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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PerM-Cloud, ALgorithms and methods of processing big genomic data repositories in computing cloud environment towards the personalized medicine.

2014/13/B/NZ2/01248

Keywords:

genomics transcriptomics cloud computing statistics big data data analytics

Descriptors:

  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ2_7: Bioinformatics

Panel:

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

Host institution :

Politechnika Warszawska, Wydział Elektroniki i Technik Informacyjnych

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Michał Okoniewski 

Number of co-investigators in the project: 7

Call: OPUS 7 - announced on 2014-03-17

Amount awarded: 499 138 PLN

Project start date (Y-m-d): 2015-03-02

Project end date (Y-m-d): 2018-09-01

Project duration:: 42 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. laptopy (10 000 PLN)

Information in the final report

  • Publication in academic press/journals (5)
  • Articles in post-conference publications (3)
  1. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort
    Authors:
    Tomasz Gambin Zeynep C. Akdemir Bo Yuan Shen Gu Theodore Chiang Claudia M.B. Carvalho Chad Shaw Shalini Jhangiani Philip M. Boone Mohammad K. Eldomery Ender Karaca Yavuz Bayram Asbjørg Stray-Pedersen Donna Muzny Wu-Lin Charng Vahid Bahrambeigi John W. Belmont Eric Boerwinkle Arthur L. Beaudet Richard A. Gibbs James R. Lupski
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45 (4), strony: 1633-1648), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkw1237 - link to the publication
  2. SeQuiLa: An elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals
    Authors:
    M. Wiewiórka, A. Szmurło, K. Stępień, M. Borowiak, M. Okoniewski, A. Leśniewska, T. Gambin
    Academic press:
    Bioinformatics (rok: 2019, tom: 35(12), strony: 2156–2158), Wydawca: Oxford Academics
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty940 - link to the publication
  3. Benchmarking distributed data warehouse solutions for storing genomic variant information
    Authors:
    Marek Wiewiórka, Dawid Wysakowicz, Michał Okoniewski, Tomasz Gambin
    Academic press:
    DATABASE - The Journal of Biological Databases and Curation (rok: 2017, tom: 2017, strony: bax049), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/database/bax049 - link to the publication
  4. Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures
    Authors:
    Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz, Michal J Okoniewski
    Academic press:
    Biology direct (rok: 2018, tom: 13(1):3, strony: -), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s13062-018-0205-x - link to the publication
  5. Iterative Sequencing and Variant Screening (ISVS) as a novel pathogenic mutations search strategy - application for TMPRSS3 mutations screen
    Authors:
    Urszula Lechowicz, Tomasz Gambin, Agnieszka Pollak, Anna Podgorska, Piotr Stawinski, Andre Franke, Britt-Sabina Petersen, Malgorzata Firczuk, Monika Oldak, Henryk Skarzynski, Rafal Ploski
    Academic press:
    Scientific Reports (rok: 2017, tom: 7(1), strony: 2543), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-017-02315-w - link to the publication
  1. Automated parameter tuning for more accurate CNV calling in WES/WGS data
    Authors:
    M. Wiewiórka, W. Kuśmirek, M. Okoniewski. T. Gambin
    Conference:
    American Society of Human Genetics meeting, ASHG 2017 (rok: 2017, ), Wydawca: ASHG
    Data:
    konferencja 17-21.10.2017
    Status:
    Published
  2. Scalable framework for the analysis of population structure using the next generation sequencing data
    Authors:
    Anastasiia Hryhorzhevska, Marek Wiewiórka, Michał Okoniewski, Tomasz Gambin
    Conference:
    23rd International Symposium on Methodologies for Intelligent Systems (rok: 2017, ), Wydawca: Springer
    Data:
    konferencja 26-29 czerwca
    Status:
    Published
    DOI:
    link to the publication
  3. Benchmarking distributed data warehouse solutions for storing genomic variant information
    Authors:
    M.S. Wiewiórka, D.P. Wysakowicz, M.J. Okoniewski, T. Gambin.
    Conference:
    American Society of Human Genetics meeting, ASHG 2016 (rok: 2016, ), Wydawca: ASHG
    Data:
    konferencja 18-22.10.2016
    Status:
    Published

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