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 | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| Revealing disease-associated pathways by network integration of untargeted metabolomics. | Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E | Nature methods | 27479327 | Nat Methods | 2016 Sep |
| Network Modeling Identifies Patient-specific Pathways in Glioblastoma. | Tuncbag N, Milani P, Pokorny JL, Johnson H, Sio TT, Dalin S, Iyekegbe DO, White FM, Sarkaria JN, Fraenkel E | Scientific reports | 27354287 | Sci Rep | 2016 Jun 29 |
| Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits. | Lim RG, Quan C, Reyes-Ortiz AM, Lutz SE, Kedaigle AJ, Gipson TA, Wu J, Vatine GD, Stocksdale J, Casale MS, Svendsen CN, Fraenkel E, Housman DE, Agalliu D, Thompson LM | Cell reports | 28514657 | Cell Rep | 2017 May 16 |
| Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. | Markmiller S, Sathe S, Server KL, Nguyen TB, Fulzele A, Cody N, Javaherian A, Broski S, Finkbeiner S, Bennett EJ, Lécuyer E, Yeo GW | Cell reports | 34496257 | Cell Rep | 2021 Sep 7 |
| Differentiation of Human Induced Pluripotent Stem Cells to Mammary-like Organoids. | Qu Y, Han B, Gao B, Bose S, Gong Y, Wawrowsky K, Giuliano AE, Sareen D, Cui X | Stem cell reports | 28132888 | Stem Cell Reports | 2017 Feb 14 |
| The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. | Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A | Cell systems | 29199020 | Cell Syst | 2018 Jan 24 |
| Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice. | HD iPSC Consortium | Nature neuroscience | 28319609 | Nat Neurosci | 2017 May |
| Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. | Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL | Mobile DNA | 30564290 | Mob DNA | 2018 |
| Stress Granule Assembly Disrupts Nucleocytoplasmic Transport. | Zhang K, Daigle JG, Cunningham KM, Coyne AN, Ruan K, Grima JC, Bowen KE, Wadhwa H, Yang P, Rigo F, Taylor JP, Gitler AD, Rothstein JD, Lloyd TE | Cell | 29628143 | Cell | 2018 May 3 |
| PCSF: An R-package for network-based interpretation of high-throughput data. | Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I | PLoS computational biology | 28759592 | PLoS Comput Biol | 2017 Jul |
| A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules. | Patel-Murray NL, Adam M, Huynh N, Wassie BT, Milani P, Fraenkel E | Scientific reports | 31969612 | Sci Rep | 2020 Jan 22 |
| Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice. | Kedaigle AJ, Reidling JC, Lim RG, Adam M, Wu J, Wassie B, Stocksdale JT, Casale MS, Fraenkel E, Thompson LM | Human molecular genetics | 31696228 | Hum Mol Genet | 2020 Jan 15 |
| Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data. | Ramamoorthy D, Severson K, Ghosh S, Sachs K, Answer ALS, Glass JD, Fournier CN, Pooled Resource Open-Access ALS Clinical Trials Consortium, ALS/MND Natural History Consortium, Herrington TM, Berry JD, Ng K, Fraenkel E | Nature computational science | 38177466 | Nat Comput Sci | 2022 Sep |
| Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures. | Ho R, Workman MJ, Mathkar P, Wu K, Kim KJ, O'Rourke JG, Kellogg M, Montel V, Banuelos MG, Arogundade OA, Diaz-Garcia S, Oheb D, Huang S, Khrebtukova I, Watson L, Ravits J, Taylor K, Baloh RH, Svendsen CN | Cell systems | 33382996 | Cell Syst | 2021 Feb 17 |
| Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease. | Finkbeiner S | Neurobiology of disease | 32977020 | Neurobiol Dis | 2020 Dec |
| PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease. | Morozko EL, Smith-Geater C, Monteys AM, Pradhan S, Lim RG, Langfelder P, Kachemov M, Kulkarni JA, Zaifman J, Hill A, Stocksdale JT, Cullis PR, Wu J, Ochaba J, Miramontes R, Chakraborty A, Hazra TK, Lau A, St-Cyr S, Orellana I, Kopan L, Wang KQ, Yeung S, Leavitt BR, Reidling JC, Yang XW, Steffan JS, Davidson BL, Sarkar PS, Thompson LM | Proceedings of the National Academy of Sciences of the United States of America | 33468657 | Proc Natl Acad Sci U S A | 2021 Jan 26 |
| Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. | Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S | Cell systems | 28131822 | Cell Syst | 2017 Feb 22 |
| Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases. | Haston KM, Finkbeiner S | Annual review of pharmacology and toxicology | 26514199 | Annu Rev Pharmacol Toxicol | 2016 |
| Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. | Milani P, Escalante-Chong R, Shelley BC, Patel-Murray NL, Xin X, Adam M, Mandefro B, Sareen D, Svendsen CN, Fraenkel E | Scientific reports | 27146274 | Sci Rep | 2016 May 5 |
| A Roadmap to Successful Clinical Proteomics. | Wright I, Van Eyk JE | Clinical chemistry | 27864386 | Clin Chem | 2017 Jan |
