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The search results on this publication page are automated on a monthly schedule based on acknowledgment 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.
Library of Integrated Network-Based Cellular Signatures (LINCS) (371)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| 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 | 2022 Aug 10 | 36419822 | |
| 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 | 2022 Nov 21 | 36409824 | |
| APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. | Blanchard, Joel W; Akay, Leyla Anne; Davila-Velderrain, Jose; von Maydell, Djuna; Mathys, Hansruedi; Davidson, Shawn M; Effenberger, Audrey; Chen, Chih-Yu; Maner-Smith, Kristal; Hajjar, Ihab; Ortlund, Eric A; Bula, Michael; Agbas, Emre; Ng, Ayesha; Jiang, Xueqiao; Kahn, Martin; Blanco-Duque, Cristina; Lavoie, Nicolas; Liu, Liwang; Reyes, Ricardo; Lin, Yuan-Ta; Ko, Tak; R'Bibo, Lea; Ralvenius, William T; Bennett, David A; Cam, Hugh P; Kellis, Manolis; Tsai, Li-Huei | Nature | 2022 Nov | 36385529 | |
| 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 | 2022 Nov 14 | 36376301 | |
| 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 | 2022 Oct 07 | 36207580 | |
| Systematic replication enables normalization of high-throughput imaging assays. | Hunt, Gregory J; Dane, Mark A; Korkola, James E; Heiser, Laura M; Gagnon-Bartsch, Johann A | Bioinformatics (Oxford, England) | 2022 10 31 | 36063034 | |
| Connecting omics signatures and revealing biological mechanisms with iLINCS. | Pilarczyk, Marcin; Fazel-Najafabadi, Mehdi; Kouril, Michal; Shamsaei, Behrouz; Vasiliauskas, Juozas; Niu, Wen; Mahi, Naim; Zhang, Lixia; Clark, Nicholas A; Ren, Yan; White, Shana; Karim, Rashid; Xu, Huan; Biesiada, Jacek; Bennett, Mark F; Davidson, Sarah E; Reichard, John F; Roberts, Kurt; Stathias, Vasileios; Koleti, Amar; Vidovic, Dusica; Clarke, Daniel J B; Schürer, Stephan C; Ma'ayan, Avi; Meller, Jarek; Medvedovic, Mario | Nature communications | 2022 08 09 | 35945222 | |
| 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 | 2022 Jul 26 | 35881481 | |
| 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 | 2022 06 23 | 35737447 | |
| 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 | 2022 06 21 | 35729113 | |
| 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 | 2022 03 23 | 35322205 | |
| 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 | 2022 Mar 05 | 35248133 | |
| Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity. | Xiong, Yuguang; Liu, Tong; Chen, Tong; Hansen, Jens; Hu, Bin; Chen, Yibang; Jayaraman, Gomathi; Schürer, Stephan; Vidovic, Dusica; Goldfarb, Joseph; Sobie, Eric A; Birtwistle, Marc R; Iyengar, Ravi; Li, Hong; Azeloglu, Evren U | Scientific data | 2022 Jan 20 | 35058449 | |
| Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors. | Meharena, Hiruy S; Marco, Asaf; Dileep, Vishnu; Lockshin, Elana R; Akatsu, Grace Y; Mullahoo, James; Watson, L Ashley; Ko, Tak; Guerin, Lindsey N; Abdurrob, Fatema; Rengarajan, Shruthi; Papanastasiou, Malvina; Jaffe, Jacob D; Tsai, Li-Huei | Cell stem cell | 2022 01 06 | 34995493 | |
| A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals. | Schaniel, Christoph; Dhanan, Priyanka; Hu, Bin; Xiong, Yuguang; Raghunandan, Teeya; Gonzalez, David M; Dariolli, Rafael; D'Souza, Sunita L; Yadaw, Arjun S; Hansen, Jens; Jayaraman, Gomathi; Mathew, Bino; Machado, Moara; Berger, Seth I; Tripodig, Joseph; Najfeld, Vesna; Garg, Jalaj; Miller, Marc; Surlyn, Colleen S; Michelis, Katherine C; Tangirala, Neelima C; Weerahandi, Himali; Thomas, David C; Beaumont, Kristin G; Sebra, Robert; Mahajan, Milind; Schadt, Eric; Vidovic, Dusica; Schürer, Stephan C; Goldfarb, Joseph; Azeloglu, Evren U; Birtwistle, Marc R; Sobie, Eric A; Kovacic, Jason C; Dubois, Nicole C; Iyengar, Ravi | Stem cell reports | 2021 Oct 26 | 34739849 | |
