Prof. Dariusz Plewczyński

email: d.plewczynski@cent.uw.edu.pl
phone: +48 22 55 43654
room: 03.63
Website: https://4dnucleome.cent.uw.edu.pl
Laboratory of Functional and Structural Genomics (Group Leader)

 

Degrees: MSc (Physics), PhD (chemistry), DSc (Habilitation, Bioinformatics)
Titles: Professor at University of Warsaw, PhD, DSc
Tel: (+48) 504 726 203 & (+4822) 554 36 54 Fax: (+4822) 554 08 01
Email: d.plewczynski@cent.uw.edu.pl & dariuszplewczynski@gmail.com

Affiliation: Center of New Technologies, University of Warsaw, Poland

Research Interests:
Dariusz Plewczynski interests are focused on functional and structural  genomics. Functional genomic attempts to make use of the vast wealth of data produced by high- throughput genomics projects, such as the structural genomics consortia, Human genome project, 1000 Genomes Project, ENCODE, and many others. The major tools that are used in this interdisciplinary research endeavor include statistical data analysis (GWAS studies, clustering, machine learning), genomic variation analysis using diverse data sources (karyotyping, confocal microscopy, aCGH microarrays, next generation sequencing: both whole genome and whole exome), bioinformatics (protein sequence analysis, protein structure prediction), and finally biophysics (polymer theory and simulations) and genomics (epigenetics, genome domains, three dimensional structure analysis of chromatin). He is presently involved in several Big Data projects at three institutes: Centre of New Technologies at University of Warsaw (his main affiliation), Jackson Laboratory for Genomic Medicine (an international partner of the TEAM project), and The Centre for Innovative Research (within the Leading National Research Centre KNOW 2012-2017) at Medical University of Bialystok (UMB). He is participating in two large projects, namely 1000 Genomes Project (NIH) by bioinformatics analysis of genomic data from aCGH arrays and NGS (next generation sequencing, deep coverage) experiments for structural variants (SV) identification; and biophysical modeling of chromatin three-dimensional conformation inside human cells using HiC and ChIA-PET techniques within the 4D Nucleome project funded by the NIH in the USA. His goal is to combine the SV data with three-dimensional cell nucleus structure for better understanding of normal genomic variation among human populations, the natural selection process during the human evolution, mammalian cell differentiation, and finally the origin, pathways, progression and development of cancer and autoimmune diseases.

Research Summary (Past & Current):

Professor at the University of Warsaw in the Center of New Technologies CeNT, Warsaw, Poland, the head of the Laboratory of Functional and Structural Genomics.
His main expertise covers computational genomics, biostatistics and bioinformatics. He is actively developing computational intelligence algorithms, performing biophysical simulations and applying computational modeling to various interdisciplinary problems in Human genomics. His recent achievements cover qualitative and quantitative biological data analysis, the general systems theory and interdisciplinary problems in the context of bioinformatics, genomics, drug design, and systems biology; ensemble learning systems, meta-clustering techniques.

He received an MS degree in Theoretical Physics (Department of Physics, UW) under the supervision of Prof. Marek Cieplak in 1995. In 2001, he defended his PhD degree in Physical Chemistry (Institute of Physical Chemistry, Polish Academy of Sciences) under supervision of Prof. Robert Hołyst. Later, He was a postdoc researcher at International Institute for Cell and Molecular Biology in 2001 collaborating closely with Prof. Adam Godzik. Dr. Dariusz Plewczynski worked in The Burnham-Sanford Institute in San Diego, CA, USA in 2002. He was a postdoc at Helsinki University, bioinformatics laboratory in 2003. In 2004 he was a visiting researcher at Merck Research Laboratories (IRBM) in Rome, Italy. From 2002 till 2011, he was the assistant professor at University of Warsaw, Warsaw, Poland. In 2011, He visited Stanford University within the Top500 Polish Ministry of Science programme. He received a DSc degree (habilitation) in Computer Science and bioinformatics in 2012 at the Institute of Computer Science Polish Academy of Sciences.