| Phosphorylated neurofilament heavy chain: A biomarker of survival for C9ORF72-associated amyotrophic lateral sclerosis. | Gendron TF, C9ORF72 Neurofilament Study Group, Daughrity LM, Heckman MG, Diehl NN, Wuu J, Miller TM, Pastor P, Trojanowski JQ, Grossman M, Berry JD, Hu WT, Ratti A, Benatar M, Silani V, Glass JD, Floeter MK, Jeromin A, Boylan KB, Petrucelli L | Annals of neurology | 28628244 | Ann Neurol | 2017 Jul |
| Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. | Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E | PLoS computational biology | 27096930 | PLoS Comput Biol | 2016 Apr |
| Methods for SWATH™: Data Independent Acquisition on TripleTOF Mass Spectrometers. | Holewinski RJ, Parker SJ, Matlock AD, Venkatraman V, Van Eyk JE | Methods in molecular biology (Clifton, N.J.) | 26867750 | Methods Mol Biol | 2016 |
| Cell death assays for neurodegenerative disease drug discovery. | Linsley JW, Reisine T, Finkbeiner S | Expert opinion on drug discovery | 31179783 | Expert Opin Drug Discov | 2019 Sep |
| Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. | Köksal AS, Beck K, Cronin DR, McKenna A, Camp ND, Srivastava S, MacGilvray ME, Bodík R, Wolf-Yadlin A, Fraenkel E, Fisher J, Gitter A | Cell reports | 30257219 | Cell Rep | 2018 Sep 25 |
| Stem cell transplantation for amyotrophic lateral sclerosis. | Baloh RH, Glass JD, Svendsen CN | Current opinion in neurology | 30080719 | Curr Opin Neurol | 2018 Oct |
| The ESCRT-III protein VPS4, but not CHMP4B or CHMP2B, is pathologically increased in familial and sporadic ALS neuronal nuclei. | Coyne AN, Rothstein JD | Acta neuropathologica communications | 34281622 | Acta Neuropathol Commun | 2021 Jul 19 |
| Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration. | Linsley JW, Shah K, Castello N, Chan M, Haddad D, Doric Z, Wang S, Leks W, Mancini J, Oza V, Javaherian A, Nakamura K, Kokel D, Finkbeiner S | Nature communications | 34489414 | Nat Commun | 2021 Sep 6 |
| An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. | NeuroLINCS Consortium, Li J, Lim RG, Kaye JA, Dardov V, Coyne AN, Wu J, Milani P, Cheng A, Thompson TG, Ornelas L, Frank A, Adam M, Banuelos MG, Casale M, Cox V, Escalante-Chong R, Daigle JG, Gomez E, Hayes L, Holewenski R, Lei S, Lenail A, Lima L, Mandefro B, Matlock A, Panther L, Patel-Murray NL, Pham J, Ramamoorthy D, Sachs K, Shelley B, Stocksdale J, Trost H, Wilhelm M, Venkatraman V, Wassie BT, Wyman S, Yang S, NYGC ALS Consortium, Van Eyk JE, Lloyd TE, Finkbeiner S, Fraenkel E, Rothstein JD, Sareen D, Svendsen CN, Thompson LM | iScience | 34746695 | iScience | 2021 Nov 19 |
| Poly(GP) proteins are a useful pharmacodynamic marker for C9ORF72-associated amyotrophic lateral sclerosis. | Gendron TF, Chew J, Stankowski JN, Hayes LR, Zhang YJ, Prudencio M, Carlomagno Y, Daughrity LM, Jansen-West K, Perkerson EA, O'Raw A, Cook C, Pregent L, Belzil V, van Blitterswijk M, Tabassian LJ, Lee CW, Yue M, Tong J, Song Y, Castanedes-Casey M, Rousseau L, Phillips V, Dickson DW, Rademakers R, Fryer JD, Rush BK, Pedraza O, Caputo AM, Desaro P, Palmucci C, Robertson A, Heckman MG, Diehl NN, Wiggs E, Tierney M, Braun L, Farren J, Lacomis D, Ladha S, Fournier CN, McCluskey LF, Elman LB, Toledo JB, McBride JD, Tiloca C, Morelli C, Poletti B, Solca F, Prelle A, Wuu J, Jockel-Balsarotti J, Rigo F, Ambrose C, Datta A, Yang W, Raitcheva D, Antognetti G, McCampbell A, Van Swieten JC, Miller BL, Boxer AL, Brown RH, Bowser R, Miller TM, Trojanowski JQ, Grossman M, Berry JD, Hu WT, Ratti A, Traynor BJ, Disney MD, Benatar M, Silani V, Glass JD, Floeter MK, Rothstein JD, Boylan KB, Petrucelli L | Science translational medicine | 28356511 | Sci Transl Med | 2017 Mar 29 |
| Mutant Huntingtin Disrupts the Nuclear Pore Complex. | Grima JC, Daigle JG, Arbez N, Cunningham KC, Zhang K, Ochaba J, Geater C, Morozko E, Stocksdale J, Glatzer JC, Pham JT, Ahmed I, Peng Q, Wadhwa H, Pletnikova O, Troncoso JC, Duan W, Snyder SH, Ranum LPW, Thompson LM, Lloyd TE, Ross CA, Rothstein JD | Neuron | 28384479 | Neuron | 2017 Apr 5 |
| Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Have Reduced Expression of Proteins Important in Neuronal Development. | Fuller HR, Mandefro B, Shirran SL, Gross AR, Kaus AS, Botting CH, Morris GE, Sareen D | Frontiers in cellular neuroscience | 26793058 | Front Cell Neurosci | 2015 |
| Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. | Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett CF, Ares M Jr, Burge CB, Taylor JP, Rigo F, Yeo GW | Neuron | 27773581 | Neuron | 2016 Nov 23 |
| ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks. | Ho R, Sances S, Gowing G, Amoroso MW, O'Rourke JG, Sahabian A, Wichterle H, Baloh RH, Sareen D, Svendsen CN | Nature neuroscience | 27428653 | Nat Neurosci | 2016 Sep |
| Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease. | Vazquez-Arango P, Vowles J, Browne C, Hartfield E, Fernandes HJ, Mandefro B, Sareen D, James W, Wade-Martins R, Cowley SA, Murphy S, O'Reilly D | Nucleic acids research | 27536002 | Nucleic Acids Res | 2016 Dec 15 |