| Functional Effects of Cardiomyocyte Injury in COVID-19. | Siddiq, Mustafa M; Chan, Angel T; Miorin, Lisa; Yadaw, Arjun S; Beaumont, Kristin G; Kehrer, Thomas; Cupic, Anastasija; White, Kris M; Tolentino, Rosa E; Hu, Bin; Stern, Alan D; Tavassoly, Iman; Hansen, Jens; Sebra, Robert; Martinez, Pedro; Prabha, Som; Dubois, Nicole; Schaniel, Christoph; Iyengar-Kapuganti, Rupa; Kukar, Nina; Giustino, Gennaro; Sud, Karan; Nirenberg, Sharon; Kovatch, Patricia; Albrecht, Randy A; Goldfarb, Joseph; Croft, Lori; McLaughlin, Maryann A; Argulian, Edgar; Lerakis, Stamatios; Narula, Jagat; García-Sastre, Adolfo; Iyengar, Ravi | Journal of virology | 2022 01 26 | 34669512 | |
| Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. | Labrie, Marilyne; Li, Allen; Creason, Allison; Betts, Courtney; Keck, Jamie; Johnson, Brett; Sivagnanam, Shamilene; Boniface, Christopher; Ma, Hongli; Blucher, Aurora; Chang, Young Hwan; Chin, Koei; Vuky, Jacqueline; Guimaraes, Alexander R; Downey, Molly; Lim, Jeong Youn; Gao, Lina; Siex, Kiara; Parmar, Swapnil; Kolodzie, Annette; Spellman, Paul T; Goecks, Jeremy; Coussens, Lisa M; Corless, Christopher L; Bergan, Raymond; Gray, Joe W; Mills, Gordon B; Mitri, Zahi I | NPJ precision oncology | 2021 Oct 19 | 34667258 | |
| Automatic Transformation and Integration to Improve Visualization and Discovery of Latent Effects in Imaging Data. | Hunt, Gregory J; Dane, Mark A; Korkola, James E; Heiser, Laura M; Gagnon-Bartsch, Johann A | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 2020 | 34531645 | |
| Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. | Markmiller, Sebastian; Sathe, Shashank; Server, Kari L; Nguyen, Thai B; Fulzele, Amit; Cody, Neal; Javaherian, Ashkan; Broski, Sara; Finkbeiner, Steven; Bennett, Eric J; Lécuyer, Eric; Yeo, Gene W | Cell reports | 2021 09 07 | 34496257 | |
| Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration. | Linsley, Jeremy W; Shah, Kevan; Castello, Nicholas; Chan, Michelle; Haddad, Dominik; Doric, Zak; Wang, Shijie; Leks, Wiktoria; Mancini, Jay; Oza, Viral; Javaherian, Ashkan; Nakamura, Ken; Kokel, David; Finkbeiner, Steven | Nature communications | 2021 09 06 | 34489414 | |
| Phenotyping Neurodegeneration in Human iPSCs. | Li, Jonathan; Fraenkel, Ernest | Annual review of biomedical data science | 2021 07 20 | 34465166 | |
| Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds. | Dele-Oni, Deborah O; Christianson, Karen E; Egri, Shawn B; Vaca Jacome, Alvaro Sebastian; DeRuff, Katherine C; Mullahoo, James; Sharma, Vagisha; Davison, Desiree; Ko, Tak; Bula, Michael; Blanchard, Joel; Young, Jennie Z; Litichevskiy, Lev; Lu, Xiaodong; Lam, Daniel; Asiedu, Jacob K; Toder, Caidin; Officer, Adam; Peckner, Ryan; MacCoss, Michael J; Tsai, Li-Huei; Carr, Steven A; Papanastasiou, Malvina; Jaffe, Jacob D | Scientific data | 2021 08 25 | 34433823 | |
| Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA. | Garay, Joseph P; Smith, Rebecca; Devlin, Kaylyn; Hollern, Daniel P; Liby, Tiera; Liu, Moqing; Boddapati, Shanta; Watson, Spencer S; Esch, Amanda; Zheng, Ting; Thompson, Wallace; Babcock, Darcie; Kwon, Sunjong; Chin, Koei; Heiser, Laura; Gray, Joe W; Korkola, James E | Breast cancer research : BCR | 2021 08 03 | 34344439 | |
| Nuclear accumulation of CHMP7 initiates nuclear pore complex injury and subsequent TDP-43 dysfunction in sporadic and familial ALS. | Coyne, Alyssa N; Baskerville, Victoria; Zaepfel, Benjamin L; Dickson, Dennis W; Rigo, Frank; Bennett, Frank; Lusk, C Patrick; Rothstein, Jeffrey D | Science translational medicine | 2021 07 28 | 34321318 | |
| Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. | Tognon, Cristina E; Sears, Rosalie C; Mills, Gordon B; Gray, Joe W; Tyner, Jeffrey W | Annual review of cancer biology | 2021 Mar | 34222745 | |
| Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma. | Lue, Hui-Wen; Derrick, Daniel S; Rao, Soumya; Van Gaest, Ahna; Cheng, Larry; Podolak, Jennifer; Lawson, Samantha; Xue, Changhui; Garg, Devin; White 3rd, Ralph; Ryan, Christopher W; Drake, Justin M; Ritz, Anna; Heiser, Laura M; Thomas, George V | Cell reports. Medicine | 2021 05 18 | 34095877 | |
| Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis. | Rossmann, Marlies P; Hoi, Karen; Chan, Victoria; Abraham, Brian J; Yang, Song; Mullahoo, James; Papanastasiou, Malvina; Wang, Ying; Elia, Ilaria; Perlin, Julie R; Hagedorn, Elliott J; Hetzel, Sara; Weigert, Raha; Vyas, Sejal; Nag, Partha P; Sullivan, Lucas B; Warren, Curtis R; Dorjsuren, Bilguujin; Greig, Eugenia Custo; Adatto, Isaac; Cowan, Chad A; Schreiber, Stuart L; Young, Richard A; Meissner, Alexander; Haigis, Marcia C; Hekimi, Siegfried; Carr, Steven A; Zon, Leonard I | Science (New York, N.Y.) | 2021 05 14 | 33986176 | |
| Protein structure-based gene expression signatures. | Rahman, Rayees; Zatorski, Nicole; Hansen, Jens; Xiong, Yuguang; van Hasselt, J G Coen; Sobie, Eric A; Birtwistle, Marc R; Azeloglu, Evren U; Iyengar, Ravi; Schlessinger, Avner | Proceedings of the National Academy of Sciences of the United States of America | 2021 May 11 | 33941686 | |
| Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. | Uzunangelov, Vladislav; Wong, Christopher K; Stuart, Joshua M | PLoS computational biology | 2021 Apr | 33861732 | |
| Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map. | Blasco, Andrea; Natoli, Ted; Endres, Michael G; Sergeev, Rinat A; Randazzo, Steven; Paik, Jin H; Macaluso, N J Maximilian; Narayan, Rajiv; Lu, Xiaodong; Peck, David; Lakhani, Karim R; Subramanian, Aravind | Bioinformatics (Oxford, England) | 2021 Apr 06 | 33824954 | |
| Integration of mechanical and ECM microenvironment signals in the determination of cancer stem cell states. | Jokela, Tiina A; LaBarge, Mark A | Current stem cell reports | 2021 Mar | 33777660 | |
| Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. | Vemulapalli, Vidyasiri; Chylek, Lily A; Erickson, Alison; Pfeiffer, Anamarija; Gabriel, Khal-Hentz; LaRochelle, Jonathan; Subramanian, Kartik; Cao, Ruili; Stegmaier, Kimberley; Mohseni, Morvarid; LaMarche, Matthew J; Acker, Michael G; Sorger, Peter K; Gygi, Steven P; Blacklow, Stephen C | eLife | 2021 Mar 23 | 33755016 | |
| Fresques, Tara; LaBarge, Mark A | Aging and cancer | 2020 Dec | 33693435 | ||
| Cell of all trades: oligodendrocyte precursor cells in synaptic, vascular, and immune function. | Akay, Leyla Anne; Effenberger, Audrey H; Tsai, Li-Huei | Genes & development | 2021 Feb 01 | 33526585 | |
| Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. | Färkkilä, Anniina; Rodríguez, Alfredo; Oikkonen, Jaana; Gulhan, Doga C; Nguyen, Huy; Domínguez, Julieta; Ramos, Sandra; Mills, Caitlin E; Pérez-Villatoro, Fernando; Lazaro, Jean-Bernard; Zhou, Jia; Clairmont, Connor S; Moreau, Lisa A; Park, Peter J; Sorger, Peter K; Hautaniemi, Sampsa; Frias, Sara; D'Andrea, Alan D | Cancer research | 2021 Jan 29 | 33514515 | |
| PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease. | Morozko, Eva L; Smith-Geater, Charlene; Monteys, Alejandro Mas; Pradhan, Subrata; Lim, Ryan G; Langfelder, Peter; Kachemov, Marketta; Hill, Austin; Stocksdale, Jennifer T; Cullis, Pieter R; Wu, Jie; Ochaba, Joseph; Miramontes, Ricardo; Chakraborty, Anirban; Hazra, Tapas K; Lau, Alice; St-Cyr, Sophie; Orellana, Iliana; Kopan, Lexi; Wang, Keona Q; Yeung, Sylvia; Leavitt, Blair R; Reidling, Jack C; Yang, X William; Steffan, Joan S; Davidson, Beverly L; Sarkar, Partha S; Thompson, Leslie M | Proceedings of the National Academy of Sciences of the United States of America | 2021 Jan 26 | 33468657 | |
| Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures. | Ho, Ritchie; Workman, Michael J; Mathkar, Pranav; Wu, Kathryn; Kim, Kevin J; O'Rourke, Jacqueline G; Kellogg, Mariko; Montel, Valerie; Banuelos, Maria G; Arogundade, Olubankole Aladesuyi; Diaz-Garcia, Sandra; Oheb, Daniel; Huang, Steven; Khrebtukova, Irina; Watson, Lisa; Ravits, John; Taylor, Kevin; Baloh, Robert H; Svendsen, Clive N | Cell systems | 2021 Feb 17 | 33382996 | |
