Biomine Kurgan Lab

College of Engineering

Dr. Lukasz Kurgan

Robert J. Mattauch Endowed Professor

Virginia Commonwealth University, Department of Computer Science
401 West Main Street, Room E4225, P.O. Box 843019, Richmond, Virginia 23284, U.S.A.
Office: E4254, East Engineering Hall, 4th floor

Phone: (804) 827-3986 | Email: lkurgan@vcu.edu | Web: http://biomine.cs.vcu.edu/

Web profiles

Education

  • 2000 – 2003
    Ph.D., Department of Computer Science, University of Colorado at Boulder, Colorado, U.S.A.
  • 1999 – 2000
    Ph. D. candidate, Department of Bioengineering, University of Toledo, Toledo, Ohio, U.S.A. (transferred to the University of Colorado at Boulder)
  • 1994 – 1999
    M.Sc. (with honors), Automation and Robotics, AGH University of Science and Technology, Krakow, Poland

Employment

  • Sept 2015 – present
    Virginia Commonwealth University, Department of Computer Science, Robert J. Mattauch Endowed Professor
  • Sept 2015 – present
    University of Alberta, Department of Electrical and Computer Engineering, Adjunct Professor
  • Jul 2013 – Aug 2015
    University of Alberta, Department of Electrical and Computer Engineering, Professor
  • Jul 2007 – Jun 2013
    The University of Alberta, Department of Electrical and Computer Engineering, Associate Professor
  • Jul 2003 – Jun 2007
    University of Alberta, Department of Electrical and Computer Engineering, Assistant Professor
  • Aug 2002 – May 2003
    University of Colorado at Denver, Department of Computer Science and Engineering, Senior Instructor
  • Jan 2002 – Aug 2002
    University of Colorado at Denver, Department of Computer Science and Engineering, Part-time Instructor
  • Aug – Dec 2001
    University of Colorado at Denver, Department of Computer Science and Engineering, Teaching Assistant
  • August 1999 – July 2000
    University of Toledo, Department of Bioengineering, Research Assistant
  • Jul 1997 – Aug 1997
    Summer co-op at KGHM Polish Copper S.A., Intern

Areas of Interest

  • Data science with focus on the development of machine learning/deep learning models
  • Structural bioinformatics
  • Structure and function prediction and modeling of proteins and short RNAs
  • Protein-ligand(drug) interactions
  • Prediction and functional characterization of intrinsic disorder in proteins
  • Structural genomics

Publications

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Editorial and Reviewer Service

Editor-in-Chief

Biomolecules 2024 - present (Section Editor-in-Chief for Bioinformatics and Systems Biology: 2018 - 2024)

Editorial Boards

  • Computational and Structural Biotechnology Journal 2023 - present
  • Bioinformatics 2019 - present
  • Machine Learning and Knowledge Extraction (MAKE) 2017 - present
  • Current Protein and Peptide Science 2016 - present

Former Membership on Editorial Boards

  • BMC Bioinformatics (area editor for Structural Bioinformatics) 2010 - 2022
  • International Journal of Molecular Sciences 2017 - 2021
  • Neurocomputing 2005 - 2019
  • Protein and Peptide Letters 2009 - 2019
  • PLoS ONE 2011 - 2019
  • PeerJ 2012 - 2019
  • Intrinsically Disordered Proteins 2015 - 2017
  • Open Proteomics Journal 2007 - 2013
  • Open Bioinformatics Journal 2008 - 2012

Guest editor

  • Special issue of the Neurocomputing on "Deep neural networks for precision medicine", 2021 (with FX Wu, M Li, and L. Rueda)
  • Special issue of the Biomolecules on "Computational Perspectives on Intrinsic Disorder-Based Functionality", 2020 (with V. Uversky and C.J. Oldfield)
  • Special issue of the International Journal of Molecular Sciences on "Intrinsically Disordered Proteins in the Norm and Pathology: In-Silico Perspective", 2017 (with V. Uversky)
  • Special issue of the International Journal of Molecular Sciences on "In-Silico Prediction and Characterization of Intrinsic Disorder in Proteins", 2015 (with V. Uversky)
  • Special issue of the Current Protein and Peptide Science on "Machine Learning Models in Protein Bioinformatics", vol. 12, no. 6, 2011 (with Y. Zhou)
  • Special issue of the IEEE Engineering in Medicine and Biology magazine on "Machine Learning in the Life Sciences", vol. 26, no. 2, March 2007 (with K. Cios and M. Reformat)
  • Special issue of the Neural Network World journal on "Biologically Inspired Computing and Computers in Biology", vol. 3, 2005 (with P. Musilek and M. Reformat)

Ad hoc reviewer for 92 journals (700+ reviews, high impact factor journals are in bold)