| C9ORF72 poly(GA) aggregates sequester and impair HR23 and nucleocytoplasmic transport proteins. | Zhang YJ, Gendron TF, Grima JC, Sasaguri H, Jansen-West K, Xu YF, Katzman RB, Gass J, Murray ME, Shinohara M, Lin WL, Garrett A, Stankowski JN, Daughrity L, Tong J, Perkerson EA, Yue M, Chew J, Castanedes-Casey M, Kurti A, Wang ZS, Liesinger AM, Baker JD, Jiang J, Lagier-Tourenne C, Edbauer D, Cleveland DW, Rademakers R, Boylan KB, Bu G, Link CD, Dickey CA, Rothstein JD, Dickson DW, Fryer JD, Petrucelli L | Nature neuroscience | 26998601 | Nat Neurosci | 2016 May |
| Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. | Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt JJFA, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya, Smith BN, Marangi G, Topp SD, Abramzon Y, Gkazi AS, Eicher JD, Kenna A, ITALSGEN Consortium, Mora G, Calvo A, Mazzini L, Riva N, Mandrioli J, Caponnetto C, Battistini S, Volanti P, La Bella V, Conforti FL, Borghero G, Messina S, Simone IL, Trojsi F, Salvi F, Logullo FO, D'Alfonso S, Corrado L, Capasso M, Ferrucci L, Genomic Translation for ALS Care (GTAC) Consortium, Moreno CAM, Kamalakaran S, Goldstein DB, ALS Sequencing Consortium, Gitler AD, Harris T, Myers RM, NYGC ALS Consortium, Phatnani H, Musunuri RL, Evani US, Abhyankar A, Zody MC, Answer ALS Foundation, Kaye J, Finkbeiner S, Wyman SK, LeNail A, Lima L, Fraenkel E, Svendsen CN, Thompson LM, Van Eyk JE, Berry JD, Miller TM, Kolb SJ, Cudkowicz M, Baxi E, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, Benatar M, Taylor JP, Rampersaud E, Wu G, Wuu J, SLAGEN Consortium, Lauria G, Verde F, Fogh I, Tiloca C, Comi GP, Sorarù G, Cereda C, French ALS Consortium, Corcia P, Laaksovirta H, Myllykangas L, Jansson L, Valori M, Ealing J, Hamdalla H, Rollinson S, Pickering-Brown S, Orrell RW, Sidle KC, Malaspina A, Hardy J, Singleton AB, Johnson JO, Arepalli S, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Al-Sarraj S, King A, Troakes C, Vance C, de Belleroche J, Baas F, Ten Asbroek ALMA, Muñoz-Blanco JL, Hernandez DG, Ding J, Gibbs JR, Scholz SW, Floeter MK, Campbell RH, Landi F, Bowser R, Pulst SM, Ravits JM, MacGowan DJL, Kirby J, Pioro EP, Pamphlett R, Broach J, Gerhard G, Dunckley TL, Brady CB, Kowall NW, Troncoso JC, Le Ber I, Mouzat K, Lumbroso S, Heiman-Patterson TD, Kamel F, Van Den Bosch L, Baloh RH, Strom TM, Meitinger T, Shatunov A, Van Eijk KR, de Carvalho M, Kooyman M, Middelkoop B, Moisse M, McLaughlin RL, Van Es MA, Weber M, Boylan KB, Van Blitterswijk M, Rademakers R, Morrison KE, Basak AN, Mora JS, Drory VE, Shaw PJ, Turner MR, Talbot K, Hardiman O, Williams KL, Fifita JA, Nicholson GA, Blair IP, Rouleau GA, Esteban-Pérez J, García-Redondo A, Al-Chalabi A, Project MinE ALS Sequencing Consortium, Rogaeva E, Zinman L, Ostrow LW, Maragakis NJ, Rothstein JD, Simmons Z, Cooper-Knock J, Brice A, Goutman SA, Feldman EL, Gibson SB, Taroni F, Ratti A, Gellera C, Van Damme P, Robberecht W, Fratta P, Sabatelli M, Lunetta C, Ludolph AC, Andersen PM, Weishaupt JH, Camu W, Trojanowski JQ, Van Deerlin VM, Brown RH Jr, van den Berg LH, Veldink JH, Harms MB, Glass JD, Stone DJ, Tienari P, Silani V, Chiò A, Shaw CE, Traynor BJ, Landers JE | Neuron | 29566793 | Neuron | 2018 Mar 21 |
| In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images. | Christiansen EM, Yang SJ, Ando DM, Javaherian A, Skibinski G, Lipnick S, Mount E, O'Neil A, Shah K, Lee AK, Goyal P, Fedus W, Poplin R, Esteva A, Berndl M, Rubin LL, Nelson P, Finkbeiner S | Cell | 29656897 | Cell | 2018 Apr 19 |
| Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites. | HD iPSC Consortium | Human molecular genetics | 30768179 | Hum Mol Genet | 2020 Jul 21 |
| Cell-based screening: extracting meaning from complex data. | Finkbeiner S, Frumkin M, Kassner PD | Neuron | 25856492 | Neuron | 2015 Apr 8 |
| Phenotyping Neurodegeneration in Human iPSCs. | Li J, Fraenkel E | Annual review of biomedical data science | 34465166 | Annu Rev Biomed Data Sci | 2021 Jul 20 |
| Nuclear accumulation of CHMP7 initiates nuclear pore complex injury and subsequent TDP-43 dysfunction in sporadic and familial ALS. | Coyne AN, Baskerville V, Zaepfel BL, Dickson DW, Rigo F, Bennett F, Lusk CP, Rothstein JD | Science translational medicine | 34321318 | Sci Transl Med | 2021 Jul 28 |
| The C9orf72 repeat expansion disrupts nucleocytoplasmic transport. | Zhang K, Donnelly CJ, Haeusler AR, Grima JC, Machamer JB, Steinwald P, Daley EL, Miller SJ, Cunningham KM, Vidensky S, Gupta S, Thomas MA, Hong I, Chiu SL, Huganir RL, Ostrow LW, Matunis MJ, Wang J, Sattler R, Lloyd TE, Rothstein JD | Nature | 26308891 | Nature | 2015 Sep 3 |
| IKKβ slows Huntington's disease progression in R6/1 mice. | Ochaba J, Fote G, Kachemov M, Thein S, Yeung SY, Lau AL, Hernandez S, Lim RG, Casale M, Neel MJ, Monuki ES, Reidling J, Housman DE, Thompson LM, Steffan JS | Proceedings of the National Academy of Sciences of the United States of America | 31088970 | Proc Natl Acad Sci U S A | 2019 May 28 |
