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<div align="center">'''Research Assistant, Ph.D. Candidate'''</div>
<div align="center">'''Ph.D., &nbsp; Assistant Professor'''</div>
[[Image:Marek_Kochanczyk.jpg|right|frame|link=|alt=Marek's photo]]
[[Image:Marek_Kochanczyk.jpg|180px|right|frameless|link=|alt=Marek's photo]]


===Contact===
===Contact===
e-mail at ippt.pan.pl: &#109;&#107;&#111;&#99;&#104;&#97;&#110;<br />
e-mail at ippt.pan.pl<!-- or ucdavis.edu-->: &#109;&#107;&#111;&#99;&#104;&#97;&#110;<br />
tel.: +48 22 8261280 ext. 161<br />
tel.: +48 22 8261280 ext. 161 <!--&nbsp;or&nbsp; +48 22 350 7270--><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 />


 
<!--''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&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 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]
 
* '''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&nbsp;J</span>, <span class="author">Tudelska&nbsp;K</span>, <span class="author">Błoński&nbsp;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]


* <span class="nopmbm">Varga A</span>, <span class="nopmbm">Ehrenreiter K</span>, <span class="nopmbm">Aschenbrenner B</span>, <span class="pmbm">Kocieniewski P</span>, <span class="pmbm">Kochanczyk M</span>, <span class="pmbm">Lipniacki&nbsp;T</span>, <span class="nopmbm">Baccarini M</span>. '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and&nbsp;ROKα''', ''Science Signaling'' <u>10</u>(469):eaai8482 (2017) [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]
* '''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&nbsp;Z</span>, <span class="author">Abdi&nbsp;A</span>, <span class="author">Błoński&nbsp;S</span>, <span class="author">Kaźmierczak B</span>, <span class="author">Lipniacki T</span><br/>''Scientific&nbsp;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]


* <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Kocieniewski P</span>, <span class="nopmbm">Kozłowska E</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="nopmbm">Sparta B</span>, <span class="nopmbm">Pargett&nbsp;M</span>, <span class="nopmbm">Albeck JG</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling''', ''Scientific Reports'' <u>6</u>:38244 (2017) [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.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]
* '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and&nbsp;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&nbsp;M</span>, <span class="author">Lipniacki&nbsp;T</span>, <span class="author">Baccarini&nbsp;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]


* <span class="pmbm">Korwek Z</span>, <span class="pmbm">Tudelska K</span>, <span class="nopmbm">Nałęcz-Jawecki P</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Lipniacki T</span>. '''Importins promote high-frequency NF-&kappa;B oscillations increasing information channel capacity''', ''Biology Direct'' <u>11</u>:61 (2016) [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]
* '''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&nbsp;M</span>, <span class="author">Albeck&nbsp;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]


* <span class="pmbm">Hat B<sup></sup></span>, <span class="pmbm">Kochańczyk M<sup></sup></span>, <span class="pmbm">Bogdał M</span>, <span class="pmbm">Lipniacki T</span>. '''Feedbacks, bifurcations, and cell fate decision-making in the p53 system''', ''PLOS Computational Biology'' <u>12</u>(2):e1004787 (2016) [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]
* '''Importins promote high-frequency NF-&kappa;B 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&nbsp;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]


* <span class="nopmbm">Cheng FHC</span>, <span class="nopmbm">Aguda BD</span>, <span class="nopmbm">Tsai J-C</span>, <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Lin JMJ</span>, <span class="nopmbm">Chen GCW</span>, <span class="nopmbm">Lai H-C</span>, <span class="nopmbm">Nephew KP</span>, <span class="nopmbm">Hwang T-W</span>, <span class="nopmbm">Chan MWY</span>. '''A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells''', ''PLOS One'' <u>9</u>(12):e116050 (2014) [http://www.ncbi.nlm.nih.gov/pubmed/25545504 PubMed] [http://dx.doi.org/10.1371/journal.pone.0116050 CrossRef] |&nbsp;[http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0116050&representation=PDF PDF]
* '''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]


* <span class="pmbm">Bogdał MN</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate''', ''BMC Systems Biology'' <u>7</u>:67 (2013) [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]
* '''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]


* <span class="pmbm">Pękalski J</span>, <span class="pmbm">Zuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Junkin M</span>, <span class="nopmbm">Kellog R</span>, <span class="nopmbm">Tay S</span>, <span class="pmbm">Lipniacki T</span>. '''Spontaneous NF-κB activation by autocrine TNFα signaling: A&nbsp;computational analysis''', ''PLOS One'' <u>8</u>(11):e78887 (2013) [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]
* '''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&nbsp;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]
<br/>
<br/>
====Chemical physics and biophysics====


* <span class="pmbm">Nałęcz-Jawecki P</span>, <span class="pmbm">Szymańska P</span>, <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Miękisz J</span>, <span class="pmbm">Lipniacki T</span>. ''' Effective reaction rates for diffusion-limited reaction cycles''', ''Journal of Chemical Physics'' <u>143</u>(21):215102 (2015) [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]
====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/>''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]
 
