Marek Kochańczyk: Difference between revisions
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<div align="center">''' | <div align="center">'''Ph.D., Assistant Professor'''</div> | ||
[[Image:Marek_Kochanczyk.jpg|right| | [[Image:Marek_Kochanczyk.jpg|180px|right|frameless|link=|alt=Marek's photo]] | ||
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===Contact=== | ===Contact=== | ||
e-mail at ippt.pan.pl: mkochan<br /> | e-mail at ippt.pan.pl: mkochan<br /> | ||
tel.: +48 22 8261280 ext. 161<br /> | tel.: +48 22 8261280 ext. 161<br /> | ||
room: 311<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 /> | |||
Dept. of Molecular and Cellular Biology<br /> | |||
University of California, Davis<br /> | |||
Briggs Hall, 550 Storer Mall, Davis, CA 95616<br />--> | |||
<br /><br /> | |||
===Publications=== | ===Publications=== | ||
<br /> | <br /> | ||
====Systems biology==== | ====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 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] | |||
* '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways'''<br/><span class="author">Czerkies M<sup>☯</sup></span>, <span class="author">Korwek Z<sup>☯</sup></span>, <span class="author">Prus W<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Jaruszewicz-Błońska J</span>, <span class="author">Tudelska K</span>, <span class="author">Błoński S</span>, <span class="author">Kimmel M</span>, <span class="author">Brasier AR</span>, <span class="author">Lipniacki T</span><br/>''Nature Communications'' <u>9</u>:493 (2018)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Czerkies-2018-NatCommun.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllSuppData.zip SuppData] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllMovies.zip SuppMovies] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-ModelCode.zip SuppCode] | |||
* '''Information processing in the NF-κB pathway'''<br/><span class="author">Tudelska K<sup>☯</sup></span>, <span class="author">Markiewicz J<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Czerkies M</span>, <span class="author">Prus W</span>, <span class="author">Korwek Z</span>, <span class="author">Abdi A</span>, <span class="author">Błoński S</span>, <span class="author">Kaźmierczak B</span>, <span class="author">Lipniacki T</span><br/>''Scientific Reports'' <u>7</u>:15926 (2017)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef] | [http://www.nature.com/articles/s41598-017-16166-y.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset1.zip SuppCode-BNGL] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset2.zip SuppCode-Py] | |||
* '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα'''<br/><span class="author">Varga A</span>, <span class="author">Ehrenreiter K</span>, <span class="author">Aschenbrenner B</span>, <span class="author">Kocieniewski P</span>, <span class="author">Kochanczyk M</span>, <span class="author">Lipniacki T</span>, <span class="author">Baccarini M</span><br/>''Science Signaling'' <u>10</u>(469):eaai8482 (2017)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/28270557 PubMed] [http://dx.doi.org/10.1126/scisignal.aai8482 CrossRef] | [http://pmbm.ippt.pan.pl/publications/supplementary/Varga-2017-SciSignal-SuppCode.bngl SuppCode-BioNetGen] | |||
* '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling'''<br/><span class="author">Kochańczyk M<sup>@</sup></span>, <span class="author">Kocieniewski P</span>, <span class="author">Kozłowska E</span>, <span class="author">Jaruszewicz-Błońska J</span>, <span class="author">Sparta B</span>, <span class="author">Pargett M</span>, <span class="author">Albeck JG</span>, <span class="author">Hlavacek WS</span>, <span class="author">Lipniacki T<sup>@</sup></span><br/>''Scientific Reports'' <u>7</u>:38244 (2017)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/28045041 PubMed] [http://dx.doi.org/10.1038/srep38244 CrossRef] | [http://www.nature.com/articles/srep38244.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeBionetgen-UPDATED.zip SuppCode-BNG] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeMatlabMatcont.zip SuppCode-MatCont] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeBionetgenNoisyEGFR.zip SuppCode-BNG-noisy] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeComsol.zip SuppCode-Comsol] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2017-SciRep-Movie.mp4 SuppMovie] | |||
