Library of Integrated Network-Based Cellular Signatures (LINCS) (244)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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
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
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
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
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
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
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
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
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
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
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
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
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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
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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
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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
Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats.Repunte-Canonigo, Vez; Lefebvre, Celine; George, Olivier; Kawamura, Tomoya; Morales, Marisela; Koob, George F; Califano, Andrea; Masliah, Eliezer; Sanna, Pietro PaoloMolecular neurodegeneration20142624980976
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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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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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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
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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
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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
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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
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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
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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
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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
Systematic identification of genomic markers of drug sensitivity in cancer cells.Garnett, Mathew J; Edelman, Elena J; Heidorn, Sonja J; Greenman, Chris D; Dastur, Anahita; Lau, King Wai; Greninger, Patricia; Thompson, I Richard; Luo, Xi; Soares, Jorge; Liu, Qingsong; Iorio, Francesco; Surdez, Didier; Chen, Li; Milano, Randy J; BignellNature2012 Mar 29570-522460902
Systematic identification of genomic markers of drug sensitivity in cancer cells.Garnett, Mathew J; Edelman, Elena J; Heidorn, Sonja J; Greenman, Chris D; Dastur, Anahita; Lau, King Wai; Greninger, Patricia; Thompson, I Richard; Luo, Xi; Soares, Jorge; Liu, Qingsong; Iorio, Francesco; Surdez, Didier; Chen, Li; Milano, Randy J; Bignell, Graham R; Tam, Ah T; Davies, Helen; Stevenson, Jesse A; Barthorpe, Syd; Lutz, Stephen R; Kogera, Fiona; Lawrence, Karl; McLaren-Douglas, Anne; Mitropoulos, Xeni; Mironenko, Tatiana; Thi, Helen; Richardson, Laura; Zhou, Wenjun; Jewitt, Frances; Zhang, Tinghu; O'Brien, Patrick; Boisvert, Jessica L; Price, Stacey; Hur, Wooyoung; Yang, Wanjuan; Deng, Xianming; Butler, Adam; Choi, Hwan Geun; Chang, Jae Won; Baselga, Jose; Stamenkovic, Ivan; Engelman, Jeffrey A; Sharma, Sreenath V; Delattre, Olivier; Saez-Rodriguez, Julio; Gray, Nathanael S; Settleman, Jeffrey; Futreal, P Andrew; Haber, Daniel A; Stratton, Michael R; Ramaswamy, Sridhar; McDermott, Ultan; Benes, Cyril HNature2012 Mar 29570-522460902
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
Toward interoperable bioscience data.Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral-Zettler, Linda; Begley, Kimberly; Booth, Tim; Bougueleret, Lydie; Burns, Gully; Chapman, Brad; Clark, Tim; Coleman, Lee-Ann; Copeland, Jay; Das, Sudeshna; de Daruvar, Antoine; de Matos, Paula; Dix, Ian; Edmunds, Scott; Evelo, Chris T; Forster, Mark J; Gaudet, Pascale; Gilbert, Jack; Goble, Carole; Griffin, Julian L; Jacob, Daniel; Kleinjans, Jos; Harland, Lee; Haug, Kenneth; Hermjakob, Henning; Ho Sui, Shannan J; Laederach, Alain; Liang, Shaoguang; Marshall, Stephen; McGrath, Annette; Merrill, Emily; Reilly, Dorothy; Roux, Magali; Shamu, Caroline E; Shang, Catherine A; Steinbeck, Christoph; Trefethen, Anne; Williams-Jones, Bryn; Wolstencroft, Katherine; Xenarios, Ioannis; Hide, WinstonNature genetics2012 Feb121-622281772
A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins.Luckert, Katrin; Gujral, Taranjit S; Chan, Marina; Joos, Thomas O; Sorger, Peter K; Macbeath, Gavin; Potz, OliverScience signaling2012 Jan 10pl122234610
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
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