyuan; Yang, Yunzhi; Zhou, XiaoboBiomaterials2012 Nov8265-7622910219
Functional characterization of an isoform-selective inhibitor of PI3K-p110ýý as a potential anticancer agent.Ni, Jing; Liu, Qingsong; Xie, Shaozhen; Carlson, Coby; Von, Thanh; Vogel, Kurt; Riddle, Steve; Benes, Cyril; Eck, Michael; Roberts, Thomas; Gray, Nathanael; Zhao, JeanCancer discovery2012 May425-3322588880
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.Kirouac, Daniel C; Saez-Rodriguez, Julio; Swantek, Jennifer; Burke, John M; Lauffenburger, Douglas A; Sorger, Peter KBMC systems biology20122922548703
Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae.Liu, Qingsong; Ren, Tao; Fresques, Tara; Oppliger, Wolfgang; Niles, Brad J; Hur, Wooyoung; Sabatini, David M; Hall, Michael N; Powers, Ted; Gray, Nathanael SACS chemical biology2012 Jun 15982-722496512
Using combination therapy to override stromal-mediated chemoresistance in mutant FLT3-positive AML: synergism between FLT3 inhibitors, dasatinib/multi-targeted inhibitors and JAK inhibitors.Weisberg, E; Liu, Q; Nelson, Erik; Kung, A L; Christie, A L; Bronson, R; Sattler, M; Sanda, T; Zhao, Z; Hur, W; Mitsiades, C; Smith, R; Daley, J F; Stone, R; Galinsky, I; Griffin, J D; Gray, NLeukemia2012 Oct2233-4422469781
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A systematic modeling study on the pathogenic role of p38 MAPK activation in myelodysplastic syndromes.Peng, Huiming; Wen, Jianguo; Zhang, Lixin; Li, Hongwei; Chang, Chung-Che; Zu, Youli; Zhou, XiaoboMolecular bioSystems2012 Apr1366-7422327869
Discovery of potent and selective covalent inhibitors of JNK.Zhang, Tinghu; Inesta-Vaquera, Francisco; Niepel, Mario; Zhang, Jianming; Ficarro, Scott B; Machleidt, Thomas; Xie, Ting; Marto, Jarrod A; Kim, NamDoo; Sim, Taebo; Laughlin, John D; Park, Hajeung; LoGrasso, Philip V; Patricelli, Matt; Nomanbhoy, Tyzoon K; Sorger, Peter K; Alessi, Dario R; Gray, Nathanael SChemistry & biology2012 Jan 27140-5422284361
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Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics.Liu, Qingsong; Kirubakaran, Sivapriya; Hur, Wooyoung; Niepel, Mario; Westover, Kenneth; Thoreen, Carson C; Wang, Jinhua; Ni, Jing; Patricelli, Matthew P; Vogel, Kurt; Riddle, Steve; Waller, David L; Traynor, Ryan; Sanda, Takaomi; Zhao, Zheng; Kang, Seong A; Zhao, Jean; Look, A Thomas; Sorger, Peter K; Sabatini, David M; Gray, Nathanael SThe Journal of biological chemistry2012 Mar 239742-5222223645
The Polya Tree Sampler: Towards Efficient and Automatic Independent Metropolis-Hastings Proposals.Hanson, Timothy E; Monteiro, João V D; Jara, AlejandroJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.2011 Mar 01;22135487
Selective aurora kinase inhibitors identified using a taxol-induced checkpoint sensitivity screen.Kwiatkowski, Nicholas; Deng, Xianming; Wang, Jinhua; Tan, Li; Villa, Fabrizio; Santaguida, Stefano; Huang, Hsiao-Chun; Mitchison, Tim; Musacchio, Andrea; Gray, NathanaelACS chemical biology2012 Jan 20185-9621992004
Crowdsourcing network inference: the DREAM predictive signaling network challenge.Prill, Robert J; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G; Sorger, Peter K; Stolovitzky, GustavoScience signaling2011 Sep 6mr721900204
High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors.Miduturu, Chandrasekhar V; Deng, Xianming; Kwiatkowski, Nicholas; Yang, Wannian; Brault, Laurent; Filippakopoulos, Panagis; Chung, Eunah; Yang, Qingkai; Schwaller, Juerg; Knapp, Stefan; King, Randall W; Lee, Jiing-Dwan; Herrgard, Sanna; Zarrinkar, PatrickChemistry & biology2011 Jul 29868-7921802008
High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors.Miduturu, Chandrasekhar V; Deng, Xianming; Kwiatkowski, Nicholas; Yang, Wannian; Brault, Laurent; Filippakopoulos, Panagis; Chung, Eunah; Yang, Qingkai; Schwaller, Juerg; Knapp, Stefan; King, Randall W; Lee, Jiing-Dwan; Herrgard, Sanna; Zarrinkar, Patrick; Gray, Nathanael SChemistry & biology2011 Jul 29868-7921802008
Adaptive informatics for multifactorial and high-content biological data.Millard, Bjorn L; Niepel, Mario; Menden, Michael P; Muhlich, Jeremy L; Sorger, Peter KNature methods2011 Jun487-9321516115