Marek Kochańczyk: Difference between revisions

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[[Image:Marek_Kochanczyk.jpg|180px|right|frameless|link=|alt=Marek's photo]]
[[Image:Marek_Kochanczyk.jpg|180px|right|frameless|link=|alt=Marek's photo]]


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===Contact===
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Institute of Fundamental Technological Research<br />
Institute of Fundamental Technological Research<br />
Polish Academy of Sciences<br />
Polish Academy of Sciences<br />
Pawińskiego 5B, 02-106 Warsaw, Poland<br />
Pawińskiego 5B, 02-106 Warsaw, Poland<br />
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''Currently '''on leave''' to:''<br />
Dioscuri Centre for Physics and Chemistry of Bacteria<br />
Institute of Physical Chemistry<br />
Polish Academy of Sciences<br />
Kasprzaka 44/52, 01-224 Warsaw, Poland


<!--''Currently on leave to:''<br />
<!--''Currently on leave to:''<br />
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<br />
<br />
====Systems biology, cell signaling====
====Systems biology, cell signaling====
* '''Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response'''<br/><span class="pmbm">Korwek&nbsp;Z<sup>☯</sup></span>, <span class="pmbm">Czerkies&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Jaruszewicz-Błońska&nbsp;J<sup>☯</sup></span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Kosiuk&nbsp;I</span>, <span class="pmbm">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/> (submitted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]
* '''Type III interferons suppress influenza A virus infection independently of STAT activation by&nbsp;triggering cell death'''<br/><span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Grabowski&nbsp;F</span>, <span class="pmbm">Koza&nbsp;P</span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Lipniacki&nbsp;T</span>.<br/>(submitted) [https://doi.org/10.1101/2024.09.09.612051 bioRxiv]
 
* '''Information transmission in a cell monolayer: A numerical study'''<br/><span class="author">Nałęcz-Jawecki&nbsp;P</span>, <span class="author">Szyc&nbsp;P</span>, <span class="author">Grabowski&nbsp;F</span>, <span class="author">Kochańczyk&nbsp;M</span>, <span class="author">Lipniacki&nbsp;T</span>.<br/>(submitted)<br/>[https://www.biorxiv.org/content/10.1101/2024.06.21.600012v1 bioRxiv]
 
* '''Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response'''<br/><span class="pmbm">Korwek&nbsp;Z<sup>☯</sup></span>, <span class="pmbm">Czerkies&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Jaruszewicz-Błońska&nbsp;J<sup>☯</sup></span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Kosiuk&nbsp;I</span>, <span class="pmbm">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/>''Science Signaling'' <u>16</u>(815):eabq1173 (2023)<br/>[https://pubmed.ncbi.nlm.nih.gov/38085817 PubMed] [https://doi.org/10.1126/scisignal.abq1173 CrossRef] | [{{SERVER}}/publications/Korwek-2023-SciSignal.pdf FullText] [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]


* '''The rate of information transmission through the MAPK/ERK signaling pathway stimulated&nbsp;in a&nbsp;pulsatile manner'''<br/><span class="pmbm">Nałęcz-Jawecki&nbsp;P</span>, <span class="author">Gagliardi&nbsp;PA</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="author">Dessauges&nbsp;C</span>, <span class="author">Pertz&nbsp;O</span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/> (submitted) [https://doi.org/10.1101/2022.03.17.484713 bioRxiv] [https://doi.org/10.5281/zenodo.7472959 Data]
* '''The MAPK/ERK channel capacity exceeds 6 bit/hour'''<br/><span class="pmbm">Nałęcz-Jawecki&nbsp;P</span>, <span class="author">Gagliardi&nbsp;PA</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="author">Dessauges&nbsp;C</span>, <span class="author">Pertz&nbsp;O</span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/>''PLOS&nbsp;Computational&nbsp;Biology'' <u>19</u>(5):e1011155 (2023)<br/> [https://pubmed.ncbi.nlm.nih.gov/37216347 PubMed] [https://doi.org/10.1371/journal.pcbi.1011155 CrossRef] | [https://doi.org/10.1101/2022.03.17.484713 bioRxiv] [https://github.com/pawelnalecz/pulsatile-information Code] [https://doi.org/10.5281/zenodo.7472959 Data]