| Investigational Treatments for COVID-19 may Increase Ventricular Arrhythmia Risk Through Drug Interactions. | Varshneya, Meera; Irurzun-Arana, Itziar; Campana, Chiara; Dariolli, Rafael; Gutierrez, Amy; Pullinger, Taylor K; Sobie, Eric A | CPT: pharmacometrics & systems pharmacology | 2021 02 | 33205613 | |
| Physiology of cardiomyocyte injury in COVID-19. | Siddiq, Mustafa M; Chan, Angel T; Miorin, Lisa; Yadaw, Arjun S; Beaumont, Kristin G; Kehrer, Thomas; White, Kris M; Cupic, Anastasija; Tolentino, Rosa E; Hu, Bin; Stern, Alan D; Tavassoly, Iman; Hansen, Jens; Martinez, Pedro; Dubois, Nicole; Schaniel, Christoph; Iyengar-Kapuganti, Rupa; Kukar, Nina; Giustino, Gennaro; Sud, Karan; Nirenberg, Sharon; Kovatch, Patricia; Goldfarb, Joseph; Croft, Lori; McLaughlin, Maryann A; Argulian, Edgar; Lerakis, Stamatios; Narula, Jagat; García-Sastre, Adolfo; Iyengar, Ravi | medRxiv : the preprint server for health sciences. | 2020 Nov 13; | 33200140 | |
| Avant-garde: an automated data-driven DIA data curation tool. | Vaca Jacome, Alvaro Sebastian; Peckner, Ryan; Shulman, Nicholas; Krug, Karsten; DeRuff, Katherine C; Officer, Adam; Christianson, Karen E; MacLean, Brendan; MacCoss, Michael J; Carr, Steven A; Jaffe, Jacob D | Nature methods. | 2020 Dec; | 33199889 | |
| Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. | Zhao, Wei; Li, Jun; Chen, Mei-Ju M; Luo, Yikai; Ju, Zhenlin; Nesser, Nicole K; Johnson-Camacho, Katie; Boniface, Christopher T; Lawrence, Yancey; Pande, Nupur T; Davies, Michael A; Herlyn, Meenhard; Muranen, Taru; Zervantonakis, Ioannis K; von Euw, Erika; Schultz, Andre; Kumar, Shwetha V; Korkut, Anil; Spellman, Paul T; Akbani, Rehan; Slamon, Dennis J; Gray, Joe W; Brugge, Joan S; Lu, Yiling; Mills, Gordon B; Liang, Han | Cancer cell | 2020 Dec 14 | 33157050 | |
| PICALM Rescues Endocytic Defects Caused by the Alzheimer's Disease Risk Factor APOE4. | Narayan, Priyanka; Sienski, Grzegorz; Bonner, Julia M; Lin, Yuan-Ta; Seo, Jinsoo; Baru, Valeriya; Haque, Aftabul; Milo, Blerta; Akay, Leyla A; Graziosi, Agnese; Freyzon, Yelena; Landgraf, Dirk; Hesse, William R; Valastyan, Julie; Barrasa, M Inmaculada; Tsai, Li-Huei; Lindquist, Susan | Cell reports | 2020 10 06 | 33027662 | |
| Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. | Yadaw, Arjun S; Li, Yan-Chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav | The Lancet. Digital health. | 2020 Oct; | 32984797 | |
| Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease. | Finkbeiner, Steven | Neurobiology of disease | 2020 12 | 32977020 | |
| Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity. | van Hasselt, J G Coen; Rahman, Rayees; Hansen, Jens; Stern, Alan; Shim, Jaehee V; Xiong, Yuguang; Pickard, Amanda; Jayaraman, Gomathi; Hu, Bin; Mahajan, Milind; Gallo, James M; Goldfarb, Joseph; Sobie, Eric A; Birtwistle, Marc R; Schlessinger, Avner; Azeloglu, Evren U; Iyengar, Ravi | Nature communications. | 2020 09 23; | 32968055 | |
| Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments. | Kimmel, Gregory J; Dane, Mark; Heiser, Laura M; Altrock, Philipp M; Andor, Noemi | Cancer research. | 2020 Nov 15; | 32938640 | |
| Systems biology approaches to measure and model phenotypic heterogeneity in cancer. | Meyer, Aaron S; Heiser, Laura M | Current opinion in systems biology. | 2019 Oct; | 32864511 | |
| Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. | Liu, Yan; Ferguson, Fleur M; Li, Lianbo; Kuljanin, Miljan; Mills, Caitlin E; Subramanian, Kartik; Harshbarger, Wayne; Gondi, Sudershan; Wang, Jinhua; Sorger, Peter K; Mancias, Joseph D; Gray, Nathanael S; Westover, Kenneth D | Cell chemical biology. | 2020 Aug 04; | 32755567 | |
| G4C2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD. | Coyne, Alyssa N; Zaepfel, Benjamin L; Hayes, Lindsey; Fitchman, Boris; Salzberg, Yuval; Luo, En-Ching; Bowen, Kelly; Trost, Hannah; Aigner, Stefan; Rigo, Frank; Yeo, Gene W; Harel, Amnon; Svendsen, Clive N; Sareen, Dhruv; Rothstein, Jeffrey D | Neuron | 2020 09 23 | 32673563 | |
| Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. | Corsello, Steven M; Nagari, Rohith T; Spangler, Ryan D; Rossen, Jordan; Kocak, Mustafa; Bryan, Jordan G; Humeidi, Ranad; Peck, David; Wu, Xiaoyun; Tang, Andrew A; Wang, Vickie M; Bender, Samantha A; Lemire, Evan; Narayan, Rajiv; Montgomery, Philip; Ben-David, Uri; Garvie, Colin W; Chen, Yejia; Rees, Matthew G; Lyons, Nicholas J; McFarland, James M; Wong, Bang T; Wang, Li; Dumont, Nancy; O'Hearn, Patrick J; Stefan, Eric; Doench, John G; Harrington, Caitlin N; Greulich, Heidi; Meyerson, Matthew; Vazquez, Francisca; Subramanian, Aravind; Roth, Jennifer A; Bittker, Joshua A; Boehm, Jesse S; Mader, Christopher C; Tsherniak, Aviad; Golub, Todd R | Nature cancer. | 2020 Feb; | 32613204 | |
| Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. | Blanchard, Joel W; Bula, Michael; Davila-Velderrain, Jose; Akay, Leyla Anne; Zhu, Lena; Frank, Alexander; Victor, Matheus B; Bonner, Julia Maeve; Mathys, Hansruedi; Lin, Yuan-Ta; Ko, Tak; Bennett, David A; Cam, Hugh P; Kellis, Manolis; Tsai, Li-Huei | Nature medicine. | 2020 06; | 32514169 | |
| Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions. | Varshneya, Meera; Irurzun-Arana, Itziar; Campana, Chiara; Dariolli, Rafael; Gutierrez, Amy; Pullinger, Taylor K; Sobie, Eric A | medRxiv : the preprint server for health sciences. | 2020 May 26; | 32511528 | |
| Clinical predictors of COVID-19 mortality. | Yadaw, Arjun S; Li, Yan-Chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav | medRxiv : the preprint server for health sciences. | 2020 May 22; | 32511520 | |
| Audit logs to enforce document integrity in Skyline and Panorama. | Rohde, Tobias; Chupalov, Rita; Shulman, Nicholas; Sharma, Vagisha; Eckels, Josh; Pratt, Brian S; MacCoss, Michael J; MacLean, Brendan X | Bioinformatics (Oxford, England) | 2020 08 01 | 32467974 | |
| Development of CDK2 and CDK5 Dual Degrader TMX-2172. | Teng, Mingxing; Jiang, Jie; He, Zhixiang; Kwiatkowski, Nicholas P; Donovan, Katherine A; Mills, Caitlin E; Victor, Chiara; Hatcher, John M; Fischer, Eric S; Sorger, Peter K; Zhang, Tinghu; Gray, Nathanael S | Angewandte Chemie (International ed. in English). | 2020 May 15; | 32415712 | |
| Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer. | Lee, Sanghoon; Zhao, Li; Rojas, Christine; Bateman, Nicholas W; Yao, Hui; Lara, Olivia D; Celestino, Joseph; Morgan, Margaret B; Nguyen, Tri V; Conrads, Kelly A; Rangel, Kelly M; Dood, Robert L; Hajek, Richard A; Fawcett, Gloria L; Chu, Randy A; Wilson, Katlin; Loffredo, Jeremy L; Viollet, Coralie; Jazaeri, Amir A; Dalgard, Clifton L; Mao, Xizeng; Song, Xingzhi; Zhou, Ming; Hood, Brian L; Banskota, Nirad; Wilkerson, Matthew D; Te, Jerez; Soltis, Anthony R; Roman, Kristin; Dunn, Andrew; Cordover, David; Eterovic, Agda Karina; Liu, Jinsong; Burks, Jared K; Baggerly, Keith A; Fleming, Nicole D; Lu, Karen H; Westin, Shannon N; Coleman, Robert L; Mills, Gordon B; Casablanca, Yovanni; Zhang, Jianhua; Conrads, Thomas P; Maxwell, George L; Futreal, P Andrew; Sood, Anil K | Cell reports. | 2020 Apr 14; | 32294438 | |
| How Machine Learning Will Transform Biomedicine. | Goecks, Jeremy; Jalili, Vahid; Heiser, Laura M; Gray, Joe W | Cell. | 2020 Apr 02; | 32243801 | |
| Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation. | Smith-Geater, Charlene; Hernandez, Sarah J; Lim, Ryan G; Adam, Miriam; Wu, Jie; Stocksdale, Jennifer T; Wassie, Brook T; Gold, Maxwell Philip; Wang, Keona Q; Miramontes, Ricardo; Kopan, Lexi; Orellana, Iliana; Joy, Shona; Kemp, Paul J; Allen, Nicholas D; Fraenkel, Ernest; Thompson, Leslie M | Stem cell reports. | 2020 03 10; | 32109367 | |
| Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS. | Mullahoo, James; Zhang, Terry; Clauser, Karl; Carr, Steven A; Jaffe, Jacob D; Papanastasiou, Malvina | Methods (San Diego, Calif.). | 2020 Jan 28; | 32004545 | |
