Curriculum Vitae

Dr. Lukasz Kurgan

Robert J. Mattauch Endowed Professor

Address

• 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

Contact Information

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

Web profiles

• Google Scholar citation profile: https://scholar.google.com/citations?hl=en&user=TrH_NF8AAAAJ
• Researcher Gate profile: https://www.researchgate.net/profile/Lukasz_Kurgan
• Semantic Scholar profile: https://www.semanticscholar.org/author/Lukasz-Kurgan/1721347
• ORCID profile: https://orcid.org/0000-0002-7749-0314
• ExpertFile profile: http://expertfile.com/experts/lukasz.kurgan
• Web of Science profile: https://www.webofscience.com/wos/author/record/273363
• LinkedIn profile: https://www.linkedin.com/in/lukasz-kurgan-36111b15b
• Faculty Opinion profile: https://facultyopinions.com/prime/thefaculty/member/1061848

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, Adjunt 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 delopment 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 Letters2009 - 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 Science
    • Career Development Award program
  • National Science Center of Poland
    • HARMONIA program
  • National Science Foundation
    • BIO 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

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

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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