* '''Limits to the rate of information transmission through the MAPK pathway'''<br/><span class="author">Grabowski F</span>, <span class="author">Czyż P</span>, <span class="author">Kochańczyk M</span><sup>@</sup>, <span class="author">Lipniacki T<sup>@</sup></span><br/>''Journal of the Royal Society Interface'' <u>16</u>(152):20180792 (2019)<br/>[https://www.ncbi.nlm.nih.gov/pubmed/30836891 PubMed] [http://dx.doi.org/10.1098/rsif.2018.0792 CrossRef] | [https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2018.0792 PDF] [{{SERVER}}/software/cce SuppCode]  
* '''Limits to the rate of information transmission through the MAPK pathway'''<br/><span class="author">Grabowski F</span>, <span class="author">Czyż P</span>, <span class="author">Kochańczyk M</span><sup>@</sup>, <span class="author">Lipniacki T<sup>@</sup></span><br/>''Journal of the Royal Society Interface'' <u>16</u>(152):20180792 (2019)<br/>[https://www.ncbi.nlm.nih.gov/pubmed/30836891 PubMed] [http://dx.doi.org/10.1098/rsif.2018.0792 CrossRef] | [https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2018.0792 PDF] [{{SERVER}}/software/cce SuppCode]  
Line 44: Line 57:


====Virology, epidemiology, public health====
====Virology, epidemiology, public health====
* '''Antagonism between viral infection and innate immunity at the single-cell level'''<br/><span class="pmbm">Grabowski&nbsp;F<sup>☯</sup></span>, <span class="pmbm">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Lipniacki&nbsp;T</span>.<br/>(submitted) [https://doi.org/10.1101/2022.11.18.517110 bioRxiv] [https://doi.org/10.5281/zenodo.7428925 Data]
* '''Antagonism between viral infection and innate immunity at the single-cell level'''<br/><span class="pmbm">Grabowski&nbsp;F<sup>☯</sup></span>, <span class="pmbm">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Lipniacki&nbsp;T</span>.<br/>''PLOS Pathogens'' <u>19</u>(9):e1011597 (2023)<br/>[https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed][https://doi.org/10.1371/journal.ppat.1011597 CrossRef] | [https://doi.org/10.1101/2022.11.18.517110 bioRxiv] [https://github.com/grfrederic/visavis Code] [https://doi.org/10.5281/zenodo.7428925 Data]


* '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by&nbsp;triggering secretion of type I and type III interferons'''<br/><span class="author">Czerkies&nbsp;M<sup>☯</sup></span>, <span class="author">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="author">Korwek&nbsp;Z</span>, <span class="author">Prus&nbsp;W</span>, <span class="author">Lipniacki&nbsp;T</span>.<br/> ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022)<br/>[https://pubmed.ncbi.nlm.nih.gov/36326278 PubMed] [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]
* '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by&nbsp;triggering secretion of type I and type III interferons'''<br/><span class="author">Czerkies&nbsp;M<sup>☯</sup></span>, <span class="author">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="author">Korwek&nbsp;Z</span>, <span class="author">Prus&nbsp;W</span>, <span class="author">Lipniacki&nbsp;T</span>.<br/> ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022)<br/>[https://pubmed.ncbi.nlm.nih.gov/36326278 PubMed] [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]

Latest revision as of 00:57, 26 November 2024

Ph.D.,   Assistant Professor
Marek's photo


Currently on leave to:
Dioscuri Centre for Physics and Chemistry of Bacteria
Institute of Physical Chemistry
Polish Academy of Sciences
Kasprzaka 44/52, 01-224 Warsaw, Poland



Publications


Systems biology, cell signaling

  • Type III interferons suppress influenza A virus infection independently of STAT activation by triggering cell death
    Prus W, Grabowski F, Koza P, Korwek Z, Czerkies M, Kochańczyk M, Lipniacki T.
    (submitted) bioRxiv
  • Information transmission in a cell monolayer: A numerical study
    Nałęcz-Jawecki P, Szyc P, Grabowski F, Kochańczyk M, Lipniacki T.
    (submitted)
    bioRxiv
  • 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, Gagliardi PA, Kochańczyk M, Dessauges C, Pertz O, 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
    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


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
    Czerkies M, Kochańczyk M, Korwek Z, Prus W, Lipniacki T.
    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
    Grabowski F, Preibisch G, Giziński S, Kochańczyk M☯,@, Lipniacki T@
    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
    Kochańczyk M@, Lipniacki T
    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
    Kochańczyk M, Grabowski F, Lipniacki T
    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
    Kochańczyk M, Grabowski F, Lipniacki T
    Mathematical Modelling of Natural Phenomena 15:28 (2020)
    CrossRef | PDF SuppCode


Chemical physics, 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