Skip to main content

Program Publications

Publications Search by Program

Search Result

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
Oncogenic RAS Regulates Long Noncoding RNA Orilnc1 in Human Cancer. Zhang D, Zhang G, Hu X, Wu L, Feng Y, He S, Zhang Y, Hu Z, Yang L, Tian T, Xu W, Wei Z, Lu Y, Flaherty KT, Zhong X, Mills GB, Gimotty PA, Xu X, Herlyn M, Zhang L Cancer research 28473531 Cancer Res 2017 Jul 15
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms. Erdem C, Gross SM, Heiser LM, Birtwistle MR Nature communications 37414767 Nat Commun 2023 Jul 6
Microenvironment-Induced Non-sporadic Expression of the AXL and cKIT Receptors Are Related to Epithelial Plasticity and Drug Resistance. Jokela TA, Engelsen AST, Rybicka A, Pelissier Vatter FA, Garbe JC, Miyano M, Tiron C, Ferariu D, Akslen LA, Stampfer MR, Lorens JB, LaBarge MA Frontiers in cell and developmental biology 29719832 Front Cell Dev Biol 2018
Systematic Functional Annotation of Somatic Mutations in Cancer. Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB Cancer cell 29533785 Cancer Cell 2018 Mar 12
Combinatorial Microenvironments Impose a Continuum of Cellular Responses to a Single Pathway-Targeted Anti-cancer Compound. Lin CH, Jokela T, Gray J, LaBarge MA Cell reports 29020637 Cell Rep 2017 Oct 10
Integration of mechanical and ECM microenvironment signals in the determination of cancer stem cell states. Jokela TA, LaBarge MA Current stem cell reports 33777660 Curr Stem Cell Rep 2021 Mar
Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA. Garay JP, Smith R, Devlin K, Hollern DP, Liby T, Liu M, Boddapati S, Watson SS, Esch A, Zheng T, Thompson W, Babcock D, Kwon S, Chin K, Heiser L, Gray JW, Korkola JE Breast cancer research : BCR 34344439 Breast Cancer Res 2021 Aug 3
AKT isoform-specific expression and activation across cancer lineages. Wang J, Zhao W, Guo H, Fang Y, Stockman SE, Bai S, Ng PK, Li Y, Yu Q, Lu Y, Jeong KJ, Chen X, Gao M, Liang J, Li W, Tian X, Jonasch E, Mills GB, Ding Z BMC cancer 30012111 BMC Cancer 2018 Jul 16
Variational Autoencoding Tissue Response to Microenvironment Perturbation. Schau GF, Thibault G, Dane MA, Gray JW, Heiser LM, Chang YH Proceedings of SPIE--the International Society for Optical Engineering 31379401 Proc SPIE Int Soc Opt Eng 2019 Feb
How Machine Learning Will Transform Biomedicine. Goecks J, Jalili V, Heiser LM, Gray JW Cell 32243801 Cell 2020 Apr 2
Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer. Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK Cell reports 32294438 Cell Rep 2020 Apr 14
Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. Heiser LM, Mills GB, Gray JW Cancer cell 30889376 Cancer Cell 2019 Mar 18
Automatic Transformation and Integration to Improve Visualization and Discovery of Latent Effects in Imaging Data. Hunt GJ, Dane MA, Korkola JE, Heiser LM, Gagnon-Bartsch JA Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America 34531645 J Comput Graph Stat 2020
Large-Scale Drug Screens Support Precision Medicine. Gray JW, Mills GB Cancer discovery 26526695 Cancer Discov 2015 Nov
Functional variomics and network perturbation: connecting genotype to phenotype in cancer. Yi S, Lin S, Li Y, Zhao W, Mills GB, Sahni N Nature reviews. Genetics 28344341 Nat Rev Genet 2017 Jul
Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. Tognon CE, Sears RC, Mills GB, Gray JW, Tyner JW Annual review of cancer biology 34222745 Annu Rev Cancer Biol 2021 Mar
<PE-AT>Contributions of Yap and Taz dysfunction to breast cancer initiation, progression, and aging-related susceptibility. Fresques T, LaBarge MA Aging and cancer 33693435 Aging Cancer 2020 Dec
Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. Labrie M, Li A, Creason A, Betts C, Keck J, Johnson B, Sivagnanam S, Boniface C, Ma H, Blucher A, Chang YH, Chin K, Vuky J, Guimaraes AR, Downey M, Lim JY, Gao L, Siex K, Parmar S, Kolodzie A, Spellman PT, Goecks J, Coussens LM, Corless CL, Bergan R, Gray JW, Mills GB, Mitri ZI NPJ precision oncology 34667258 NPJ Precis Oncol 2021 Oct 19
A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis. Ternes L, Dane M, Gross S, Labrie M, Mills G, Gray J, Heiser L, Chang YH Communications biology 35322205 Commun Biol 2022 Mar 23
An altered extracellular matrix-integrin interface contributes to Huntington's disease-associated CNS dysfunction in glial and vascular cells. Hernandez SJ, Lim RG, Onur T, Dane MA, Smith R, Wang K, Jean GE, Reyes-Ortiz A, Devlin K, Miramontes R, Wu J, Casale M, Kilburn D, Heiser LM, Korkola JE, Van Vactor D, Botas J, Thompson-Peer KL, Thompson LM Human molecular genetics 36547263 Hum Mol Genet 2023 Apr 20
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. Copperman J, Mclean IC, Gross SM, Singh J, Chang YH, Zuckerman DM, Heiser LM bioRxiv : the preprint server for biology 38293173 bioRxiv 2024 Jun 25
Improved Prediction of Drug-Induced Torsades de Pointes Through Simulations of Dynamics and Machine Learning Algorithms. Lancaster MC, Sobie EA Clinical pharmacology and therapeutics 26950176 Clin Pharmacol Ther 2016 Oct
A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR Scientific reports 29116112 Sci Rep 2017 Nov 7
Disruption of podocyte cytoskeletal biomechanics by dasatinib leads to nephrotoxicity. Calizo RC, Bhattacharya S, van Hasselt JGC, Wei C, Wong JS, Wiener RJ, Ge X, Wong NJ, Lee JJ, Cuttitta CM, Jayaraman G, Au VH, Janssen W, Liu T, Li H, Salem F, Jaimes EA, Murphy B, Campbell KN, Azeloglu EU Nature communications 31053734 Nat Commun 2019 May 3
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. Yadaw AS, Li YC, Bose S, Iyengar R, Bunyavanich S, Pandey G The Lancet. Digital health 32984797 Lancet Digit Health 2020 Oct
Physiology of cardiomyocyte injury in COVID-19. Siddiq MM, Chan AT, Miorin L, Yadaw AS, Beaumont KG, Kehrer T, White KM, Cupic A, Tolentino RE, Hu B, Stern AD, Tavassoly I, Hansen J, Martinez P, Dubois N, Schaniel C, Iyengar-Kapuganti R, Kukar N, Giustino G, Sud K, Nirenberg S, Kovatch P, Goldfarb J, Croft L, McLaughlin MA, Argulian E, Lerakis S, Narula J, García-Sastre A, Iyengar R medRxiv : the preprint server for health sciences 33200140 medRxiv 2020 Nov 16
