Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Spatial network model of sequence and structure diversity of Human genome at a population scale

2019/35/O/ST6/02484

Keywords:

bioinformatics structural variants chromatin loops mammalian 3D genome Topologically Associating Domains deep learning spatial network model Biophysical Modelling Cell differentiation Hematopoietic development oncogenesis immortalization

Descriptors:

  • ST6_013:
  • ST6_012:
  • NZ2_007:

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Politechnika Warszawska, Wydział Matematyki i Nauk Informacyjnych

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: 2

Call: PRELUDIUM BIS 1 - announced on 2019-09-16

Amount awarded: 528 000 PLN

Project start date (Y-m-d): 2020-10-01

Project end date (Y-m-d): 2025-06-30

Project duration:: 57 months (the same as in the proposal)

Project status: Project completed

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 (37)
  1. 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
  2. 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
  3. 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
  4. 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
  5. ConsensuSV-ONT-a modern method for accurate structural variant calling
    Authors:
    Antoni Pietryga, Mateusz Chiliński, Sachin Gadakh, Dariusz Plewczynski
    Academic press:
    bioRxiv (rok: 2024, tom: -, strony: -), Wydawca: Cold Spring Harbor Laboratory
    Status:
    Published
    DOI:
    10.1101/2024.07.26.605267 - link to the publication
  6. FGVC8 based foliar diseases identification with use of multi-label classifiers
    Authors:
    Mateusz Chiliński, Piotr Góralewski, Tomasz Lehmann, Adam Nowacki, Justyna Stypułkowska
    Academic press:
    International Journal of Computer Information Systems and Industrial Management Applications (rok: 2022, tom: 14, strony: 92-99), Wydawca: Machine Intelligence Research Labs
    Status:
    Published
    DOI:
    link to the publication
  7. 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
  8. 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, strony: 5758), Wydawca: Multidisciplinary Digital Publishing Institute
    Status:
    Published
    DOI:
    10.3390/ijms25115758 - link to the publication
  9. Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions
    Authors:
    Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan, Dariusz Plewczyński
    Academic press:
    Scientific Reports (rok: 2023, tom: 13, strony: 11693), Wydawca: Springer Nature Limited
    Status:
    Published
    DOI:
    10.1038/s41598-023-38865-5 - link to the publication
  10. COVID-DeepPredictor: Recurrent Neural Network to Predict SARS-CoV-2 and Other Pathogenic Viruses
    Authors:
    Indrajit Saha, Nimisha Ghosh, Debasree Maity, Arjit Seal and Dariusz Plewczynski
    Academic press:
    Frontiers in Genetics (rok: 2021, tom: 12, strony: 45669), Wydawca: Frontiers Media S.A.
    Status:
    Published
    DOI:
    10.3389/fgene.2021.569120 - link to the publication
  11. Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes
    Authors:
    Karolina Jodkowska, Zofia Parteka-Tojek, Abhishek Agarwal, Michal Denkiewicz, Sevastianos Korsak, Mateusz Chilinski, Krzysztof Banecki, Dariusz Plewczynski
    Academic press:
    bioRxiv (rok: 2024, tom: -, strony: -), Wydawca: Cold Spring Harbor Laboratory
    Status:
    Published
    DOI:
    10.1101/2024.05.16.594268 - link to the publication
  12. 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
  13. Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis
    Authors:
    Karolina Vanickova, Mirko Milosevic, Irina Ribeiro Bas, Monika Burocziova, Asumi Yokota, Petr Danek, Srdjan Grusanovic, Mateusz Chiliński, Dariusz Plewczyński, Jakub Rohlena, Hideyo Hirai, Katerina Rohlenova, Meritxell Alberich-Jorda
    Academic press:
    EMBO Journal (rok: 2023, tom: 23, strony: 45675), Wydawca: EMBO Press
    Status:
    Published
    DOI:
    10.15252/embj.2023113527 - link to the publication
  14. Chromatin image-driven modelling
    Authors:
    Michał Kadlof, Krzysztof Banecki, Mateusz Chiliński, Dariusz Plewczynski
    Academic press:
    Methods (rok: 2024, tom: -, strony: -), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2024.04.006 - link to the publication
  15. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology
    Authors:
    Anna Czmil, Michal Wronski, Sylwester Czmil, Marta Sochacka-Pietal, Michal Cmil, Jan Gawor, Tomasz Wołkowicz, Dariusz Plewczynski, Dominik Strzalka, Michal Pietal
    Academic press:
    PeerJ (rok: 2022, tom: 10, strony: e13056), Wydawca: PeerJ
    Status:
    Published
    DOI:
    10.7717/peerj.13056 - link to the publication
  16. Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN
    Authors:
    Anik Banik, Souvik Podder, Sovan Saha, Piyali Chatterjee, Anup Kumar Halder, Mita Nasipuri, Subhadip Basu, Dariusz Plewczynski
    Academic press:
    Cells (rok: 2022, tom: 11, strony: 2648), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/cells11172648 - link to the publication
  17. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
    Authors:
    Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski
    Academic press:
    Bioinformatics (rok: 2023, tom: 39(8), strony: 468), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad468 - link to the publication
  18. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
    Authors:
    Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng
    Academic press:
