Marek Kochańczyk: Difference between revisions

Revision as of 21:46, 23 September 2020

Ph.D., Assistant Professor

Contact

e-mail at ippt.pan.pl or ucdavis.edu: 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

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

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

Epidemiology and public health

Evaluation of national responses to COVID-19 pandemic based on Pareto optimality
Kochańczyk M, Lipniacki T
(submitted) MedRxiv CrossRef | PDF GitHub

Accounting for super-spreading gives the basic reproduction number R₀ of COVID-19 that is higher than initially estimated
Kochańczyk M, Grabowski F, Lipniacki T
Royal Society Open Science (2020)
CrossRef | PDF SuppInfo

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

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 67: / Line 67: @@
 * '''Evaluation of national responses to COVID-19 pandemic based on Pareto optimality'''<br/><span class="author">Kochańczyk M</span>, <span class="author">Lipniacki T</span><br/>(''submitted'') &nbsp;[https://www.medrxiv.org/content/10.1101/2020.06.27.20141747v1 MedRxiv]  [https://dx.doi.org/10.1101/2020.06.27.20141747 CrossRef] | [https://www.medrxiv.org/content/10.1101/2020.06.27.20141747v1.full.pdf PDF] [https://github.com/kochanczyk/covid19-pareto GitHub]
-* '''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/>''Royal Society Open Science'' (accepted)<br/>[https://www.medrxiv.org/content/10.1101/2020.04.26.20080788v1 MedRxiv] [https://doi.org/10.1101/2020.04.26.20080788 CrossRef] | [https://www.medrxiv.org/content/10.1101/2020.04.26.20080788v2.full.pdf PDF]
+* '''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/>''Royal Society Open Science'' (2020)<br/> [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]
 * '''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]