Investigational Treatments for COVID-19 may Increase Ventricular Arrhythmia Risk Through Drug Interactions. Varshneya M, Irurzun-Arana I, Campana C, Dariolli R, Gutierrez A, Pullinger TK, Sobie EA CPT: pharmacometrics & systems pharmacology 33205613 CPT Pharmacometrics Syst Pharmacol 2021 Feb
Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells. Stillitano F, Hansen J, Kong CW, Karakikes I, Funck-Brentano C, Geng L, Scott S, Reynier S, Wu M, Valogne Y, Desseaux C, Salem JE, Jeziorowska D, Zahr N, Li R, Iyengar R, Hajjar RJ, Hulot JS eLife 28134617 Elife 2017 Jan 30
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data. Smith GR, Birtwistle MR PloS one 27326762 PLoS One 2016
Building Containerized Workflows Using the BioDepot-Workflow-Builder. Hung LH, Hu J, Meiss T, Ingersoll A, Lloyd W, Kristiyanto D, Xiong Y, Sobie E, Yeung KY Cell systems 31521606 Cell Syst 2019 Nov 27
Mitochondrial origins of fractional control in regulated cell death. Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P Nature communications 30899020 Nat Commun 2019 Mar 21
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. Zatorski N, Stein D, Rahman R, Iyengar R, Schlessinger A Database : the journal of biological databases and curation 35881481 Database (Oxford) 2022 Jul 26
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR Nature communications 35729113 Nat Commun 2022 Jun 21
Ambiguous interactions between diastolic and SR Ca(2+) in the regulation of cardiac Ca(2+) release. Sobie EA, Williams GSB, Lederer WJ The Journal of general physiology 28798276 J Gen Physiol 2017 Sep 4
A privileged role for neuronal Na(+) channels in regulating ventricular [Ca(2+)] and arrhythmias. Jones DC, Gong JQX, Sobie EA The Journal of general physiology 29899058 J Gen Physiol 2018 Jul 2
Drug response consistency in CCLE and CGP. Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR Nature 27905419 Nature 2016 Nov 30
I love it when a plan comes together: Insight gained through convergence of competing mathematical models. Gong JQ, Shim JV, Núñez-Acosta E, Sobie EA Journal of molecular and cellular cardiology 27913283 J Mol Cell Cardiol 2017 Jan
Cell size assays for mass cytometry. Stern AD, Rahman AH, Birtwistle MR Cytometry. Part A : the journal of the International Society for Analytical Cytology 27768827 Cytometry A 2017 Jan
Network pharmacodynamic models for customized cancer therapy. Gallo JM, Birtwistle MR Wiley interdisciplinary reviews. Systems biology and medicine 25914386 Wiley Interdiscip Rev Syst Biol Med 2015 Jul-Aug
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR Scientific reports 30054510 Sci Rep 2018 Jul 27
A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals. Schaniel C, Dhanan P, Hu B, Xiong Y, Raghunandan T, Gonzalez DM, Dariolli R, D'Souza SL, Yadaw AS, Hansen J, Jayaraman G, Mathew B, Machado M, Berger SI, Tripodi J, Najfeld V, Garg J, Miller M, Surlyn CS, Michelis KC, Tangirala NC, Weerahandi H, Thomas DC, Beaumont KG, Sebra R, Mahajan M, Schadt E, Vidovic D, Schürer SC, Goldfarb J, Azeloglu EU, Birtwistle MR, Sobie EA, Kovacic JC, Dubois NC, Iyengar R Stem cell reports 34739849 Stem Cell Reports 2021 Dec 14
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity. van Hasselt JGC, Rahman R, Hansen J, Stern A, Shim JV, Xiong Y, Pickard A, Jayaraman G, Hu B, Mahajan M, Gallo JM, Goldfarb J, Sobie EA, Birtwistle MR, Schlessinger A, Azeloglu EU, Iyengar R Nature communications 32968055 Nat Commun 2020 Sep 23
Analytical reduction of combinatorial complexity arising from multiple protein modification sites. Birtwistle MR Journal of the Royal Society, Interface 25519995 J R Soc Interface 2015 Feb 6
Protein structure-based gene expression signatures. Rahman R, Zatorski N, Hansen J, Xiong Y, van Hasselt JGC, Sobie EA, Birtwistle MR, Azeloglu EU, Iyengar R, Schlessinger A Proceedings of the National Academy of Sciences of the United States of America 33941686 Proc Natl Acad Sci U S A 2021 May 11
Holistic optimization of an RNA-seq workflow for multi-threaded environments. Hung LH, Lloyd W, Agumbe Sridhar R, Athmalingam Ravishankar SD, Xiong Y, Sobie E, Yeung KY Bioinformatics (Oxford, England) 30859176 Bioinformatics 2019 Oct 15
In silico model-based inference: an emerging approach for inverse problems in engineering better medicines. Klinke DJ 2nd, Birtwistle MR Current opinion in chemical engineering 26309811 Curr Opin Chem Eng 2015 Nov 1
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR PLoS computational biology 29579036 PLoS Comput Biol 2018 Mar
Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics. Shim JV, Chun B, van Hasselt JGC, Birtwistle MR, Saucerman JJ, Sobie EA Frontiers in physiology 28951721 Front Physiol 2017
Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity. Xiong Y, Liu T, Chen T, Hansen J, Hu B, Chen Y, Jayaraman G, Schürer S, Vidovic D, Goldfarb J, Sobie EA, Birtwistle MR, Iyengar R, Li H, Azeloglu EU Scientific data 35058449 Sci Data 2022 Jan 20
Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions. Varshneya M, Irurzun-Arana I, Campana C, Dariolli R, Gutierrez A, Pullinger TK, Sobie EA medRxiv : the preprint server for health sciences 32511528 medRxiv 2020 May 26
Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates. Zadeh CO, Huggins JR, Sarmah D, Westbury BC, Interiano WR, Jordan MC, Phillips SA, Dodd WB, Meredith WO, Harold NJ, Erdem C, Birtwistle MR ACS omega 36033686 ACS Omega 2022 Aug 23
MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets. Erdem C, Birtwistle MR Frontiers in systems biology 38269333 Front Syst Biol 2023
Multiscale mapping of transcriptomic signatures for cardiotoxic drugs. Hansen J, Xiong Y, Siddiq MM, Dhanan P, Hu B, Shewale B, Yadaw AS, Jayaraman G, Tolentino RE, Chen Y, Martinez P, Beaumont KG, Sebra R, Vidovic D, Schürer SC, Goldfarb J, Gallo JM, Birtwistle MR, Sobie EA, Azeloglu EU, Berger SI, Chan A, Schaniel C, Dubois NC, Iyengar R Nature communications 39261481 Nat Commun 2024 Sep 11
A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML. Gopal S, Lu Q, Man JJ, Baur W, Rao SP, Litichevskiy L, Papanastasiou M, Creech AL, DeRuff KC, Mullahoo J, Officer A, Egri SB, Davison D, Jaffe JD, Jaffe IZ Blood advances 30021779 Blood Adv 2018 Jul 24
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ Nature communications 30510204 Nat Commun 2018 Dec 3
APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Blanchard JW, Akay LA, Davila-Velderrain J, von Maydell D, Mathys H, Davidson SM, Effenberger A, Chen CY, Maner-Smith K, Hajjar I, Ortlund EA, Bula M, Agbas E, Ng A, Jiang X, Kahn M, Blanco-Duque C, Lavoie N, Liu L, Reyes R, Lin YT, Ko T, R'Bibo L, Ralvenius WT, Bennett DA, Cam HP, Kellis M, Tsai LH Nature 36385529 Nature 2022 Nov
JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K Cancer research 36409824 Cancer Res 2023 Jan 18
PICALM Rescues Endocytic Defects Caused by the Alzheimer's Disease Risk Factor APOE4. Narayan P, Sienski G, Bonner JM, Lin YT, Seo J, Baru V, Haque A, Milo B, Akay LA, Graziosi A, Freyzon Y, Landgraf D, Hesse WR, Valastyan J, Barrasa MI, Tsai LH, Lindquist S Cell reports 33027662 Cell Rep 2020 Oct 6
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD Molecular & cellular proteomics : MCP 26912667 Mol Cell Proteomics 2016 May
Activity of the PI3K-δ,γ inhibitor duvelisib in a phase 1 trial and preclinical models of T-cell lymphoma. Horwitz SM, Koch R, Porcu P, Oki Y, Moskowitz A, Perez M, Myskowski P, Officer A, Jaffe JD, Morrow SN, Allen K, Douglas M, Stern H, Sweeney J, Kelly P, Kelly V, Aster JC, Weaver D, Foss FM, Weinstock DM Blood 29233821 Blood 2018 Feb 22
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ Nature methods 28783153 Nat Methods 2017 Sep
Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline. Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B Molecular & cellular proteomics : MCP 29487113 Mol Cell Proteomics 2018 Jun
Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns. Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon I Genome research 30166406 Genome Res 2018 Oct
A Curated Resource for Phosphosite-specific Signature Analysis. Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR Molecular & cellular proteomics : MCP 30563849 Mol Cell Proteomics 2019 Mar
Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories. Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ Analytical chemistry 30350613 Anal Chem 2018 Nov 6
Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. Blanchard JW, Bula M, Davila-Velderrain J, Akay LA, Zhu L, Frank A, Victor MB, Bonner JM, Mathys H, Lin YT, Ko T, Bennett DA, Cam HP, Kellis M, Tsai LH Nature medicine 32514169 Nat Med 2020 Jun
Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors. Meharena HS, Marco A, Dileep V, Lockshin ER, Akatsu GY, Mullahoo J, Watson LA, Ko T, Guerin LN, Abdurrob F, Rengarajan S, Papanastasiou M, Jaffe JD, Tsai LH Cell stem cell 34995493 Cell Stem Cell 2022 Jan 6
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ Mass spectrometry reviews 28691345 Mass Spectrom Rev 2020 May
Multiplexed peptide analysis using data-independent acquisition and Skyline. Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ Nature protocols 25996789 Nat Protoc 2015 Jun
Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis. Rossmann MP, Hoi K, Chan V, Abraham BJ, Yang S, Mullahoo J, Papanastasiou M, Wang Y, Elia I, Perlin JR, Hagedorn EJ, Hetzel S, Weigert R, Vyas S, Nag PP, Sullivan LB, Warren CR, Dorjsuren B, Greig EC, Adatto I, Cowan CA, Schreiber SL, Young RA, Meissner A, Haigis MC, Hekimi S, Carr SA, Zon LI Science (New York, N.Y.) 33986176 Science 2021 May 14
Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS. Papanastasiou M, Mullahoo J, DeRuff KC, Bajrami B, Karageorgos I, Johnston SE, Peckner R, Myers SA, Carr SA, Jaffe JD Molecular & cellular proteomics : MCP 31409669 Mol Cell Proteomics 2019 Oct
Thesaurus: quantifying phosphopeptide positional isomers. Searle BC, Lawrence RT, MacCoss MJ, Villén J Nature methods 31363206 Nat Methods 2019 Aug
Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds. Dele-Oni DO, Christianson KE, Egri SB, Vaca Jacome AS, DeRuff KC, Mullahoo J, Sharma V, Davison D, Ko T, Bula M, Blanchard J, Young JZ, Litichevskiy L, Lu X, Lam D, Asiedu JK, Toder C, Officer A, Peckner R, MacCoss MJ, Tsai LH, Carr SA, Papanastasiou M, Jaffe JD Scientific data 34433823 Sci Data 2021 Aug 25
Cell of all trades: oligodendrocyte precursor cells in synaptic, vascular, and immune function. Akay LA, Effenberger AH, Tsai LH Genes & development 33526585 Genes Dev 2021 Feb 1
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ Journal of the American Society for Mass Spectrometry 30671891 J Am Soc Mass Spectrom 2019 Apr
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Hinohara K, Wu HJ, Sébastien Vigneau, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K Cancer cell 30753830 Cancer Cell 2019 Feb 11
The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity. Li A, Lu X, Natoli T, Bittker J, Sipes NS, Subramanian A, Auerbach S, Sherr DH, Monti S Environmental health perspectives 30964323 Environ Health Perspect 2019 Apr
Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms. Jaffe JD, Feeney CM, Patel J, Lu X, Mani DR Journal of the American Society for Mass Spectrometry 27562500 J Am Soc Mass Spectrom 2016 Nov
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS. Mullahoo J, Zhang T, Clauser K, Carr SA, Jaffe JD, Papanastasiou M Methods (San Diego, Calif.) 32004545 Methods 2020 Dec 1
Avant-garde: an automated data-driven DIA data curation tool. Vaca Jacome AS, Peckner R, Shulman N, Krug K, DeRuff KC, Officer A, Christianson KE, MacLean B, MacCoss MJ, Carr SA, Jaffe JD Nature methods 33199889 Nat Methods 2020 Dec
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K Cancer cell 30472020 Cancer Cell 2018 Dec 10
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD Nature methods 29608554 Nat Methods 2018 May
Pharmacogenomic agreement between two cancer cell line data sets. Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium Nature 26570998 Nature 2015 Dec 3
Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR. Liu Q, Xu C, Kirubakaran S, Zhang X, Hur W, Liu Y, Kwiatkowski NP, Wang J, Westover KD, Gao P, Ercan D, Niepel M, Thoreen CC, Kang SA, Patricelli MP, Wang Y, Tupper T, Altabef A, Kawamura H, Held KD, Chou DM, Elledge SJ, Janne PA, Wong KK, Sabatini DM, Gray NS Cancer research 23436801 Cancer Res 2013 Apr 15
TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer. Si H, Lu H, Yang X, Mattox A, Jang M, Bian Y, Sano E, Viadiu H, Yan B, Yau C, Ng S, Lee SK, Romano RA, Davis S, Walker RL, Xiao W, Sun H, Wei L, Sinha S, Benz CC, Stuart JM, Meltzer PS, Van Waes C, Chen Z Oncogene 27132513 Oncogene 2016 Nov 3
Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM Cell 27499020 Cell 2016 Aug 11
Functionalizing genomic data for personalization of medicine. Benes CH Clinical pharmacology and therapeutics 23321554 Clin Pharmacol Ther 2013 Apr
Crowdsourcing network inference: the DREAM predictive signaling network challenge. Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G Science signaling 21900204 Sci Signal 2011 Aug 30
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM Bioinformatics (Oxford, England) 22962493 Bioinformatics 2012 Sep 15
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK BMC systems biology 22548703 BMC Syst Biol 2012 May 1
Upregulation of IGF1R by mutant RAS in leukemia and potentiation of RAS signaling inhibitors by small-molecule inhibition of IGF1R. Weisberg E, Nonami A, Chen Z, Nelson E, Chen Y, Liu F, Cho H, Zhang J, Sattler M, Mitsiades C, Wong KK, Liu Q, Gray NS, Griffin JD Clinical cancer research : an official journal of the American Association for Cancer Research 25186968 Clin Cancer Res 2014 Nov 1
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma'ayan A Bioinformatics (Oxford, England) 25100688 Bioinformatics 2014 Nov 15
A-770041 reverses paclitaxel and doxorubicin resistance in osteosarcoma cells. Duan Z, Zhang J, Ye S, Shen J, Choy E, Cote G, Harmon D, Mankin H, Hua Y, Zhang Y, Gray NS, Hornicek FJ BMC cancer 25236161 BMC Cancer 2014 Sep 19
Discovery of type II inhibitors of TGFβ-activated kinase 1 (TAK1) and mitogen-activated protein kinase kinase kinase kinase 2 (MAP4K2). Tan L, Nomanbhoy T, Gurbani D, Patricelli M, Hunter J, Geng J, Herhaus L, Zhang J, Pauls E, Ham Y, Choi HG, Xie T, Deng X, Buhrlage SJ, Sim T, Cohen P, Sapkota G, Westover KD, Gray NS Journal of medicinal chemistry 25075558 J Med Chem 2015 Jan 8
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A Nucleic acids research 24906883 Nucleic Acids Res 2014 Jul
A coding single-nucleotide polymorphism in lysine demethylase KDM4A associates with increased sensitivity to mTOR inhibitors. Van Rechem C, Black JC, Greninger P, Zhao Y, Donado C, Burrowes PD, Ladd B, Christiani DC, Benes CH, Whetstine JR Cancer discovery 25564517 Cancer Discov 2015 Mar
Using combination therapy to override stromal-mediated chemoresistance in mutant FLT3-positive AML: synergism between FLT3 inhibitors, dasatinib/multi-targeted inhibitors and JAK inhibitors. Weisberg E, Liu Q, Nelson E, Kung AL, Christie AL, Bronson R, Sattler M, Sanda T, Zhao Z, Hur W, Mitsiades C, Smith R, Daley JF, Stone R, Galinsky I, Griffin JD, Gray N Leukemia 22469781 Leukemia 2012 Oct
mTOR inhibition specifically sensitizes colorectal cancers with KRAS or BRAF mutations to BCL-2/BCL-XL inhibition by suppressing MCL-1. Faber AC, Coffee EM, Costa C, Dastur A, Ebi H, Hata AN, Yeo AT, Edelman EJ, Song Y, Tam AT, Boisvert JL, Milano RJ, Roper J, Kodack DP, Jain RK, Corcoran RB, Rivera MN, Ramaswamy S, Hung KE, Benes CH, Engelman JA Cancer discovery 24163374 Cancer Discov 2014 Jan
Effects of the selective MPS1 inhibitor MPS1-IN-3 on glioblastoma sensitivity to antimitotic drugs. Tannous BA, Kerami M, Van der Stoop PM, Kwiatkowski N, Wang J, Zhou W, Kessler AF, Lewandrowski G, Hiddingh L, Sol N, Lagerweij T, Wedekind L, Niers JM, Barazas M, Nilsson RJ, Geerts D, De Witt Hamer PC, Hagemann C, Vandertop WP, Van Tellingen O, Noske DP, Gray NS, Würdinger T Journal of the National Cancer Institute 23940287 J Natl Cancer Inst 2013 Sep 4
EMT twists the road to PI3K. Niederst MJ, Benes CH Cancer discovery 24501304 Cancer Discov 2014 Feb
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. Uzunangelov V, Wong CK, Stuart JM PLoS computational biology 33861732 PLoS Comput Biol 2021 Apr
Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment. Liu TT, Achrol AS, Mitchell LA, Rodriguez SA, Feroze A, Iv M, Kim C, Chaudhary N, Gevaert O, Stuart JM, Harsh GR, Chang SD, Rubin DL Neuro-oncology 28007759 Neuro Oncol 2017 Jul 1
High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors. Miduturu CV, Deng X, Kwiatkowski N, Yang W, Brault L, Filippakopoulos P, Chung E, Yang Q, Schwaller J, Knapp S, King RW, Lee JD, Herrgard S, Zarrinkar P, Gray NS Chemistry & biology 21802008 Chem Biol 2011 Jul 29
Systematic identification of genomic markers of drug sensitivity in cancer cells. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH Nature 22460902 Nature 2012 Mar 28
Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN Cell reports 28297679 Cell Rep 2017 Mar 14
Selective Akt inhibitors synergize with tyrosine kinase inhibitors and effectively override stroma-associated cytoprotection of mutant FLT3-positive AML cells. Weisberg E, Liu Q, Zhang X, Nelson E, Sattler M, Liu F, Nicolais M, Zhang J, Mitsiades C, Smith RW, Stone R, Galinsky I, Nonami A, Griffin JD, Gray N PloS one 23437141 PLoS One 2013
A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS Journal of the American Society of Nephrology : JASN 26260164 J Am Soc Nephrol 2016 Apr
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC Journal of biomolecular screening 24518066 J Biomol Screen 2014 Jun
Discovery of a potent, covalent BTK inhibitor for B-cell lymphoma. Wu H, Wang W, Liu F, Weisberg EL, Tian B, Chen Y, Li B, Wang A, Wang B, Zhao Z, McMillin DW, Hu C, Li H, Wang J, Liang Y, Buhrlage SJ, Liang J, Liu J, Yang G, Brown JR, Treon SP, Mitsiades CS, Griffin JD, Liu Q, Gray NS ACS chemical biology 24556163 ACS Chem Biol 2014 May 16
A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins. Luckert K, Gujral TS, Chan M, Sevecka M, Joos TO, Sorger PK, Macbeath G, Pötz O Science signaling 22234610 Sci Signal 2012 Jan 10
Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines. Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Schoeberl B, Sorger PK Science signaling 24065145 Sci Signal 2013 Sep 24
Network2Canvas: network visualization on a canvas with enrichment analysis. Tan CM, Chen EY, Dannenfelser R, Clark NR, Ma'ayan A Bioinformatics (Oxford, England) 23749960 Bioinformatics 2013 Aug 1
Metasignatures identify two major subtypes of breast cancer. Duan Q, Kou Y, Clark NR, Gordonov S, Ma'ayan A CPT: pharmacometrics & systems pharmacology 23836026 CPT Pharmacometrics Syst Pharmacol 2013 Mar 27
Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones. Deng X, Elkins JM, Zhang J, Yang Q, Erazo T, Gomez N, Choi HG, Wang J, Dzamko N, Lee JD, Sim T, Kim N, Alessi DR, Lizcano JM, Knapp S, Gray NS European journal of medicinal chemistry 24239623 Eur J Med Chem 2013
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A BMC bioinformatics 23586463 BMC Bioinformatics 2013 Apr 15
Differential determinants of cancer cell insensitivity to antimitotic drugs discriminated by a one-step cell imaging assay. Tang Y, Xie T, Florian S, Moerke N, Shamu C, Benes C, Mitchison TJ Journal of biomolecular screening 23788527 J Biomol Screen 2013 Oct
Using Transcriptional Signatures to Find Cancer Drivers with LURE. Haan D, Tao R, Friedl V, Anastopoulos IN, Wong CK, Weinstein AS, Stuart JM Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 31797609 Pac Symp Biocomput 2020
Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities. Lapek JD Jr, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W Nature biotechnology 28892078 Nat Biotechnol 2017 Oct
Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models. Corcoran RB, Cheng KA, Hata AN, Faber AC, Ebi H, Coffee EM, Greninger P, Brown RD, Godfrey JT, Cohoon TJ, Song Y, Lifshits E, Hung KE, Shioda T, Dias-Santagata D, Singh A, Settleman J, Benes CH, Mino-Kenudson M, Wong KK, Engelman JA Cancer cell 23245996 Cancer Cell 2013 Jan 14
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM Bioinformatics (Oxford, England) 23986566 Bioinformatics 2013 Nov 1
Discovery of potent and selective covalent inhibitors of JNK. Zhang T, Inesta-Vaquera F, Niepel M, Zhang J, Ficarro SB, Machleidt T, Xie T, Marto JA, Kim N, Sim T, Laughlin JD, Park H, LoGrasso PV, Patricelli M, Nomanbhoy TK, Sorger PK, Alessi DR, Gray NS Chemistry & biology 22284361 Chem Biol 2012 Jan 27
Discovery of a potent and selective DDR1 receptor tyrosine kinase inhibitor. Kim HG, Tan L, Weisberg EL, Liu F, Canning P, Choi HG, Ezell SA, Wu H, Zhao Z, Wang J, Mandinova A, Griffin JD, Bullock AN, Liu Q, Lee SW, Gray NS ACS chemical biology 23899692 ACS Chem Biol 2013 Oct 18
The UCSC Interaction Browser: multidimensional data views in pathway context. Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM Nucleic acids research 23748957 Nucleic Acids Res 2013 Jul
Mass spectrometry based method to increase throughput for kinome analyses using ATP probes. McAllister FE, Niepel M, Haas W, Huttlin E, Sorger PK, Gygi SP Analytical chemistry 23607489 Anal Chem 2013 May 7
Selective aurora kinase inhibitors identified using a taxol-induced checkpoint sensitivity screen. Kwiatkowski N, Deng X, Wang J, Tan L, Villa F, Santaguida S, Huang HC, Mitchison T, Musacchio A, Gray N ACS chemical biology 21992004 ACS Chem Biol 2012 Jan 20
Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics. Liu Q, Kirubakaran S, Hur W, Niepel M, Westover K, Thoreen CC, Wang J, Ni J, Patricelli MP, Vogel K, Riddle S, Waller DL, Traynor R, Sanda T, Zhao Z, Kang SA, Zhao J, Look AT, Sorger PK, Sabatini DM, Gray NS The Journal of biological chemistry 22223645 J Biol Chem 2012 Mar 23
Identification of Wee1 as a novel therapeutic target for mutant RAS-driven acute leukemia and other malignancies. Weisberg E, Nonami A, Chen Z, Liu F, Zhang J, Sattler M, Nelson E, Cowens K, Christie AL, Mitsiades C, Wong KK, Liu Q, Gray N, Griffin JD Leukemia 24791855 Leukemia 2015 Jan
The characteristic direction: a geometrical approach to identify differentially expressed genes. Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A BMC bioinformatics 24650281 BMC Bioinformatics 2014 Mar 21
Metrics other than potency reveal systematic variation in responses to cancer drugs. Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK Nature chemical biology 24013279 Nat Chem Biol 2013 Nov
Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Crystal AS, Shaw AT, Sequist LV, Friboulet L, Niederst MJ, Lockerman EL, Frias RL, Gainor JF, Amzallag A, Greninger P, Lee D, Kalsy A, Gomez-Caraballo M, Elamine L, Howe E, Hur W, Lifshits E, Robinson HE, Katayama R, Faber AC, Awad MM, Ramaswamy S, Mino-Kenudson M, Iafrate AJ, Benes CH, Engelman JA Science (New York, N.Y.) 25394791 Science 2014 Dec 19
A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Gujral TS, Chan M, Peshkin L, Sorger PK, Kirschner MW, MacBeath G Cell 25417160 Cell 2014 Nov 6
Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Lee S, Shang Y, Redmond SA, Urisman A, Tang AA, Li KH, Burlingame AL, Pak RA, Jovičić A, Gitler AD, Wang J, Gray NS, Seeley WW, Siddique T, Bigio EH, Lee VM, Trojanowski JQ, Chan JR, Huang EJ Neuron 27321923 Neuron 2016 Jul 6
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M Cell 29625051 Cell 2018 Apr 5
Prophetic Granger Causality to infer gene regulatory networks. Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM PloS one 29211761 PLoS One 2017
A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro. Ramm S, Todorov P, Chandrasekaran V, Dohlman A, Monteiro MB, Pavkovic M, Muhlich J, Shankaran H, Chen WW, Mettetal JT, Vaidya VS Toxicological sciences : an official journal of the Society of Toxicology 30649541 Toxicol Sci 2019 May 1
Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Van Rechem C, Black JC, Boukhali M, Aryee MJ, Gräslund S, Haas W, Benes CH, Whetstine JR Cancer discovery 25564516 Cancer Discov 2015 Mar
Lean Big Data integration in systems biology and systems pharmacology. Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y Trends in pharmacological sciences 25109570 Trends Pharmacol Sci 2014 Sep
Assessment of ABT-263 activity across a cancer cell line collection leads to a potent combination therapy for small-cell lung cancer. Faber AC, Farago AF, Costa C, Dastur A, Gomez-Caraballo M, Robbins R, Wagner BL, Rideout WM 3rd, Jakubik CT, Ham J, Edelman EJ, Ebi H, Yeo AT, Hata AN, Song Y, Patel NU, March RJ, Tam AT, Milano RJ, Boisvert JL, Hicks MA, Elmiligy S, Malstrom SE, Rivera MN, Harada H, Windle BE, Ramaswamy S, Benes CH, Jacks T, Engelman JA Proceedings of the National Academy of Sciences of the United States of America 25737542 Proc Natl Acad Sci U S A 2015 Mar 17
A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. Tang Y Current protocols in chemical biology 24652619 Curr Protoc Chem Biol 2014 Mar 14
