Marek Kochańczyk
From Laboratory of Modeling in Biology and Medicine
Ph.D., Assistant Professor
![Marek's photo](/images/thumb/3/38/Marek_Kochanczyk.jpg/180px-Marek_Kochanczyk.jpg)
Contact
e-mail at ippt.pan.pl: 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, cell signaling
- Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response
Korwek Z☯, Czerkies M☯, Jaruszewicz-Błońska J☯, Prus W, Kosiuk I, Kochańczyk M☯, Lipniacki T
Science Signaling 16(815):eabq1173 (2023)
PubMed CrossRef | FullText bioRxiv
- The MAPK/ERK channel capacity exceeds 6 bit/hour
Nałęcz-Jawecki P, , Kochańczyk M, , , Lipniacki T
PLOS Computational Biology 19(5):e1011155 (2023)
PubMed CrossRef | bioRxiv Code Data
- Limits to the rate of information transmission through the MAPK pathway
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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
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Nature Communications 9:493 (2018)
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- Information processing in the NF-κB pathway
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Scientific Reports 7:15926 (2017)
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- RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα
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Science Signaling 10(469):eaai8482 (2017)
PubMed CrossRef | SuppCode-BioNetGen
- Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
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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
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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
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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
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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
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BMC Systems Biology 7:67 (2013)
PubMed CrossRef | PDF Code-Matlab
- Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis
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PLOS One 8(11):e78887 (2013)
PubMed CrossRef | PDF Supp-PDF Code-Matlab Code-BioNetGen Code-MatCont
Virology, epidemiology, public health
- Antagonism between viral infection and innate immunity at the single-cell level
Grabowski F☯, Kochańczyk M☯, Korwek Z, Czerkies M, Prus W, Lipniacki T.
PLOS Pathogens 19(9):e1011597 (2023)
PubMedCrossRef | bioRxiv Code Data
- Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons
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Journal of Virology 96:22 e01341-22 (2022)
PubMed CrossRef bioRxiv
- The spread of SARS-CoV-2 variant Omicron with the doubling time of 2.0–3.3 days can be explained by immune evasion
Grabowski F, Kochańczyk M, Lipniacki T.
Viruses 14(2):294 (2022)
PubMed CrossRef medRxiv | PDF Correspondence
- SARS-CoV-2 Variant of Concern 202012/01 has about twofold replicative advantage and acquires concerning mutations
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Viruses 13(3):392 (2021)
PubMed CrossRef medRxiv | PDF SuppInfo-ZIP Correspondence
- Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives
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Scientific Reports 11:2425 (2021)
PubMed CrossRef medRxiv | PDF GitHub
- Super-spreading events initiated the exponential growth phase of COVID-19 with R0 higher than initially estimated
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Royal Society Open Science 7:200786 (2020)
PubMed CrossRef | PDF SuppInfo-PDF Correspondence
- Dynamics of COVID-19 pandemic at constant and time-dependent contact rates
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Mathematical Modelling of Natural Phenomena 15:28 (2020)
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Chemical physics, biophysics
- Sampling rare events in stochastic reaction–diffusion systems within trajectory looping
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Physical Review E 98:022401 (2018)
PubMed CrossRef | PDF-ms Www
- Effective reaction rates for diffusion-limited reaction cycles
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Journal of Chemical Physics 143(21):215102 (2015)
PubMed CrossRef | PDF-ms
- Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles
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Physical Review E 91:022702 (2015)
PubMed CrossRef | PDF-ms
- Stochastic transitions in a bistable reaction system on the membrane
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Journal of the Royal Society Interface 10(84):20130151 (2013)
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- Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process
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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
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
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Chemistry & Biodiversity 6(12):2311–2336 (2009)
PubMed CrossRef
- Prediction of functional sites based on the fuzzy oil drop model
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PLoS Computational Biology 3(5):e94 (2007)
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- Localization of ligand binding site in proteins identified in silico
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Journal of Molecular Modeling 13(6–7):665–675 (2007)
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Software tools
- Spatkin: a simulator for rule-based modeling of biomolecular site dynamics on surfaces
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Bioinformatics 33(22):3667–3669 (2017)
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- ShuttleTracker: a tool for analysing nucleocytoplasmic shuttling of fluorescent reporters
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