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=== | ===Contact=== | ||
e-mail at ippt.pan.pl | e-mail at ippt.pan.pl: mkochan<br /> | ||
tel.: +48 22 8261280 ext. 161 | tel.: +48 22 8261280 ext. 161<br /> | ||
room: 311<br /><br /> | room: 311<br /><br /> | ||
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==== | ||
* ''' | * '''Type III interferons suppress influenza A virus infection independently of STAT activation by triggering cell death'''<br/><span class="pmbm">Prus W</span>, <span class="pmbm">Grabowski F</span>, <span class="pmbm">Koza P</span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki 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 P</span>, <span class="author">Szyc P</span>, <span class="author">Grabowski F</span>, <span class="author">Kochańczyk M</span>, <span class="author">Lipniacki 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 Z<sup>☯</sup></span>, <span class="pmbm">Czerkies M<sup>☯</sup></span>, <span class="pmbm">Jaruszewicz-Błońska J<sup>☯</sup></span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Kosiuk I</span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Lipniacki 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 | * '''The MAPK/ERK channel capacity exceeds 6 bit/hour'''<br/><span class="pmbm">Nałęcz-Jawecki P</span>, <span class="author">Gagliardi PA</span>, <span class="pmbm">Kochańczyk M</span>, <span class="author">Dessauges C</span>, <span class="author">Pertz O</span>, <span class="pmbm">Lipniacki T</span><br/>''PLOS Computational 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 F<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Lipniacki T</span>.<br/>( | * '''Antagonism between viral infection and innate immunity at the single-cell level'''<br/><span class="pmbm">Grabowski F<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Lipniacki 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 triggering secretion of type I and type III interferons'''<br/><span class="author">Czerkies M<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Korwek Z</span>, <span class="author">Prus W</span>, <span class="author">Lipniacki 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 triggering secretion of type I and type III interferons'''<br/><span class="author">Czerkies M<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Korwek Z</span>, <span class="author">Prus W</span>, <span class="author">Lipniacki 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
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
, , , , .
(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, , 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
, , @,
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
, , , , , , , , ,
Nature Communications 9:493 (2018)
PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode
- Information processing in the NF-κB pathway
, , , , , , , , ,
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
, , , , , ,
Science Signaling 10(469):eaai8482 (2017)
PubMed CrossRef | SuppCode-BioNetGen
- 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
- 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
- Feedbacks, bifurcations, and cell fate decision-making in the p53 system
, , ,
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
, , , , , , , , ,
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
, , ,
BMC Systems Biology 7:67 (2013)
PubMed CrossRef | PDF Code-Matlab
- 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
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
, , , , .
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
, , , ,
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
,
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
, ,
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
, ,
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
, ,
Physical Review E 98:022401 (2018)
PubMed CrossRef | PDF-ms Www
- Effective reaction rates for diffusion-limited reaction cycles
, , , ,
Journal of Chemical Physics 143(21):215102 (2015)
PubMed CrossRef | PDF-ms
- Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles
, , ,
Physical Review E 91:022702 (2015)
PubMed CrossRef | PDF-ms
- 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
- 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
- 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
, , , , , , , , , , , ,
Chemistry & Biodiversity 6(12):2311–2336 (2009)
PubMed CrossRef
- Prediction of functional sites based on the fuzzy oil drop model
, , , , , ,
PLoS Computational Biology 3(5):e94 (2007)
PubMed CrossRef | PDF
- Localization of ligand binding site in proteins identified in silico
, , ,
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
, ,
Bioinformatics 33(22):3667–3669 (2017)
PubMed CrossRef | Www
- ShuttleTracker: a tool for analysing nucleocytoplasmic shuttling of fluorescent reporters
(unpublished) Www