| A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules. | Patel-Murray, Natasha L; Adam, Miriam; Huynh, Nhan; Wassie, Brook T; Milani, Pamela; Fraenkel, Ernest | Scientific reports. | 2020 Jan 22; | 31969612 | |
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| Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells. | Chopra, Sameer S; Jenney, Anne; Palmer, Adam; Niepel, Mario; Chung, Mirra; Mills, Caitlin; Sivakumaren, Sindhu Carmen; Liu, Qingsong; Chen, Jia-Yun; Yapp, Clarence; Asara, John M; Gray, Nathanael S; Sorger, Peter K | Cell systems. | 2020 Jan 22; | 31812693 | |
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| Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy. | Fang, Yong; McGrail, Daniel J; Sun, Chaoyang; Labrie, Marilyne; Chen, Xiaohua; Zhang, Dong; Ju, Zhenlin; Vellano, Christopher P; Lu, Yiling; Li, Yongsheng; Jeong, Kang Jin; Ding, Zhiyong; Liang, Jiyong; Wang, Steven W; Dai, Hui; Lee, Sanghoon; Sahni, Nidhi; Mercado-Uribe, Imelda; Kim, Tae-Beom; Chen, Ken; Lin, Shiaw-Yih; Peng, Guang; Westin, Shannon N; Liu, Jinsong; O'Connor, Mark J; Yap, Timothy A; Mills, Gordon B | Cancer cell. | 2019 Jun 10; | 31185210 | |
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| Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming. | Wang, Huan; Sheehan, Robert P; Palmer, Adam C; Everley, Robert A; Boswell, Sarah A; Ron-Harel, Noga; Ringel, Alison E; Holton, Kristina M; Jacobson, Connor A; Erickson, Alison R; Maliszewski, Laura; Haigis, Marcia C; Sorger, Peter K | Cell systems. | 2019 May 22; | 31078528 | |
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| Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. | Ferguson, Fleur M; Doctor, Zainab M; Ficarro, Scott B; Browne, Christopher M; Marto, Jarrod A; Johnson, Jared L; Yaron, Tomer M; Cantley, Lewis C; Kim, Nam Doo; Sim, Taebo; Berberich, Matthew J; Kalocsay, Marian; Sorger, Peter K; Gray, Nathanael S | Cell chemical biology. | 2019 Mar 11; | 30930164 | |
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| Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. | Heiser, Laura M; Mills, Gordon B; Gray, Joe W | Cancer cell. | 2019 Mar 18; | 30889376 | |
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| 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 E | Cell systems. | 2018 Mar 28; | 29550255 | |
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| 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 B | Cancer 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 A | Science 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, Sandro | Neuro-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, Brendan | Molecular & 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 A | Journal of proteome research. | 2018 Apr 06; | 29461835 | |
| Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis. | Tan, Hua; Zhou, Xiaobo | Methods in molecular biology (Clifton, N.J.). | 2018; | 29344882 | |
| A systems biology approach to studying the molecular mechanisms of osteoblastic differentiation under cytokine combination treatment. | Tan, Hua; Chen, Ruoying; Li, Wenyang; Zhao, Weiling; Zhang, Yuanyuan; Yang, Yunzhi; Su, Jing; Zhou, Xiaobo | NPJ Regenerative medicine. | 2017; | 29302342 | |
| Laser-fabricated cell patterning stencil for single cell analysis. | Messner, Jacob J; Glenn, Honor L; Meldrum, Deirdre R | BMC 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 M | Blood. | 2018 Feb 22; | 29233821 | |
| Prophetic Granger Causality to infer gene regulatory networks. | Carlin, Daniel E; Paull, Evan O; Graim, Kiley; Wong, Christopher K; Bivol, Adrian; Ryabinin, Peter; Ellrott, Kyle; Sokolov, Artem; Stuart, Joshua M | PloS one. | 2017; | 29211761 | |