* '''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&nbsp;F</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Lipniacki&nbsp;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="pmbm">Szymańska P<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup></sup></span>, <span class="nopmbm">Miększ J</span>, <span class="pmbm">Lipniacki T</span>. '''Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles''', ''Physical Review&nbsp;E'' <u>91</u>:022702 (2015) [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]
* '''SARS-CoV-2 Variant of Concern 202012/01 has about twofold replicative advantage and acquires concerning mutations'''<br/><span class="author">Grabowski&nbsp;F<sup>☯</sup></span>, <span class="author">Preibisch&nbsp;G</span>, <span class="author">Giziński&nbsp;S</span>, <span class="author">Kochańczyk&nbsp;M<sup>☯,@</sup></span>, <span class="author">Lipniacki&nbsp;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]


* <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz J</span>, <span class="pmbm">Lipniacki T</span>. '''Stochastic transitions in a bistable reaction system on the membrane''', ''Journal of the Royal Society Interface'' <u>10</u>(84):20130151 (2013) [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]
* '''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]


* <span class="pmbm">Żuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz J</span>, <span class="nopmbm">Bednorz W</span>, <span class="pmbm">Lipniacki T</span>. '''Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth-death process''', ''Physical Biology'' <u>5</u>(9):055002 (2012) [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]
* '''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]
<br/>
<br/>
====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&nbsp;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&nbsp;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]
* '''Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles'''<br/><span class="author">Szymańska P<sup>☯</sup></span>, <span class="author">Kochańczyk&nbsp;M<sup>☯</sup></span>, <span class="author">Miękisz J</span>, <span class="author">Lipniacki T</span><br/>''Physical Review&nbsp;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]
* '''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]
* '''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]
<br/>
====Computational structural biology====
====Computational structural biology====


* <span class="pmbm">Kochańczyk M</span>. '''Prediction of functionally important residues in globular proteins from unusual central distances of amino acids''', ''BMC Structural Biology'' <u>11</u>(1):34 (2011) [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]
* '''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="nopmbm">Prymula K</span>, <span class="nopmbm">Piwowar M</span>, <span class="nopmbm">Kochańczyk M</span>, <span class="nopmbm">Flis L</span>, <span class="nopmbm">Malawski M</span>, <span class="nopmbm">Szepieniec T</span>, <span class="nopmbm">Evangelista G</span>, <span class="nopmbm">Minervini G</span>, <span class="nopmbm">Polticelli F</span>, <span class="nopmbm">Wiśniowski Z</span>, <span class="nopmbm">Sałapa K</span>, <span class="nopmbm">Matczyńska E</span>, <span class="nopmbm">Roterman I</span>. '''In silico structural study of random amino acid sequence proteins not present in nature''', ''Chemistry &amp;&nbsp;Biodiversity'' <u>6</u>(12):2311-2336 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/20020465 PubMed] [http://dx.doi.org/10.1002/cbdv.200800338 CrossRef]
* '''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 &amp;&nbsp;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="nopmbm">Bryliński M</span>, <span class="nopmbm">Prymula K</span>, <span class="nopmbm">Jurkowski W</span>, <span class="nopmbm">Kochańczyk M</span>, <span class="nopmbm">Stawowczyk E</span>, <span class="nopmbm">Konieczny L</span>, <span class="nopmbm">Roterman I</span>. '''Prediction of functional sites based on the fuzzy oil drop model''', ''PLoS&nbsp;Computational Biology'' <u>3</u>(5):e94 (2007) [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]
* '''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&nbsp;M</span>, <span class="author">Stawowczyk&nbsp;E</span>, <span class="author">Konieczny&nbsp;L</span>, <span class="author">Roterman I</span><br/>''PLoS&nbsp;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="nopmbm">Bryliński M</span>, <span class="nopmbm">Kochańczyk M</span>, <span class="nopmbm">Broniatowska E</span>, <span class="nopmbm">Roterman I</span>. '''Localization of ligand binding site in proteins identified in silico''', ''Journal of Molecular Modeling'' <u>13</u>(6-7):665-675 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17394030 PubMed] [http://dx.doi.org/10.1007/s00894-007-0191-x CrossRef]
* '''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="nopmbm">Bryliński M</span>, <span class="nopmbm">Kochańczyk M</span>, <span class="nopmbm">Konieczny L</span>, <span class="nopmbm">Roterman I</span>. '''Sequence-structure-function relation characterized in silico''', ''In&nbsp;Silico Biology'' <u>6</u>(6):589-600 (2006) [http://www.ncbi.nlm.nih.gov/pubmed/17518766 PubMed] | [http://www.bioinformatics.org/reveal Server]
<!--* <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&nbsp;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>-->
<br/>
====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&nbsp;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 17:06, 14 September 2024

Ph.D.,   Assistant Professor
Marek's photo

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

  • 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