Library of Integrated Network-based Cellular Signatures (LINCS)
Library of Integrated Network-based Cellular Signatures (LINCS)
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| Adaptive informatics for multifactorial and high-content biological data. | Millard, Bjorn L; Niepel, Mario; Menden, Michael P; Muhlich, Jeremy L; Sorger, Peter K | Nature methods | 21516115 | 2011 Jun |
| 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 S | Chemistry & biology | 21802008 | 2011 Jul 29 |
| Crowdsourcing network inference: the DREAM predictive signaling network challenge. | Prill, Robert J; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G; Sorger, Peter K; Stolovitzky, Gustavo | Science signaling | 21900204 | 2011 Sep 6 |
| 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, Nathanael | ACS chemical biology | 21992004 | 2012 Jan 20 |
| The Polya Tree Sampler: Towards Efficient and Automatic Independent Metropolis-Hastings Proposals. | Hanson, Timothy E; Monteiro, João V D; Jara, Alejandro | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. | 22135487 | 2011 Mar 01; |
| 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 S | The Journal of biological chemistry | 22223645 | 2012 Mar 23 |
| 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, Oliver | Science signaling | 22234610 | 2012 Jan 10 |
| 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, Winston | Nature genetics | 22281772 | 2012 Feb |
| 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 S | Chemistry & biology | 22284361 | 2012 Jan 27 |
| 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, Xiaobo | Molecular bioSystems | 22327869 | 2012 Apr |
| 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 H | Nature | 22460902 | 2012 Mar 29 |
| 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, N | Leukemia | 22469781 | 2012 Oct |
| 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 S | ACS chemical biology | 22496512 | 2012 Jun 15 |
| 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 K | BMC systems biology | 22548703 | 2012 |
| 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, Jean | Cancer discovery | 22588880 | 2012 May |
| 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, Xiaobo | Biomaterials | 22910219 | 2012 Nov |
| 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, Xiaobo | BMC bioinformatics | 22935054 | 2012 |
| 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 M | Bioinformatics (Oxford, England) | 22962493 | 2012 Sep 15 |
| Brain Penetrant LRRK2 Inhibitor. | Choi, Hwan Geun; Zhang, Jinwei; Deng, Xianming; Hatcher, John M; Patricelli, Matthew P; Zhao, Zheng; Alessi, Dario R; Gray, Nathanael S | ACS medicinal chemistry letters | 23066449 | 2012 Aug 9 |
| 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 C | PloS one | 23155465 | 2012 |
| Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models. | Wang, Hongyan; Zhou, Xiaobo | Chinese journal of cancer | 23237214 | 2013 Apr |
| 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 A | Cancer cell | 23245996 | 2013 Jan 14 |
| Kinome-wide activity modeling from diverse public high-quality data sets. | Schurer, Stephan C; Muskal, Steven M | Journal of chemical information and modeling | 23259810 | 2013 Jan 28 |
| A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosis. | Shao, Hongwei; He, Ying; Li, King C P; Zhou, Xiaobo | Molecular bioSystems | 23287963 | 2013 Mar |
| Functionalizing genomic data for personalization of medicine. | Benes, C H | Clinical pharmacology and therapeutics | 23321554 | 2013 Apr |
| Systems pharmacology meets predictive, preventive, personalized and participatory medicine. | Jenkins, Sherry L; Ma'ayan, Avi | Pharmacogenomics | 23327571 | 2013 Jan |
| 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, Xiaobo | Chinese journal of cancer | 23327800 | 2013 Apr |
| 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, Rong | Analytical chemistry | 23339603 | 2013 Feb 19 |
| 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 S | Cancer research | 23436801 | 2013 Apr 15 |
| 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, Nathanael | PloS one | 23437141 | 2013 |
