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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:

Komorowski M, Tawfik DS. The limited information capacity of cross-reactive sensors drives the evolutionary expansion of signaling, Cell Syst 8(1):76–85.e6 (2019) PubMed CrossRef

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, Nature Communications 9:4591 (2018) PubMed 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

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 28(10):2001–2067 (2018) CrossRef

More publications...

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

@@ Line 42: / Line 42: @@
 ====Recent publications of our Lab:====
+* <span class="pmbm">Komorowski M</span>, <span class="nopmbm">Tawfik DS</span>. '''The limited information capacity of cross-reactive sensors drives the evolutionary expansion of signaling''', ''Cell Syst'' <u>8</u>(1):76–85.e6 (2019) [https://www.ncbi.nlm.nih.gov/pubmed/30660612 PubMed] [http://doi.org/10.1016/j.cels.2018.12.006 CrossRef]
 * <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]
@@ Line 48: / Line 50: @@
 * <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&nbsp;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]
-* <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''<span style="font-variant:small-caps">Spatkin</span>: a simulator for rule-based modeling of biomolecular site dynamics on surfaces''', ''Bioinformatics'' (2017) <u>33</u>(22):3667–3669 [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 class="pmbm">Pierini F</span>, <span class="nopmbm">Lanzi M</span>, <span class="pmbm">Nakielski P</span>, <span class="pmbm">Pawłowska S</span>, <span class="nopmbm">Urbanek O</span>, <span class="pmbm">Zembrzycki K</span>, <span class="pmbm">Kowalewski TA</span>. '''Single-material organic solar cells based on electrospun fullerene-grafted polythiophene nanofibers''', ''Macromolecules'' <u>50</u>(13):4972–81 (2017) [http://dx.doi.org/10.1021/acs.macromol.7b00857 CrossRef]