| A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. | Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium, Gray JW, Birtwistle MR, Heiser LM, Sorger PK | Cell systems | 31302153 | Cell Syst | 2019 Jul 24 |
| A three-groups model for high-throughput survival screens. | Shaby BA, Skibinski G, Ando M, LaDow ES, Finkbeiner S | Biometrics | 26821783 | Biometrics | 2016 Sep |
| Assessing microscope image focus quality with deep learning. | Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar A, Finkbeiner S, Nelson P | BMC bioinformatics | 29540156 | BMC Bioinformatics | 2018 Mar 15 |
| Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy. | Woo CJ, Maier VK, Davey R, Brennan J, Li G, Brothers J 2nd, Schwartz B, Gordo S, Kasper A, Okamoto TR, Johansson HE, Mandefro B, Sareen D, Bialek P, Chau BN, Bhat B, Bullough D, Barsoum J | Proceedings of the National Academy of Sciences of the United States of America | 28193854 | Proc Natl Acad Sci U S A | 2017 Feb 21 |
| Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation. | Smith-Geater C, Hernandez SJ, Lim RG, Adam M, Wu J, Stocksdale JT, Wassie BT, Gold MP, Wang KQ, Miramontes R, Kopan L, Orellana I, Joy S, Kemp PJ, Allen ND, Fraenkel E, Thompson LM | Stem cell reports | 32109367 | Stem Cell Reports | 2020 Mar 10 |
| G(4)C(2) Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD. | Coyne AN, Zaepfel BL, Hayes L, Fitchman B, Salzberg Y, Luo EC, Bowen K, Trost H, Aigner S, Rigo F, Yeo GW, Harel A, Svendsen CN, Sareen D, Rothstein JD | Neuron | 32673563 | Neuron | 2020 Sep 23 |
| NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency. | Matlock AD, Vaibhav V, Holewinski R, Venkatraman V, Dardov V, Manalo DM, Shelley B, Ornelas L, Banuelos M, Mandefro B, Escalante-Chong R, Li J, Finkbeiner S, Fraenkel E, Rothstein J, Thompson L, Sareen D, Svendsen CN, NIH NeuroLINCS Consortium, Van Eyk JE | Scientific data | 36631473 | Sci Data | 2023 Jan 11 |
| Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins. | Fote GM, Eapen VV, Lim RG, Yu C, Salazar L, McClure NR, McKnight J, Nguyen TB, Heath MC, Lau AL, Villamil MA, Miramontes R, Kratter IH, Finkbeiner S, Reidling JC, Paulo JA, Kaiser P, Huang L, Housman DE, Thompson LM, Steffan JS | Proceedings of the National Academy of Sciences of the United States of America | 39074279 | Proc Natl Acad Sci U S A | 2024 Aug 6 |
| A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. | Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma'ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM | Communications biology | 36207580 | Commun Biol | 2022 Oct 7 |
| A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. | Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR | Cell | 29195078 | Cell | 2017 Nov 30 |
| The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices. | Enache OM, Lahr DL, Natoli TE, Litichevskiy L, Wadden D, Flynn C, Gould J, Asiedu JK, Narayan R, Subramanian A | Bioinformatics (Oxford, England) | 30203022 | Bioinformatics | 2019 Apr 15 |
| The Drug Repurposing Hub: a next-generation drug library and information resource. | Corsello SM, Bittker JA, Liu Z, Gould J, McCarren P, Hirschman JE, Johnston SE, Vrcic A, Wong B, Khan M, Asiedu J, Narayan R, Mader CC, Subramanian A, Golub TR | Nature medicine | 28388612 | Nat Med | 2017 Apr 7 |
| Drug and disease signature integration identifies synergistic combinations in glioblastoma. | Stathias V, Jermakowicz AM, Maloof ME, Forlin M, Walters W, Suter RK, Durante MA, Williams SL, Harbour JW, Volmar CH, Lyons NJ, Wahlestedt C, Graham RM, Ivan ME, Komotar RJ, Sarkaria JN, Subramanian A, Golub TR, Schürer SC, Ayad NG | Nature communications | 30552330 | Nat Commun | 2018 Dec 14 |
| Genomic evolution of cancer models: perils and opportunities. | Ben-David U, Beroukhim R, Golub TR | Nature reviews. Cancer | 30578414 | Nat Rev Cancer | 2019 Feb |
| Genetic and transcriptional evolution alters cancer cell line drug response. | Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR | Nature | 30089904 | Nature | 2018 Aug |
| Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. | Corsello SM, Nagari RT, Spangler RD, Rossen J, Kocak M, Bryan JG, Humeidi R, Peck D, Wu X, Tang AA, Wang VM, Bender SA, Lemire E, Narayan R, Montgomery P, Ben-David U, Garvie CW, Chen Y, Rees MG, Lyons NJ, McFarland JM, Wong BT, Wang L, Dumont N, O'Hearn PJ, Stefan E, Doench JG, Harrington CN, Greulich H, Meyerson M, Vazquez F, Subramanian A, Roth JA, Bittker JA, Boehm JS, Mader CC, Tsherniak A, Golub TR | Nature cancer | 32613204 | Nat Cancer | 2020 Feb |
| Targeting MTHFD2 in acute myeloid leukemia. | Pikman Y, Puissant A, Alexe G, Furman A, Chen LM, Frumm SM, Ross L, Fenouille N, Bassil CF, Lewis CA, Ramos A, Gould J, Stone RM, DeAngelo DJ, Galinsky I, Clish CB, Kung AL, Hemann MT, Vander Heiden MG, Banerji V, Stegmaier K | The Journal of experimental medicine | 27325891 | J Exp Med | 2016 Jun 27 |
