Marek Kochańczyk

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Ph.D.,   Assistant Professor
Marek's photo

Contact

e-mail at ippt.pan.pl or ucdavis.edu: mkochan
tel.: +48 22 8261280 ext. 161
room: 311

Institute of Fundamental Technological Research
Polish Academy of Sciences
Pawińskiego 5B, 02-106 Warsaw, Poland



Publications


Systems biology

  • Limits to the rate of information transmission through the MAPK pathway
    Grabowski F, Czyż P, Kochańczyk M@, Lipniacki T@
    Journal of the Royal Society Interface 16(152):20180792 (2019)
    PubMed CrossRef | PDF SuppCode
  • Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways
    Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T
    Nature Communications 9:493 (2018)
    PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode
  • Information processing in the NF-κB pathway
    Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T
    Scientific Reports 7:15926 (2017)
    PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNGL SuppCode-Py
  • RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα
    Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M
    Science Signaling 10(469):eaai8482 (2017)
    PubMed CrossRef | SuppCode-BioNetGen
  • Feedbacks, bifurcations, and cell fate decision-making in the p53 system
    Hat B, Kochańczyk M, Bogdał M, Lipniacki T
    PLOS Computational Biology 12(2):e1004787 (2016)
    PubMed CrossRef | PDF SuppText SuppFigs SuppCode
  • A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells
    Cheng FHC, Aguda BD, Tsai J-C, Kochańczyk M, Lin JMJ, Chen GCW, Lai H-C, Nephew KP, Hwang T-W, Chan MWY
    PLOS One 9(12):e116050 (2014)
    PubMed CrossRef | PDF
  • Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate
    Bogdał MN, Hat B, Kochańczyk M, Lipniacki T
    BMC Systems Biology 7:67 (2013)
    PubMed CrossRef | PDF Code-Matlab


Chemical physics and biophysics

  • Sampling rare events in stochastic reaction–diffusion systems within trajectory looping
    Zuk PJ, Kochańczyk M, Lipniacki T
    Physical Review E 98:022401 (2018)
    PubMed CrossRef | PDF-ms Www
  • Effective reaction rates for diffusion-limited reaction cycles
    Nałęcz-Jawecki P, Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T
    Journal of Chemical Physics 143(21):215102 (2015)
    PubMed CrossRef | PDF-ms
  • Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles
    Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T
    Physical Review E 91:022702 (2015)
    PubMed CrossRef | PDF-ms
  • Stochastic transitions in a bistable reaction system on the membrane
    Kochańczyk M, Jaruszewicz J, Lipniacki T
    Journal of the Royal Society Interface 10(84):20130151 (2013)
    PubMed CrossRef | PDF Supp-PDF Supp-movies
  • Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process
    Żuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T
    Physical Biology 5(9):055002 (2012)
    PubMed CrossRef | PDF-ms


Computational structural biology

  • Prediction of functionally important residues in globular proteins from unusual central distances of amino acids
    Kochańczyk M
    BMC Structural Biology 11(1):34 (2011)
    PubMed CrossRef | PDF PDF+supp Code Server
  • In silico structural study of random amino acid sequence proteins not present in nature
    Prymula K, Piwowar M, Kochańczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wiśniowski Z, Sałapa K, Matczyńska E, Roterman I
    Chemistry & Biodiversity 6(12):2311–2336 (2009)
    PubMed CrossRef
  • Prediction of functional sites based on the fuzzy oil drop model
    Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I
    PLoS Computational Biology 3(5):e94 (2007)
    PubMed CrossRef | PDF
  • Localization of ligand binding site in proteins identified in silico
    Bryliński M, Kochańczyk M, Broniatowska E, Roterman I
    Journal of Molecular Modeling 13(6–7):665–675 (2007)
    PubMed CrossRef


Software tools

  • Spatkin: a simulator for rule-based modeling of biomolecular site dynamics on surfaces
    Kochańczyk M@, Hlavacek WS, Lipniacki T
    Bioinformatics 33(22):3667–3669 (2017)
    PubMed CrossRef | Www
  • ShuttleTracker: a tool for analysing nucleocytoplasmic shuttling of fluorescent reporters
    (unpublished) Www