| The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. | Keenan, Alexandra B; Jenkins, Sherry L; Jagodnik, Kathleen M; Koplev, Simon; He, Edward; Torre, Denis; Wang, Zichen; Dohlman, Anders B; Silverstein, Moshe C; Lachmann, Alexander; Kuleshov, Maxim V; Ma'ayan, Avi; Stathias, Vasileios; Terryn, Raymond; Cooper, Daniel; Forlin, Michele; Koleti, Amar; Vidovic, Dusica; Chung, Caty; Schürer, Stephan C; Vasiliauskas, Jouzas; Pilarczyk, Marcin; Shamsaei, Behrouz; Fazel, Mehdi; Ren, Yan; Niu, Wen; Clark, Nicholas A; White, Shana; Mahi, Naim; Zhang, Lixia; Kouril, Michal; Reichard, John F; Sivaganesan, Siva; Medvedovic, Mario; Meller, Jaroslaw; Koch, Rick J; Birtwistle, Marc R; Iyengar, Ravi; Sobie, Eric A; Azeloglu, Evren U; Kaye, Julia; Osterloh, Jeannette; Haston, Kelly; Kalra, Jaslin; Finkbiener, Steve; Li, Jonathan; Milani, Pamela; Adam, Miriam; Escalante-Chong, Renan; Sachs, Karen; Lenail, Alex; Ramamoorthy, Divya; Fraenkel, Ernest; Daigle, Gavin; Hussain, Uzma; Coye, Alyssa; Rothstein, Jeffrey; Sareen, Dhruv; Ornelas, Loren; Banuelos, Maria; Mandefro, Berhan; Ho, Ritchie; Svendsen, Clive N; Lim, Ryan G; Stocksdale, Jennifer; Casale, Malcolm S; Thompson, Terri G; Wu, Jie; Thompson, Leslie M; Dardov, Victoria; Venkatraman, Vidya; Matlock, Andrea; Van Eyk, Jennifer E; Jaffe, Jacob D; Papanastasiou, Malvina; Subramanian, Aravind; Golub, Todd R; Erickson, Sean D; Fallahi-Sichani, Mohammad; Hafner, Marc; Gray, Nathanael S; Lin, Jia-Ren; Mills, Caitlin E; Muhlich, Jeremy L; Niepel, Mario; Shamu, Caroline E; Williams, Elizabeth H; Wrobel, David; Sorger, Peter K; Heiser, Laura M; Gray, Joe W; Korkola, James E; Mills, Gordon B; LaBarge, Mark; Feiler, Heidi S; Dane, Mark A; Bucher, Elmar; Nederlof, Michel; Sudar, Damir; Gross, Sean; Kilburn, David F; Smith, Rebecca; Devlin, Kaylyn; Margolis, Ron; Derr, Leslie; Lee, Albert; Pillai, Ajay | Cell 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 R | Cell. | 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 G | PLoS 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, Dhruv | Scientific 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 K | Scientific 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 M | Cancer 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, Han | Cancer 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 K | Nature 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 C | Oncogene. | 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, Mario | BMC 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 A | Cell 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 A | Cell 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 A | Frontiers in physiology. | ; | 28951721 | |
| Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials. | Barrette, Anne Marie; Bouhaddou, Mehdi; Birtwistle, Marc R | ACS 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 K | Scientific 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, Xiaobo | Carcinogenesis. | 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, Wilhelm | Nature 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 J | The 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 J | Nature 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, Ivo | PLoS computational biology. | 2017 Jul; | 28759592 | |
| The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. | Pino, Lindsay K; Searle, Brian C; Bollinger, James G; Nunn, Brook; MacLean, Brendan; MacCoss, Michael J | Mass spectrometry reviews | 2020 05 | 28691345 | |
| 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, Mich | Annals of neurology. | 2017 Jul; | 28628244 | |
| Designing Drug-Response Experiments and Quantifying their Results. | Hafner, Marc; Niepel, Mario; Subramanian, Kartik; Sorger, Peter K | Current 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 K | Current protocols in chemical biology. | 2017 Jun 19; | 28628199 | |
| Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics. | Hafner, Marc; Niepel, Mario; Sorger, Peter K | Nature biotechnology. | 2017 Jun 07; | 28591115 | |
