Marek Kochańczyk: Difference between revisions

Revision as of 12:13, 28 August 2017

Research Assistant, Ph.D. Candidate

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

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 6:38244 (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

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 (accepted) CrossRef Www

@@ Line 18: / Line 18: @@
 * <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&nbsp;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]
-* <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]
+* <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>. '''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]
 * <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]