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Latest revision as of 11:03, 19 December 2023

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
phone: +48 22 8261281 ext. 409
room: 325

Recent publications of our Lab (selected highlights):

Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response
Korwek Z, Czerkies M, Jaruszewicz-Błońska J, Prus W, Kosiuk I, Kochańczyk M, Lipniacki T
Science Signaling 16(815):eabq1173 (2023) PubMed CrossRef | FullText bioRxiv

Antagonism between viral infection and innate immunity at the single-cell level
Grabowski F, Kochańczyk M, Korwek Z, Czerkies M, Prus W, Lipniacki T
PLOS Pathogens 19(9):e1011597 (2023) PubMed CrossRef | bioRxiv Code Data

Concentration on demand – a microfluidic system for precise adjustment of the content of single droplets
Zaremba D, Błoński S, Korczyk PM
Chemical Engineering Journal 430(3):132935 (2022) CrossRef | PDF

Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants
Koehler M, Ray A, Moreira RA, Juniku B, Poma AB, Alsteens D
Nature Communications 12(1):6977 (2021) CrossRef | PDF

Direction of epithelial folding defines impact of mechanical forces on epithelial state,
Błoński S, J Aureille, S Badawi, D Zaremba, L Pernet, A Grichine, S Fraboulet, PM Korczyk, P Recho, Ch Guilluy, ME Dolega
Developmental Cell 56:3222–3234 (2021) CrossRef

Fractional response analysis reveals logarithmic cytokine responses in cellular populations
Nienałtowski K, Rigby RE, Walczak J, Zakrzewska KE, Rehwinkel J, Komorowski M
Nature Communications 12:4175 (2021) CrossRef | PDF

Super-spreading events initiated the exponential growth phase of COVID-19 with R₀ higher than initially estimated
Kochańczyk M, Grabowski F, Lipniacki T
Royal Society Open Science 7:200786 (2020) CrossRef | PDF SuppInfo-PDF Correspondence

Quantitative determination of mechanical stability in the novel coronavirus spike protein
Moreira RA, Chwastyk M, Baker JL, Guzman HV, Poma AB
Nanoscale 12:16409 (2020) CrossRef

Multifunctional platform based on electrospun nanofibers and plasmonic hydrogel: A smart nanostructured pillow for near-infrared light-driven biomedical applications
Nakielski P, Pawłowska S, Rinoldi C, Ziai Y, De Sio L, Urbanek O, Zembrzycki K, Pruchniewski M, Lanzi M, Salatelli E, Calogero A, Kowalewski TA, Yarin AL, Pierini F
ACS Applied Materials & Interfaces 12(49):54328–5434 (2020) CrossRef | PDF

Ultraviolet light-assisted electrospinning of core–shell fully cross-linked P(NIPAAm-co-NIPMAAm) hydrogel-based nanofibers for thermally-induced drug delivery self-regulation
Pawłowska S, Rinoldi C, Nakielski P, Ziai Y, Urbanek O, Li X, Kowalewski TA, Ding B, Pierini F
Advanced Materials Interfaces 2000247 (2020) CrossRef | SuppInfo-PDF SuppMovie-MP4 CoverPicture

Accounting for corner flow unifies the understanding of droplet formation
in microfluidic channels
Korczyk PM, van Steijn V, Blonski S, Zaremba D, Beattie DA, Garstecki P
Nature Communications 10:2528 (2019) CrossRef | PDF SuppInfo-PDF

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

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

An information-theoretic framework for deciphering pleiotropic and noisy
biochemical signaling
Jetka T, Nienałtowski K, Filippi S, Stumpf MPH, Komorowski M
Nature Communications 9:4591 (2018) PubMed CrossRef | PDF SuppInfo-PDF