| A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations. | Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD | Cell systems | 29655704 | Cell Syst | 2018 Apr 25 |
| Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map. | Smith I, Greenside PG, Natoli T, Lahr DL, Wadden D, Tirosh I, Narayan R, Root DE, Golub TR, Subramanian A, Doench JG | PLoS biology | 29190685 | PLoS Biol | 2017 Nov |
| Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis. | Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK | Molecular systems biology | 25814555 | Mol Syst Biol | 2015 Mar 26 |
| Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. | Wang J, Erazo T, Ferguson FM, Buckley DL, Gomez N, Muñoz-Guardiola P, Diéguez-Martínez N, Deng X, Hao M, Massefski W, Fedorov O, Offei-Addo NK, Park PM, Dai L, DiBona A, Becht K, Kim ND, McKeown MR, Roberts JM, Zhang J, Sim T, Alessi DR, Bradner JE, Lizcano JM, Blacklow SC, Qi J, Xu X, Gray NS | ACS chemical biology | 30102854 | ACS Chem Biol | 2018 Sep 21 |
| A High Content Screen in Macrophages Identifies Small Molecule Modulators of STING-IRF3 and NFkB Signaling. | Koch PD, Miller HR, Yu G, Tallarico JA, Sorger PK, Wang Y, Feng Y, Thomas JR, Ross NT, Mitchison T | ACS chemical biology | 29553248 | ACS Chem Biol | 2018 Apr 20 |
| Characterization of a highly selective inhibitor of the Aurora kinases. | Ferguson FM, Doctor ZM, Chaikuad A, Sim T, Kim ND, Knapp S, Gray NS | Bioorganic & medicinal chemistry letters | 28818446 | Bioorg Med Chem Lett | 2017 Sep 15 |
| Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. | Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS | Science signaling | 27405981 | Sci Signal | 2016 Jul 12 |
| Proteomic profiling across breast cancer cell lines and models. | Kalocsay M, Berberich MJ, Everley RA, Nariya MK, Chung M, Gaudio B, Victor C, Bradshaw GA, Eisert RJ, Hafner M, Sorger PK, Mills CE, Subramanian K | Scientific data | 37542042 | Sci Data | 2023 Aug 4 |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK | Nature communications | 36376301 | Nat Commun | 2022 Nov 14 |
| Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. | Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD | Cell chemical biology | 32755567 | Cell Chem Biol | 2020 Oct 15 |
| Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. | Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK | Cell chemical biology | 30956147 | Cell Chem Biol | 2019 May 16 |
| Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. | Lin JR, Fallahi-Sichani M, Sorger PK | Nature communications | 26399630 | Nat Commun | 2015 Sep 24 |
| Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation. | Jones DS, Jenney AP, Swantek JL, Burke JM, Lauffenburger DA, Sorger PK | Nature chemical biology | 27820799 | Nat Chem Biol | 2017 Jan |
| Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. | Lin JR, Fallahi-Sichani M, Chen JY, Sorger PK | Current protocols in chemical biology | 27925668 | Curr Protoc Chem Biol | 2016 Dec 7 |
| Structure-guided development of covalent TAK1 inhibitors. | Tan L, Gurbani D, Weisberg EL, Hunter JC, Li L, Jones DS, Ficarro SB, Mowafy S, Tam CP, Rao S, Du G, Griffin JD, Sorger PK, Marto JA, Westover KD, Gray NS | Bioorganic & medicinal chemistry | 28011204 | Bioorg Med Chem | 2017 Feb 1 |
| Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. | Tan L, Gurbani D, Weisberg EL, Jones DS, Rao S, Singer WD, Bernard FM, Mowafy S, Jenney A, Du G, Nonami A, Griffin JD, Lauffenburger DA, Westover KD, Sorger PK, Gray NS | Bioorganic & medicinal chemistry | 28038940 | Bioorg Med Chem | 2017 Feb 15 |
| Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. | Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK | Molecular systems biology | 28069687 | Mol Syst Biol | 2017 Jan 9 |
| Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics. | Hafner M, Niepel M, Sorger PK | Nature biotechnology | 28591115 | Nat Biotechnol | 2017 Jun 7 |
| GRcalculator: an online tool for calculating and mining dose-response data. | Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M | BMC cancer | 29065900 | BMC Cancer | 2017 Oct 24 |
| Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition. | Jones DS, Jenney AP, Joughin BA, Sorger PK, Lauffenburger DA | Science signaling | 29511118 | Sci Signal | 2018 Mar 6 |
| Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. | Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK | eLife | 29993362 | Elife | 2018 Jul 11 |
| A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line. | Song Y, Subramanian K, Berberich MJ, Rodriguez S, Latorre IJ, Luria CM, Everley R, Albers MW, Mitchison TJ, Sorger PK | Scientific data | 30778261 | Sci Data | 2019 Feb 19 |
| PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction. | Graim K, Friedl V, Houlahan KE, Stuart JM | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 30864317 | Pac Symp Biocomput | 2019 |
| Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. | Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK | Cell chemical biology | 31178407 | Cell Chem Biol | 2019 Aug 15 |
| A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification. | Browne CM, Jiang B, Ficarro SB, Doctor ZM, Johnson JL, Card JD, Sivakumaren SC, Alexander WM, Yaron TM, Murphy CJ, Kwiatkowski NP, Zhang T, Cantley LC, Gray NS, Marto JA | Journal of the American Chemical Society | 30518210 | J Am Chem Soc | 2019 Jan 9 |
| Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming. | Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK | Cell systems | 31078528 | Cell Syst | 2019 May 22 |
| Multi omics analysis of fibrotic kidneys in two mouse models. | Pavkovic M, Pantano L, Gerlach CV, Brutus S, Boswell SA, Everley RA, Shah JV, Sui SH, Vaidya VS | Scientific data | 31201317 | Sci Data | 2019 Jun 14 |
| Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics. | Hafner M, Heiser LM, Williams EH, Niepel M, Wang NJ, Korkola JE, Gray JW, Sorger PK | Scientific data | 29112189 | Sci Data | 2017 Nov 7 |
| Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials. | Barrette AM, Bouhaddou M, Birtwistle MR | ACS chemical neuroscience | 28950062 | ACS Chem Neurosci | 2018 Jan 17 |
| Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. | Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK | eLife | 35737447 | Elife | 2022 Jun 23 |
| Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. | Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D'Andrea AD | Cancer research | 33514515 | Cancer Res | 2021 May 15 |
| Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. | Wu HJ, Temko D, Maliga Z, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ, Michor F | Cell genomics | 36419822 | Cell Genom | 2022 Aug 10 |
| N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells. | Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, Witte ON | Cancer cell | 27050099 | Cancer Cell | 2016 Apr 11 |
| Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells. | Niepel M, Hafner M, Chung M, Sorger PK | Current protocols in chemical biology | 28628199 | Curr Protoc Chem Biol | 2017 Jun 19 |
| Designing Drug-Response Experiments and Quantifying their Results. | Hafner M, Niepel M, Subramanian K, Sorger PK | Current protocols in chemical biology | 28628201 | Curr Protoc Chem Biol | 2017 Jun 19 |
| Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. | Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP | Journal of proteome research | 27978624 | J Proteome Res | 2017 Feb 3 |
| A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. | Erickson BK, Rose CM, Braun CR, Erickson AR, Knott J, McAlister GC, Wühr M, Paulo JA, Everley RA, Gygi SP | Molecular cell | 28065596 | Mol Cell | 2017 Jan 19 |
| Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane. | Werbin JL, Avendaño MS, Becker V, Jungmann R, Yin P, Danuser G, Sorger PK | Scientific reports | 28939861 | Sci Rep | 2017 Sep 22 |
| MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments. | Berberich MJ, Paulo JA, Everley RA | Journal of proteome research | 29461835 | J Proteome Res | 2018 Apr 6 |
| A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. | Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA | Cell systems | 28988802 | Cell Syst | 2017 Nov 22 |
| Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. | Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma'ayan A, Sorger PK | Nature communications | 29084964 | Nat Commun | 2017 Oct 30 |
| Development of CDK2 and CDK5 Dual Degrader TMX-2172. | Teng M, Jiang J, He Z, Kwiatkowski NP, Donovan KA, Mills CE, Victor C, Hatcher JM, Fischer ES, Sorger PK, Zhang T, Gray NS | Angewandte Chemie (International ed. in English) | 32415712 | Angew Chem Int Ed Engl | 2020 Aug 10 |
| Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. | Hafner M, Niepel M, Chung M, Sorger PK | Nature methods | 27135972 | Nat Methods | 2016 Jun |
| A High-Throughput Immune-Oncology Screen Identifies EGFR Inhibitors as Potent Enhancers of Antigen-Specific Cytotoxic T-lymphocyte Tumor Cell Killing. | Lizotte PH, Hong RL, Luster TA, Cavanaugh ME, Taus LJ, Wang S, Dhaneshwar A, Mayman N, Yang A, Kulkarni M, Badalucco L, Fitzpatrick E, Kao HF, Kuraguchi M, Bittinger M, Kirschmeier PT, Gray NS, Barbie DA, Jänne PA | Cancer immunology research | 30242021 | Cancer Immunol Res | 2018 Dec |
| Development and Characterization of a Wee1 Kinase Degrader. | Li Z, Pinch BJ, Olson CM, Donovan KA, Nowak RP, Mills CE, Scott DA, Doctor ZM, Eleuteri NA, Chung M, Sorger PK, Fischer ES, Gray NS | Cell chemical biology | 31735695 | Cell Chem Biol | 2020 Jan 16 |
| Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. | Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D | eLife | 31961323 | Elife | 2020 Jan 21 |
| Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells. | Chopra SS, Jenney A, Palmer A, Niepel M, Chung M, Mills C, Sivakumaren SC, Liu Q, Chen JY, Yapp C, Asara JM, Gray NS, Sorger PK | Cell systems | 31812693 | Cell Syst | 2020 Jan 22 |
| Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. | Rao S, Gurbani D, Du G, Everley RA, Browne CM, Chaikuad A, Tan L, Schröder M, Gondi S, Ficarro SB, Sim T, Kim ND, Berberich MJ, Knapp S, Marto JA, Westover KD, Sorger PK, Gray NS | Cell chemical biology | 30982749 | Cell Chem Biol | 2019 Jun 20 |
| Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. | Vemulapalli V, Chylek LA, Erickson A, Pfeiffer A, Gabriel KH, LaRochelle J, Subramanian K, Cao R, Stegmaier K, Mohseni M, LaMarche MJ, Acker MG, Sorger PK, Gygi SP, Blacklow SC | eLife | 33755016 | Elife | 2021 Mar 23 |
| A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers. | Rao S, Du G, Hafner M, Subramanian K, Sorger PK, Gray NS | The Journal of biological chemistry | 30858179 | J Biol Chem | 2019 May 24 |
| Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. | Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ, Kalocsay M, Sorger PK, Gray NS | Cell chemical biology | 30930164 | Cell Chem Biol | 2019 Jun 20 |
| Dual Inhibition of GSK3β and CDK5 Protects the Cytoskeleton of Neurons from Neuroinflammatory-Mediated Degeneration In Vitro and In Vivo. | Reinhardt L, Kordes S, Reinhardt P, Glatza M, Baumann M, Drexler HCA, Menninger S, Zischinsky G, Eickhoff J, Fröb C, Bhattarai P, Arulmozhivarman G, Marrone L, Janosch A, Adachi K, Stehling M, Anderson EN, Abo-Rady M, Bickle M, Pandey UB, Reimer MM, Kizil C, Schöler HR, Nussbaumer P, Klebl B, Sterneckert JL | Stem cell reports | 30773488 | Stem Cell Reports | 2019 Mar 5 |
| Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer. | Chong CR, Bahcall M, Capelletti M, Kosaka T, Ercan D, Sim T, Sholl LM, Nishino M, Johnson BE, Gray NS, Jänne PA | Clinical cancer research : an official journal of the American Association for Cancer Research | 27370605 | Clin Cancer Res | 2017 Jan 1 |
| Suppression of the metastatic spread of breast cancer by DN10764 (AZD7762)-mediated inhibition of AXL signaling. | Park JS, Lee C, Kim HK, Kim D, Son JB, Ko E, Cho JH, Kim ND, Nan HY, Kim CY, Yoon S, Lee SH, Choi HG | Oncotarget | 27829217 | Oncotarget | 2016 Dec 13 |
| Functional kinomics establishes a critical node of volume-sensitive cation-Cl(-) cotransporter regulation in the mammalian brain. | Zhang J, Gao G, Begum G, Wang J, Khanna AR, Shmukler BE, Daubner GM, de Los Heros P, Davies P, Varghese J, Bhuiyan MI, Duan J, Zhang J, Duran D, Alper SL, Sun D, Elledge SJ, Alessi DR, Kahle KT | Scientific reports | 27782176 | Sci Rep | 2016 Oct 26 |
| Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype. | Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS | Cell chemical biology | 30905681 | Cell Chem Biol | 2019 Jun 20 |
| Pathway-Based Genomics Prediction using Generalized Elastic Net. | Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM | PLoS computational biology | 26960204 | PLoS Comput Biol | 2016 Mar |
| Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold. | Roux J, Hafner M, Bandara S, Sims JJ, Hudson H, Chai D, Sorger PK | Molecular systems biology | 25953765 | Mol Syst Biol | 2015 May 7 |
| ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES. | Sokolov A, Paull EO, Stuart JM | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 26776204 | Pac Symp Biocomput | 2016 |
| Revealing cancer subtypes with higher-order correlations applied to imaging and omics data. | Graim K, Liu TT, Achrol AS, Paull EO, Newton Y, Chang SD, Harsh GR 4th, Cordero SP, Rubin DL, Stuart JM | BMC medical genomics | 28359308 | BMC Med Genomics | 2017 Mar 31 |
| Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases. | Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK | Cell systems | 29886111 | Cell Syst | 2018 Jun 27 |
| Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma. | Coy S, Rashid R, Lin JR, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S | Neuro-oncology | 29509940 | Neuro Oncol | 2018 Jul 5 |
| TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. | Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM | Cancer research | 29092953 | Cancer Res | 2017 Nov 1 |
| Organoid culture promotes dedifferentiation of mouse myoblasts into stem cells capable of complete muscle regeneration. | Price FD, Matyas MN, Gehrke AR, Chen W, Wolin EA, Holton KM, Gibbs RM, Lee A, Singu PS, Sakakeeny JS, Poteracki JM, Goune K, Pfeiffer IT, Boswell SA, Sorger PK, Srivastava M, Pfaff KL, Gussoni E, Buchanan SM, Rubin LL | Nature biotechnology | 39261590 | Nat Biotechnol | 2024 Sep 11 |
| Systematic replication enables normalization of high-throughput imaging assays. | Hunt GJ, Dane MA, Korkola JE, Heiser LM, Gagnon-Bartsch JA | Bioinformatics (Oxford, England) | 36063034 | Bioinformatics | 2022 Oct 31 |
| Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma. | Lue HW, Derrick DS, Rao S, Van Gaest A, Cheng L, Podolak J, Lawson S, Xue C, Garg D, White R 3rd, Ryan CW, Drake JM, Ritz A, Heiser LM, Thomas GV | Cell reports. Medicine | 34095877 | Cell Rep Med | 2021 May 18 |
| Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes. | Watson SS, Dane M, Chin K, Tatarova Z, Liu M, Liby T, Thompson W, Smith R, Nederlof M, Bucher E, Kilburn D, Whitman M, Sudar D, Mills GB, Heiser LM, Jonas O, Gray JW, Korkola JE | Cell systems | 29550255 | Cell Syst | 2018 Mar 28 |
| AACR Project GENIE: Powering Precision Medicine through an International Consortium. | AACR Project GENIE Consortium | Cancer discovery | 28572459 | Cancer Discov | 2017 Aug |
| Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer. | Smith R, Devlin K, Kilburn D, Gross S, Sudar D, Bucher E, Nederlof M, Dane M, Gray JW, Heiser L, Korkola JE | Journal of visualized experiments : JoVE | 31180341 | J Vis Exp | 2019 May 21 |
| Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy. | Fang Y, McGrail DJ, Sun C, Labrie M, Chen X, Zhang D, Ju Z, Vellano CP, Lu Y, Li Y, Jeong KJ, Ding Z, Liang J, Wang SW, Dai H, Lee S, Sahni N, Mercado-Uribe I, Kim TB, Chen K, Lin SY, Peng G, Westin SN, Liu J, O'Connor MJ, Yap TA, Mills GB | Cancer cell | 31185210 | Cancer Cell | 2019 Jun 10 |
| Individual Cells Can Resolve Variations in Stimulus Intensity along the IGF-PI3K-AKT Signaling Axis. | Gross SM, Dane MA, Bucher E, Heiser LM | Cell systems | 31838146 | Cell Syst | 2019 Dec 18 |
| Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments. | Kimmel GJ, Dane M, Heiser LM, Altrock PM, Andor N | Cancer research | 32938640 | Cancer Res | 2020 Nov 15 |
| Systems biology approaches to measure and model phenotypic heterogeneity in cancer. | Meyer AS, Heiser LM | Current opinion in systems biology | 32864511 | Curr Opin Syst Biol | 2019 Oct |
| Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. | Zhao W, Li J, Chen MM, Luo Y, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NT, Davies MA, Herlyn M, Muranen T, Zervantonakis IK, von Euw E, Schultz A, Kumar SV, Korkut A, Spellman PT, Akbani R, Slamon DJ, Gray JW, Brugge JS, Lu Y, Mills GB, Liang H | Cancer cell | 33157050 | Cancer Cell | 2020 Dec 14 |
| Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. | Goodspeed A, Heiser LM, Gray JW, Costello JC | Molecular cancer research : MCR | 26248648 | Mol Cancer Res | 2016 Jan |
| Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas. | Li J, Akbani R, Zhao W, Lu Y, Weinstein JN, Mills GB, Liang H | Cancer research | 29092939 | Cancer Res | 2017 Nov 1 |
| ZEB1-repressed microRNAs inhibit autocrine signaling that promotes vascular mimicry of breast cancer cells. | Langer EM, Kendsersky ND, Daniel CJ, Kuziel GM, Pelz C, Murphy KM, Capecchi MR, Sears RC | Oncogene | 29084210 | Oncogene | 2018 Feb 22 |
| Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments. | Jokela TA, Dane MA, Smith RL, Devlin KL, Shalabi S, Lopez JC, Miyano M, Stampfer MR, Korkola JE, Gray JW, Heiser LM, LaBarge MA | Cellular signalling | 37935340 | Cell Signal | 2024 Jan |
| Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer. | Lu Y, Ling S, Hegde AM, Byers LA, Coombes K, Mills GB, Akbani R | Seminars in oncology | 27663479 | Semin Oncol | 2016 Aug |
| Neomorphic mutations create therapeutic challenges in cancer. | Takiar V, Ip CK, Gao M, Mills GB, Cheung LW | Oncogene | 27841866 | Oncogene | 2017 Mar 23 |
| Annot: a Django-based sample, reagent, and experiment metadata tracking system. | Bucher E, Claunch CJ, Hee D, Smith RL, Devlin K, Thompson W, Korkola JE, Heiser LM | BMC bioinformatics | 31675914 | BMC Bioinformatics | 2019 Nov 1 |
| Systems biology approach reveals a link between mTORC1 and G2/M DNA damage checkpoint recovery. | Hsieh HJ, Zhang W, Lin SH, Yang WH, Wang JZ, Shen J, Zhang Y, Lu Y, Wang H, Yu J, Mills GB, Peng G | Nature communications | 30266942 | Nat Commun | 2018 Sep 28 |
| A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity. | Mohammadi F, Visagan S, Gross SM, Karginov L, Lagarde JC, Heiser LM, Meyer AS | Communications biology | 36396800 | Commun Biol | 2022 Nov 17 |
| INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer. | Liu M, Smith R, Liby T, Chiotti K, López CS, Korkola JE | Breast cancer research : BCR | 35248133 | Breast Cancer Res | 2022 Mar 5 |
| Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays. | Li J, Zhao W, Akbani R, Liu W, Ju Z, Ling S, Vellano CP, Roebuck P, Yu Q, Eterovic AK, Byers LA, Davies MA, Deng W, Gopal YN, Chen G, von Euw EM, Slamon D, Conklin D, Heymach JV, Gazdar AF, Minna JD, Myers JN, Lu Y, Mills GB, Liang H | Cancer cell | 28196595 | Cancer Cell | 2017 Feb 13 |
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