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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Virtual High Throughput Screening (vHTS) derivation of a cross-immunity model for the Influenza-A Virus Infections.

2013/09/B/NZ2/00121

Keywords:

bioinformatics genomics influenza epidemiology protein structure sequence analysis

Descriptors:

  • NZ2_1: Molecular genetics
  • NZ2_10: Biological systems analysis, modelling and simulation
  • NZ2_11: Genetic epidemiology

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):

dr hab. Dariusz Plewczyński 

Number of co-investigators in the project: 5

Call: OPUS 5 - announced on 2013-03-15

Amount awarded: 987 900 PLN

Project start date (Y-m-d): 2014-02-17

Project end date (Y-m-d): 2017-09-16

Project duration:: 43 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Jednostka obliczeniowa, który będzie używana jako serwer internetowy oraz prototyp rozwiązania w większej skali. (20 000 PLN)
  2. komputery robocze dla wykonawców projektu.
  3. Oprogramowanie biomolekularne do dokowania: GOLD lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności. (24 000 PLN)
  4. Komputery robocze dla wykonawców projektu (3 szt.) (45 000 PLN)
  5. Komputery mobilne dla wykonawców projektu (3 szt.) (30 000 PLN)
  6. Oprogramowanie biomolekularne Schrodiner lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności. (29 000 PLN)
  7. oprogramowanie biomolekularne Tripos Sybyl i/lub Accelrys Discovery Studio lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności. (25 000 PLN)
  8. oprogramowanie biomolekularne eHiTS lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności. (31 000 PLN)