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

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

→ All 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 (selected highlights):<br style="line-height: 10%; margin-bottom:5px"/>====
+*'''Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response'''<br/><span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Jaruszewicz-Błońska&nbsp;J</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Kosiuk&nbsp;I</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/>  ''Science&nbsp;Signaling'' <u>16</u>(815):eabq1173 (2023) [https://pubmed.ncbi.nlm.nih.gov/38085817 PubMed] [https://doi.org/10.1126/scisignal.abq1173 CrossRef] | [{{SERVER}}/publications/Korwek-2023-SciSignal.pdf FullText] [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:16px">
+* '''Antagonism between viral infection and innate immunity at the single-cell level'''<br/><span class="pmbm">Grabowski&nbsp;F</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Lipniacki&nbsp;T</span><br/>''PLOS&nbsp;Pathogens'' <u>19</u>(9):e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef] | [https://doi.org/10.1101/2022.11.18.517110 bioRxiv] [https://github.com/grfrederic/visavis Code] [https://doi.org/10.5281/zenodo.7428925 Data]<br style="line-height: 100%; margin-bottom:16px">
 * '''Concentration on demand – a microfluidic system for precise adjustment of the content of single droplets'''<br/><span class="pmbm">Zaremba&nbsp;D</span>, <span class="pmbm">Błoński&nbsp;S</span>, <span class="pmbm">Korczyk&nbsp;PM</span><br/> ''Chemical Engineering Journal'' <u>430</u>(3):132935 (2022) [https://doi.org/10.1016/j.cej.2021.132935 CrossRef] | [https://www.sciencedirect.com/science/article/pii/S1385894721045113/pdfft?md5=da0fd906b3e86fba9f62b68f21d8230f&pid=1-s2.0-S1385894721045113-main.pdf PDF]<br style="line-height: 100%; margin-bottom:16px">
-* '''Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants'''<br/><span class="nopmbm">M&nbsp;Koehler</span>, <span class="nopmbm">A&nbsp;Ray</span>, <span class="pmbm">RA&nbsp;Moreira</span>, <span class="nopmbm">B&nbsp;Juniku</span>, <span class="pmbm">AB&nbsp;Poma</span>, <span class="nopmbm">D&nbsp;Alsteens </span><br/>''Nature Communications'' <u>12</u>(1):6977 (2021) [http://dx.doi.org/10.1038/s41467-021-27325-1 CrossRef] | [https://www.nature.com/articles/s41467-021-27325-1.pdf PDF]
+* '''Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants'''<br/><span class="nopmbm">Koehler&nbsp;M</span>, <span class="nopmbm">Ray&nbsp;A</span>, <span class="pmbm">Moreira&nbsp;RA</span>, <span class="nopmbm">Juniku&nbsp;B</span>, <span class="pmbm">Poma&nbsp;AB</span>, <span class="nopmbm">Alsteens&nbsp;D</span><br/>''Nature Communications'' <u>12</u>(1):6977 (2021) [http://dx.doi.org/10.1038/s41467-021-27325-1 CrossRef] | [https://www.nature.com/articles/s41467-021-27325-1.pdf PDF]<br style="line-height: 100%; margin-bottom:16px">
 * '''Direction of epithelial folding defines impact of mechanical forces on epithelial state''',<br/><span class="pmbm">Błoński&nbsp;S</span>, <span class="nopmbm">J&nbsp;Aureille</span>, <span class="nopmbm">S&nbsp;Badawi</span>, <span class="pmbm">D&nbsp;Zaremba</span>, <span class="nopmbm">L&nbsp;Pernet</span>, <span class="nopmbm">A&nbsp;Grichine</span>, <span class="nopmbm">S&nbsp;Fraboulet</span>, <span class="pmbm">PM&nbsp;Korczyk</span>, <span class="nopmbm">P&nbsp;Recho</span>, <span class="nopmbm">Ch&nbsp;Guilluy</span>, <span class="nopmbm">ME&nbsp;Dolega</span><br/>''Developmental Cell'' <u>56</u>:3222–3234 (2021) [https://doi.org/10.1016/j.devcel.2021.11.008 CrossRef]<br style="line-height: 100%; margin-bottom:16px">
@@ Line 71: / Line 75: @@
 * '''Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis'''<span class="nopmbm"><br style="line-height: 50%; margin-bottom:10px"/>Adimy M</span>, <span class="nopmbm">Chekroun A</span>, <span class="pmbm">Kaźmierczak B</span><br style="line-height: 50%; margin-bottom:10px"/>''Journal of Differential Equations'' <u>262</u>(7):4085–4128 (2017) [http://dx.doi.org/10.1016/j.jde.2016.12.009 CrossRef]<br style="line-height: 100%; margin-bottom:16px">
-* '''The propagation phenomenon of solutions of a parabolic problem on the sphere'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Kazmierczak B</span>, <span class="nopmbm">Tsai J-C</span>, <span class="pmbm">Bialecki S</span><br style="line-height: 50%; margin-bottom:10px"/>''Mathematical Models and Methods in Applied Sciences'' <u>28</u>(10):2001–2067 (2018) [http://doi.org/10.1142/S0218202518500483 CrossRef]
+<!--* '''The propagation phenomenon of solutions of a parabolic problem on the sphere'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Kazmierczak B</span>, <span class="nopmbm">Tsai J-C</span>, <span class="pmbm">Bialecki S</span><br style="line-height: 50%; margin-bottom:10px"/>''Mathematical Models and Methods in Applied Sciences'' <u>28</u>(10):2001–2067 (2018) [http://doi.org/10.1142/S0218202518500483 CrossRef]
-<br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Publications | &rarr; All publications]]
+<br/>-->&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Publications | &rarr; All publications]]
 <br/>
 To learn more on our research, you may read [http://pmbm.ippt.pan.pl/publications/chapters/Kochanczyk_i_inni_2018_rozdzial_22.pdf our perspective on regulatory pathway modeling (a&nbsp;book chapter in Polish)].
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