Bioinformatics and Computational Genomics

What We Do

The research interests of Laboratory of Bioinformatics and Computational Genomics are focused on the application of bioinformatics and computational modelling methods in functional and structural genomics. We make use of the vast wealth of data produced by high-throughput genomics projects, such as 4DNucleome, 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 experiments (karyotyping, confocal microscopy, aCGH microarrays, short and long reads next generation sequencing), bioinformatics (protein sequence analysis, protein structure prediction), and finally biophysics (polymer theory and simulations) and various genomics data sources (DNA sequence, epigenomics, chromatin organization, topologically associating domains, three dimensional structure of chromatin identified by 3C technologies). We are 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 (Centre of New Technologies University of Warsaw and Mathematics and Information Science Department of Warsaw  University of Technology). We perform 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, HiChIP and ChIA-PET techniques. Our 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 constrains for the natural selection during the evolutionary processes, mammalian cell differentiation, and finally autoimmune diseases and cancer origin and development.

Grants

,,Theoretical and practical challenges of modern immunotherapy''

Ministry of Science and Higher Education, applied PhD, 0056/DW/2018/01/1
in cooperation with Ardigen S.A. from Krakow
Warsaw University of Technology; Faculty of Mathematics and Information Sciences
Time: 2018-2021

,,iCell: information processing in living organisms. The role of three-dimensional structure and multi-scale properties in controlling the biological processes in a cell''

National Science Centre, OPUS, 2014/15/B/ST6/05082
University of Warsaw; Centre of New Technologies
Time: 2015-2019
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1) 2019-2023 Grant COST EU action CA18127, International Nucleome Consortium, Management Committee Substitute;

2) 2017-2021 Grant COST EU action CA16212, Impact of Nuclear Domains On Gene Expression and Plant Traits, Management Committee Substitute;

3) 2018-2021 Grant H2020 RIA Full Application, EDCPT European & Developing Countries Clinical Trials Partnership – Emergency Funding Mechanism 2018, Biochemical Adjustments of native EBOV Glycoprotein in Patient Sample to Unmask target-Epitopes for Rapid Diagnostic Testing, Polish co-PI;

4) 2017-2019 Polish-India government funded collaborative grant number DST/INT/POL/P-36/2016, Genetic biomarkers for breast cancer subtypes: the role of membrane receptors in modeling of heterogeneous populations of tumor cells, Polish co-PI;

5) 2016-2019 Grant 4D Nucleome from NIH, USA number 1U54DK107967-01, Nucleome Positioning System for Spatiotemporal Genome Organization and Regulation;

6) 2013-2018 Grant COST EU action BM1405, Non-globular proteins: from sequence to structure, function and application in molecular physiopathology, Management Committee member;

7) 2013-2018 Grant COST EU action BM1408, A collaborative European network of C. elegans early-stage researchers and young principal investigators (GENiE), Management Committee member

8)Foundation of Polish Science, TEAM, 0087/3/2016; Title: 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; University of Warsaw; Centre of New Technologies; Time: 2017-2020

Virtual High Throughput Screening (vHTS) derivation of a cross-immunity model for the Influenza-A Virus Infections

National Science Centre, OPUS, 2013/09/B/NZ2/00121
University of Warsaw; Centre of New Technologies
Time: 2013-2017

Publications

Key works

  • “Spatial chromatin architecture alteration by structural variations in human genomes at the population scale” Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D. Genome Biol. 2019 Jul 30;20(1):148. doi: 10.1186/s13059-019-1728-x. Erratum in: Genome Biol. 2019 Sep 3;20(1):188. PMID: 31362752
  • “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
  • “An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization” by 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.
  • “3D-GNOME: an integrated web service for structural modeling of the 3D genome” by Szalaj P, Michalski PJ, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D. Nucleic Acids Res. 2016 May 16. pii: gkw437. pmid:27185892
  • ”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. doi: 10.1016/j.cell.2015.11.024
  • “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. doi: 10.1038/nature15393.

Recent contributions

  • “Spatial chromatin architecture alteration by structural variations in human genomes at the population scale” Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D. Genome Biol. 2019 Jul 30;20(1):148. doi: 10.1186/s13059-019-1728-x. Erratum in: Genome Biol. 2019 Sep 3;20(1):188. PMID: 31362752
  • “Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells” by Al Bkhetan Z, Kadlof M, Kraft A, Plewczynski D. Methods. 2019 Mar 7. pii: S1046-2023(18)30334-7. doi: 10.1016/j.ymeth.2019.03.002. PMID: 30853548.
  • “One protein to rule them all: the role of CCCTC-binding factor in shaping Human genome in health and disease” by Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. Semin Cell Dev Biol. 2018 Aug 7. pii: S1084-9521(17)30591-8. doi: 10.1016/j.semcdb.2018.08.003.
  • “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
  • “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 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
  • “Social adaptation in multi-agent model of linguistic categorization is affected by network information flow” by J. Zubek, M. Denkiewicz, J. Barański, P. Wróblewski, J. Rączaszek-Leonardi, D. Plewczynski, PLoS ONE, 2017, 12(8), e0182490.

Team

Dr hab. Dariusz Plewczyński, prof. PW & UW

Founder

Zofia Parteka

Member

Agnieszka Kraft

Member

Michał Włanowolski

Member

Michał Denkiewicz

Member

Alexander Myronov

Member

Katarzyna Gruba

Member

Have a Project in Mind?

Please get in touch with the head of the group.