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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Integrative systems biology: inferring from massive heterogeneous data

2011/01/B/NZ2/00864

Keywords:

MCMC estimation bayesian inference ODE sensitivity analysis cis-regulation LC-MS next generation sequencing

Descriptors:

  • NZ2_7: Bioinformatics
  • NZ2_9: Systems biology
  • NZ2_10: Biological systems analysis, modelling and simulation

Panel:

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

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. Anna Gambin 

Number of co-investigators in the project: 10

Call: OPUS 1 - announced on 2011-03-15

Amount awarded: 561 000 PLN

Project start date (Y-m-d): 2011-12-27

Project end date (Y-m-d): 2015-06-26

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

Project status: Project settled

Equipment purchased [PL]

  1. laptop (3 szt.) (4 729 PLN)
  2. drukarka.

Information in the final report

  • Publication in academic press/journals (20)
  • Articles in post-conference publications (1)
  1. Delete or merge regressors for linear model selection.
    Authors:
    A. Maj-Kanska, P. Pokarowski and A. Prochenka
    Academic press:
    Electronic Journal of Statistics (rok: 2015, tom: 9, strony: 1749-1778), Wydawca: The Institute of Mathematical Statistics and the Bernoulli Society
    Status:
    Published
    DOI:
    10.1214/15-EJS1050 - link to the publication
  2. Modelling the efficacy of hyperthermia treatment.
    Authors:
    Rybinski M, Szymanska Z, Lasota S, Gambin A.
    Academic press:
    Journal of the Royal Society Interface (rok: 2013, tom: 10(88), strony: 20130527), Wydawca: The Royal Society
    Status:
    Published
    DOI:
    0.1098/rsif.2013.0527 - link to the publication
  3. Sensitivity analysis of mathematical models of signaling pathways
    Authors:
    Agata Charzyńska, Anna Nałęcz, Mikołaj Rybiński, Anna Gambin
    Academic press:
    Biotechnologia (rok: 2012, tom: 93(3), strony: 291-308), Wydawca: Biotechnology Committee Polish Academy of Sciences and the Institute of Bioorganic Chemistry Polish Academy of Sciences
    Status:
    Published
    DOI:
    brak - link to the publication
  4. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder.
    Authors:
    Szafranski P, Dharmadhikari AV, Brosens E, Gurha P, Kolodziejska KE, Zhishuo O, Dittwald P, Majewski T, Mohan KN, Chen B, Person RE, Tibboel D, de Klein A, Pinner J, Chopra M, Malcolm G, Peters G, Arbuckle S, Guiang SF 3rd, Hustead VA, Jessurun J, Hirsch R, Witte DP, Maystadt I, Sebire N, Fisher R, Langston C, Sen P, Stankiewicz P.
    Academic press:
    Genome Research (rok: 2013, tom: 23(1), strony: 23-33), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1101/gr.141887.112 - link to the publication
  5. StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems.
    Authors:
    Jetka T, Charzyńska A, Gambin A, Stumpf MP, Komorowski M.
    Academic press:
    Bioinformatics. (rok: 2014, tom: 30(1), strony: 137-138), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btt631 - link to the publication
  6. BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry.
    Authors:
    Dittwald P, Claesen J, Burzykowski T, Valkenborg D, Gambin A.
    Academic press:
    Analytical Chemistry (rok: 2013, tom: 85(4), strony: 1991-1994), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ac303439m. - link to the publication
  7. Comment on Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform"
    Authors:
    Hu H, Dittwald P, Zaia J, Valkenborg D.
    Academic press:
    Analytical Chemistry (rok: 2013, tom: 85(24), strony: 12189-12192), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ac402731h - link to the publication
  8. Inferring serum proteolytic activity from LC-MS/MS data.
    Authors:
    Dittwald P, Ostrowski J, Karczmarski J, Gambin A.
    Academic press:
    BMC Bioinformatics (rok: 2012, tom: 5:S7, strony: 45300), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/1471-2105-13-S5-S7 - link to the publication
  9. Multiple samples aCGH analysis for rare CNVs detection
    Authors:
    Sykulski M, Gambin T, Bartnik M, Derwińska K, Wiśniowiecka-Kowalnik B, Stankiewicz P, Gambin A.
    Academic press:
    Journal of Clinical Bioinformatics (rok: 2013, tom: 11;3(1):12., strony: -), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/2043-9113-3-12 - link to the publication
  10. Computational modeling of sphingolipid metabolism.
    Authors:
