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Laboratory of Modeling in Biology and Medicine

biophysics | systems biology | bioengineering

Head:
Prof. Tomasz Lipniacki — institutional www
e-mail: tlipnia@ippt.pan.pl or tomek@rice.edu
tel.: +48 22 8261281 ext. 409
room: 325

Recent publications of our Lab:

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

Jetka T, Nienałtowski K, Filippi S, Stumpf MPH, Komorowski M. An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling, Nat Commun 9:4591 (2018) CrossRef

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

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

Pierini F, Lanzi M, Nakielski P, Pawłowska S, Urbanek O, Zembrzycki K, Kowalewski TA. Single-material organic solar cells based on electrospun fullerene-grafted polythiophene nanofibers, Macromolecules 50(13):4972–81 (2017) CrossRef

Adimy M, Chekroun A, Kaźmierczak B. Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis, Journal of Differential Equations 262(7):4085–4128 (2017) CrossRef

Kazmierczak B, Tsai J-C, Bialecki S. The propagation phenomenon of solutions of a parabolic problem on the sphere, Math Model Meth Appl Sci (accepted) CrossRef

More publications...

To learn more on our research, you may read our perspective on regulatory pathway modeling (a book chapter in Polish).

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 * <span class="pmbm">Czerkies M</span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="pmbm">Tudelska K</span>, <span class="pmbm">Błoński S</span>, <span class="nopmbm">Kimmel M</span>, <span class="nopmbm">Brasier AR</span>, <span class="pmbm">Lipniacki T</span>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [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]
-* <span class="pmbm">Jetka T</span>, <span class="pmbm">Nienałtowski K</span>, <span class="nopmbm">Filippi S</span>, <span class="nopmbm">Stumpf MPH</span>, <span class="pmbm">Komorowski M</span>. '''An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling''', ''Nat Commun'' <u>9</u>: 4591 (2018) [http://dx.doi.org/10.1038/s41467-018-07085-1 CrossRef]
+* <span class="pmbm">Jetka T</span>, <span class="pmbm">Nienałtowski K</span>, <span class="nopmbm">Filippi S</span>, <span class="nopmbm">Stumpf MPH</span>, <span class="pmbm">Komorowski M</span>. '''An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling''', ''Nat Commun'' <u>9</u>:4591 (2018) [http://dx.doi.org/10.1038/s41467-018-07085-1 CrossRef]
 * <span class="pmbm">Tudelska K</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Korwek Z</span>, <span class="nopmbm">Abdi A</span>, <span class="pmbm">Błoński S</span>, <span class="pmbm">Kaźmierczak B</span>, <span class="pmbm">Lipniacki T</span>. '''Information processing in the NF-κB pathway''', ''Scientific&nbsp;Reports'' <u>7</u>:15926 (2017) [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]