Analysis of growth factor signaling in genetically diverse breast cancer lines. Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Muhlich JL, Schoeberl B, Sorger PK BMC biology 24655548 BMC Biol 2014 Mar 21
Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI, Card JD, Adelmant G, He H, Askenazi M, Marshall AG, Young NL, Gray NS, Marto JA Journal of the American Society for Mass Spectrometry 24496597 J Am Soc Mass Spectrom 2014 Apr
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. Hays T, Ma'ayan A, Clark NR, Tan CM, Teixeira A, Teixeira A, Choi JW, Burdis N, Jung SY, Bajaj AO, O'Malley BW, He JC, Hyink DP, Klotman PE PloS one 24949636 PLoS One 2014
Drugging MYCN through an allosteric transition in Aurora kinase A. Gustafson WC, Meyerowitz JG, Nekritz EA, Chen J, Benes C, Charron E, Simonds EF, Seeger R, Matthay KK, Hertz NT, Eilers M, Shokat KM, Weiss WA Cancer cell 25175806 Cancer Cell 2014 Sep 8
Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Kwiatkowski N, Zhang T, Rahl PB, Abraham BJ, Reddy J, Ficarro SB, Dastur A, Amzallag A, Ramaswamy S, Tesar B, Jenkins CE, Hannett NM, McMillin D, Sanda T, Sim T, Kim ND, Look T, Mitsiades CS, Weng AP, Brown JR, Benes CH, Marto JA, Young RA, Gray NS Nature 25043025 Nature 2014 Jul 31
Adaptive informatics for multifactorial and high-content biological data. Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK Nature methods 21516115 Nat Methods 2011 Jun
Brain Penetrant LRRK2 Inhibitor. Choi HG, Zhang J, Deng X, Hatcher JM, Patricelli MP, Zhao Z, Alessi DR, Gray NS ACS medicinal chemistry letters 23066449 ACS Med Chem Lett 2012 Aug 9
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase. Zhong Y, Chen EY, Liu R, Chuang PY, Mallipattu SK, Tan CM, Clark NR, Deng Y, Klotman PE, Ma'ayan A, He JC Journal of the American Society of Nephrology : JASN 23559582 J Am Soc Nephrol 2013 Apr
Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Jenkins SL, Ma'ayan A Pharmacogenomics 23327571 Pharmacogenomics 2013 Jan
Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas. Liu TT, Achrol AS, Mitchell LA, Du WA, Loya JJ, Rodriguez SA, Feroze A, Westbroek EM, Yeom KW, Stuart JM, Chang SD, Harsh GR 4th, Rubin DL AJNR. American journal of neuroradiology 26744442 AJNR Am J Neuroradiol 2016 Apr
Landscape of Targeted Anti-Cancer Drug Synergies in Melanoma Identifies a Novel BRAF-VEGFR/PDGFR Combination Treatment. Friedman AA, Amzallag A, Pruteanu-Malinici I, Baniya S, Cooper ZA, Piris A, Hargreaves L, Igras V, Frederick DT, Lawrence DP, Haber DA, Flaherty KT, Wargo JA, Ramaswamy S, Benes CH, Fisher DE PloS one 26461489 PLoS One 2015
Functional characterization of an isoform-selective inhibitor of PI3K-p110β as a potential anticancer agent. Ni J, Liu Q, Xie S, Carlson C, Von T, Vogel K, Riddle S, Benes C, Eck M, Roberts T, Gray N, Zhao J Cancer discovery 22588880 Cancer Discov 2012 May
Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae. Liu Q, Ren T, Fresques T, Oppliger W, Niles BJ, Hur W, Sabatini DM, Hall MN, Powers T, Gray NS ACS chemical biology 22496512 ACS Chem Biol 2012 Jun 15
Toward interoperable bioscience data. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W Nature genetics 22281772 Nat Genet 2012 Jan 27
Reverse Phase Protein Arrays for Compound Profiling. Moerke N, Fallahi-Sichani M Current protocols in chemical biology 27622568 Curr Protoc Chem Biol 2016 Sep 13
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist S Science (New York, N.Y.) 23869022 Science 2013 Jul 19
Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME Neuron 26711116 Neuron 2016 Jan 6
A functional landscape of resistance to ALK inhibition in lung cancer. Wilson FH, Johannessen CM, Piccioni F, Tamayo P, Kim JW, Van Allen EM, Corsello SM, Capelletti M, Calles A, Butaney M, Sharifnia T, Gabriel SB, Mesirov JP, Hahn WC, Engelman JA, Meyerson M, Root DE, Jänne PA, Garraway LA Cancer cell 25759024 Cancer Cell 2015 Mar 9
Genetic modifiers of EGFR dependence in non-small cell lung cancer. Sharifnia T, Rusu V, Piccioni F, Bagul M, Imielinski M, Cherniack AD, Pedamallu CS, Wong B, Wilson FH, Garraway LA, Altshuler D, Golub TR, Root DE, Subramanian A, Meyerson M Proceedings of the National Academy of Sciences of the United States of America 25512530 Proc Natl Acad Sci U S A 2014 Dec 30
An unbiased approach to identify endogenous substrates of "histone" deacetylase 8. Olson DE, Udeshi ND, Wolfson NA, Pitcairn CA, Sullivan ED, Jaffe JD, Svinkina T, Natoli T, Lu X, Paulk J, McCarren P, Wagner FF, Barker D, Howe E, Lazzaro F, Gale JP, Zhang YL, Subramanian A, Fierke CA, Carr SA, Holson EB ACS chemical biology 25089360 ACS Chem Biol 2014 Oct 17
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map. Blasco A, Natoli T, Endres MG, Sergeev RA, Randazzo S, Paik JH, Macaluso NJM, Narayan R, Lu X, Peck D, Lakhani KR, Subramanian A Bioinformatics (Oxford, England) 33824954 Bioinformatics 2021 Sep 29
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray MA, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, Clemons PA Proceedings of the National Academy of Sciences of the United States of America 25024206 Proc Natl Acad Sci U S A 2014 Jul 29
A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Johannessen CM, Johnson LA, Piccioni F, Townes A, Frederick DT, Donahue MK, Narayan R, Flaherty KT, Wargo JA, Root DE, Garraway LA Nature 24185007 Nature 2013 Dec 5
Connecting omics signatures and revealing biological mechanisms with iLINCS. Pilarczyk M, Fazel-Najafabadi M, Kouril M, Shamsaei B, Vasiliauskas J, Niu W, Mahi N, Zhang L, Clark NA, Ren Y, White S, Karim R, Xu H, Biesiada J, Bennett MF, Davidson SE, Reichard JF, Roberts K, Stathias V, Koleti A, Vidovic D, Clarke DJB, Schürer SC, Ma'ayan A, Meller J, Medvedovic M Nature communications 35945222 Nat Commun 2022 Aug 9
Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. Chen J, Hu Z, Phatak M, Reichard J, Freudenberg JM, Sivaganesan S, Medvedovic M PLoS computational biology 24039560 PLoS Comput Biol 2013
In utero exposure of rats to high-fat diets perturbs gene expression profiles and cancer susceptibility of prepubertal mammary glands. Govindarajah V, Leung YK, Ying J, Gear R, Bornschein RL, Medvedovic M, Ho SM The Journal of nutritional biochemistry 26895667 J Nutr Biochem 2016 Mar
Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. Repunte-Canonigo V, Lefebvre C, George O, Kawamura T, Morales M, Koob GF, Califano A, Masliah E, Sanna PP Molecular neurodegeneration 24980976 Mol Neurodegener 2014 Jul 1
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P Genome research 25378249 Genome Res 2015 Feb
Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A Cell 26186195 Cell 2015 Jul 16
Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models. Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A Cell reports 26387954 Cell Rep 2015 Sep 29
Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. Repunte-Canonigo V, Shin W, Vendruscolo LF, Lefebvre C, van der Stap L, Kawamura T, Schlosburg JE, Alvarez M, Koob GF, Califano A, Sanna PP Genome biology 25886852 Genome Biol 2015 Feb 2
A community computational challenge to predict the activity of pairs of compounds. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community Nature biotechnology 25419740 Nat Biotechnol 2014 Dec
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). Vempati UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, Visser U, Lemmon VP, Schürer SC PloS one 23155465 PLoS One 2012
Epigenetic pathways and glioblastoma treatment: insights from signaling cascades. Allen BK, Stathias V, Maloof ME, Vidovic D, Winterbottom EF, Capobianco AJ, Clarke J, Schurer S, Robbins DJ, Ayad NG Journal of cellular biochemistry 25290986 J Cell Biochem 2015 Mar
Using the BioAssay Ontology for analyzing high-throughput screening data. Zander Balderud L, Murray D, Larsson N, Vempati U, Schürer SC, Bjäreland M, Engkvist O Journal of biomolecular screening 25512330 J Biomol Screen 2015 Mar
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action. Vidović D, Koleti A, Schürer SC Frontiers in genetics 25324859 Front Genet 2014
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. Clark AM, Bunin BA, Litterman NK, Schürer SC, Visser U PeerJ 25165633 PeerJ 2014
Minimum information about a spinal cord injury experiment: a proposed reporting standard for spinal cord injury experiments. Lemmon VP, Ferguson AR, Popovich PG, Xu XM, Snow DM, Igarashi M, Beattie CE, Bixby JL, MIASCI Consortium Journal of neurotrauma 24870067 J Neurotrauma 2014 Aug 1
Kinome-wide activity modeling from diverse public high-quality data sets. Schürer SC, Muskal SM Journal of chemical information and modeling 23259810 J Chem Inf Model 2013 Jan 28
Systems modeling of anti-apoptotic pathways in prostate cancer: psychological stress triggers a synergism pattern switch in drug combination therapy. Sun X, Bao J, Nelson KC, Li KC, Kulik G, Zhou X PLoS computational biology 24339759 PLoS Comput Biol 2013
Compound signature detection on LINCS L1000 big data. Liu C, Su J, Yang F, Wei K, Ma J, Zhou X Molecular bioSystems 25609570 Mol Biosyst 2015 Mar
RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information. Suresh V, Liu L, Adjeroh D, Zhou X Nucleic acids research 25609700 Nucleic Acids Res 2015 Feb 18
Drug Signature Detection Based on L1000 Genomic and Proteomic Big Data. Chen W, Zhou X Methods in molecular biology (Clifton, N.J.) 30848467 Methods Mol Biol 2019
Genome-wide mutational spectra analysis reveals significant cancer-specific heterogeneity. Tan H, Bao J, Zhou X Scientific reports 26212640 Sci Rep 2015 Jul 27
Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway. Sun X, Su J, Bao J, Peng T, Zhang L, Zhang Y, Yang Y, Zhou X Biomaterials 22910219 Biomaterials 2012 Nov
A systematic modeling study on the pathogenic role of p38 MAPK activation in myelodysplastic syndromes. Peng H, Wen J, Zhang L, Li H, Chang CC, Zu Y, Zhou X Molecular bioSystems 22327869 Mol Biosyst 2012 Apr
Modeling the relationship of epigenetic modifications to transcription factor binding. Liu L, Jin G, Zhou X Nucleic acids research 25820421 Nucleic Acids Res 2015 Apr 30
In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. Tan H, Wei K, Bao J, Zhou X Molecular bioSystems 24056678 Mol Biosyst 2013 Nov
Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects. Shao H, Peng T, Ji Z, Su J, Zhou X PloS one 24339888 PLoS One 2013
Computational systems biology in cancer brain metastasis. Peng H, Tan H, Zhao W, Jin G, Sharma S, Xing F, Watabe K, Zhou X Frontiers in bioscience (Scholar edition) 26709906 Front Biosci (Schol Ed) 2016 Jan 1
Pathway bridge based multiobjective optimization approach for lurking pathway prediction. Zhang R, Zhao C, Xiong Z, Zhou X BioMed research international 24949437 Biomed Res Int 2014
A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosis. Shao H, He Y, Li KC, Zhou X Molecular bioSystems 23287963 Mol Biosyst 2013 Mar
SNVHMM: predicting single nucleotide variants from next generation sequencing. Bian J, Liu C, Wang H, Xing J, Kachroo P, Zhou X BMC bioinformatics 23855743 BMC Bioinformatics 2013 Jul 15
Integrating genomics and proteomics data to predict drug effects using binary linear programming. Ji Z, Su J, Liu C, Wang H, Huang D, Zhou X PloS one 25036040 PLoS One 2014
Modeling cell-cell interactions in regulating multiple myeloma initiating cell fate. Peng T, Peng H, Choi DS, Su J, Chang CC, Zhou X IEEE journal of biomedical and health informatics 24058033 IEEE J Biomed Health Inform 2014 Mar
Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis. Sun X, Zhang L, Tan H, Bao J, Strouthos C, Zhou X BMC bioinformatics 22935054 BMC Bioinformatics 2012 Aug 30
Matrix factorization reveals aging-specific co-expression gene modules in the fat and muscle tissues in nonhuman primates. Wang Y, Zhao W, Zhou X Scientific reports 27703186 Sci Rep 2016 Oct 5
OCIAD2 suppressed tumor growth and invasion via AKT pathway in Hepatocelluar carcinoma. Wu D, Yang X, Peng H, Guo D, Zhao W, Zhao C, Zhou X Carcinogenesis 28911005 Carcinogenesis 2017 Sep 1
A systems biology approach to studying the molecular mechanisms of osteoblastic differentiation under cytokine combination treatment. Tan H, Chen R, Li W, Zhao W, Zhang Y, Yang Y, Su J, Zhou X NPJ Regenerative medicine 29302342 NPJ Regen Med 2017
Prediction of treatment efficacy for prostate cancer using a mathematical model. Peng H, Zhao W, Tan H, Ji Z, Li J, Li K, Zhou X Scientific reports 26868634 Sci Rep 2016 Feb 12
Drug Effect Prediction by Integrating L1000 Genomic and Proteomic Big Data. Chen W, Zhou X Methods in molecular biology (Clifton, N.J.) 30848468 Methods Mol Biol 2019
