Marek Kochańczyk: Difference between revisions

Revision as of 20:23, 1 February 2019

Ph.D., Assistant Professor

Contact

e-mail at ippt.pan.pl: mkochan

Institute of Fundamental Technological Research
Polish Academy of Sciences
Pawińskiego 5B, 02-106 Warsaw, Poland

Currently on leave to:
Dept. of Molecular and Cellular Biology
University of California, Davis
Briggs Hall, 550 Storer Mall, Davis, CA 95616

Publications

Systems biology

Limits to the rate of information transmission through MAPK pathway
Grabowski F, Czyż P, Kochańczyk M, Lipniacki T
(submitted)
bioRxiv Www

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

Chemical physics and 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

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 ====Systems biology====
-* '''Limits to the rate of information transmission through MAPK pathway'''<br/><span class="nopmbm">Grabowski F</span>, <span class="nopmbm">Czyż P</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span><br/> (''submitted'')<br/>[http://www.biorxiv.org/content/early/2018/08/28/402750 bioRxiv] [http://pmbm.ippt.pan.pl/software/cce/ Www]
+* '''Limits to the rate of information transmission through MAPK pathway'''<br/><span class="author">Grabowski F</span>, <span class="author">Czyż P</span>, <span class="author">Kochańczyk M</span>, <span class="author">Lipniacki T</span><br/> (''submitted'')<br/>[http://www.biorxiv.org/content/early/2018/08/28/402750 bioRxiv] [http://pmbm.ippt.pan.pl/software/cce/ Www]
-* '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways'''<br/><span class="pmbm">Czerkies M<sup>☯</sup></span>, <span class="pmbm">Korwek Z<sup>☯</sup></span>, <span class="pmbm">Prus W<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Jaruszewicz-Błońska&nbsp;J</span>, <span class="pmbm">Tudelska&nbsp;K</span>, <span class="pmbm">Błoński&nbsp;S</span>, <span class="nopmbm">Kimmel M</span>, <span class="nopmbm">Brasier AR</span>, <span class="pmbm">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]
+* '''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]
-* '''Information processing in the NF-κB pathway'''<br/><span class="pmbm">Tudelska K<sup>☯</sup></span>, <span class="pmbm">Markiewicz J<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="nopmbm">Abdi&nbsp;A</span>, <span class="pmbm">Błoński&nbsp;S</span>, <span class="pmbm">Kaźmierczak B</span>, <span class="pmbm">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]
+* '''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]
-* '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and&nbsp;ROKα'''<br/><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&nbsp;M</span>, <span class="pmbm">Lipniacki&nbsp;T</span>, <span class="nopmbm">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]
+* '''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]
-* '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling'''<br/><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&nbsp;JG</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</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]
+* '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling'''<br/><span class="author">Kochańczyk M</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</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-&kappa;B oscillations increasing information channel capacity'''<br/><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><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]
+* '''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]
-* '''Feedbacks, bifurcations, and cell fate decision-making in the p53 system'''<br/><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><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]
+* '''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="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><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]
+* '''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="pmbm">Bogdał MN</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">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]
+* '''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="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><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]
+*  '''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====
-* '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping'''<br/><span class="nopmbm">Zuk PJ<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">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]
+* '''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="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><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 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]
-* '''Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles'''<br/><span class="pmbm">Szymańska P<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="nopmbm">Miękisz J</span>, <span class="pmbm">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]
+* '''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&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="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz J</span>, <span class="pmbm">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]
+* '''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="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><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]
+* '''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====
-* '''Prediction of functionally important residues in globular proteins from unusual central distances of amino acids'''<br/><span class="pmbm">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]
+* '''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]
-* '''In silico structural study of random amino acid sequence proteins not present in nature'''<br/><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><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]
+* '''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]
-* '''Prediction of functional sites based on the fuzzy oil drop model'''<br/><span class="nopmbm">Bryliński M</span>, <span class="nopmbm">Prymula K</span>, <span class="nopmbm">Jurkowski W</span>, <span class="nopmbm">Kochańczyk&nbsp;M</span>, <span class="nopmbm">Stawowczyk&nbsp;E</span>, <span class="nopmbm">Konieczny&nbsp;L</span>, <span class="nopmbm">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]
+* '''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]
-* '''Localization of ligand binding site in proteins identified in silico'''<br/><span class="nopmbm">Bryliński M</span>, <span class="nopmbm">Kochańczyk M</span>, <span class="nopmbm">Broniatowska E</span>, <span class="nopmbm">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]
+* '''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)<br/>[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>-->
 <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="pmbm">Kochańczyk M</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">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">Spatkin</span>: a simulator for rule-based modeling of biomolecular site dynamics on surfaces'''<br/><span class="author">Kochańczyk M</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]