Simon Koplev, Curriculum Vitae

Academic Positions & Education

2015-current PhD student, University of Cambridge, Cancer Research UK, Cambridge Institute, Cambridge, UK
2016-2018 Bioinformatician II, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, USA
2015-2016 Bioinformatician, Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, USA
2014-2015 Research assistant, Biotech Research and Innovation Centre, University of Copenhagen, Denmark
2013-2014 Research scholar, Department of Medicine, Dana-Farber Cancer Institute, Harvard Medical School, USA
2013-2014 MScEng in Systems Biology and Bioinformatics,Technical University of Denmark, Denmark
2013-2014 BSc in Biochemistry, University of Copenhagen, Denmark

Publications

2018

[15] Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes

R Malik, G Chauhan, M Traylor, M Sargurupremraj, Y Okada, A Mishra, L Rutten-Jacobs, A Giese, SW van der Laan, S Gretarsdottir, CD Anderson, M Chong, HHH Adams, T Ago, P Almgren, P Amouyel, H Ay, TM Bartz, OR Benavente, S Bevan, GB Boncoraglio, RD Brown, AS Butterworth, C Carrera, CL Carty, DI Chasman, W Chen, JW Cole, A Correa, I Cotlarciuc, C Cruchaga, J Danesh, PIW de Bakker, AL DeStefano, M den Hoed, Q Duan, ST Engelter, GJ Falcone, RF Gottesman, RP Grewal, V Gudnason, S Gustafsson, J Haessler, TB Harris, A Hassan, AS Havulinna, SR Heckbert, EG Holliday, G Howard, F Hsu, HI Hyacinth, MA Ikram, E Ingelsson, MR Irvin, X Jian, J Jimenez-Conde, JA Johnson, JW Jukema, M Kanai, KL Keene, BM Kissela, DO Kleindorfer, C Kooperberg, M Kubo, LA Lange, CD Langefeld, C Langenberg, LJ Launer, J Lee, R Lemmens, D Leys, CM Lewis, W Lin, AG Lindgren, E Lorentzen, PK Magnusson, J Maguire, A Manichaikul, PF McArdle, JF Meschia, BD Mitchell, TH Mosley, MA Nalls, T Ninomiya, MJ O'Donnell, BM Psaty, SL Pulit, K Rannikmae, AP Reiner, KM Rexrode, K Rice, SS Rich, PM Ridker, NS Rost, PM Rothwell, JI Rotter, T Rundek, RL Sacco, S Sakaue, MM Sale, V Salomaa, BR Sapkota, R Schmidt, CO Schmidt, U Schminke, P Sharma, A Slowik, CLM Sudlow, C Tanislav, T Tatlisumak, KD Taylor, VNS Thijs, G Thorleifsson, U Thorsteinsdottir, S Tiedt, S Trompet, C Tzourio, CM van Duijn, M Walters, NJ Wareham, S Wassertheil-Smoller, JG Wilson, KL Wiggins, Q Yang, S Yusuf, JC Bis, T Pastinen, A Ruusalepp, EE Schadt, S Koplev, JLM Bjorkegren, et al, {AFGen Consortium}, {Cohorts for Heart, Aging Research in Genomic Epidemiology (CHARGE) Consortium}, {International Genomics of Blood Pressure (iGEN-BP) Consortium}, {INVENT Consortium}, STARNET, {BioBank Japan Cooperative Hospital Group}, {COMPASS Consortium}, {EPIC-CVD Consortium}, {EPIC-InterAct Consortium}, {International Stroke Genetics Consortium (ISGC)}, {METASTROKE Consortium}, {Neurology Working Group of the CHARGE Consortium}, {NINDS Stroke Genetics Network (SiGN)}, {UK Young Lacunar DNA Study}, {MEGASTROKE Consortium}, {MEGASTROKE Consortium:

Nature genetics 50(4), 524--537 (2018)

[14] A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers

BA Smith, NG Balanis, A Nanjundiah, KM Sheu, BL Tsai, Q Zhang, JW Park, M Thompson, J Huang, ON Witte, TG Graeber

Cell Reports 24(12), 3353--3366.e5 (2018)

[13] The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

AB Keenan, SL Jenkins, KM Jagodnik, S Koplev, E He, D Torre, Z Wang, AB Dohlman, MC Silverstein, A Lachmann, MV Kuleshov, A Ma'ayan, V Stathias, R Terryn, D Cooper, M Forlin, A Koleti, D Vidovic, C Chung, SC Schurer, J Vasiliauskas, M Pilarczyk, B Shamsaei, M Fazel, Y Ren, W Niu, NA Clark, S White, N Mahi, L Zhang, M Kouril, JF Reichard, S Sivaganesan, M Medvedovic, J Meller, RJ Koch, MR Birtwistle, R Iyengar, EA Sobie, EU Azeloglu, J Kaye, J Osterloh, K Haston, J Kalra, S Finkbiener, J Li, P Milani, M Adam, R Escalante-Chong, K Sachs, A Lenail, D Ramamoorthy, E Fraenkel, G Daigle, U Hussain, A Coye, J Rothstein, D Sareen, L Ornelas, M Banuelos, B Mandefro, R Ho, CN Svendsen, RG Lim, J Stocksdale, MS Casale, TG Thompson, J Wu, LM Thompson, V Dardov, V Venkatraman, A Matlock, JE {Van Eyk}, JD Jaffe, M Papanastasiou, A Subramanian, TR Golub, SD Erickson, M Fallahi-Sichani, M Hafner, NS Gray, J Lin, CE Mills, JL Muhlich, M Niepel, CE Shamu, EH Williams, D Wrobel, PK Sorger, LM Heiser, JW Gray, JE Korkola, GB Mills, M LaBarge, HS Feiler, MA Dane, E Bucher, M Nederlof, D Sudar, S Gross, DF Kilburn, R Smith, K Devlin, R Margolis, L Derr, A Lee, A Pillai