* '''Importins promote high-frequency NF-κB oscillations increasing information channel capacity'''<br/><span class="author">Korwek Z</span>, <span class="author">Tudelska K</span>, <span class="author">Nałęcz-Jawecki P</span>, <span class="author">Czerkies M</span>, <span class="author">Prus W</span>, <span class="author">Markiewicz J</span>, <span class="author">Kochańczyk M</span>, <span class="author">Lipniacki T</span><br/>''Biology Direct'' <u>11</u>:61 (2016)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/27835978 PubMed] [http://dx.doi.org/10.1186/s13062-016-0164-z CrossRef] | [http://pmbm.ippt.pan.pl/publications/Korwek-2016-BiolDirect.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Korwek-2016-BiolDirect-Fig1d-HiRes.pdf Scheme-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Korwek-2016-BiolDirect-AddFile1-ModelDescription.pdf SuppModelInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Korwek-2016-BiolDirect-AddFile2-NFkBImportinsModel.bngl SuppModelCode-BNGL] [http://pmbm.ippt.pan.pl/publications/supplementary/Korwek-2016-BiolDirect-AddFile3-SuppFigs-S1-to-S7.pdf SuppFigs-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Korwek-2016-BiolDirect-AddFiles4567-SuppImages.zip SuppImages-ZIP] | |||
* '''Feedbacks, bifurcations, and cell fate decision-making in the p53 system'''<br/><span class="author">Hat B<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Bogdał M</span>, <span class="author">Lipniacki T</span><br/>''PLOS Computational Biology'' <u>12</u>(2):e1004787 (2016)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/26928575 PubMed] [http://dx.doi.org/10.1371/journal.pcbi.1004787 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Hat-2016-PLOSComputBiol.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Hat-2016-PLOSComputBiol-SuppText.pdf SuppText] [http://pmbm.ippt.pan.pl/publications/supplementary/Hat-2016-PLOSComputBiol-SuppFigures.zip SuppFigs] [http://pmbm.ippt.pan.pl/publications/supplementary/Hat-2016-PLOSComputBiol-SuppCode.zip SuppCode] | |||
* '''A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells'''<br/><span class="author">Cheng FHC</span>, <span class="author">Aguda BD</span>, <span class="author">Tsai J-C</span>, <span class="author">Kochańczyk M</span>, <span class="author">Lin JMJ</span>, <span class="author">Chen GCW</span>, <span class="author">Lai H-C</span>, <span class="author">Nephew KP</span>, <span class="author">Hwang T-W</span>, <span class="author">Chan MWY</span><br/>''PLOS One'' <u>9</u>(12):e116050 (2014)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/25545504 PubMed] [http://dx.doi.org/10.1371/journal.pone.0116050 CrossRef] | [http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0116050&representation=PDF PDF] | |||
* '''Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate'''<br/><span class="author">Bogdał MN</span>, <span class="author">Hat B</span>, <span class="author">Kochańczyk M</span>, <span class="author">Lipniacki T</span><br/>''BMC Systems Biology'' <u>7</u>:67 (2013)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/23883471 PubMed] [http://dx.doi.org/10.1186/1752-0509-7-67 CrossRef] | [http://www.biomedcentral.com/content/pdf/1752-0509-7-67.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Bogdal-2013-BMCSystBiol-SourceCode.zip Code-Matlab] | |||
* '''Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis'''<br/><span class="author">Pękalski J</span>, <span class="author">Zuk PJ</span>, <span class="author">Kochańczyk M</span>, <span class="author">Junkin M</span>, <span class="author">Kellog R</span>, <span class="author">Tay S</span>, <span class="author">Lipniacki T</span><br/>''PLOS One'' <u>8</u>(11):e78887 (2013)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/24324544 PubMed] [http://dx.doi.org/10.1371/journal.pone.0078887 CrossRef] | [http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0078887&representation=PDF PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Pekalski-2013-PLOSOne-SuppText-S1.pdf Supp-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S1.zip Code-Matlab] [http://pmbm.ippt.pan.pl/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S2.zip Code-BioNetGen] [http://pmbm.ippt.pan.pl/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S3.zip Code-MatCont] | |||
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* <span class=" | ====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/>''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] | ||
* | * '''The spread of SARS-CoV-2 variant Omicron with the doubling time of 2.0–3.3 days can be explained by immune evasion'''<br/><span class="pmbm">Grabowski F</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>.<br/>''Viruses'' <u>14</u>(2):294 (2022)<br/>[https://pubmed.ncbi.nlm.nih.gov/35215887 PubMed] [https://doi.org/10.3390/v14020294 CrossRef] [https://dx.doi.org/10.1101/2021.12.08.21267494 medRxiv] | [https://www.mdpi.com/1999-4915/14/2/294/pdf PDF] [https://susy.mdpi.com/user/review/displayFile/23340271/tDGR6nk0?file=author-coverletter&report=16624478 Correspondence] | ||
