Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

Delete all

Multiscale spatial reorganization of chromatin in response to replication stress and its role in cellular protection against genomic instability

2020/37/B/NZ2/03757

Keywords:

replication stress genetic instability DNA double-strand breaks DNA fragile sites genomics bioinformatics chromatin loops mammalian 3D genome Topologically Associating Domains polimer modelling cell differentiation chromatin higher order organization human genome

Descriptors:

  • NZ2_007:
  • NZ2_002:
  • ST6_013:

Panel:

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

Host institution :

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Dariusz Michał Plewczyński 

Number of co-investigators in the project: 6

Call: OPUS 19 - announced on 2020-03-16

Amount awarded: 2 950 920 PLN

Project start date (Y-m-d): 2021-02-01

Project end date (Y-m-d): 2027-01-31

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

Project status: Pending project

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (36)
  1. Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt
    Authors:
    Miguel Montez, Maria Majchrowska, Michal Krzyszton, Grzegorz Bokota, Sebastian Sacharowski, Magdalena Wrona, Ruslan Yatusevich, Ferran Massana, Dariusz Plewczynski, Szymon Swiezewski
    Academic press:
    EMBO Journal (rok: 2023, tom: 42(5), strony: e112443), Wydawca: EMBO Press
    Status:
    Published
    DOI:
    10.15252/embj.2022112443 - link to the publication
  2. Unveiling the Biomarkers of Cancer and COVID-19 and Their Regulations in Different Organs by Integrating RNA-Seq Expression and Protein–Protein Interactions
    Authors:
    Nimisha Ghosh, Indrajit Saha, Dariusz Plewczynski
    Academic press:
    ACS Omega (rok: 2022, tom: 7, strony: 43589-43602), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acsomega.2c04389 - link to the publication
  3. Online Predictor Using Machine Learning to Predict Novel Coronavirus and Other Pathogenic Viruses
    Authors:
    Jnanendra Prasad Sarkar, Indrajit Saha, Nimisha Ghosh, Debasree Maity, Dariusz Plewczynski
    Academic press:
    ACS Omega (rok: 2022, tom: 7, strony: 23069—23074), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acsomega.2c00215 - link to the publication
  4. Structural Variants and Implicated Processes Associated with Familial Tourette Syndrome
    Authors:
    Jakub P Fichna, Mateusz Chiliński, Anup Kumar Halder, Paweł Cięszczyk, Dariusz Plewczynski, Cezary Żekanowski, Piotr Janik
    Academic press:
    International Journal of Molecular Sciences (rok: 2024, tom: 25(11), strony: 5758), Wydawca: MPDPI
    Status:
    Published
    DOI:
    10.3390/ijms25115758 - link to the publication
  5. The 3D enhancer network of the developing T cell genome is shaped by SATB1
    Authors:
    Tomas Zelenka, Antonios Klonizakis, Despina Tsoukatou, Dionysios-Alexandros Papamatheakis, Sören Franzenburg, Petros Tzerpos, Ioannis-Rafail Tzonevrakis, George Papadogkonas, Manouela Kapsetaki, Christoforos Nikolaou, Dariusz Plewczynski & Charalampos Spilianakis
    Academic press:
    Nature Communications (rok: 2022, tom: 14, strony: 6954), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41467-022-34345-y - link to the publication
  6. 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells
    Authors:
    Karolina Jodkowska, Vera Pancaldi, Maria Rigau, Ricardo Almeida, José M Fernández-Justel, Osvaldo Graña-Castro, Sara Rodríguez-Acebes, Miriam Rubio-Camarillo, Enrique Carrillo-de Santa Pau, David Pisano, Fátima Al-Shahrour, Alfonso Valencia, María Gómez, Juan Méndez
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: 12149–12165), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac1111 - link to the publication
  7. PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms
    Authors:
    Sengupta K, Saha S, Halder AK, Chatterjee P, Nasipuri M, Basu S and Plewczynski D