| 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 Cijiang | Journal of the American Society of Nephrology : JASN | 23559582 | 2013 Apr |
| 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, Xiaobo | Biomaterials | 23566802 | 2013 Jul |
| 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, Avi | BMC bioinformatics | 23586463 | 2013 |
| 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 P | Analytical chemistry | 23607489 | 2013 May 7 |
| The UCSC Interaction Browser: multidimensional data views in pathway context. | Wong, Christopher K; Vaske, Charles J; Ng, Sam; Sanborn, J Zachary; Benz, Stephen C; Haussler, David; Stuart, Joshua M | Nucleic acids research. | 23748957 | 2013 Jul; |
| Network2Canvas: network visualization on a canvas with enrichment analysis. | Tan, Christopher M; Chen, Edward Y; Dannenfelser, Ruth; Clark, Neil R; Ma'ayan, Avi | Bioinformatics (Oxford, England) | 23749960 | 2013 Aug 1 |
| Single cell functional proteomics for assessing immune response in cancer therapy: technology, methods, and applications. | Ma, Chao; Fan, Rong; Elitas, Meltem | Frontiers in oncology. | 23755371 | 2013; |
| 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 J | Journal of biomolecular screening | 23788527 | 2013 Jun 20 |
| Metasignatures identify two major subtypes of breast cancer. | Duan, Q; Kou, Y; Clark, N R; Gordonov, S; Ma'ayan, A | CPT: pharmacometrics & systems pharmacology. | 23836026 | 2013 Mar 27; |
| SNVHMM: predicting single nucleotide variants from next generation sequencing. | Bian, Jiawen; Liu, Chenglin; Wang, Hongyan; Xing, Jing; Kachroo, Priyanka; Zhou, Xiaobo | BMC bioinformatics | 23855743 | 2013 |
| 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, Susan | Science (New York, N.Y.) | 23869022 | 2013 Jul 19 |
| 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 S | ACS chemical biology | 23899692 | 2013 Oct 18 |
| 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; Nilsson | Journal of the National Cancer Institute | 23940287 | 2013 Sep 4 |
| 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 M | Bioinformatics (Oxford, England) | 23986566 | 2013 Nov 1 |
| 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 K | Nature chemical biology | 24013279 | 2013 Nov |
| 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, Mario | PLoS computational biology | 24039560 | 2013 Sep |
| In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. | Tan, Hua; Wei, Kun; Bao, Jiguang; Zhou, Xiaobo | Molecular bioSystems | 24056678 | 2013 Nov |
| 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, Xiaobo | IEEE journal of biomedical and health informatics | 24058033 | 2014 Mar |
| Red blood cell tracking using optical flow methods. | Guo, Dongmin; van de Ven, Anne L; Zhou, Xiaobo | IEEE journal of biomedical and health informatics. | 24058034 | 2014 May; |
| 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 K | Science signaling | 24065145 | 2013 |
| 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 R | Sensors and actuators. B, Chemical | 24078772 | 2013 Oct |
| A dual sensor for real-time monitoring of glucose and oxygen. | Zhang, Liqiang; Su, Fengyu; Buizer, Sean; Lu, Hongguang; Gao, Weimin; Tian, Yanqing; Meldrum, Deirdre | Biomaterials | 24090834 | 2013 Dec |
| 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 discovery | 24163374 | 2014 Jan |
| 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 A | Nature | 24185007 | 2013 Dec 5 |
| 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 S | European journal of medicinal chemistry | 24239623 | 2013 Dec |
| 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, Xiaobo | PLoS computational biology | 24339759 | 2013 Dec |
| Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects. | Shao, Hongwei; Peng, Tao; Ji, Zhiwei; Su, Jing; Zhou, Xiaobo | PloS one | 24339888 | 2013 |
| 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 A | Journal of the American Society for Mass Spectrometry | 24496597 | 2014 Apr |
| EMT twists the road to PI3K. | Niederst, Matthew J; Benes, Cyril H | Cancer discovery. | 24501304 | 2014 Feb; |