Multi-scale modeling for the transmission of influenza and the evaluation of interventions toward it. Guo D, Li KC, Peters TR, Snively BM, Poehling KA, Zhou X Scientific reports 25757402 Sci Rep 2015 Mar 11
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach. Peng H, Peng T, Wen J, Engler DA, Matsunami RK, Su J, Zhang L, Chang CC, Zhou X Bioinformatics (Oxford, England) 24618474 Bioinformatics 2014 Jul 1
Modeling vascularized bone regeneration within a porous biodegradable CaP scaffold loaded with growth factors. Sun X, Kang Y, Bao J, Zhang Y, Yang Y, Zhou X Biomaterials 23566802 Biomaterials 2013 Jul
Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models. Wang H, Zhou X Chinese journal of cancer 23237214 Chin J Cancer 2013 Apr
Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays. Fan J, Dy JG, Chang CC, Zhou X Chinese journal of cancer 23327800 Chin J Cancer 2013 Apr
Red blood cell tracking using optical flow methods. Guo D, van de Ven AL, Zhou X IEEE journal of biomedical and health informatics 24058034 IEEE J Biomed Health Inform 2014 May
Systemic modeling myeloma-osteoclast interactions under normoxic/hypoxic condition using a novel computational approach. Ji Z, Wu D, Zhao W, Peng H, Zhao S, Huang D, Zhou X Scientific reports 26282073 Sci Rep 2015 Aug 18
Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis. Tan H, Zhou X Methods in molecular biology (Clifton, N.J.) 29344882 Methods Mol Biol 2018
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. Liu K, Beck D, Thoms JAI, Liu L, Zhao W, Pimanda JE, Zhou X Bioinformatics (Oxford, England) 28472271 Bioinformatics 2017 Sep 1
Intraglomerular crosstalk elaborately regulates podocyte injury and repair in diabetic patients: insights from a 3D multiscale modeling study. Tan H, Yi H, Zhao W, Ma JX, Zhang Y, Zhou X Oncotarget 27683034 Oncotarget 2016 Nov 8
Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features. Chen H, Chen W, Liu C, Zhang L, Su J, Zhou X Scientific reports 27427091 Sci Rep 2016 Jul 18
"Pop-slide" patterning: Rapid fabrication of microstructured PDMS gasket slides for biological applications. Ramji R, Khan NT, Muñoz-Rojas A, Miller-Jensen K RSC advances 26949529 RSC Adv 2015
High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. Lu Y, Chen JJ, Mu L, Xue Q, Wu Y, Wu PH, Li J, Vortmeyer AO, Miller-Jensen K, Wirtz D, Fan R Analytical chemistry 23339603 Anal Chem 2013 Feb 19
A microchip platform for interrogating tumor-macrophage paracrine signaling at the single-cell level. Elitas M, Brower K, Lu Y, Chen JJ, Fan R Lab on a chip 25057779 Lab Chip 2014 Sep 21
Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation. Xue Q, Lu Y, Eisele MR, Sulistijo ES, Khan N, Fan R, Miller-Jensen K Science signaling 26082435 Sci Signal 2015 Jun 16
Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Lu Y, Xue Q, Eisele MR, Sulistijo ES, Brower K, Han L, Amir el-AD, Pe'er D, Miller-Jensen K, Fan R Proceedings of the National Academy of Sciences of the United States of America 25646488 Proc Natl Acad Sci U S A 2015 Feb 17
Single cell functional proteomics for assessing immune response in cancer therapy: technology, methods, and applications. Ma C, Fan R, Elitas M Frontiers in oncology 23755371 Front Oncol 2013
A polymer-based ratiometric intracellular glucose sensor. Zhang L, Su F, Buizer S, Kong X, Lee F, Day K, Tian Y, Meldrum DR Chemical communications (Cambridge, England) 24840577 Chem Commun (Camb) 2014 Jul 4
A fluorescent colorimetric pH sensor and the influences of matrices on sensing performances. Tian Y, Fuller E, Klug S, Lee F, Su F, Zhang L, Chao SH, Meldrum DR Sensors and actuators. B, Chemical 24078772 Sens Actuators B Chem 2013 Oct
A highly selective mitochondria-targeting fluorescent K(+) sensor. Kong X, Su F, Zhang L, Yaron J, Lee F, Shi Z, Tian Y, Meldrum DR Angewandte Chemie (International ed. in English) 26302172 Angew Chem Int Ed Engl 2015 Oct 5
The oxindole Syk inhibitor OXSI-2 blocks nigericin-induced inflammasome signaling and pyroptosis independent of potassium efflux. Yaron JR, Rao MY, Gangaraju S, Zhang L, Kong X, Su F, Tian Y, Glenn HL, Meldrum DR Biochemical and biophysical research communications 26970308 Biochem Biophys Res Commun 2016 Apr 8
A platform for high-throughput bioenergy production phenotype characterization in single cells. Kelbauskas L, Glenn H, Anderson C, Messner J, Lee KB, Song G, Houkal J, Su F, Zhang L, Tian Y, Wang H, Bussey K, Johnson RH, Meldrum DR Scientific reports 28349963 Sci Rep 2017 Mar 28
Ratiometric fluorescent pH-sensitive polymers for high-throughput monitoring of extracellular pH. Zhang L, Su F, Kong X, Lee F, Day K, Gao W, Vecera ME, Sohr JM, Buizer S, Tian Y, Meldrum DR RSC advances 27721974 RSC Adv 2016
1,8-Naphthalimide Derivative Dyes with Large Stokes Shifts for Targeting Live-Cell Mitochondria. Zhang L, Su F, Kong X, Lee F, Sher S, Day K, Tian Y, Meldrum DR Chembiochem : a European journal of chemical biology 27319799 Chembiochem 2016 Sep 15
A dual sensor for real-time monitoring of glucose and oxygen. Zhang L, Su F, Buizer S, Lu H, Gao W, Tian Y, Meldrum D Biomaterials 24090834 Biomaterials 2013 Dec
K(+) regulates Ca(2+) to drive inflammasome signaling: dynamic visualization of ion flux in live cells. Yaron JR, Gangaraju S, Rao MY, Kong X, Zhang L, Su F, Tian Y, Glenn HL, Meldrum DR Cell death & disease 26512962 Cell Death Dis 2015 Oct 29
Laser-fabricated cell patterning stencil for single cell analysis. Messner JJ, Glenn HL, Meldrum DR BMC biotechnology 29258486 BMC Biotechnol 2017 Dec 19
Panorama: a targeted proteomics knowledge base. Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B Journal of proteome research 25102069 J Proteome Res 2014 Sep 5
Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG Methods in molecular biology (Clifton, N.J.) 26867747 Methods Mol Biol 2016
Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD Methods (San Diego, Calif.) 25448295 Methods 2015 Jan 15
CPTAC Assay Portal: a repository of targeted proteomic assays. Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H, Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG Nature methods 24972168 Nat Methods 2014 Jul
Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A Nature genetics 27322546 Nat Genet 2016 Aug

This page last reviewed on March 13, 2025