„Announcement about the competition for a PhD student in the field of bioinformatics and computational genomics, the discipline of computer science”

Dean of Faculty of Mathematics and Information Science of the Warsaw University of Technology, with the PRELUDIUM BIS Project Leader, announce opening of the competition for the position of PhD Student in the Interdisciplinary Laboratory of Bioinformatics and Computational Genomics.

Research Project:

Scientific goal of the PRELUDIUM BIS (National Science Centre, panel ST6) project „Spatial network model of sequence diversity and structure of the human genome on a population scale” is to analyze the impact of structural variants (SVs, such as deletions, duplications, insertions, inversions, translocations, etc.) and single nucleotide polymorphisms (single molecule polymorphism, SNP) on the three-dimensional structure of the human genome. We want to understand how rewiring (i.e. changing the set of chromatin loops) of the genome in different cell types disrupts gene expression, and thus leads to the tumor formation process. Public and private datasets from the large-scale next generation sequencing (NGS) experiments will be used to implement the project, and computational methods developed by Principal Investigator (PI), such as statistical data analysis, machine learning and computer simulations. The project will finish with the publicizing the web server and the source code of the proprietary 3D-OME algorithm predicting the three-dimensional structure of the mammalian genome based on DNA sequencing data, biopolymer theory and biophysical properties of chromatin. We want to show that modeling allows to describe the transformation of the local three- dimensional structure of chromatin, and the disruption of expression of genes in the genomic domain after a change in the DNA sequence (single nucleotide mutation, deletion, duplication, insertion, etc.).

 

Principal Investigator:

Dariusz Plewczynski, PhD is the head of the Laboratory of Bioinformatics and Computational Genomics, the Faculty of Mathematics and Information Sciences at Warsaw University of Technology. His 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 University of Technology). He is actively participating in multinational 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 constrains for the natural selection during the evolutionary processes, mammalian cell differentiation, and finally cancer origin and development.

 

Contact:

Dariusz Plewczynski, PhD

Laboratory of Bioinformatics and Computational Genomics,

Faculty of Mathematics and Information Science

Warsaw University of Technology

Koszykowa 75, 00-662 Warsaw, Poland

phone: +48 22 234 7219, e-mail: darman@mini.pw.edu.pl,

www: http://4dnucleome.mini.pw.edu.pl

 

Selected Publications:

  • “3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome” by Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. Nucleic Acids Res. 2020 May 22:gkaa388. doi: 10.1093/nar/gkaa388. PMID: 32442297
  • “Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia” by Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Genome Biol. 2020 May 11;21(1):110. doi: 10.1186/s13059-020-02030-2. PMID: 32393309
  • “Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization” by Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM. Nat Commun. 2020 May 1;11(1):2120. doi: 10.1038/s41467-020-15987-2. PMID: 32358536
  • „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.
  • Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction” Xu H, Zhang S, Yi X, Plewczynski D, Li MJ. Comput Struct Biotechnol J. 2020 Feb 28;18:558-570. doi: 10.1016/j.csbj.2020.02.013. eCollection 2020. PMID: 32226593
  • “Oncogenes expand during evolution to withstand somatic amplification” by Wang X, Li X, Zhang L, Wong SH, Wang MHT, Tse G, Dai RZW, Nakatsu G, Coker OO, Chen Z, Ko H, Chan JYK, Liu T, Cheng CHK, Cheng ASL, To KF, Plewczynski D, Sung JJY, Yu J, Gin T, Chan MTV, Wu WKK. Ann Oncol. 2018 Sep 11. doi: 10.1093/annonc/mdy397.
  • “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
  • “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. Epub 2015 Dec 10.
  • 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.