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Dmitry Korkin, Ph.D. E-Mail: [email protected] WWW

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Dmitry Korkin, Ph.D. E-Mail: Dkorkin@Wpi.Edu WWW Bioinformatics and Computational Biology Program Department of Computer Science Worcester Polytechnic Institute, Worcester, MA Dmitry Korkin, Ph.D. e-mail: [email protected] WWW: http://korkinlab.org Education • Postdoc in Bioinformatics and Computational Biology University of California San Francisco: 2003-2007; Rockefeller University: 2002 Research topic: Structural bioinformatics and systems biology of protein-protein interactions • Ph.D. in Computer Science Faculty of Computer Science, University of New Brunswick, NB, Canada: 2003 Research topic: Machine learning with applications to computer-aided drug design • M.Sc. in Mathematics, Applied Mathematics Faculty of Mechanics and Mathematics, Moscow State University, Moscow, Russia: 1999 Research Topic: Application of information theory to Security Policy • B.Sc. in Mathematics, Applied Mathematics Faculty of Mechanics and Mathematics, Moscow State University, Moscow, Russia: 1997 Academic positions • Director, Bioinformatics and Computational Biology Program 2017-present Worcester Polytechnic Institute, Worcester, MA, USA • Associate Professor in Bioinformatics and Computer Science with tenure 2014–present Dept. of Computer Science and Program in Bioinformatics and Computational Biology Courtesy appointment with Data Science Program and Depts. of Applied Mathematics, Biology and Biotechnology, Worcester Polytechnic Institute, MA, USA • Associate Professor in Bioinformatics and Computer Science with tenure 2013–2014 Dept. of Computer Science and Informatics Institute, University of Missouri-Columbia Affiliated with Bond Life Science Center, University of Missouri-Columbia, MO, USA • Associate Director of Graduate Studies in Bioinformatics 2008–2010 Informatics Institute, University of Missouri-Columbia, Columbia, USA • Assistant Professor in Bioinformatics and Computer Science 2007–2013 Dept. of Computer Science and Informatics Institute, University of Missouri-Columbia Affiliated with Bond Life Science Center, University of Missouri-Columbia, MO, USA • Postdoctoral Fellow 2003–2007 University of California San Francisco, San Francisco, USA; Advisor: Prof. Andrej Sali • Postdoctoral Fellow 2002–2003 Rockefeller University, New York, USA; Advisor: Prof. Andrej Sali • Graduate Fellow 2000–2002 University of New Brunswick, NB, Canada; Advisor: Prof. Lev Goldfarb • Visiting Researcher 1999 University of New Brunswick, Fredericton, Canada, 1999 Non-Academic positions • Consultant in Bioinformatics and Biomedical Data Analytics 2018-present Syndax Pharmaceuticals, Inc., MA, USA • President and Co-Founder 2018-present In Virtu Data Solutions, LLC, MA, USA A startup focusing on consulting in biomedical data analytics Honors, awards, and other recognition To Dmitry Korkin • 2019: Senior Member, International Society for Computational Biology (ISCB) • 2018: MA Acorn Award 2018 Finalist • 2013: Junior Research Faculty of the Year Award, College of Engineering, University of Missouri-Columbia • 2009: NSF CAREER Award (see Grants for details) • 2002: ISCB Travel Fellowship, The International Society for Computational Biology • 2001: Sasi Mohal Pal Memorial Prize (the best academic performance), University of New Brunswick, Canada • 1999: Gold medal and Diploma with Excellence (excellent academic performance), Moscow State University To Dmitry Korkin’s Advised and Co-Advised Students • 2019 Fulbright Fellow: Winnie Mkandawire • 2019 WPI Graduate Student Travel Fund, Hongzhu Cui • 2nd place (CS and Data Science) in 2019 WPI GRIE Poster Competition, Suhas Srinivasan • 1st place (CS and Data Science) in 2018 WPI GRIE Poster Competition, Suhas Srinivasan • 2018 WPI Graduate Student Travel Fund, Suhas Srinivasan • 2017 Fulbright Fellow: Anastasia Leshchyk • 2016 WPI Graduate Student Travel Fund, Katelyn Hughes • Cold Spring Harbor Labs (CSHL) Travel Stipend, to present work at “Systems Biology: Global Regulation of Gene Expression, 2016" meeting at CSHL, Katelyn Hughes • Finalist for the 2014 WPI GRIE Poster Competition, Andi Dhroso • Undergraduate Award at the 2014 MU Life Science Annual poster competition, Jeff King • 2014 ISCB Travel Fellowship to present our work at the ISMB 2014 conference (the main conference in bioinformatics and computational biology), Samantha Warren • 1st place at MU CS Annual poster competition, Samantha Warren • 2013 Keystone Symposia Future of Science Fund scholarship, Andi Dhroso • 3rd place in Missouri Informatics Symposium 2013, Samantha Warren • 1st place in poster competition at the 2012 MU Life