| AACR Project GENIE: Powering Precision Medicine through an International Consortium. | AACR Project GENIE Consortium | Cancer 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 B | Science 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, Sach | Bioinformatics (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 M | Cell 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, Lin | Cancer 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, Xiaobo | Bioinformatics (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 R | Nature 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 D | Neuron. | 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 M | BMC 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, Leonard | Science translational medicine. | 2017 Mar 29; | 28356511 | |
| A platform for high-throughput bioenergy production phenotype characterization in single cells. | Kelbauskas, Laimonas; Glenn, Honor; Anderson, Clifford; Messner, Jacob; Lee, Kristen B; Song, Ganquan; Houkal, Jeff; Su, Fengyu; Zhang, Liqiang; Tian, Yanqing; Wang, Hong; Bussey, Kimberly; Johnson, Roger H; Meldrum, Deirdre R | Scientific reports. | 2017 03 28; | 28349963 | |
| Functional variomics and network perturbation: connecting genotype to phenotype in cancer. | Yi, Song; Lin, Shengda; Li, Yongsheng; Zhao, Wei; Mills, Gordon B; Sahni, Nidhi | Nature reviews. Genetics. | 2017 Mar 27; | 28344341 | |
| Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice. | HD iPSC Consortium | Nature 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 N | Cell 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, Han | Cancer 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, James | Proceedings 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-Sébastien | eLife. | 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, Xiaojiang | Stem cell reports. | 2017 Feb 14; | 28132888 | |
| Genome-Scale Networks Link Neurodegenerative Disease Genes to ?-Synuclein through Specific Molecular Pathways. | Khurana, Vikram; Peng, Jian; Chung, Chee Yeun; Auluck, Pavan K; Fanning, Saranna; Tardiff, Daniel F; Bartels, Theresa; Koeva, Martina; Eichhorn, Stephen W; Benyamini, Hadar; Lou, Yali; Nutter-Upham, Andy; Baru, Valeriya; Freyzon, Yelena; Tuncbag, Nurcan; | Cell systems. | 2017 02 22; | 28131822 | |
| Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. | Fallahi-Sichani, Mohammad; Becker, Verena; Izar, Benjamin; Baker, Gregory J; Lin, Jia-Ren; Boswell, Sarah A; Shah, Parin; Rotem, Asaf; Garraway, Levi A; Sorger, Peter K | Molecular systems biology. | 2017 Jan 09; | 28069687 | |
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| 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. | 2014 Oct 17; | 2210-6 | 25089360 |
| 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. | 2015 Jan 8; | 183-96 | 25075558 |
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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, | Nature | 2014 Jul 31 | 616-20 | 25043025 |
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| A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. | Tang, Yangzhong | Current protocols in chemical biology | 2014 Mar | 5-Jan | 24652619 |
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| 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 | 2014 Jan | 42-52 | 24163374 |
| 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 | 2013 Dec | 9779-88 | 24090834 |
| 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 | 2013 Oct | 10-Jan | 24078772 |
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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, Xiaobo | IEEE journal of biomedical and health informatics | 2014 Mar | 484-91 | 24058033 |
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| 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 | 2013 Nov | 708-14 | 24013279 |
| 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) | 2013 Nov 1 | 2757-64 | 23986566 |
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