Projects search

Epistasis in genomic and survival data of cancer patients

Authors:

Dariusz Matlak, Ewa Szczurek

Academic press:

PLoS Computational Biology (year: 2017, volume: 2017, pages: 46038), Publisher: Public library of science

Status:

Published

DOI:

10.1371/journal.pcbi.1005626 – link to the publication

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 (year: 2018, volume: 8, pages: 4390), Publisher: Nature publishing group

Status:

Published

DOI:

10.1038/s41598-018-22829-1 – link to the publication

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 (year: 2017, volume: 46(4), pages: 1724-1740), Publisher: Oxford University press

Status:

Published

DOI:

10.1093/nar/gkx1214 – link to the publication

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 (year: 2016, volume: 44(19), pages: 9110-9120), Publisher: Oxford University Press

Status:

Published

DOI:

10.1093/nar/gkw800 – link to the publication

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 (year: 2019, volume: 20(14), pages: 3478), Publisher: MDPI

Status:

Published

DOI:

10.3390/ijms20143478 – link to the publication

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 (year: 2017, volume: 1,14652777777778, pages: 571), Publisher: Bio Med Central

Status:

Published

DOI:

10.1186/s12864-017-3950-9 – link to the publication

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 (year: 2016, volume: 37(9), pages: 904-913), Publisher: Wiley Inc.

Status:

Published

DOI:

10.1002/humu.23014 – link to the publication

BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations

Authors:

Rafał Zaborowski, Bartek Wilczyński

Academic press:

Journal of Computational Biology (year: 2019, volume: 26(4), pages: 305-314), Publisher: Mary Ann Liebert, Inc

Status:

Published

DOI:

10.1089/cmb.2018.0162 – link to the publication

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 (year: 2021, volume: 11 (1), pages: 46037), Publisher: Nature Publishing Group

Status:

Published

DOI:

10.1038/s41598-021-95009-3 – link to the publication

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 (year: 2021, volume: 5(3), pages: 900-912), Publisher: American society for Hematology

Status:

Published

DOI:

10.1182/bloodadvances.2020003709 – link to the publication

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 (year: 2021, volume: 12, 3621, pages: 46039), Publisher: Nature Publishing Group

Status:

Published

DOI:

10.1038/s41467-021-23922-2 – link to the publication

Automated inference of gene regulatory networks using explicit regulatory modules

Authors:

Clémence Réda Bartek Wilczyński

Academic press:

Journal of Theoretical Biology (year: 2020, volume: 486, pages: 11091), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.jtbi.2019.110091 – link to the publication

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 (year: 2018, volume: 8, pages: 4390), Publisher: Nature Publishing

Status:

Published

DOI:

10.1038/s41598-018-22829-1 – link to the publication

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 (year: 2021, volume: 43 (1), pages: 46059), Publisher: Morion LLC

Status:

Published

DOI:

10.32471/exp-oncology.2312-8852.vol-43-no-1.15925 – link to the publication

QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models

Authors:

Bartłomiej Zawalski IrinaTuszyńska Bartek Wilczyński

Academic press:

Methods (year: 2020, volume: 181, pages: 80-85), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.ymeth.2019.08.006 – link to the publication

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 (year: 2016, volume: 0,98125, pages: 46032), Publisher: Springer Verlag

Status:

Published

DOI:

10.1186/s12859-016-1259-3 – link to the publication

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 (year: 2020, volume: 1202, pages: 259-279), Publisher: Springer

Status:

Published

DOI:

link to the publication