e-mail: d.plewczynski@cent.uw.edu.pl
Position: Lab 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. His functional attempts make use of the vast wealth of data produced by high-throughput genomics projects, such as 4DNucleome (structural genomics consortium), 1000 Genomes Project, UK BioBank, Simons Genome Diversity Project, Earth BioGenome 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), bioinformatics (protein sequence analysis, protein structure prediction), and finally biophysics (polymer theory and simulations) and genomics (epigenetics, genome domains, three dimensional structure of chromatin). He is presently involved in several Big Data projects both in US (4DN at Jackson Laboratory for Genomic Medicine, Earth BioGenome at University of California Davis), EU (INDEPTH, INC COST actions, ENHPATHY ITN) and in Poland (CeNT University of Warsaw and MINI Warsaw Technical University). He is actively participating in two large consortia projects, namely bioinformatics and genomic analysis of 1000 Genomes Project population data for structural variants (SV) and single nucleotide polymorphism (SNP) identification in the context of 3D nuclear structure; and biophysical modeling of chromatin three-dimensional conformation within 4Dnucleome project for multiple human cell lines using HiC and ChIA-PET techniques. His goal is to combine SV, epigenomic, transcriptional and super-resolution imaging data with spatial and temporal nucleus structure for better understanding of the biological function of genomes, the genomic structural variation within populations of cells and between individuals from different species, the spatial constraints for the natural selection during the evolutionary processes, mammalian cell differentiation, and finally cancer and autoimmune diseases origin and development.
Research Summary (Past & Current):
Dariusz Plewczynski, PhD is a professor at University of Warsaw in Center of New Technologies CeNT, Warsaw, Poland, the head of Laboratory of Functional and Structural Genomics and the principal investigator at Mathematics and Information Science Department at Warsaw University of Technology. His main expertise covers computational genomics, biostatistics and bioinformatics. He is actively developing the computational intelligence algorithms, perform biophysical simulations and apply 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 the MS, and PhD degrees in Theoretical Physics (phase transitions) and Physical Chemistry (stochastic processes) in 1995, and 2001, respectively. He was postdoc researcher at International Institute for Cell and Molecular Biology in 2001 under the supervision of Dr. Leszek Rychlewski. Dr. Dariusz Plewczynski worked with Dr. Adam Godzik in The Burnham-Sanford Institute in San Diego, CA, USA in 2002. He was a postdoc at Helsinki University, bioinformatics laboratory of Prof. Liisa Holm in 2003. In 2004 he was visiting researcher hosted by Dr Uwe Koch at Merck Research Laboratories (IRBM) in Rome, Italy. From 2002 till 2011, he was the assistant professor at University of Warsaw, Warsaw, Poland and the head of chemo-informatics unit at BioInfoBank Institute, Poznan, Poland. In 2011, He visited Stanford University within Top500 Polish Ministry of Science programme. He received DSc degree (habilitation) in Computer Science and Bioinformatics in 2012 at the Computer Science Institute of Polish Academy of Sciences.
From 2012 up to now, He conducts research as a professor at University of Warsaw, and from 2017 He performs educational duties at Warsaw University of Technology. He is involved in bioinformatics projects in the Leading National Research Centre of Medical University of Bialystok (Prof. Adam Krętowski) and Medical University of Warsaw (Prof. Rafał Płoski and Prof. Dominika Nowis) from 2012. He was visiting professor at The Jackson Laboratory for Genomic Medicine & Yale University within the senior Fulbright fellowship in 2013-2014 working with Prof. Charles Lee. In 2019, He is co-affiliated with University of California, Davis in 2019 as the sabbatical fellow at Computer Science and Engineering Department collaborating with Raissa D’Souza and Harris A. Lewin.
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
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“Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction” by Al Bkhetan Z, Plewczynski D. Sci Rep. 2018 Mar 26;8(1):5217. doi: 10.1038/s41598-018-23276-8. PMID: 29581440
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“Three-dimensional organization and dynamics of the genome” by Szalaj P, Plewczynski D. Cell Biol Toxicol. 2018 Mar 22. doi: 10.1007/s10565-018-9428-y. PMID: 29568981
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“The structural variability of the influenza A hemagglutinin receptor-binding site” by Lazniewski M, Dawson WK, Szczepinska T, Plewczynski D. Brief Funct Genomics. 2017 Dec 13. doi: 10.1093/bfgp/elx042.
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”The 4D nucleome project” by Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network. Nature 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884
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“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. - “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. - “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.
- “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.
- ”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.
- “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.
- “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.
- “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
- “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);
- “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);
- “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.