Cell systems 6(1), 13--24 (2018)

[12] Multi-stage Differentiation Defines Melanoma Subtypes with Differential Vulnerability to Drug-Induced Iron-Dependent Oxidative Stress

J Tsoi, L Robert, K Paraiso, C Galvan, KM Sheu, J Lay, DJ Wong, M Atefi, R Shirazi, X Wang, D Braas, CS Grasso, N Palaskas, A Ribas, TG Graeber

Cancer Cell 33(5), 890--904.e5 (2018)

[11] Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition

S Koplev, K Lin, AB Dohlman, A Ma'ayan

PLoS computational biology 14(1), e1005911 (2018)

[10] A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism

MM Seldin, S Koplev, P Rajbhandari, L Vergnes, GM Rosenberg, Y Meng, C Pan, TMN Phuong, R Gharakhanian, N Che, S Makinen, DM Shih, M Civelek, BW Parks, ED Kim, F Norheim, K {Chella Krishnan}, Y Hasin-Brumshtein, M Mehrabian, M Laakso, CA Drevon, HA Koistinen, P Tontonoz, K Reue, RM Cantor, JLM Bjorkegren, AJ Lusis

Cell metabolism 27(5), 1138--1155.e6 (2018)

[9] Functional and transcriptomic insights into pathogenesis of R9C phospholamban mutation using human induced pluripotent stem cell-derived cardiomyocytes

DK Ceholski, IC Turnbull, C Kong, S Koplev, J Mayourian, PA Gorski, F Stillitano, AA Skodras, M Nonnenmacher, N Cohen, JLM Bjorkegren, DR Stroik, RL Cornea, DD Thomas, RA Li, KD Costa, RJ Hajjar

Journal of molecular and cellular cardiology 119(), 147--154 (2018)

[8] JCAD, a Gene at the 10p11 Coronary Artery Disease Locus, Regulates Hippo Signaling in Endothelial Cells

PD Jones, MA Kaiser, M {Ghaderi Najafabadi}, S Koplev, Y Zhao, G Douglas, T Kyriakou, S Andrews, R Rajmohan, H Watkins, KM Channon, S Ye, X Yang, JLM Bjorkegren, NJ Samani, TR Webb

Arteriosclerosis, thrombosis, and vascular biology 38(8), 1711--1722 (2018)

[7] CD90 Identifies Adventitial Mesenchymal Progenitor Cells in Adult Human Medium- and Large-Sized Arteries

KC Michelis, A Nomura-Kitabayashi, L Lecce, O Franzen, S Koplev, Y Xu, MP Santini, V D'Escamard, JTL Lee, V Fuster, R Hajjar, RC Reddy, J Chikwe, P Stelzer, F Filsoufi, A Stewart, A Anyanwu, JLM Bjorkegren, JC Kovacic

Stem cell reports 11(1), 242--257 (2018)

[6] Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus

V Nanda, T Wang, M Pjanic, B Liu, T Nguyen, LP Matic, U Hedin, S Koplev, L Ma, O Franzen, A Ruusalepp, EE Schadt, JLM Bjorkegren, SB Montgomery, MP Snyder, T Quertermous, NJ Leeper, CL Miller

PLoS genetics 14(11), e1007755 (2018)

[5] Macrophage Trafficking, Inflammatory Resolution, and Genomics in Atherosclerosis: JACC Macrophage in CVD Series (Part 2)

KJ Moore, S Koplev, EA Fisher, I Tabas, JLM Bjorkegren, AC Doran, JC Kovacic

Journal of the American College of Cardiology 72(18), 2181--2197 (2018)

2017

[4] MicroRNA-210, MicroRNA-331, and MicroRNA-7 Are Differentially Regulated in Treated HIV-1-Infected Individuals and Are Associated With Markers of Systemic Inflammation

V Ballegaard, U Ralfkiaer, KK Pedersen, M Hove, S Koplev, P Br{\ae}ndstrup, LP Ryder, HO Madsen, J Gerstoft, K Gr{\o}nb{\ae}k, SD Nielsen

Journal of acquired immune deficiency syndromes (1999) 74(4), e104--e113 (2017)

[3] Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

KM Jagodnik, S Koplev, SL Jenkins, L Ohno-Machado, B Paten, SC Schurer, M Dumontier, R Verborgh, A Bui, P Ping, NJ McKenna, R Madduri, A Pillai, A Ma'ayan

Journal of biomedical informatics 71(), 49--57 (2017)

[2] Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments

S Koplev, J Longden, J Ferkinghoff-Borg, M {Blicher Bjerreg{\aa}rd}, TR Cox, JT Erler, JT Pedersen, F Voellmy, MOA Sommer, R Linding

Cell reports 20(12), 2784--2791 (2017)

2016

[1] Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

MV Kuleshov, MR Jones, AD Rouillard, NF Fernandez, Q Duan, Z Wang, S Koplev, SL Jenkins, KM Jagodnik, A Lachmann, MG McDermott, CD Monteiro, GW Gundersen, A Ma'ayan

Nucleic acids research 44(W1), W90--7 (2016)