From 2011, He was the head of the bioinformatics team at the University of Warsaw (first at ICM, and later from 2015 at Centre of New Technologies). He has been involved in bioinformatics projects in the Leading National Research Centre of the Medical University of Bialystok from 2012. He was a visiting professor at The Jackson Laboratory for Genomic Medicine; Yale University within the senior Fulbright fellowship (2013-2014).

Education

  • MA: 1995, Faculty of Physics, Warsaw University, Poland. Major: theoretical physics.
    Thesis title:
    “Statistical physics of phase transitions in thin magnetic layers”;
  • PhD: 2001, Institute of Physical Chemistry, Poland. Major: physical chemistry. Dissertation title:
    „Diffusion of curved surfaces”;
  • PostDoc: 2001 – Warsaw, Poland, The International Molecular and Cell Biology Institute. Major:
    bioinformatics. Research project: „Structural Comparison of proteins“;
  • 2002 – San Diego, CA, The Sanford-Burnham Institute. Major: bioinformatics. Research project:
    „Improving the sequence alignment quality using predicted local 3D structure of a protein chain“;
  • 2003 – Helsinki, Finland, Helsinki University. Major: bioinformatics. Research project:
    “Structural alignment of proteins using DALI”
  • Habilitation: 2012, Institute of Computer Science Polish Academy of Sciences, Poland. Major: Computer
    Science. Dissertation title: „Applications of machine learning and data analysis techniques to biological
    function prediction of biomolecules”

Positions held

  • Starting from January 2015 – Assistant Professor, DSc, PhD, the head of Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw
  • 2013 till 2016 – Research consultant, Centre for Innovative Research, Faculty of Medicine, Medical University of Bialystok, Poland.
  • 2002 till 2015 – Assistant Professor, Bioinformatics and Systems Biology Laboratory, Statistical Data Analysis & Systems Theory Unit, Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Poland.
  • 2011 till 2013 – Assistant Professor, Department of Physical Chemistry, Bioinformatics and Applied Mathematics Unit, Faculty of Pharmacy, Medical University of Warsaw, Poland.

Visiting Researcher

  • 2004 – Rome, Italy, Merck Laboratories. Major: bioinformatics, chemoinformatics. Research project:
    “Applications of machine learning algorithms in virtual High-throughput screening”
  • 2005 – Helsinki, Finland, Helsinki University. Major: bioinformatics. Research project: “Prediction of
    protein-protein interactions”
  • 2003-2008 – Poznan, Poland, BioInfoBank Institute, Major: bioinformatics. Research project: „Prediction of
    protein function using sequence and structual information“.
  • 2011 – Stanford University, Centre of Professional Development, Top500 Innovators
  • 2013/2014 – The Jackson Laboratory & Yale University, Farmington, CT, USA

Other professional activities and memberships

  • Member of the Polish Bioinformatics Society
  • Member of the Polish Physics Society
  • Member of the International Society for Computational Biology

Editorships & Reviewing boards

  • Member of the Editor Board: “BMC Bioinformatics”, BioMedCentral, UK
  • Reviewer for: Genome Research, BMC Genome Biology, Nature Methods, Bioinformatics, J Chem Inf Modeling, BMC Bioinformatics, Chemical Biology and Drug Design and many other journals in the field of “omics-“, computational genomics, drug design, bioinformatics and systems biology.

Recent major publications

  1. “An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization” Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D. Genome Res. 2016 Oct 27.
  2. “3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale” Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D. Database (Oxford).
    2016 Oct 2;2016.
  3. “3D-GNOME: an integrated web service for structural modeling of the 3D genome” Szalaj P, Michalski PJ, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D. Nucleic Acids Res. 2016 Jul 8;44(W1):W288-93.
  4. “2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity” Basu S, Plewczynski D, Saha S, Roszkowska M, Magnowska M, Baczynska E, Wlodarczyk J. Bioinformatics. 2016 Aug 15;32(16):2490-8.
  5. ”CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription” Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad- Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y. Cell 2015, Dec 17;163(7):1611-27. Epub 2015 Dec 10.
  6. “An integrated map of structural variation in 2,504 human genomes” by Sudmant PH, …, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Nature. 2015 Oct 1;526(7571):75-81.
  7. “A global reference for human genetic variation” by 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. Nature. 2015 Oct 1;526(7571):68-74.
  8. “Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods” Plewczynski D, Gruca S, Szałaj P, Gulik K, de Oliveira SF and Malhotra A. book chapter in “Clinical Applications for Next-Generation Sequencing” book, Elsevier, 2015
  9. “A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium” by Kazakiewicz D, Karr JR, Langner KM, Plewczynski D. Comput Biol Chem. S1476-9271 (2015);
  10. “Binding Activity Prediction of Cyclin-Dependent Inhibitors” Saha I, Rak B, Bhowmick SS, Maulik U, Bhattacharjee D, Koch U, Lazniewski M, Plewczynski D. J Chem Inf Model. 55(7):1469-82. (2015);
  11. “Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models” by Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P. PLoS Comput Biol. 28;11(5) (2015);

