Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Atlas of brain regulatory regions and regulatory networks - a novel systems biology approach to pathogenesis of selected neurological disorders

2015/16/W/NZ2/00314

Keywords:

DNAse-Seq open chromatin ChIPseq epigenetics regulatory DNA gliomas neuropsychiatric disorders

Descriptors:

  • NZ2_2: Genomics, transcriptomics, epigenomics
  • NZ1_1: Molecular biology

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Uniwersytet Warszawski, Wydział Matematyki, Informatyki i Mechaniki

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Bartosz Wilczyński 

Number of co-investigators in the project: 25

Call: SYMFONIA 3 - announced on 2014-12-15

Amount awarded: 6 842 014 PLN

Project start date (Y-m-d): 2015-11-18

Project end date (Y-m-d): 2021-11-17

Project duration:: 72 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Stacje robocze IPI PAN.
  2. KOMORA DO PCR.
  3. Komputery osobiste (2 szt.) (10 000 PLN)
  4. The CHEF Mapper® XA system - aparat do pulsacyjnej elekroforezy DNA (120 000 PLN)
  5. komputery osobiste (MIM UW).
  6. Dwie stacje robocze z monitorami (10000 zł/każda) (2 szt.) (20 000 PLN)
  7. Serwer danych do przechowywania danych eksperymentalnych i atlasu obszarów (90 000 PLN)
  8. Stacja robocza MIM UW.
  9. Wysokowydajny serwer (21 912 PLN)
  10. Zamrażarka niskotemperaturowa.
  11. Automatyczna stacja pipetująca (170 000 PLN)
  12. Macierz dyskowa do serwera w instytucie Nenckiego.