| 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 C | Journal of biomolecular screening. | 24518066 | 2014 Jun; |
| 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 biology | 24556163 | 2014 May 16 |
| 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, Xiaobo | Bioinformatics (Oxford, England) | 24618474 | 2014 Jul 1 |
| 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, Avi | BMC bioinformatics | 24650281 | 2014 |
| A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. | Tang, Yangzhong | Current protocols in chemical biology | 24652619 | 2014 Mar |
| 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 K | BMC biology | 24655548 | 2014 |
| 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 D | Leukemia. | 24791855 | 2015 Jan; |
| A polymer-based ratiometric intracellular glucose sensor. | Zhang, Liqiang; Su, Fengyu; Buizer, Sean; Kong, Xiangxing; Lee, Fred; Day, Kevin; Tian, Yanqing; Meldrum, Deirdre R | Chemical communications (Cambridge, England) | 24840577 | 2014 Jul 4 |
| 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 Consortium | Journal of neurotrauma. | 24870067 | 2014 Aug 1; |
| 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, Avi | Nucleic acids research | 24906883 | 2014 Jul |
| Pathway bridge based multiobjective optimization approach for lurking pathway prediction. | Zhang, Rengjing; Zhao, Chen; Xiong, Zixiang; Zhou, Xiaobo | BioMed research international | 24949437 | 2014 |
| 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 E | PloS one | 24949636 | 2014 |
| 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 Con | Nature methods | 24972168 | 2014 Jul |
| 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 Paolo | Molecular neurodegeneration | 24980976 | 2014 |
| 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 A | Proceedings of the National Academy of Sciences of the United States of America. | 25024206 | 2014 Jul 29; |
| Integrating genomics and proteomics data to predict drug effects using binary linear programming. | Ji, Zhiwei; Su, Jing; Liu, Chenglin; Wang, Hongyan; Huang, Deshuang; Zhou, Xiaobo | PloS one | 25036040 | 2014 |
| 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, | Nature | 25043025 | 2014 Jul 31 |
| A microchip platform for interrogating tumor-macrophage paracrine signaling at the single-cell level. | Elitas, Meltem; Brower, Kara; Lu, Yao; Chen, Jonathan J; Fan, Rong | Lab on a chip | 25057779 | 2014 Sep 21 |
| 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 S | Journal of medicinal chemistry. | 25075558 | 2015 Jan 8; |
| 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 B | ACS chemical biology. | 25089360 | 2014 Oct 17; |
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| INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer. | Liu, Moqing; Smith, Rebecca; Liby, Tiera; Chiotti, Kami; López, Claudia S; Korkola, James E | Breast cancer research : BCR | 35248133 | 2022 Mar 05 |
| A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis. | Ternes, Luke; Dane, Mark; Gross, Sean; Labrie, Marilyne; Mills, Gordon; Gray, Joe; Heiser, Laura; Chang, Young Hwan | Communications biology | 35322205 | 2022 03 23 |
| A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. | Erdem, Cemal; Mutsuddy, Arnab; Bensman, Ethan M; Dodd, William B; Saint-Antoine, Michael M; Bouhaddou, Mehdi; Blake, Robert C; Gross, Sean M; Heiser, Laura M; Feltus, F Alex; Birtwistle, Marc R | Nature communications | 35729113 | 2022 06 21 |
| Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. | Doherty, Laura M; Mills, Caitlin E; Boswell, Sarah A; Liu, Xiaoxi; Hoyt, Charles Tapley; Gyori, Benjamin; Buhrlage, Sara J; Sorger, Peter K | eLife | 35737447 | 2022 06 23 |
| Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. | Zatorski, Nicole; Stein, David; Rahman, Rayees; Iyengar, Ravi; Schlessinger, Avner | Database : the journal of biological databases and curation | 35881481 | 2022 Jul 26 |