* <span class=" | * '''SARS-CoV-2 Variant of Concern 202012/01 has about twofold replicative advantage and acquires concerning mutations'''<br/><span class="author">Grabowski F<sup>☯</sup></span>, <span class="author">Preibisch G</span>, <span class="author">Giziński S</span>, <span class="author">Kochańczyk M<sup>☯,@</sup></span>, <span class="author">Lipniacki T<sup>@</sup></span><br/>''Viruses'' <u>13</u>(3):392 (2021)<br/>[https://pubmed.ncbi.nlm.nih.gov/33804556 PubMed] [https://doi.org/10.3390/v13030392 CrossRef] [https://doi.org/10.1101/2020.12.28.20248906 medRxiv] | [https://www.mdpi.com/1999-4915/13/3/392/pdf PDF] [https://www.mdpi.com/1999-4915/13/3/392/s1 SuppInfo-ZIP] [https://www.mdpi.com/1999-4915/13/3/392/review_report Correspondence] | ||
* | * '''Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives'''<br/><span class="author">Kochańczyk M<sup>@</sup></span>, <span class="author">Lipniacki T</span><br/>''Scientific Reports'' <u>11</u>:2425 (2021)<br/>[https://pubmed.ncbi.nlm.nih.gov/33510274 PubMed] [https://doi.org/10.1038/s41598-021-81869-2 CrossRef] [https://www.medrxiv.org/content/10.1101/2020.06.27.20141747v2 medRxiv] | [https://www.nature.com/articles/s41598-021-81869-2.pdf PDF] [https://github.com/kochanczyk/covid19-pareto GitHub] | ||
* < | * '''Super-spreading events initiated the exponential growth phase of COVID-19 with <i>R</i><sub>0</sub> higher than initially estimated'''<br/><span class="author">Kochańczyk M</span>, <span class="author">Grabowski F</span>, <span class="author">Lipniacki T</span><br/>''Royal Society Open Science'' <u>7</u>:200786 (2020)<br/> [https://pubmed.ncbi.nlm.nih.gov/33047040 PubMed] [https://doi.org/10.1098/rsos.200786 CrossRef] | [https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.200786 PDF] [https://royalsocietypublishing.org/doi/suppl/10.1098/rsos.200786 SuppInfo-PDF] [https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098/rsos.200786&file=rsos200786_review_history.pdf Correspondence] | ||
* < | * '''Dynamics of COVID-19 pandemic at constant and time-dependent contact rates'''<br/><span class="author">Kochańczyk M</span>, <span class="author">Grabowski F</span>, <span class="author">Lipniacki T</span><br/>''Mathematical Modelling of Natural Phenomena'' <u>15</u>:28 (2020)<br/>[https://doi.org/10.1051/mmnp/2020011 CrossRef] | [https://www.mmnp-journal.org/articles/mmnp/pdf/forth/mmnp200048.pdf PDF] [http://pmbm.ippt.pan.pl/model/covid19/covid19_model.nb SuppCode] | ||
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* <span class="pmbm">Nałęcz-Jawecki P</span>, <span class=" | ====Chemical physics, biophysics==== | ||
* '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping'''<br/><span class="author">Zuk PJ<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Lipniacki T</span><br/>''Physical Review E'' <u>98</u>:022401 (2018)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/30253540 PubMed] [http://doi.org/10.1103/PhysRevE.98.022401 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Zuk-2018-PhysRevE-MS.pdf PDF-ms] [http://pmbm.ippt.pan.pl/software/looping Www] | |||
* '''Effective reaction rates for diffusion-limited reaction cycles'''<br/><span class="author">Nałęcz-Jawecki P</span>, <span class="author">Szymańska P</span>, <span class="author">Kochańczyk M</span>, <span class="author">Miękisz J</span>, <span class="author">Lipniacki T</span><br/>''Journal of Chemical Physics'' <u>143</u>(21):215102 (2015)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/26646890 PubMed] [http://dx.doi.org/10.1063/1.4936131 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Nalecz-Jawecki-2015-JChemPhys-MS.pdf PDF-ms] | |||
* <span class=" | * '''Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles'''<br/><span class="author">Szymańska P<sup>☯</sup></span>, <span class="author">Kochańczyk M<sup>☯</sup></span>, <span class="author">Miękisz J</span>, <span class="author">Lipniacki T</span><br/>''Physical Review E'' <u>91</u>:022702 (2015)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/25768526 PubMed] [http://dx.doi.org/10.1103/PhysRevE.91.022702 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Szymanska-2015-PhysRevE-MS.pdf PDF-ms] | ||
* <span class=" | * '''Stochastic transitions in a bistable reaction system on the membrane'''<br/><span class="author">Kochańczyk M</span>, <span class="author">Jaruszewicz J</span>, <span class="author">Lipniacki T</span><br/>''Journal of the Royal Society Interface'' <u>10</u>(84):20130151 (2013)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/23635492 PubMed] [http://dx.doi.org/10.1098/rsif.2013.0151 CrossRef] | [http://rsif.royalsocietypublishing.org/content/10/84/20130151.full.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2013-JRSocInterface-Supp.pdf Supp-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2013-JRSocInterface-Movies.zip Supp-movies] | ||
