Marek Kochańczyk

Ph.D.,   Assistant Professor

Contact

e-mail at ippt.pan.pl or ucdavis.edu: mkochan

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

Currently on leave to:
Dept. of Molecular and Cellular Biology
University of California, Davis
Briggs Hall, 550 Storer Mall, Davis, CA 95616

Publications

Systems biology

• Limits to the rate of information transmission through MAPK pathway
  Grabowski F, Czyż P, Kochańczyk M, Lipniacki T.
  (submitted) bioRxiv Www

• 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

• Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
  Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T.
  Scientific Reports 7:38244 (2017) PubMed CrossRef
  PDF SuppInfo-PDF SuppCode-BNG SuppCode-MatCont SuppCode-BNG-noisy SuppCode-Comsol SuppMovie

• Importins promote high-frequency NF-κB oscillations increasing information channel capacity
  Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T.
  Biology Direct 11:61 (2016) PubMed CrossRef
  PDF Scheme-PDF SuppModelInfo-PDF SuppModelCode-BNGL SuppFigs-PDF SuppImages-ZIP

• 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

• Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis
  Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellog R, Tay S, Lipniacki T.
  PLOS One 8(11):e78887 (2013) PubMed CrossRef
  PDF Supp-PDF Code-Matlab Code-BioNetGen Code-MatCont

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^☯, Miększ 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