    Academic press:
    Frontiers in Genetics (rok: 2022, tom: 13, strony: 969915), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fgene.2022.969915 - link to the publication
  8. Dormancy and heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size
    Authors:
    Michal Krzyszton, Sebastian P. Sacharowski, Veena Halale Manjunath, Katarzyna Muter, Grzegorz Bokota, Ce Wang, Dariusz Plewczyński, Tereza Dobisova, Szymon Swiezewski
    Academic press:
    Plant Commun. (rok: 2024, tom: 5(2), strony: 100732), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.xplc.2023.100732 - link to the publication
  9. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction
    Authors:
    Anup Kumar Halder, Abhishek Agarwal, Karolina Jodkowska, Dariusz Plewczynski
    Academic press:
    Briefings in Functional Genomics (rok: 2024, tom: 23(5), strony: 538-548), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elae009 - link to the publication
  10. A Gibbs sampler for learning DAG: a unification for discrete and Gaussian domains
    Authors:
    Hamid Zareifard, Vahid Rezaei Tabar & Dariusz Plewczynski
    Academic press:
    Journal of Statistical Computation and Simulation (rok: 2021, tom: 91, strony: 2833-2853), Wydawca: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/00949655.2021.1909026 - link to the publication
  11. Identification of Human miRNA Biomarkers Targeting the SARS-CoV-2 Genome
    Authors:
    Indrajit Saha, Nimisha Ghosh, Dariusz Plewczynski
    Academic press:
    ACS Omega (rok: 2022, tom: 7, strony: 46411–46420), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acsomega.2c05091 - link to the publication
  12. The 3D enhancer network of the developing T cell genome is shaped by SATB1
    Authors:
    Tomas Zelenka, Antonios Klonizakis, Despina Tsoukatou, Dionysios-Alexandros Papamatheakis, Sören Franzenburg, Petros Tzerpos, Ioannis-Rafail Tzonevrakis, George Papadogkonas, Manouela Kapsetaki, Christoforos Nikolaou, Dariusz Plewczynski & Charalampos Spilianakis
    Academic press:
    Nature Communications (rok: 2022, tom: 14, strony: 6954), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41467-022-34345-y - link to the publication
  13. In vitro immune evaluation of adenoviral vector-based platform for infectious diseases
    Authors:
    Joanna Baran, Łukasz Kuryk, Teresa Szczepińska, Michał Łaźniewski, Mariangela Garofalo, Anna Mazurkiewicz-Pisarek, Diana Mikiewicz, Alina Mazurkiewicz, Maciej Trzaskowski, Magdalena Wieczorek, Katarzyna Pancer, Ewelina Hallmann, Lidia Brydak, Dariusz Plewczynski, Tomasz Ciach, Jolanta Mierzejewska, Monika Staniszewska
    Academic press:
    BioTechnologia (rok: 2023, tom: 104(4), strony: 403-419), Wydawca: Institute of Bioorganic Chemistry, Polish Academy of Sciences
    Status:
    Published
    DOI:
    10.5114/bta.2023.132775 - link to the publication
  14. cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling
    Authors:
    Michal Wlasnowolski, Pawel Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: 588), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad588 - link to the publication
  15. HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences
    Authors:
    Mateusz Chiliński, Dariusz Plewczynski
    Academic press:
    BMC Genomics (rok: 2024, tom: 25, strony: -), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/s12864-024-10885-z - link to the publication
  16. Chromatin image-driven modelling
    Authors:
    Michał Kadlof, Krzysztof Banecki, Mateusz Chiliński, Dariusz Plewczynski
    Academic press:
    Methods (rok: 2024, tom: 226, strony: 54-60), Wydawca: ScienceDirect
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2024.04.006 - link to the publication
  17. Unveiling the Molecular Mechanism of Trastuzumab Resistance in SKBR3 and BT474 Cell Lines for HER2 Positive Breast Cancer
    Authors:
