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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Incorporating genomic variation information into DNA sequencing data analysis

2016/21/B/ST6/01471

Keywords:

DNA sequencing reference genome genomic diversity

Descriptors:

  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • ST6_12: Scientific computing, simulation and modelling tools
  • NZ2_2: Genomics, transcriptomics, epigenomics

Panel:

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

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 hab. Norbert Dojer 

Number of co-investigators in the project: 7

Call: OPUS 11 - announced on 2016-03-15

Amount awarded: 637 600 PLN

Project start date (Y-m-d): 2017-02-06

Project end date (Y-m-d): 2022-02-05

Project duration:: 60 months (the same as in the proposal)

Project status: Project settled

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.

Equipment purchased [PL]

  1. komputer - laptop (2 szt.) (16 000 PLN)
  2. komputer - stacja robocza (13 900 PLN)
  3. monitory komputerowe (3 500 PLN)
  4. projektor.
  5. komputer - laptop (3 szt.) (18 000 PLN)
  6. urządzenie wielofunkcyjne (3 959 PLN)
  7. komputer - laptop (12 595 PLN)
  8. serwer obliczeniowy (50 000 PLN)

Information in the final report

  • Publication in academic press/journals (6)
  1. Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes
    Authors:
    Krzyszton, M., Zakrzewska-Placzek, M., Kwasnik, A., Dojer, N., Karlowski, W. and Kufel, J.
    Academic press:
    The Plant Journal (rok: 2018, tom: 93, strony: 1017–1031), Wydawca: John Wiley & Sons, Ltd
    Status:
    Published
    DOI:
    10.1111/tpj.13826 - link to the publication
  2. Linearization of genome sequence graphs revisited
    Authors:
    Anna Lisiecka, Norbert Dojer
    Academic press:
    iScience (rok: 2021, tom: 1,00486111111111, strony: 102755:1 - 102755:14), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.isci.2021.102755 - link to the publication
  3. Getting insight into the pan-genome structure with PangTree
    Authors:
    Paulina Dziadkiewicz, Norbert Dojer
    Academic press:
    BMC Genomics (rok: 2020, tom: 21, strony: 274), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12864-020-6610-4 - link to the publication
  4. Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application
    Authors:
    Wiktor Kuśmirek, Wiktor Franus, Robert Nowak
    Academic press:
    BioMed Research International (rok: 2019, tom: 2019, strony: 7847064), Wydawca: Hindawi
    Status:
    Published
    DOI:
    10.1155/2019/7847064 - link to the publication
  5. Comprehensive mapping of histone modifications at DNA double-strand breaks deciphers repair pathway chromatin signatures
    Authors:
    Thomas Clouaire, Vincent Rocher, Anahita Lashgari, Coline Arnould, Marion Aguirrebengoa, Anna Biernacka, Magdalena Skrzypczak, Franćcois Aymard, Bernard Fongang, Norbert Dojer, Jason Iacovoni, Maga Rowicka, Krzysztof Ginalski, Jacques Côté, Gaëlle Legube
    Academic press:
    MOLECULAR CELL (rok: 2018, tom: 72, strony: 250-262), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.molcel.2018.08.020 - link to the publication
  6. qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing
    Authors:
    Yingjie Zhu, Anna Biernacka, Benjamin Pardo, Norbert Dojer, Romain Forey, Magdalena Skrzypczak, Bernard Fongang, Jules Nde, Razie Yousefi, Philippe Pasero, Krzysztof Ginalski, Maga Rowicka
    Academic press:
    Nature Communications (rok: 2019, tom: 10(1), strony: 2313), Wydawca: Nature Publishing Group UK
    Status:
    Published
    DOI:
    10.1038/s41467-019-10332-8 - link to the publication

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