ACM Computing Surveys; Acta Crystallographica D; Amino Acids; Analytical Biochemistry; Artificial Intelligence; Artificial Intelligence in Medicine; BBA Proteins and Proteomics; Biochimie; Biochemistry; Bioinformatics; Biomolecules; BMC Bioinformatics; BMC Structural Biology; Briefings in Bioinformatics; BMC Genomics; Cell Biochemistry and Biophysics; Chemical Reviews; Computational Biology and Chemistry; Computers and Mathematics with Applications; Computers in Biology and Medicine; Computing and Informatics; Current Bioinformatics; Current Protein Peptide Science; Current Protocols; Data and Knowledge Engineering; Data Mining and Knowledge Discovery; Database; Digital Signal Processing; European Neuropsychopharmacology; Expert Opinion On Drug Discovery; Food Technology and Biotechnology; Gene; Genomics; Genomics, Proteomics & Bioinformatics; Human Mutation; IEEE ACM Trans on Computational Biology and Bioinformatics; IEEE Trans Biomedical Engineering; IEEE Trans on Evolutionary Computing; IEEE Trans on Fuzzy Systems; IEEE Trans on Knowledge and Data Engineering; IEEE Trans on Systems Man and Cybernetics Parts A; B; and C; IEEE Engineering in Medicine and Biology; IEEE Trans on NanoBioscience; Information Fusion; Information Sciences; International Journal of Approximate Reasoning; International Journal of Biological Science; International Journal of Computational Intelligence Research; International Journal of Molecular Sciences; International Journal of Proteomics; Intrinsically Disordered Proteins; Journal of Applied Science; Journal of Bioinformatics and Computational Biology; Journal of Biomolecular Structure and Dynamics; Journal of Chemical Information and Modeling; Journal of Computational Chemistry; Journal of Computer Aided Molecular Design; Journal of Information Sciences Engineering; Journal of Modeling and Simulation; Journal of Molecular Biology; Journal of Multi-Valued Logic and Soft Computing; Journal of Proteome Research; Journal of Structural Biology; Journal of Theoretical Biology; Knowledge Engineering Review; Methods; Molecular BioSystems; Molecules; Nature; Nature Communications; Nature Computational Science; Nature Protocols; Neurocomputing; Nucleic Acids Research; Open Bioinformatics; Pattern Recognition; Physics Letters A; Plant Molecular Biology; PLOS Computational Biology; PLoS ONE; Proceedings of the National Academy of Science (PNAS); Protein Peptide Letters; Protein Engineering Design and Selection; Protein Journal; Protein Science; Proteins; Proteomics; Scientific Reports; RNA; RSC Advances; and Trends in Biochemical Sciences.

Member of review panel for the following funding agencies (in alphabetical order):

  • CIHR (Canadian Institutes of Health Research)Genomics Committee

Reviewer for the following funding agencies (in alphabetical order):

  • CFI (Canada Foundation for Innovation)Leaders Opportunity Fund program
  • CIHR (Canadian Institutes of Health Research)Operating Grants program
  • Human Frontier ScienceCareer Development Award program
  • National Science Center of PolandHARMONIA program
  • National Science FoundationBIO Career program
    • IIS Information Integration and Informatics program
    • MCB Cellular Dynamics and Function program
    • MCB Molecular Biophysics program
    • MCB Molecular and Cellular Biosciences program
    • MCB Systems and Synthetic Biology program
  • NSERC (Natural Sciences and Engineering Research Council of Canada)Discovery program
    • Collaborative Health Research Projects (CHRP) program
    • Collaborative Research and Development (CRD) program
  • NWO (Netherlands Organisation for Scientific Research and Dutch National Science Foundation)Computational Life Sciences program
    • Physical Sciences Free Competition program
  • QNRF (Qatar National Research Foundation)National Priorities Research program (NPRP)

Membership is Professional Societies

Current Membership

  • RSB (Royal Society of Biology) (Fellow) 2023-present
  • EASA (European Academy of Sciences and Arts) (Member) 2022-present
  • AAIA (Asia-Pacific Artificial Intelligence Association) (Member) 2021-present
  • Kosciuszko Foundation Collegium of Eminent Scientists (Fellow) 2018-present
  • AIMBE (American Institute for Medical and Biological Engineering) (Fellow) 2018-present
  • PTBI (Polish Bioinformatics Society) (Member) 2010-present
  • ISCB (International Society for Computational Biology) (Senior Member) 2005-present
  • ACM (Association for Computing Machinery) (Senior Member) 2002-present

Past Membership

  • APEGGA (Association of Professional Engineers, Geologists, and Geophysicists of Alberta) (Member) 2009-2016
  • CAN (Canadian Arthritis Network) (Member) 2006-2013
  • IEEE (Institute of Electrical and Electronics Engineers) 2002-2012
    • IEEE Computer Society (Senior Member) 2003-2012
    • IEEE Computational Intelligence Society (Member) 2004-2011
    • IEEE System, Man, and Cybernetics Society (Member) 2004-2010
  • SIGKDD (ACM Special Interest Group on Knowledge Discovery in Data and Data Mining) (Member) 2003-2010
  • MITACS (Mathematics of Information Technology and Complex Systems) (Member) 2005-2010
  • SIAM (Society of Industrial and Applied Mathematics) (Member) 2004-2005