    Wronowska W, Charzyńska A, Nienałtowski K, Gambin A.
    Academic press:
    BMC Syst Biol. (rok: 2015, tom: 0,407638888888889, strony: 45307), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12918-015-0176-9. - link to the publication
  11. On the Fine Isotopic Distribution and Limits to Resolution in Mass Spectrometry.
    Authors:
    Dittwald P, Valkenborg D, Claesen J, Rockwood AL, Gambin A.
    Academic press:
    J Am Soc Mass Spectrom. (rok: 2015, tom: 1, strony: 45305), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s13361-015-1180-4 - link to the publication
  12. An efficient method to calculate the aggregated isotopic distribution and exact center-masses.
    Authors:
    Claesen J, Dittwald P, Burzykowski T, Valkenborg D.
    Academic press:
    J Am Soc Mass Spectrom (rok: 2012, tom: 23(4), strony: 753-763), Wydawca: Springer Science+Business Media (USA)
    Status:
    Published
    DOI:
    10.1007/s13361-011-0326-2 - link to the publication
  13. Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles
    Authors:
    Paulina Szymańska, Marek Kochańczyk, Jacek Miękisz, and Tomasz Lipniacki
    Academic press:
    Phys. Rev. E (rok: 2015, tom: 91, strony: 22702), Wydawca: American Physical Society
    Status:
    Published
    DOI:
    10.1103/PhysRevE.91.022702 - link to the publication
  14. Functional performance of aCGH design for clinical cytogenetics.
    Authors:
    Gambin T, Stankiewicz P, Sykulski M, Gambin A.
    Academic press:
    Computers in Biology and Medicine (rok: 2013, tom: 43(6), strony: 775-785), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiomed.2013.02.008 - link to the publication
  15. Computational models of the JAK1/2-STAT1 signaling.
    Authors:
    Gambin A, Charzyńska A, Ellert-Miklaszewska A, Rybiński M.
    Academic press:
    Jak Stat (rok: 2013, tom: 0,0854166666666667, strony: e24672), Wydawca: Landes Bioscience
    Status:
    Published
    DOI:
    10.4161/jkst.24672 - link to the publication
  16. Inverted low-copy repeats and genome instability--a genome-wide analysis.
    Authors:
    Dittwald P, Gambin T, Gonzaga-Jauregui C, Carvalho CM, Lupski JR, Stankiewicz P, Gambin A.
    Academic press:
    Human Mutation (rok: 2013, tom: 34(1), strony: 210-220), Wydawca: Wiley-Liss on behalf of the Human Genome Variation Society
    Status:
    Published
    DOI:
    10.1002/humu.22217 - link to the publication
  17. NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits.
    Authors:
    Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Rodríguez Rojas LX, Elton LE, Scott DA, Schaaf CP, Torres-Martinez W, Stevens AK, Rosenfeld JA, Agadi S, Francis D, Kang SH, Breman A, Lalani SR, Bacino CA, Bi W, Milosavljevic A, Beaudet AL, Patel A, Shaw CA, Lupski JR, Gambin A, Cheung SW, Stankiewicz P
    Academic press:
    Genome Research (rok: 2013, tom: 23(9), strony: 1395-13409), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1101/gr.152454.112 - link to the publication
  18. State-dependent swap strategies and automatic reduction of number of temperatures in adaptive parallel tempering algorithm
    Authors:
    MK Łącki B Miasojedow
    Academic press:
    Stat Comput (rok: 2015, tom: 1, strony: 45306), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s11222-015-9579-0 - link to the publication
  19. Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma.
    Authors:
    Szczurek E, Misra N, Vingron M.
    Academic press:
    Int J Cancer (rok: 2013, tom: 133(9), strony: 2123-2132), Wydawca: John Wiley & Sons on behalf of the Union for International Cancer Control
    Status:
    Published
    DOI:
    10.1002/ijc.28235 - link to the publication
  20. Towards automated discrimination of lipids versus peptides from full scan mass spectra.
    Authors:
    Dittwald P, Nghia VT, Harris GA, Caprioli RM, Van de Plas R, Laukens K, Gambin A, Valkenborg D.
    Academic press:
    EuPA Open Proteom. (rok: 2014, tom: 4, strony: 87-100), Wydawca: Elsevier ( European Proteomics Association )
    Status:
    Published
    DOI:
    10.1016/j.euprot.2014.05.002 - link to the publication
  1. Efficient and Error-Tolerant Sequencing Read Mapping
    Authors:
    Piotr Jaroszyński, Norbert Dojer
    Conference:
    International Work-Conference on Bioinformatics and Biomedical Engineering (rok: 2013, ), Wydawca: Francisco Ortuno, Ignacio Rojas
    Data:
    konferencja 18-20.03
    Status:
    Published

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