    Anna Kokot, Sachin Gadakh, Indrajit Saha, Ewa Gajda, Michał Łaźniewski, Somnath Rakshit, Kaustav Sengupta, Ayatullah Faruk Mollah, Michał Denkiewicz, Katarzyna Górczak, Jürgen Claesen, Tomasz Burzykowski, Dariusz Plewczynski
    Academic press:
    Curr. Issues Mol. Biol. (rok: 2024, tom: 46(3), strony: 2713-2740), Wydawca: MPDPI
    Status:
    Published
    DOI:
    10.3390/cimb46030171 - link to the publication
  18. Advancements and future directions in single-cell Hi-C based 3D chromatin modeling
    Authors:
    Krzysztof Banecki, Sevastianos Korsak, Dariusz Plewczynski
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2024, tom: -, strony: -), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.csbj.2024.09.026 - link to the publication
  19. The dynamic role of cohesin in maintaining human genome architecture
    Authors:
    Abhishek Agarwal, Sevastianos Korsak, Ashutosh Choudhury, Dariusz Plewczynski
    Academic press:
    BioEssays (rok: 2023, tom: 45(10), strony: e2200240), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/bies.202200240 - link to the publication
  20. Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
    Authors:
    Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski & Yijun Ruan
    Academic press:
    Scientific Reports (rok: 2022, tom: 12, strony: 8582), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-022-12568-9 - link to the publication
  21. Editorial: SARS-CoV-2: From Genetic Variability to Vaccine Design
    Authors:
    Saha I, Ghosh N and Plewczynski D
    Academic press:
    Frontiers in Genetics (rok: 2022, tom: 13, strony: 960107), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fgene.2022.960107 - link to the publication
  22. Unveiling novel aspects of SARS-CoV-2 to combat COVID-19
    Authors:
    Nimisha Ghosh, Indrajit Saha, Dariusz Plewczynski
    Academic press:
    Front Genet. (rok: 2024, tom: 15, strony: 1383640), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fgene.2024.1383640 - link to the publication
  23. TBC1D24 emerges as an important contributor to progressive postlingual dominant hearing loss
    Authors:
    Dominika Oziębło, Marcin L. Leja, Michal Lazniewski, Anna Sarosiak, Grażyna Tacikowska, Krzysztof Kochanek, Dariusz Plewczynski, Henryk Skarżyński & Monika Ołdak
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 45671), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-021-89645-y - link to the publication
  24. Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size
    Authors:
    Michal Krzyszton, Sebastian P. Sacharowski, Veena Halale Manjunath, Katarzyna Muter, Grzegorz Bokota, Ce Wang, Dariusz Plewczyński, Tereza Dobisova, Szymon Swiezewski
    Academic press:
    Plant Communications (rok: 2023, tom: 5(12), strony: 100723), Wydawca: Science Direct
    Status:
    Published
    DOI:
    10.1016/j.xplc.2023.100732 - link to the publication
  25. PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms
    Authors:
    Sengupta K, Saha S, Halder AK, Chatterjee P, Nasipuri M, Basu S and Plewczynski D
    Academic press:
    Frontiers in Genetics (rok: 2022, tom: 13, strony: 969915), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fgene.2022.969915 - link to the publication
  26. Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome
    Authors:
    Sevastianos Korsak, Krzysztof Banecki, Dariusz Plewczynski
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2024, tom: -, strony: -), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.csbj.2024.09.025 - link to the publication
  27. Potent but transient immunosuppression of T-cells is a general feature of CD71+ erythroid cells
    Authors:
    Tomasz M. Grzywa, Anna Sosnowska, Zuzanna Rydzynska, Michal Lazniewski, Dariusz Plewczynski, Klaudia Klicka, Milena Malecka-Gieldowska, Anna Rodziewicz-Lurzynska, Olga Ciepiela, Magdalena Justyniarska, Paulina Pomper, Marcin M. Grzybowski, Roman Blaszczyk, Michal Wegrzynowicz, Agnieszka Tomaszewska, Grzegorz Basak, Jakub Golab & Dominika Nowis