Research projects

  • 2017-2020 FNP TEAM grant “Three-dimensional Human Genome structure at the population scale:
    computational algorithm and experimental validation for lymphoblastoid cell lines of selected families from
    1000 Genomes Project” to D. Plewczynski, PI;
  • 2016-2017 NCN Grant ETIUDA “Modelling and analysis of three dimensional structure and its dynamics in cel
    nucleus” to Przemyslaw Szalaj (PhD student), D. Plewczynski – scientific advisor;
  • 2015-2018 EU COST action BM1405 “Non-globular proteins: from sequence to structure, function and
    application in molecular physiopathology” to D. Plewczynski, polish PI;
  • 2016-2017 NCN Grant PRELUDIUM “Analysis of mechanisms of drug resistance to trastuzumab in HER2
    overexpressing breast cancer based on gene expression changes in selected cell lines” to Anna Rusek (PhD
    student), D. Plewczynski – scientific advisor;
  • 2015-2018 NCN Grant OPUS “iCell: information processing in living organisms. The role of three-dimensional
    structure and multi-scale properties in controlling the biological processes in a cell” to D. Plewczynski, PI;
  • 2015-2016 NCN Grant ETIUDA “Integration of information in biological and synthetic systems” to J. Zubek
    (PhD student), D. Plewczynski – scientific advisor;
  • 2014-2017 NCN Grant OPUS “Virtual High Throughput Screening (vHTS) derivation of a cross-immunity model
    for the Influenza-A Virus Infections” to D. Plewczynski, PI;
  • 2008-2011 KBN Grant “Application of machine learning methods to prediction of protein-protein interactions” –
    Polish Ministry of Science grant to dr D. Plewczynski, PI;
  • Grant LSHG-CT- 2003-503265 BIOSAPIENS, a large-scale effort to annotate human genome using both
    informatics tools and input from experimentalists. 6 th Framework EC Project, participant;
  • Grant SP22-CT- 2004-003831 SEPSDA, Combatting and eventually eradicating the new coronavirus causing
    Severe Acute Respiratory Syndrome (SARS) requires specific and efficient antiviral drugs and improved
    diagnostics. 6 th Framework EC Project, participant;
  • Grant QLRT-CT2000- 00127 ELM, The four principal objectives of the ELM consortium are to (1) design, (2)
    develop, (3) maintain and (4) apply, a novel infrastructure resource devoted to the prediction of functional
    motifs in protein sequences. 6 th Framework EC Project, participant;

Teaching experience

  • Lectures: Genome Biology (UW); Genomes Biophysics (UW); Bioinformatics (UW,WUT); Drug
    Design (WUM); Machine Learning (UW); statistical data analysis (UW).
  • Seminars and laboratories: Bioinformatics; Systems Biology; Machine Learning & Statistics.

Awards

  • 2013 – Senior Fulbright Fellowship to visit Harvard University, and Yale Univ., USA;
  • 2011 – Top500 Innovators: Science, Management and Commercialization Award; Polish Ministry of Science and Higher Education
  • 1994 – Sosnowski Award (for outstanding physicists); Polish Physical Society
  • 1993 – 1994 Polish Ministry of Education and Science Award
  • 1986 – 1987 Polish Ministry of Education

Languages:
Polish (native), English (fluent), German (basic), Russian (basic)

Hobby:
Photography, History, Traveling, Robotics and Artificial Intelligence.