Information in the final report

  • Publication in academic press/journals (16)
  • Book publications / chapters in book publications (1)
  1. A non-coding cancer mutation disrupting an HNF4α binding motif affects an enhancer regulating genes associated to the progression of liver cancer
    Authors:
    Marco Cavalli, Klev Diamanti, Gang Pan, Michał J. Dąbrowski, Jan Komorowski, Claes Wadelius
    Academic press:
    Experimental Oncology (rok: 2021, tom: 43 (1), strony: 45328), Wydawca: Morion LLC
    Status:
    Published
    DOI:
    10.32471/exp-oncology.2312-8852.vol-43-no-1.15925 - link to the publication
  2. Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival.
    Authors:
    Dabrowski, Michal J., Michal Draminski, Klev Diamanti, Karolina Stepniak, Magdalena A. Mozolewska, Paweł Teisseyre, Jacek Koronacki, Jan Komorowski, Bozena Kaminska, and Bartosz Wojtas.
    Academic press:
    Scientific reports (rok: 2018, tom: 8, strony: 4390), Wydawca: Nature Publishing
    Status:
    Published
    DOI:
    10.1038/s41598-018-22829-1 - link to the publication
  3. Combinatorial identification of DNA methylation patterns over age in the human brain
    Authors:
    Behrooz Torabi Moghadam, Michal Dabrowski, Bozena Kaminska, Manfred G. Grabherr and Jan KomorowskiEmail author
    Academic press:
    BMC Bioinformatics (rok: 2016, tom: 0,98125, strony: 45301), Wydawca: Springer Verlag
    Status:
    Published
    DOI:
    10.1186/s12859-016-1259-3 - link to the publication
  4. Epistasis in genomic and survival data of cancer patients
    Authors:
    Dariusz Matlak, Ewa Szczurek
    Academic press:
    PLoS Computational Biology (rok: 2017, tom: 2017, strony: 45307), Wydawca: Public library of science
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1005626 - link to the publication
  5. Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets
    Authors:
    Svea Stratmann, Sara A. Yones, Markus Mayrhofer, Nina Norgren, Aron Skaftason, Jitong Sun, Karolina Smolińska, Jan Komorowski, Morten K. Herlin, Christer Sundström, Anna Eriksson, Martin Höglund, Josefine Palle, Jonas Abrahamsson, Kirsi Jahnukainen, Monica Cheng Munthe-Kaas, Bernward Zeller, Katja Pokrovskaja Tamm, Lucia Cavelier, Linda Holmfeldt
    Academic press:
    Blood Advances (rok: 2021, tom: 5(3), strony: 900-912), Wydawca: American society for Hematology
    Status:
    Published
    DOI:
    10.1182/bloodadvances.2020003709 - link to the publication
  6. QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models
    Authors:
    Bartłomiej Zawalski IrinaTuszyńska Bartek Wilczyński
    Academic press:
    Methods (rok: 2020, tom: 181, strony: 80-85), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2019.08.006 - link to the publication
  7. Unveiling new interdependencies between signifcant DNA methylation sites, gene expression profles and glioma patients survival
    Authors:
    Michal J. Dabrowski, Michal Draminski, Klev Diamanti, Karolina Stepniak, Magdalena A. Mozolewska, Paweł Teisseyre, Jacek Koronacki, Jan Komorowski, Bozena Kaminska, Bartosz Wojtas
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 4390), Wydawca: Nature publishing group
    Status:
    Published
    DOI:
    10.1038/s41598-018-22829-1 - link to the publication
  8. A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers
    Authors:
    Husen M. Umer, Marco Cavalli, Michal J. Dabrowski, Klev Diamanti, Marcin Kruczyk, Gang Pan, Jan Komorowski, and Claes Wadelius
    Academic press:
    Human Mutation (rok: 2016, tom: 37(9), strony: 904-913), Wydawca: Wiley Inc.
    Status:
    Published
    DOI:
    10.1002/humu.23014 - link to the publication
  9. BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations
    Authors:
    Rafał Zaborowski, Bartek Wilczyński
    Academic press:
    Journal of Computational Biology (rok: 2019, tom: 26(4), strony: 305-314), Wydawca: Mary Ann Liebert, Inc
    Status:
    Published
    DOI:
    10.1089/cmb.2018.0162 - link to the publication
  10. PiiL: visualization of DNA methylation and gene expression data in gene pathways
    Authors:
    Behrooz Torabi Moghadam , Neda Zamani, Jan Komorowski and Manfred Grabherr
    Academic press:
    BMC Genomics (rok: 2017, tom: 1,14652777777778, strony: 571), Wydawca: Bio Med Central
    Status:
    Published
    DOI:
    10.1186/s12864-017-3950-9 - link to the publication
  11. The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes
    Authors:
    Ilona Grabowicz, Bartosz Wilczyński, Bożena Kamińska, Adria‐Jaume Roura, Bartosz Wojtaś, Michał J. Dąbrowski
    Academic press:
    Scientific Reports (rok: 2021, tom: 11 (1), strony: 45306), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-021-95009-3 - link to the publication
  12. Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications
    Authors:
    Michal J. Dabrowski, Bartosz Wojtas
    Academic press:
    International Journal of Molecular Sciences (rok: 2019, tom: 20(14), strony: 3478), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms20143478 - link to the publication
  13. Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas
    Authors:
    Karolina Stępniak, Magdalena A. Machnicka, Jakub Mieczkowski, Anna Macioszek, Bartosz Wojtaś, Bartłomiej Gielniewski, Katarzyna Poleszak, Małgorzata Perycz, Sylwia K. Król, Rafał Guzik, Michał J. Dąbrowski, Michał Dramiński, Marta Jardanowska, Ilona Grabowicz, Agata Dziedzic, Hanna Kranas, Karolina Sienkiewicz, Klev Diamanti, Katarzyna Kotulska, Wiesława Grajkowska, Marcin Roszkowski, Tomasz Czernicki, Andrzej Marchel, Jan Komorowski, Bożena Kamińska, Bartosz Wilczyński
    Academic press:
    Nature Communications (rok: 2021, tom: 12, 3621, strony: 45308), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41467-021-23922-2 - link to the publication
  14. Maps of context-dependent putative regulatory regions and genomic signal interactions
    Authors:
    Klev Diamanti Husen M. Umer Marcin Kruczyk Michał J. Dąbrowski Marco Cavalli Claes Wadelius Jan Komorowski
    Academic press:
    Nucleic Acids Research (rok: 2016, tom: 44(19), strony: 9110-9120), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw800 - link to the publication
  15. Automated inference of gene regulatory networks using explicit regulatory modules
    Authors:
    Clémence Réda Bartek Wilczyński
    Academic press:
    Journal of Theoretical Biology (rok: 2020, tom: 486, strony: 11091), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jtbi.2019.110091 - link to the publication
  16. Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions
    Authors:
    Henri Niskanen Irina Tuszynska Rafal Zaborowski Merja Heinäniemi Seppo Ylä-Herttuala Bartek Wilczynski Minna U Kaikkonen
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 46(4), strony: 1724-1740), Wydawca: Oxford University press
    Status:
    Published
    DOI:
    10.1093/nar/gkx1214 - link to the publication
  1. Histone Modifying Enzymes and Chromatin Modifiers in Glioma Pathobiology and Therapy Responses
    Authors:
    Iwona A. Ciechomska, Chinchu Jayaprakash, Marta Maleszewska, Bozena Kaminska
    Book:
    Glioma Signaling (rok: 2020, tom: 1202, strony: 259-279), Wydawca: Springer
    Status:
    Published
    DOI:
    link to the publication

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