Marek Kochańczyk: Difference between revisions

Latest revision as of 17:06, 14 September 2024

Ph.D., Assistant Professor

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

Relaxation oscillations and hierarchy of feedbacks in MAPK signaling
Kochańczyk M^@, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T^@
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
Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T
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
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

Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis
Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellog R, Tay S, Lipniacki T
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)
PubMed CrossRef | 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

@@ Line 3: / Line 3: @@
 ===Contact===
-e-mail at ippt.pan.pl or ucdavis.edu: &#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 <!--&nbsp;or&nbsp; +48 22 350 7270--><br />
 room: 311<br /><br />
@@ Line 17: / Line 17: @@
 ===Publications===
 <br />
-====Epidemiology====
+====Systems biology, cell signaling====
-* '''Accounting for super-spreading gives the basic reproduction number <i>R</i><sub>0</sub> of COVID-19 that&nbsp;is&nbsp;higher than initially estimated'''<br/><span class="author">Kochańczyk M</span>, <span class="author">Grabowski F</span>, <span class="author">Lipniacki T</span><br/>(submitted)<br/>[https://doi.org/10.1101/2020.04.26.20080788 CrossRef]
+* '''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]
-* '''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/>
-====Systems biology====
 * '''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 43: / Line 46: @@
 *  '''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/>
-====Chemical physics and biophysics====
+====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]
+* '''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]
+* '''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]
+<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]
@@ Line 69: / Line 89: @@
 </span>-->
 <br/>
 ====Software tools====