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Library of Integrated Network-Based Cellular Signatures (LINCS) (99)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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
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
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
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
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
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
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
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
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
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
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
Modeling the relationship of epigenetic modifications to transcription factor binding.Liu, Liang; Jin, Guangxu; Zhou, XiaoboNucleic acids research.2015 Apr 30;3873-8525820421
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
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
Panorama: a targeted proteomics knowledge base.Sharma, Vagisha; Eckels, Josh; Taylor, Greg K; Shulman, Nicholas J; Stergachis, Andrew B; Joyner, Shannon A; Yan, Ping; Whiteaker, Jeffrey R; Halusa, Goran N; Schilling, Birgit; Gibson, Bradford W; Colangelo, Christopher M; Paulovich, Amanda G; Carr, Steven A; Jaffe, Jacob D; MacCoss, Michael J; MacLean, BrendanJournal of proteome research.2014 Sep 5;4205-1025102069
An unbiased approach to identify endogenous substrates of ''histone'' deacetylase 8.Olson, David E; Udeshi, Namrata D; Wolfson, Noah A; Pitcairn, Carol Ann; Sullivan, Eric D; Jaffe, Jacob D; Svinkina, Tanya; Natoli, Ted; Lu, Xiaodong; Paulk, Joshiawa; McCarren, Patrick; Wagner, Florence F; Barker, Doug; Howe, Eleanor; Lazzaro, Fanny; Gale, Jennifer P; Zhang, Yan-Ling; Subramanian, Aravind; Fierke, Carol A; Carr, Steven A; Holson, Edward BACS chemical biology.2014 Oct 17;2210-625089360
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
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
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
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
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
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
Minimum information about a spinal cord injury experiment: a proposed reporting standard for spinal cord injury experiments.Lemmon, Vance P; Ferguson, Adam R; Popovich, Phillip G; Xu, Xiao-Ming; Snow, Diane M; Igarashi, Michihiro; Beattie, Christine E; Bixby, John L; MIASCI ConsortiumJournal of neurotrauma.2014 Aug 1;1354-6124870067
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
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
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
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 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
Lean Big Data integration in systems biology and systems pharmacology.Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, YanTrends in pharmacological sciences2014 Sep450-46025109570
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
A polymer-based ratiometric intracellular glucose sensor.Zhang, Liqiang; Su, Fengyu; Buizer, Sean; Kong, Xiangxing; Lee, Fred; Day, Kevin; Tian, Yanqing; Meldrum, Deirdre RChemical communications (Cambridge, England)2014 Jul 46920-224840577
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach.Peng, Huiming; Peng, Tao; Wen, Jianguo; Engler, David A; Matsunami, Rise K; Su, Jing; Zhang, Le; Chang, Chung-Che Jeff; Zhou, XiaoboBioinformatics (Oxford, England)2014 Jul 11899-90724618474
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, AviNucleic acids research2014 JulW449-6024906883
CPTAC Assay Portal: a repository of targeted proteomic 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; Rodriguez, Henry; Clinical Proteomic Tumor Analysis ConNature methods2014 Jul703-424972168
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
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
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
A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells.Tang, YangzhongCurrent protocols in chemical biology2014 Mar5-Jan24652619
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
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
Analysis of growth factor signaling in genetically diverse breast cancer lines.Niepel, Mario; Hafner, Marc; Pace, Emily A; Chung, Mirra; Chai, Diana H; Zhou, Lili; Muhlich, Jeremy L; Schoeberl, Birgit; Sorger, Peter KBMC biology20142024655548
Pathway bridge based multiobjective optimization approach for lurking pathway prediction.Zhang, Rengjing; Zhao, Chen; Xiong, Zixiang; Zhou, XiaoboBioMed research international201435109524949437
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
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
Integrating genomics and proteomics data to predict drug effects using binary linear programming.Ji, Zhiwei; Su, Jing; Liu, Chenglin; Wang, Hongyan; Huang, Deshuang; Zhou, XiaoboPloS one2014e10279825036040
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
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 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
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
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
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
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
In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase.Tan, Hua; Wei, Kun; Bao, Jiguang; Zhou, XiaoboMolecular bioSystems2013 Nov2764-7424056678
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
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
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
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
Network2Canvas: network visualization on a canvas with enrichment analysis.Tan, Christopher M; Chen, Edward Y; Dannenfelser, Ruth; Clark, Neil R; Ma'ayan, AviBioinformatics (Oxford, England)2013 Aug 11872-823749960
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state.Santagata, Sandro; Mendillo, Marc L; Tang, Yun-chi; Subramanian, Aravind; Perley, Casey C; Roche, Stephane P; Wong, Bang; Narayan, Rajiv; Kwon, Hyoungtae; Koeva, Martina; Amon, Angelika; Golub, Todd R; Porco Jr, John A; Whitesell, Luke; Lindquist, SusanScience (New York, N.Y.)2013 Jul 19123830323869022
Modeling vascularized bone regeneration within a porous biodegradable CaP scaffold loaded with growth factors.Sun, Xiaoqiang; Kang, Yunqing; Bao, Jiguang; Zhang, Yuanyuan; Yang, Yunzhi; Zhou, XiaoboBiomaterials2013 Jul4971-8123566802
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
Mass spectrometry based method to increase throughput for kinome analyses using ATP probes.McAllister, F E; Niepel, M; Haas, W; Huttlin, E; Sorger, P K; Gygi, S PAnalytical chemistry2013 May 74666-7423607489
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
Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models.Wang, Hongyan; Zhou, XiaoboChinese journal of cancer2013 Apr186-9423237214
Functionalizing genomic data for personalization of medicine.Benes, C HClinical pharmacology and therapeutics2013 Apr309-1123321554
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
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase.Zhong, Yifei; Chen, Edward Y; Liu, Ruijie; Chuang, Peter Y; Mallipattu, Sandeep K; Tan, Christopher M; Clark, Neil R; Deng, Yueyi; Klotman, Paul E; Ma'ayan, Avi; He, John CijiangJournal of the American Society of Nephrology : JASN2013 Apr801-1123559582
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
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
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
Systems pharmacology meets predictive, preventive, personalized and participatory medicine.Jenkins, Sherry L; Ma'ayan, AviPharmacogenomics2013 Jan119-2223327571
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
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, AviBMC bioinformatics201312823586463
SNVHMM: predicting single nucleotide variants from next generation sequencing.Bian, Jiawen; Liu, Chenglin; Wang, Hongyan; Xing, Jing; Kachroo, Priyanka; Zhou, XiaoboBMC bioinformatics201322523855743
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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


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