Marek Kochańczyk: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
mNo edit summary |
mNo edit summary |
||
Line 19: | Line 19: | ||
====Systems biology==== | ====Systems biology==== | ||
* '''Non-self RNA rewires IFNβ 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/> (submitted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv] | * '''Non-self RNA rewires IFNβ 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/> (submitted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv] | ||
* '''The rate of information transmission through the MAPK/ERK signaling pathway stimulated in a pulsatile manner'''<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/> (submitted) [https://doi.org/10.1101/2022.03.17.484713 CrossRef] | |||
* '''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] |
Revision as of 15:13, 20 March 2022
Ph.D., Assistant Professor
Contact
e-mail at ippt.pan.pl or ucdavis.edu: 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
- Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response
Korwek Z☯, Czerkies M☯, Jaruszewicz-Błońska J☯, Prus W, Kosiuk I, Kochańczyk M☯, Lipniacki T
(submitted) bioRxiv
- The rate of information transmission through the MAPK/ERK signaling pathway stimulated in a pulsatile manner
Nałęcz-Jawecki P, , Kochańczyk M, , , Lipniacki T
(submitted) CrossRef
- 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 and public health
RSV immunizes bystander cells to IAV infection using interferons β and λ
(submitted) bioRxiv , , , , .
- Grabowski F, Kochańczyk M, Lipniacki T.
The spread of SARS-CoV-2 variant Omicron with the doubling time of 2.0–3.3 days can be explained by immune evasion
Viruses 14(2):294 (2022) 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 and 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