    Briefings in Bioinformatics (rok: 2022, tom: 23, strony: bbac380), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bib/bbac380 - link to the publication
  19. Multi-scale phase separation by explosive percolation with single chromatin loop resolution
    Authors:
    Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2022, tom: 20, strony: 3591-3603), Wydawca: Elsevier B.V.
    Status:
    Published
    DOI:
    10.1016/j.csbj.2022.06.063 - link to the publication
  20. 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
  21. HiCDiffusion-diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences
    Authors:
    Mateusz Chiliński, Dariusz Plewczyński
    Academic press:
    bioRxiv (rok: 2024, tom: -, strony: -), Wydawca: Cold Spring Harbor Laboratory
    Status:
    Published
    DOI:
    10.1101/2024.02.01.578389 - link to the publication
  22. PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
    Authors:
    Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska & Dariusz Plewczynski
    Academic press:
    BMC Bioinformatics (rok: 2021, tom: 22, strony: 45672), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-021-03984-1 - link to the publication
  23. Prediction of chromatin looping using deep hybrid learning (DHL)
    Authors:
    Mateusz Chiliński, Anup Kumar Halder, Dariusz Plewczynski
    Academic press:
    Quantitative Biology (rok: 2023, tom: 2, strony: 155-162), Wydawca: Higher Education Press
    Status:
    Published
    DOI:
    10.15302/j-qb-022-0315 - link to the publication
  24. 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
  25. Single-Hit Inactivation Drove Tumor Suppressor Genes Out of the X Chromosome during Evolution
    Authors:
    Xiansong Wang; Wei Hu; Xiangchun Li; Dan Huang; Qing Li; Hung Chan; Judeng Zeng; Chuan Xie; Huarong Chen; Xiaodong Liu; Tony Gin; Maggie Haitian Wang; Alfred Sze Lok Cheng; Wei Kang; Ka-Fai To; Dariusz Plewczynski; Qingpeng Zhang; Xiaoting Chen; Danny Cheuk Wing Chan; Ho Ko; Sunny Hei Wong; Jun Yu; Matthew Tak Vai Chan; Lin Zhang; William Ka Kei Wu
    Academic press:
    CANCER RESEARCH (rok: 2022, tom: 82, strony: 1482–1491), Wydawca: AACR
    Status:
    Published
    DOI:
    10.1158/0008-5472.CAN-21-3458 - link to the publication
  26. 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
  27. ConsensuSV—from the whole-genome sequencing data to the complete variant list
    Authors:
    Mateusz Chiliński, Dariusz Plewczynski
    Academic press:
    Bioinformatics (rok: 2022, tom: 38/24, strony: 5440-5442), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac709 - link to the publication
  28. Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism
    Authors:
    Nimisha Ghosh, Indrajit Saha, Nikhil Sharma, Suman Nandi, Dariusz Plewczynski
    Academic press:
    Virus Research (rok: 2021, tom: 298, strony: 45676), Wydawca: Elsevier B.V.
    Status:
    Published
    DOI:
    10.1016/j.virusres.2021.198401 - link to the publication
  29. ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19
    Authors:
    Sovan Saha, Piyali Chatterjee, Anup Kumar Halder, Mita Nasipuri, Subhadip Basu, Dariusz Plewczynski
    Academic press:
    Vaccines (rok: 2022, tom: 10, strony: 1643), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/vaccines10101643 - link to the publication
  30. 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
  31. Consensus-based identification and comparative analysis of structural variants and their influence on 3D genome structure using long- and short-read sequencing technologies in polish families
    Authors:
    Mateusz Chiliński, Sachin Gadakh, Kaustav Sengupta, Karolina Jodkowska, Natalia Zawrotna, Jan Gawor, Michal Pietal, Dariusz Plewczynski
    Academic press:
    Lecture Notes in Networks and Systems (rok: 2022, tom: 404, strony: 41-49), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1007/978-981-19-0105-8_5 - link to the publication
  32. 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
  33. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
    Authors:
    Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski
    Academic press:
    Bioinformatics (rok: 2023, tom: 39(8), strony: 468), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad468 - link to the publication
  34. 3DGenBench: a web-server to benchmark computational models for 3D Genomics
    Authors:
    International Nucleome Consortium (Polina Belokopytova, Emil Viesná, Mateusz Chiliński, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea M. Chiariello, Vladimir B. Teif, Dariusz Plewczynski, Bin Zhang, Daniel Jost, Veniamin Fishman)
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50/W1, strony: W4-W12), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac396 - link to the publication
  35. Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations
    Authors:
    Michal Lazniewski, Doni Dermawan, Syahrul Hidayat, Muchtaridi Muchtaridi, Wayne Dawson, Dariusz Plewczyński
    Academic press:
    Methods (rok: 2022, tom: 203, strony: 498—510), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2022.02.004 - link to the publication
  36. 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
  37. Multi-scale phase separation by explosive percolation with single chromatin loop resolution
    Authors:
    Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2022, tom: 20, strony: 3591-3603), Wydawca: Elsevier B.V.
    Status:
    Published
    DOI:
    10.1016/j.csbj.2022.06.063 - link to the publication

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