Laboratory of Functional and Structural Genomics
kierownik zespołu:
Dariusz Plewczyński

Team

MSc Grzegorz Bokota
PhD Wayne Dawson
postdoc
MSc Michał Kadlof
PhD student, Faculty of Physics
MSc Denis Kazakiewicz
PhD, Medical University of Bialystok
MSc Jan Kostrzewa
doktorant
Agnieszka Kraft
student, Faculty of Mathematics, Informatics and Mechanics
MSc Giovanni Mazzocco
PhD Piotr Migdal
Zofia Parteka
student, Faculty of Mathematics, Informatics and Mechanics
MSc Benedykt Rak
PhD student, WUM
Michał Sadowski
student, Faculty of Physics
MSc Przemysław Szałaj
PhD, Medical University of Bialystok
PhD Teresa Szczepińska
postdoc
MSc Marcin Tatjewski
MSc Przemysław Wróblewski
MSc Weronika Wronowska
PhD student, Faculty of Biology
PhD Michał Łaźniewski

O laboratorium

In the Laboratory of Functional and Structural Genomics we perform theoretical studies, whose main objective is to analyze and predict the three-dimensional structure of the human genome, and its relation with the genomic diversity of human populations, both natural and pathological. In particular, we investigate structural variants, copy number variants observed in various sub-populations and the groups of patients, and their three-dimensional localization in the structure of the nucleus.

We also examine the relationship of the expression levels of selected genes from their location in three-dimensional space. In addition, we use structural information to enrich the sequential genomic analysis in order to better define the function of selected genomic regions that are important in the context of personalized medicine.

For this purpose, first we are developing a variety of large-scale computational tools for analysis of whole genome sequences, the identification of structural variants, determining the statistical significance of the observed number of copies of genomic regions in selected cohorts of patients. Secondly, we evaluate their uniqueness comparing the observed changes with typical and natural genomic diversity that has been cataloged for example in the 1000 Genomes Project Consortium. Thirdly, we infer the biological function of these genomic regions using publicly available databases. Fourthly, we identify unique local three-dimensional environment for selected sites, eg. regulatory ones. In the fifth step, we analyze the impact of structural re-arrangements of those local neighborhoods on the gene expression profiles, which is related to the presence of transcription factories.

Współpraca krajowa:
  • Prof. Grzegorz Wilczyński, Institute of Experimental Biology, Polish Academy of Sciences
  • Dr hab. Jakub Włodarczyk, Institute of Experimental Biology, Polish Academy of Sciences
  • Prof. dr hab. Marek Kuś,Center for Theoretical Physics Polish Academy of Science 
  • Prof. dr hab. Krystian Jażdżewski, CeNT University of Warsaw
  • Prof. dr hab. Dominika Nowis, CeNT University of Warsaw
  • Prof. dr hab. Jakub Gołąb, Medical University of Warsaw
  • Prof. dr hab. Rafał Płoski, Medical University of Warsaw
  • Prof. dr hab. Adam Krętowski, Medical University of Bialystok
  • Dr Jan Radomski, ICM University of Warsaw
  • Dr Zuzanna Szymańska, ICM University of Warsaw
  • Dr Maciej Cytowski, ICM University of Warsaw
  • Dr Franciszek Rakowski, ICM University of Warsaw
  • Prof. dr hab. Joanna Rączaszek-Leonardii, University of Warsaw
Współpraca zagraniczna:
  • Prof. Charles Lee, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Prof. Yijun Ruan, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Prof. Subhadip Basu, Jadavpur University, Kolkata, India
  • Prof. Ujjwal Maulik, Jadavpur University, Kolkata, India
  • Prof. Sanghamitra Bandyopadhyay, Indian Statistical Institute, Kolkata, India
  • Prof. Bing Ren, University of California San Diego, San Diego, USA
  • Prof. Jonathan Sebat, University of California San Diego, San Diego, USA
  • Prof. Erez Lieberman Aiden, Baylor College of Medicine & Rice University, Houston, TX 77030, USA
  • Prof. Tomasz Burzykowski, Hasselt University, Belgium
  • Dr Jonathan Karr, Mount Sinai School of Medicine, NY, USA
  • Dr Karol Langer, University of Virginia, Charlottesville,VA, USA
  • Prof. Adam Godzik, Sanford-Burnham Medical Research Institute, San Diego, CA, USA
  • Prof. Benjamin Audit, Ecole Normale Supérieure de Lyon, France
  • Dr Uwe Koch, Lead Discovery Center GmbH, Dortmund, Germany
  • Prof. Michael Stitzel, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Prof. Duygu Ucar, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Prof. Marcin von Grotthuss, The Broad Institute of MIT and Harvard Medical School, MA, USA
  • Prof. de Oliveira SF, Laboratório de Genética, Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil 

 

News

Wednesday, June 1, 2016 - 09:51

New publication taken by Lab members has been published in Cell magazine: CTCF-Mediated Human Genome Architecture Reveals 3D Topology for Chromatin Transcription....

Thursday, March 17, 2016 - 14:48

Program gives group of scientists, chosen through an open call, possibility to prepare their calculations, test processing capabilities of the Okeanos system (e.g. scalability...

Thursday, October 8, 2015 - 11:11
A global reference for human genetic variation  and  An integrated map of structural variation in 2,504 human genomes were recently published with the participation of...
Thursday, October 8, 2015 - 10:52

Julian Zubek, MSc received ETIUDA scholarship within the NCN competition. Aplication was submitted on behalf of Institute of Computer Science Polish Academy of Sciences....