Artem Sokolov, Ph.D.
Artem Sokolov, Ph.D.
Instructor in Biomedical Informatics

Artem Sokolov completed his PhD under the supervision of Asa Ben-Hur at Colorado State University, where he worked on developing state-of-the-art methods for protein function prediction. Sokolov's postdoctoral research at the University of California Santa Cruz focused on building robust, interpretable in silico models of human cancers and correlating these models with biological and clinical outcomes as part of his involvement in The Cancer Genome Atlas (TCGA) and the West Coast Dream Team (WCDT) consortia.

As Director of Informatics and Modeling at the Laboratory of Systems Pharmacology (LSP), Artem leads a group of computational biologists and software engineers who model pre-clinical, translational and clinical data using a wide range of machine learning and artificial intelligence approaches. He plays a leading role in training and mentoring a diverse group of students and postdocs in managing the lab’s collaborations with academic and industrial groups.

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.
Authors: Aggarwal R, Huang J, Alumkal JJ, Zhang L, Feng FY, Thomas GV, Weinstein AS, Friedl V, Zhang C, Witte ON, Lloyd P, Gleave M, Evans CP, Youngren J, Beer TM, Rettig M, Wong CK, True L, Foye A, Playdle D, Ryan CJ, Lara P, Chi KN, Uzunangelov V, Sokolov A, Newton Y, Beltran H, Demichelis F, Rubin MA, Stuart JM, Small EJ.
J Clin Oncol
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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.
Authors: Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kaminska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwinska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.
Cell
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Prophetic Granger Causality to infer gene regulatory networks.
Authors: Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM.
PLoS One
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N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells.
Authors: 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
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Inferring causal molecular networks: empirical assessment through a community-based effort.
Authors: Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.
Nat Methods
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Pathway-Based Genomics Prediction using Generalized Elastic Net.
Authors: Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM.
PLoS Comput Biol
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ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.
Authors: Sokolov A, Paull EO, Stuart JM.
Pac Symp Biocomput
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A basal stem cell signature identifies aggressive prostate cancer phenotypes.
Authors: Smith BA, Sokolov A, Uzunangelov V, Baertsch R, Newton Y, Graim K, Mathis C, Cheng D, Stuart JM, Witte ON.
Proc Natl Acad Sci U S A
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Assessing the clinical utility of cancer genomic and proteomic data across tumor types.
Authors: Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H.
Nat Biotechnol
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A large-scale evaluation of computational protein function prediction.
Authors: Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.
Nat Methods
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