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| A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. | Gross, Sean M; Dane, Mark A; Smith, Rebecca L; Devlin, Kaylyn L; McLean, Ian C; Derrick, Daniel S; Mills, Caitlin E; Subramanian, Kartik; London, Alexandra B; Torre, Denis; Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Erdem, Cemal; Lyons, Nicholas; Natoli, Ted; Pessa, Sarah; Lu, Xiaodong; Mullahoo, James; Li, Jonathan; Adam, Miriam; Wassie, Brook; Liu, Moqing; Kilburn, David F; Liby, Tiera A; Bucher, Elmar; Sanchez-Aguila, Crystal; Daily, Kenneth; Omberg, Larsson; Wang, Yunguan; Jacobson, Connor; Yapp, Clarence; Chung, Mirra; Vidovic, Dusica; Lu, Yiling; Schurer, Stephan; Lee, Albert; Pillai, Ajay; Subramanian, Aravind; Papanastasiou, Malvina; Fraenkel, Ernest; Feiler, Heidi S; Mills, Gordon B; Jaffe, Jake D; Ma'ayan, Avi; Birtwistle, Marc R; Sorger, Peter K; Korkola, James E; Gray, Joe W; Heiser, Laura M | Communications biology | 36207580 | 2022 Oct 07 |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills, Caitlin E; Subramanian, Kartik; Hafner, Marc; Niepel, Mario; Gerosa, Luca; Chung, Mirra; Victor, Chiara; Gaudio, Benjamin; Yapp, Clarence; Nirmal, Ajit J; Clark, Nicholas; Sorger, Peter K | Nature communications | 36376301 | 2022 Nov 14 |
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| A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity. | Mohammadi, Farnaz; Visagan, Shakthi; Gross, Sean M; Karginov, Luka; Lagarde, J C; Heiser, Laura M; Meyer, Aaron S | Communications biology | 36396800 | 2022 Nov 17 |
| JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states. | Stevens, Laura E; Peluffo, Guillermo; Qiu, Xintao; Temko, Daniel; Fassl, Anne; Li, Zheqi; Trinh, Anne; Seehawer, Marco; Jovanovic, Bojana; Aleckovic, Masa; Wilde, Callahan M; Geck, Renee C; Shu, Shaokun; Kingston, Natalie L; Harper, Nicholas W; Almendro, Vanessa; Pyke, Alanna L; Egri, Shawn B; Papanastasiou, Malvina; Clement, Kendell; Zhou, Ningxuan; Walker, Sarah; Salas, Jacqueline; Park, So Yeon; Frank, David A; Meissner, Alexander; Jaffe, Jacob D; Sicinski, Piotr; Toker, Alex; Michor, Franziska; Long, Henry W; Overmoyer, Beth A; Polyak, Kornelia | Cancer research | 36409824 | 2022 Nov 21 |
| Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. | Wu, Hua-Jun; Temko, Daniel; Maliga, Zoltan; Moreira, Andre L; Sei, Emi; Minussi, Darlan Conterno; Dean, Jamie; Lee, Charlotte; Xu, Qiong; Hochart, Guillaume; Jacobson, Connor A; Yapp, Clarence; Schapiro, Denis; Sorger, Peter K; Seeley, Erin H; Navin, Nicholas; Downey, Robert J; Michor, Franziska | Cell genomics | 36419822 | 2022 Aug 10 |
| An altered extracellular matrix-integrin interface contributes to Huntington's disease-associated CNS dysfunction in glial and vascular cells. | Hernandez, Sarah J; Lim, Ryan G; Onur, Tarik; Dane, Mark A; Smith, Rebecca; Wang, Keona; Jean, Grace En-Hway; Reyes-Ortiz, Andrea; Devlin, Kaylyn; Miramontes, Ricardo; Wu, Jie; Casale, Malcolm; Kilburn, David; Heiser, Laura M; Korkola, James E; Van Vactor, David; Botas, Juan; Thompson-Peer, Katherine L; Thompson, Leslie M | Human molecular genetics | 36547263 | 2023 Apr 20 |
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| Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects. | Gross, Sean M; Mohammadi, Farnaz; Sanchez-Aguila, Crystal; Zhan, Paulina J; Liby, Tiera A; Dane, Mark A; Meyer, Aaron S; Heiser, Laura M | Nature communications | 37301933 | 2023 Jun 10 |
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| Proteomic profiling across breast cancer cell lines and models. | Kalocsay, Marian; Berberich, Matthew J; Everley, Robert A; Nariya, Maulik K; Chung, Mirra; Gaudio, Benjamin; Victor, Chiara; Bradshaw, Gary A; Eisert, Robyn J; Hafner, Marc; Sorger, Peter K; Mills, Caitlin E; Subramanian, Kartik | Scientific data | 37542042 | 2023 Aug 04 |
| Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments. | Jokela, Tiina A; Dane, Mark A; Smith, Rebecca L; Devlin, Kaylyn L; Shalabi, Sundus; Lopez, Jennifer C; Miyano, Masaru; Stampfer, Martha R; Korkola, James E; Gray, Joe W; Heiser, Laura M; LaBarge, Mark A | Cellular signalling | 37935340 | 2024 Jan |
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