Marek Kochańczyk: Difference between revisions

Revision as of 11:51, 23 July 2018

Research Assistant

Contact

e-mail at ippt.pan.pl: mkochan
tel.: +48 22 8261280 ext. 161 or +48 22 350 7270
room: 311

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

Publications

Systems biology

Czerkies M^☯, Korwek Z^☯, Prus W^☯, Kochańczyk M^☯, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications 9:493 (2018) PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode

Tudelska K^☯, Markiewicz J^☯, Kochańczyk M^☯, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway, Scientific Reports 7:15926 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNGL SuppCode-Py

Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M. RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Science Signaling 10(469):eaai8482 (2017) PubMed CrossRef | SuppCode-BioNetGen

Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T. Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Scientific Reports 7:38244 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNG SuppCode-MatCont SuppCode-BNG-noisy SuppCode-Comsol SuppMovie

Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T. Importins promote high-frequency NF-κB oscillations increasing information channel capacity, Biology Direct 11:61 (2016) PubMed CrossRef | PDF Scheme-PDF SuppModelInfo-PDF SuppModelCode-BNGL SuppFigs-PDF SuppImages-ZIP

Hat B^☯, Kochańczyk M^☯, Bogdał M, Lipniacki T. Feedbacks, bifurcations, and cell fate decision-making in the p53 system, PLOS Computational Biology 12(2):e1004787 (2016) PubMed CrossRef | PDF SuppText SuppFigs SuppCode

Cheng FHC, Aguda BD, Tsai J-C, Kochańczyk M, Lin JMJ, Chen GCW, Lai H-C, Nephew KP, Hwang T-W, Chan MWY. A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells, PLOS One 9(12):e116050 (2014) PubMed CrossRef | PDF

Bogdał MN, Hat B, Kochańczyk M, Lipniacki T. Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate, BMC Systems Biology 7:67 (2013) PubMed CrossRef | PDF Code-Matlab

Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellog R, Tay S, Lipniacki T. Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis, PLOS One 8(11):e78887 (2013) PubMed CrossRef | PDF Supp-PDF Code-Matlab Code-BioNetGen Code-MatCont

Chemical physics and biophysics

Zuk PJ^☯, Kochańczyk M^☯, Lipniacki T. Sampling rare events in stochastic reaction–diffusion systems within trajectory looping', Phys Rev E (accepted) Www

Nałęcz-Jawecki P, Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T. Effective reaction rates for diffusion-limited reaction cycles, Journal of Chemical Physics 143(21):215102 (2015) PubMed CrossRef | PDF-ms

Szymańska P^☯, Kochańczyk M^☯, Miększ J, Lipniacki T. Effective reaction rates in diffusion-limited phosphorylation–dephosphorylation cycles, Physical Review E 91:022702 (2015) PubMed CrossRef | PDF-ms

Kochańczyk M, Jaruszewicz J, Lipniacki T. Stochastic transitions in a bistable reaction system on the membrane, Journal of the Royal Society Interface 10(84):20130151 (2013) PubMed CrossRef | PDF Supp-PDF Supp-movies

Żuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T. Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process, Physical Biology 5(9):055002 (2012) PubMed CrossRef | PDF-ms

Computational structural biology

Kochańczyk M. Prediction of functionally important residues in globular proteins from unusual central distances of amino acids, BMC Structural Biology 11(1):34 (2011) PubMed CrossRef | PDF PDF+supp Code Server

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. In silico structural study of random amino acid sequence proteins not present in nature, Chemistry & Biodiversity 6(12):2311–2336 (2009) PubMed CrossRef

Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I. Prediction of functional sites based on the fuzzy oil drop model, PLoS Computational Biology 3(5):e94 (2007) PubMed CrossRef | PDF

Bryliński M, Kochańczyk M, Broniatowska E, Roterman I. Localization of ligand binding site in proteins identified in silico, Journal of Molecular Modeling 13(6-7):665–675 (2007) PubMed CrossRef

Software tools

Kochańczyk M, Hlavacek WS, Lipniacki T. Spatkin: a simulator for rule-based modeling of biomolecular site dynamics on surfaces, Bioinformatics (2017) 33(22):3667–3669 PubMed CrossRef Www

@@ Line 36: / Line 36: @@
 ====Chemical physics and biophysics====
-* <span class="nopmbm">Zuk PJ<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction-diffusion systems within trajectory looping''', ''Physical Review&nbsp;E'' (accepted)
+* <span class="nopmbm">Zuk PJ<sup>☯</sup></span>, <span class="pmbm">Kochańczyk M<sup>☯</sup></span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping''', '''Phys Rev&nbsp;E'' (accepted) [http://pmbm.ippt.pan.pl/software/looping Www]
 * <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]
@@ Line 44: / Line 44: @@
 * <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]
-* <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]
+* <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]
 <br/>
 ====Computational structural biology====
@@ Line 50: / Line 50: @@
 * <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]
-* <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]
+* <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]
 * <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]
-* <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]
+* <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]
-<!--* <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="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>-->
 <br/>