Information in the final report

  • Publication in academic press/journals (20)
  • Articles in post-conference publications (3)
  • Book publications / chapters in book publications (4)
  1. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale
    Authors:
    Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D
    Academic press:
    Database (rok: 2016, tom: -, strony: -), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/database/baw130 - link to the publication
  2. Binding Activity Prediction of Cyclin-Dependent Inhibitors
    Authors:
    Saha I, Rak B, Bhowmick SS, Maulik U, Bhattacharjee D, Koch U, Lazniewski M, Plewczynski D
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2015, tom: 55, strony: 1469-1482), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ci500633c - link to the publication
  3. Mapping of the influenza A hemagglutinin serotypes evolution by the ISSCOR method
    Authors:
    Jan Radomski ,Piotr Słonimski ,Włodzimierz Zagórski-Ostoja ,Piotr Borowicz
    Academic press:
    Acta Biochimica Polonica (rok: 2014, tom: 61, strony: 441-451), Wydawca: The Journal of the Polish Biochemical Society and of the Committee of Biochemistry and Biophysics Polish Academy of Sciences
    Status:
    Published
    DOI:
    brak - link to the publication
  4. Social adaptation in multi-agent model of linguistic categorization is affected by network information flow
    Authors:
    Julian Zubek, Michał Denkiewicz, Juliusz Barański, Przemysław Wróblewski, Joanna Rączaszek-Leonardi, Dariusz Plewczynski
    Academic press:
    PLoS One (rok: 2017, tom: 12(8), strony: e0182490), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0182490 - link to the publication
  5. Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods
    Authors:
    Srivastava A, Mazzocco G, Kel A, Wyrwicz LS, Plewczynski D
    Academic press:
    Molecular BioSystems (rok: 2016, tom: 12, strony: 778-785), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C5MB00672D - link to the publication
  6. Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae
    Authors:
    Zubek J, Tatjewski M, Boniecki A, Mnich M, Basu S, Plewczynski D.
    Academic press:
    PeerJ (rok: 2015, tom: -, strony: -), Wydawca: PeerJ Inc.
    Status:
    Published
    DOI:
    10.7717/peerj.1041 - link to the publication
  7. PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.
    Authors:
    Chatterjee P, Basu S, Zubek J, Kundu M, Nasipuri M, Plewczynski D
    Academic press:
    J Mol Model (rok: 2016, tom: 22(4), strony: 22-72), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-016-2933-0 - link to the publication
  8. 3gClust: Human Protein Cluster Analysis
    Authors:
    Halder AK, Chatterjee P, Nasipuri M, Plewczynski D, Basu S.
    Academic press:
    IEEE/ACM Trans Comput Biol Bioinform (rok: 2018, tom: -, strony: 45292), Wydawca: IEEE
    Status:
    Published
    DOI:
    10.1109/TCBB.2018.2840996 - link to the publication
  9. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
    Authors:
    Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y.
    Academic press:
    Cell (rok: 2015, tom: 163, strony: 1611-1627), Wydawca: Elsevier Inc.
    Status:
    Published
    DOI:
    10.1016/j.cell.2015.11.024 - link to the publication
  10. Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis
    Authors:
    Bokota G, Magnowska M, Kuśmierczyk T, Łukasik M, Roszkowska M, Plewczynski D
    Academic press:
    Front Comput Neurosci (rok: 2016, tom: -, strony: -), Wydawca: Frontiers Inc.
    Status:
    Published
    DOI:
    10.3389/fncom.2016.00140 - link to the publication
  11. Novel neuro-audiological findings and further evidence for TWNK involvement in Perrault syndrome
    Authors:
    Ołdak M, Oziębło D, Pollak A, Stępniak I, Lazniewski M, Lechowicz U, Kochanek K, Furmanek M, Tacikowska G, Plewczynski D, Wolak T, Płoski R, Skarżyński H
    Academic press:
    J Trans Med (rok: 2017, tom: 15(1), strony: -), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12967-017-1129-4 - link to the publication
  12. Role of the host genetic variability in the influenza A virus susceptibility
    Authors:
    Ana Carolina Arcanjo, Giovanni Mazzocco, Silviene Fabiana de Oliveira, Dariusz Plewczynski and Jan P. Radomski
    Academic press:
    Acta Biochimica Polonica (rok: 2014, tom: 61, strony: 403-419), Wydawca: The Journal of the Polish Biochemical Society and of the Committee of Biochemistry and Biophysics Polish Academy of Sciences
    Status:
    Published
    DOI:
    brak - link to the publication
  13. Computational inference of H3K4me3 and H3K27ac domain length
    Authors:
    Zubek J, Stitzel ML, Ucar D, Plewczynski D
    Academic press:
    PeerJ (rok: 2016, tom: -, strony: -), Wydawca: PeerJ Inc.
    Status:
    Published
    DOI:
    10.7717/peerj.1750 - link to the publication
  14. The structural variability of the influenza A hemagglutinin receptor binding site
    Authors:
    Michal Lazniewski, Wayne K Dawson, Teresa Szczepińska , Dariusz Plewczynski
    Academic press:
    Briefings in Functional Genomics (rok: 2018, tom: 17(6), strony: 415-427), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elx042 - link to the publication
  15. 3D-GNOME: an integrated web service for structural modeling of the 3D genome
    Authors:
    Szalaj P, Michalski PJ, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D
    Academic press:
    Nucleic Acids Res (rok: 2016, tom: 44, strony: 288-293), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkw437 - link to the publication
  16. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium
    Authors:
    Kazakiewicz D, Karr JR, Langner KM, Plewczynski D
    Academic press:
    Computational Biology and Chemistry (rok: 2015, tom: 59, strony: 91-97), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiolchem.2015.07.007 - link to the publication
  17. An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization
    Authors:
    Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D
    Academic press:
    Genome Res (rok: 2016, tom: 26(12), strony: 1697-1709), Wydawca: CSH Press
    Status:
    Published
    DOI:
    10.1101/gr.205062.116 - link to the publication
  18. Ensemble learning prediction of protein-protein interactions using proteins functional annotations
    Authors:
    Saha I, Zubek J, Klingström T, Forsberg S, Wikander J, Kierczak M, Maulik U, Plewczynski D.
    Academic press:
    Mol Biosyst (rok: 2014, tom: 10, strony: 820), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c3mb70486f - link to the publication
  19. RNA structure interactions and ribonucleoprotein processes of the influenza A virus
    Authors:
    Dawson W, Lazniewski M, Plewczynski D
    Academic press:
    Brief Funct Genomics (rok: 2018, tom: 17(6), strony: 402-414), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elx028 - link to the publication
  20. The Proline-Rich Region of Glyceraldehyde-3-Phosphate Dehydrogenase from Human Sperm May Bind SH3 Domains, as Revealed by a Bioinformatic Study of Low-Complexity Protein Segments
    Authors:
    Marcin Tatjewski, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg
    Academic press:
    Molecular Reproduction & Development (rok: 2016, tom: 83, strony: 144-148), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/mrd.22606 - link to the publication
  1. Distributional Proteomics: Modelling amino acid relationships by measuring their patterns of statistical occurrence across proteins
    Authors:
    Marcin Tatjewski, Dariusz Plewczynski
    Conference:
    2nd Conference of the Project Information Technologies: research and their interdisciplinary applications" (rok: 2015, ), Wydawca: Instytut Podstaw Informatyki PAN
    Data:
    konferencja 22-24.10.2015
    Status:
    Published
  2. MaER: A New Multiclass Classifier for BindingActivity Prediction of HLA Class II Proteins
    Authors:
    Mazzocco G, Bhowmick S.S., Saha I., Maulik U., Bhattacharjee D., and Plewczynski D.
    Conference:
    PReMI: 6th International Conference on Pattern Recognition and Machine Intelligence (rok: 2015, ), Wydawca: Springer in Lecture Notes in Computer Science
    Data:
    konferencja 30/6-3/7
    Status:
    Published
  3. Evaluating multi-level machine learning prediction of protein-protein interactions
    Authors:
    Julian Zubek, Marcin Tatjewski, Subhadip Basu, Dariusz Plewczynski
    Conference:
    2nd Conference of the Project Information Technologies: research and their interdisciplinary applications" (rok: 2015, ), Wydawca: Instytut Podstaw Informatyki PAN
    Data:
    konferencja 22-24.10.2015
    Status:
    Published
    DOI:
    link to the publication
  1. Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods
    Authors:
    Plewczynski D, Gruca S, Szałaj P, Gulik K, de Oliveira SF and Malhotra A.
    Book:
    Clinical Applications for Next-Generation Sequencing (rok: 2015, tom: -, strony: 39-61), Wydawca: Elsevier
    Status:
    Published
  2. PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier
    Authors:
    Piyali Chatterjee, Subhadip Basu, Julian Zubek, Mahantapas Kundu, Mita Nasipuri, Dariusz Plewczynski
    Book:
    Pattern Recognition and Machine Intelligence in the series of Lecture Notes in Computer Science (rok: 2015, tom: 9124, strony: 441-450), Wydawca: Springer International Publishing
    Status:
    Published
  3. Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer
    Authors:
    Indrajit Saha, Shib Sankar Bhowmick, Filippo Geraci, Marco Pellegrini, Debotosh Bhattacharjee, Ujjwal Maulik, Dariusz Plewczynski
    Book:
    SEMCCO 2015: Swarm, Evolutionary, and Memetic Computing in Lecture Notes in Computer Science book series (LNCS) (rok: 2015, tom: 9873, strony: 116-127), Wydawca: Springer
    Status:
    Published
    DOI:
    link to the publication
  4. Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices
    Authors:
    Tatjewski M, Kierczak M, Plewczynski D
    Book:
    Prediction of Protein Secondary Structure (rok: 2016, tom: 1484, strony: 275-300), Wydawca: Springer Protocols
    Status:
    Published

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