    Academic press:
    Communications Biology (rok: 2021, tom: 4, strony: 45676), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s42003-021-02914-4 - link to the publication
  28. Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
    Authors:
    Teresa Szczepińska, Ayatullah Faruk Mollah and Dariusz Plewczynski
    Academic press:
    International Journal of Molecular Sciences (rok: 2021, tom: 22, strony: 45670), Wydawca: MDPI, Basel, Switzerland
    Status:
    Published
    DOI:
    10.3390/ijms222111591 - link to the publication
  29. Novel combinatorial therapy of oncolytic adenovirus AdV5/3-D24-ICOSL-CD40L with anti PD-1 exhibits enhanced anti-cancer efficacy through promotion of intratumoral T-cell infiltration and modulation of tumour microenvironment in mesothelioma mouse model
    Authors:
    Mariangela Garofalo, Magdalena Wieczorek, Ines Anders, Monika Staniszewska, Michal Lazniewski, Marta Prygiel, Aleksandra Anna Zasada, Teresa Szczepińska, Dariusz Plewczynski, Stefano Salmaso, Paolo Caliceti, Vincenzo Cerullo, Ramon Alemany, Beate Rinner, Katarzyna Pancer, Lukasz Kuryk
    Academic press:
    Frontiers in Oncology (rok: 2023, tom: 13, strony: 1259314), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fonc.2023.1259314 - link to the publication
  30. 3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome
    Authors:
    Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski
    Academic press:
    Nucleic Acids Research (rok: 2023, tom: 51, strony: W5-W10), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkad354 - link to the publication
  31. Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies
    Authors:
    Maciej Wiśniewski, Peace Babirye, Carol Musubika, Eleni Papakonstantinou, Samuel Kirimunda, Michal Łaźniewski, Teresa Szczepińska, Moses L Joloba, Elias Eliopoulos, Erik Bongcam-Rudloff, Dimitrios Vlachakis, Anup Kumar Halder, Dariusz Plewczyński, Misaki Wayengera
    Academic press:
    Briefings in Functional Genomics (rok: 2024, tom: 23(6), strony: 765–774), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elae012 - link to the publication
  32. Editorial: SARS-CoV-2: From Genetic Variability to Vaccine Design
    Authors:
    Saha I, Ghosh N and Plewczynski D
    Academic press:
    Frontiers in Genetics (rok: 2022, tom: 13, strony: 960107), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fgene.2022.960107 - link to the publication
  33. Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
    Authors:
    Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski & Yijun Ruan
    Academic press:
    Scientific Reports (rok: 2022, tom: 12, strony: 8582), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-022-12568-9 - link to the publication
  34. 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines
    Authors:
    Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk & Subhadip Basu
    Academic press:
    Neuroinformatics (rok: 2021, tom: -, strony: 45677), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1007/s12021-021-09549-0 - link to the publication
  35. From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect
    Authors:
    Mateusz Chiliński, Kaustav Sengupta, Dariusz Plewczynski
    Academic press:
    Seminars in Cell & Developmental Biology (rok: 2021, tom: 121, strony: 171-185), Wydawca: Elsevier Ltd.
    Status:
    Published
    DOI:
    10.1016/j.semcdb.2021.08.007 - link to the publication
  36. LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin
    Authors:
    Sevastianos Korsak, Dariusz Plewczynski
    Academic press:
    Methods (rok: 2024, tom: 223, strony: 106-117), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2024.01.015 - link to the publication

O Narodowym Centrum Nauki

Finansowanie nauki

Współpraca zagraniczna

Centrum prasowe

Deklaracja dostępności
Przetwarzanie danych osobowych
Polityka cookies

Partnerzy