* <span class=" | * '''Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process'''<br/><span class="author">Żuk PJ</span>, <span class="author">Kochańczyk M</span>, <span class="author">Jaruszewicz J</span>, <span class="author">Bednorz W</span>, <span class="author">Lipniacki T</span><br/>''Physical Biology'' <u>5</u>(9):055002 (2012)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/23011381 PubMed] [http://dx.doi.org/10.1088/1478-3975/9/5/055002 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Zuk-2012-PhysBiol-MS.pdf PDF-ms] | ||
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====Computational structural biology==== | ====Computational structural biology==== | ||
* | * '''Prediction of functionally important residues in globular proteins from unusual central distances of amino acids'''<br/><span class="author">Kochańczyk M</span><br/>''BMC Structural Biology'' <u>11</u>(1):34 (2011)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/21923943 PubMed] [http://dx.doi.org/10.1186/1472-6807-11-34 CrossRef] | [http://www.biomedcentral.com/content/pdf/1472-6807-11-34.pdf PDF] [http://pmbm.ippt.pan.pl/publications/Kochanczyk-2011-BMCStructBiol.pdf PDF+supp] [http://pmbm.ippt.pan.pl/publications/supplementary/Kochanczyk-2011-BMCStructBiol-SourceCode.tar.gz Code] [http://pmbm.ippt.pan.pl/services/surpresi/ Server] | ||
* <span class=" | * '''In silico structural study of random amino acid sequence proteins not present in nature'''<br/><span class="author">Prymula K</span>, <span class="author">Piwowar M</span>, <span class="author">Kochańczyk M</span>, <span class="author">Flis L</span>, <span class="author">Malawski M</span>, <span class="author">Szepieniec T</span>, <span class="author">Evangelista G</span>, <span class="author">Minervini G</span>, <span class="author">Polticelli F</span>, <span class="author">Wiśniowski Z</span>, <span class="author">Sałapa K</span>, <span class="author">Matczyńska E</span>, <span class="author">Roterman I</span><br/>''Chemistry & Biodiversity'' <u>6</u>(12):2311–2336 (2009)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/20020465 PubMed] [http://dx.doi.org/10.1002/cbdv.200800338 CrossRef] | ||
* <span class=" | * '''Prediction of functional sites based on the fuzzy oil drop model'''<br/><span class="author">Bryliński M</span>, <span class="author">Prymula K</span>, <span class="author">Jurkowski W</span>, <span class="author">Kochańczyk M</span>, <span class="author">Stawowczyk E</span>, <span class="author">Konieczny L</span>, <span class="author">Roterman I</span><br/>''PLoS Computational Biology'' <u>3</u>(5):e94 (2007)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/17530916 PubMed] [http://dx.doi.org/10.1371/journal.pcbi.0030094 CrossRef] | [http://www.ploscompbiol.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0030094&representation=PDF PDF] | ||
* <span class=" | * '''Localization of ligand binding site in proteins identified in silico'''<br/><span class="author">Bryliński M</span>, <span class="author">Kochańczyk M</span>, <span class="author">Broniatowska E</span>, <span class="author">Roterman I</span><br/> ''Journal of Molecular Modeling'' <u>13</u>(6–7):665–675 (2007)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/17394030 PubMed] [http://dx.doi.org/10.1007/s00894-007-0191-x CrossRef] | ||
<!--* <span style="display: inline"><span class=" | <!--* <span style="display: inline"><span class="author">Bryliński M</span>, <span class="author">Kochańczyk M</span>, <span class="author">Konieczny L</span>, <span class="author">Roterman I</span>. '''Sequence-structure-function relation characterized in silico''', ''In Silico Biology'' <u>6</u>(6):589–600 (2006)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/17518766 PubMed] | [http://www.bioinformatics.org/reveal Server] | ||
</span>--> | </span>--> | ||
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====Software tools==== | |||
* '''<span style="font-variant:small-caps">Spatkin</span>: a simulator for rule-based modeling of biomolecular site dynamics on surfaces'''<br/><span class="author">Kochańczyk M<sup>@</sup></span>, <span class="author">Hlavacek WS</span>, <span class="author">Lipniacki T</span> <br/>''Bioinformatics'' <u>33</u>(22):3667–3669 (2017)<br/>[http://www.ncbi.nlm.nih.gov/pubmed/29036531 PubMed] [http://doi.org/10.1093/bioinformatics/btx456 CrossRef] | [http://pmbm.ippt.pan.pl/software/spatkin Www] | |||
* '''<span style="font-variant:small-caps">ShuttleTracker</span>: a tool for analysing nucleocytoplasmic shuttling of fluorescent reporters'''<br/>(unpublished) [http://pmbm.ippt.pan.pl/software/shuttletracker Www] |
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