Community Service

  • Steering Committee, the ICMLA conference series
  • Program Co-Chair (with F. Luo and Y. Huang) of the 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'21)
  • Co-Chair (with V. Palade) of the 2015 International Conference on Machine Learning and Applications (ICMLA'15)
  • Co-organizer (with D. Kihara) of the Special Session on "Proteins in Motion" at GLBIO'12
  • Program Chair (with A. Qi) of the 2009 International Conference on Machine Learning and Applications (ICMLA'09)
  • Program Chair (with T. Hu) of the 2008 International Conference on Machine Learning and Applications (ICMLA'08)
  • Co-Chair (with W. Stach and W. Pedrycz) of the special session on "Fuzzy Cognitive Maps - Theory, Learning, and Applications" at the 2008 World Congress on Computational Intelligence
  • Special Sessions Co-chair (with S.Mitra) of the 2007 International Conference on Machine Learning and Applications (ICMLA'07)
  • Program Chair (with J. Ye) of the 2006 International Conference on Machine Learning and Applications (ICMLA'06)
  • Program Chair (with M. Reformat) of the 2005 International Conference on Machine Learning and Applications (ICMLA'05)
  • Co-organizer of the Special Session on Applications of Machine Learning in Medicine and Biology at ICMLA'05
  • Program Chair of the 2005 Symposium on Human-Centric Computing (HC2 2005)
  • Publicity Chair of the ICMLA'04 conference
  • Invited Sessions Chair of the NAFIPS'04 conference
  • Keynotes Chair of the 4th ASERC Workshop on Quantitative and Soft Software Engineering
  • Chair of the "Inductive Learning and Applications" session at ICMLA'02
  • Program committee member: IRI'01, ICMLA'02, ICMLA'03, QSSE'04, ICMLA'04, ICCI'04, BIOT'05, ICMLA'06, IEEE-GrC'06, BIOT'06, KES'06, ACM-SAC'07, IEEE CIBCB'07, ICMLA'07, ICBBE'07, IEEE-GrC'07, PRIB'07, MLDM'07, CCECE'08, IEEE-GrC'08, ICMLA'08, PRIB'08, ICAIS'09, IEEE-GrC'09, CEC'09, IEEE-GrC'10, AAIA'10, IEEE CEC'10, IMCSIT'10, BIOINFORMATICS 2011, IEEE-GrC'11, IEEE CEC'11, ICAIS'11, BIBM'11, CIBCB12, BIOINFORMATICS 2012, BIBM'12, BIOINFORMATICS 2013, PRIB'13, ICAT'2013, IEEE-GrC'13, BIBM'13, GLBIO'14, ICBBT'14, BIOINFORMATICS 2014, BIBM'14, GLBIO'15, AlCoB'16, IJCAI'16, BIBM'16, ISMB'16, AlCoB'17, ISMB/ECCB'17, ISMB'18, BIBM'18, ISMB/ECCB'19, ISMB'20, BIBM'20, ISMB/ECCB'21, BIBM'21, ISMB'22, BIBM'22, ISMB/ECCB'23, BIBM'23, and ISMB'24.

Visiting Positions

  • June 2016
    Visiting Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • May 2014
    Visiting Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • June 2013
    Visiting Associate Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • June 2012
    Visiting Associate Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • May 2011
    Visiting Associate Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • April-June 2010
    Visiting Associate Professor, Center for Computational Biology and Bioinformatics, IUPUI, Indianapolis, USA
  • January 2010
    Visiting Associate Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • May 2009
    Visiting Associate Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China
  • May-June 2006
    Visiting Assistant Professor at the Chern Institute of Mathematics, Nankai University, Tianjin, China

Awards and Honors

  • Fellow of the Royal Society of Biology (RSB), 2023
  • Winner of the CAID2 competition, 2023
  • Member of European Academy of Sciences and Arts, 2022
  • Member of Faculty Opinions in the "Bioinformatics, Biomedical Informatics and Computational Biology" area, 2021
  • Fellow of the Asia-Pacific Artificial Intelligence Association (AAIA), 2021
  • Winner of the CAID1 competition, 2021
  • Senior Member of the International Society for Computational Biology (ISCB), 2019
  • Fellow of the American Institute for Medical and Biological Engineering (AIMBE), 2018
  • Fellow of the Kosciuszko Foundation Collegium of Eminent Scientists, 2018
  • Senior member of Association for Computing Machinery (ACM), 2012
  • Outstanding Graduate Student Award, AGH University of Science and Technology, 1999
  • Gold Medal of Stanislaw Staszic, 1999
  • Silver Medal of Stanislaw Staszic, 1998
  • Bronze Medal of Stanislaw Staszic, 1997

Teaching

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