Science Week, Samantha Warren • 2nd place in poster competition at 2012 MCBIOS Conference, Xingyan Kuang • 3rd place in poster competition at 2012 MCBIOS Conference, Bin Pang • NSF Educational Workshop Travel award for ABRF 2012 (17 awarded nation-wide), Nan Zhao • DOE GAANN Fellowship, Samantha Warren • Shumaker Fellowships: Xingyan Kuang, Nan Zhao, Bin Pang • 3rd place in poster competition at the 2011 MU Life Science Week, Nan Zhao • Best undergraduate poster at the 2010 MU Life Science Week, Samantha Warren Research and Scholarship Summary: My research crosses the fields of bioinformatics, computation systems biology, genomics, biomedical data mining, machine learning, artificial intelligence, and biovisualization. My group has strong expertise in developing cutting-edge AI, machine learning, and visualization methods to deal with large volumes of biological and biomedical data. I have published 61 articles, including: 1 book chapter, 49 journal publications including 1 cover journal paper (FEBS, 2014) in the top bioinformatics, computational biology, computer science, and life sciences journals and preprints, and 11 conference proceedings. My co-authors include Elizabeth Blackburn (recipient of the 2009 Nobel Prize in Physiology or Medicine), as well as David Baker, Andrej Sali, and Michael Freeling (all three are members of the National Academy of Sciences of USA). Notes: 1. For the life sciences, computational sciences, informatics and other interdisciplinary journals, the key authors are usually (i) the last author (a senior author coordinating the project, designing the approaches, writing the paper, etc.) and (ii) the first author (a junior author responsible for the implementation of the approaches, their assessment, and result analysis). In a joint interdisciplinary project between multiple labs, senior authors, one from each research group, occupy the last several positions in the citation, while key junior authors occupy the first positions. 2. Supervised and co-supervised students are underscored. WPI students are underscored and italicized. 3. IF corresponds to the ISI impact factor of the journal at the time the paper was published (when available). Journal articles and preprints J1 Cui H, Zhou C, X Dai, Y Liang, R Paffenroth, D Korkin, “Boosting Gene Expression Clustering with System-Wide Biological Information: A Robust Autoencoder Approach”, International Journal of Computational Biology and Drug Design. 2020, In press J2 Narykov O, Bogatov D, and Korkin D. "DISPOT: A simple knowledge-based protein domain interaction statistical potential." Bioinformatics. (IF: 4.531) 2019, Dec 15; 35 (24): 5374– 5378 J3 Cui H, Srinivasan S, and Korkin D. Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases. Genes. (IF: 2.638) 2019, Nov;10(11):933 J4 Srinivasan S, Johnson NT, and Korkin D. "A Hybrid Deep Clustering Approach for Robust Cell Type Profiling Using Single-cell RNA-seq Data." bioRxiv. 2019: 511626 J5 Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, ..., Srinivasan S, Cui H, Narykov O, Dhroso A, Johnson NT, Korkin D, ... , Natoli T. “Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases.” Nature Methods. (IF: 25.062) 2019 J6 Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG and Mimee B, “The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.” BMC genomics. (IF: 3.730) 2019, 20(1), p.119 J7 Cui H, Zhao N, Korkin D. Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling. Journal of molecular biology. (IF: 4.894) 2018, Sep 14; 430(18):2974-92. J8 Dhroso A, Eidson S, Korkin D. “Genome-wide prediction of bacterial effectors across six secretion system types using a feature-based supervised learning framework.” Scientific reports. (IF: 4.609) 2018: 8 (1), 17209 J9 Narykov O, Johnson NT, Korkin D. “Determining rewiring effects of alternatively spliced isoforms on protein-protein interactions using a computational approach.” bioRxiv. 2018, Jan 1:256834 J10 Gardner M, Dhroso A, Johnson NT, Davis EL, Baum TJ, Korkin D, Mitchum MG. “Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines.” Scientific reports. (IF: 4.609) 2018, Feb 6;8(1):2505 J11 Johnson NT, Dhroso A, Hughes KJ, D Korkin, “Biological classification with RNA-Seq data: Can alternative splicing enhance machine learning classifier?” RNA. 2018, 24 (9), 1119- 1132 J12 V Gruzdev, D Korkin, BP Mooney, JF Havelund, IM Møller, JJ Thelen, “Controlled modification of biomolecules by ultrashort laser pulses in polar liquids”, Scientific Reports. (IF: 4.609 ) 2017, 7(1), 5550 J13 Kandoth PK, Liu S, Prenger E, Ludwig A, Lakhssassi N, Heinz R, Zhou Z, Howland A, Gunther J, Eidson S, Dhroso A., …, Korkin D, Meksem K, Mitchum M. “Systematic
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