Marek Kochańczyk

Research Assistant

Contact

e-mail at ippt.pan.pl: mkochan
tel.: +48 22 8261280 ext. 161  or  +48 22 350 7270
room: 311

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

Publications

Systems biology

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

• Czerkies M^☯, Korwek Z^☯, Prus W^☯, Kochańczyk M^☯, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications 9:493 (2018) PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode

• Tudelska K^☯, Markiewicz J^☯, Kochańczyk M^☯, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway, Scientific Reports 7:15926 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNGL SuppCode-Py

• Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M. RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Science Signaling 10(469):eaai8482 (2017) PubMed CrossRef | SuppCode-BioNetGen

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

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

• Hat B^☯, Kochańczyk M^☯, Bogdał M, Lipniacki T. Feedbacks, bifurcations, and cell fate decision-making in the p53 system, PLOS Computational Biology 12(2):e1004787 (2016) PubMed CrossRef | PDF SuppText SuppFigs SuppCode

• Cheng FHC, Aguda BD, Tsai J-C, Kochańczyk M, Lin JMJ, Chen GCW, Lai H-C, Nephew KP, Hwang T-W, Chan MWY. A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells, PLOS One 9(12):e116050 (2014) PubMed CrossRef | PDF

• Bogdał MN, Hat B, Kochańczyk M, Lipniacki T. Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate, BMC Systems Biology 7:67 (2013) PubMed CrossRef | PDF Code-Matlab

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

Chemical physics and biophysics

• Zuk PJ^☯, Kochańczyk M^☯, Lipniacki T. Sampling rare events in stochastic reaction–diffusion systems within trajectory looping, Physical Review E 98:022401 (2018) CrossRef | PDF-ms Www

• Nałęcz-Jawecki P, Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T. Effective reaction rates for diffusion-limited reaction cycles, Journal of Chemical Physics 143(21):215102 (2015) PubMed CrossRef | PDF-ms

• Szymańska P^☯, Kochańczyk M^☯, Miększ J, Lipniacki T. Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles, Physical Review E 91:022702 (2015) PubMed CrossRef | PDF-ms

• Kochańczyk M, Jaruszewicz J, Lipniacki T. Stochastic transitions in a bistable reaction system on the membrane, Journal of the Royal Society Interface 10(84):20130151 (2013) PubMed CrossRef | PDF Supp-PDF Supp-movies

• Żuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T. Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process, Physical Biology 5(9):055002 (2012) PubMed CrossRef | PDF-ms

Computational structural biology

• Kochańczyk M. Prediction of functionally important residues in globular proteins from unusual central distances of amino acids, BMC Structural Biology 11(1):34 (2011) PubMed CrossRef | PDF PDF+supp Code Server

• 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. In silico structural study of random amino acid sequence proteins not present in nature, Chemistry & Biodiversity 6(12):2311–2336 (2009) PubMed CrossRef

• Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I. Prediction of functional sites based on the fuzzy oil drop model, PLoS Computational Biology 3(5):e94 (2007) PubMed CrossRef | PDF

• Bryliński M, Kochańczyk M, Broniatowska E, Roterman I. Localization of ligand binding site in proteins identified in silico, Journal of Molecular Modeling 13(6-7):665–675 (2007) PubMed CrossRef

Software tools

• Kochańczyk M, Hlavacek WS, Lipniacki T. Spatkin: a simulator for rule-based modeling of biomolecular site dynamics on surfaces, Bioinformatics 33(22):3667–3669 (2017) PubMed CrossRef | Www