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<br />[[Image:Group_photo_2013.jpg|780px|center|link=|alt=Photo by Marek Bukowicki, June 2013|(Nearly all) members of our laboratory in June 2013.]]<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">Members of our laboratory in June 2013.</div>
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== Laboratory of Modeling in Biology and Medicine ==
 
 
<span style="font-size:large;">
<span style="color: #444;">'''biophysics &nbsp;<span style="color: grey;"><!--🙵-->&middot;</span>&nbsp; systems biology &nbsp;<span style="color: grey;"><!--🙵-->&middot;</span>&nbsp; bioengineering'''</span>
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[[Image:Tomasz_Lipniacki.jpg|left|link=|alt=]]
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'''Head''':<br />
'''Head''':<br />
Prof. Tomasz Lipniacki  &#8212; [http://www.ippt.pan.pl/en/staff/tlipnia institutional www]
Prof. Tomasz Lipniacki  &#8212; [http://www.ippt.pan.pl/en/staff/tlipnia institutional www]
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e-mail: [mailto://tlipnia@ippt.pan.pl tlipnia@ippt.pan.pl] or [mailto://tomek@rice.edu tomek@rice.edu]<br />
e-mail: [mailto://tlipnia@ippt.pan.pl tlipnia@ippt.pan.pl] or [mailto://tomek@rice.edu tomek@rice.edu]<br />
tel.: +48 22 8261281 ext. 409<br />
phone: +48 22 8261281 ext. 409<br />
room: 325
room: 325
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'''Address''':<br />
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Institute of Fundamental Technological Research<br />
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Polish Academy of Sciences<br />
Pawińskiego 5B, 02-106 Warsaw, Poland<br />
[http://www.google.pl/maps/place/Instytut+Podstawowych+Problem%C3%B3w+Techniki+PAN/@52.2067717,20.9805232,809m/data=!3m2!1e3!4b1!4m2!3m1!1s0x471eccb6d3fd7141:0xe6962ade97a84a58?hl=pl View on the map]
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'''Secretary's office''':<br />
Institute of Fundamental Technological Research ([http://www.ippt.pan.pl/en IPPT])<br/>
Ms. Agnieszka Ponarska<br />
of the Polish Academy of Sciences (PAN) in Warsaw, Poland
e-mail: [mailto://aponar@ippt.pan.pl aponar@ippt.pan.pl]<br />
tel.: +48 22 8269803 or<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;+48 22 8261281 ext. 228<br />
room: 329<br />
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<br/><br/>
====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">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">
*'''Fractional response analysis reveals logarithmic cytokine responses in cellular populations'''<br/><span class="pmbm">Nienałtowski&nbsp;K</span>, <span class="nopmbm">Rigby&nbsp;RE</span>, <span class="pmbm">Walczak&nbsp;J</span>, <span class="pmbm">Zakrzewska&nbsp;KE</span>, <span class="nopmbm">Rehwinkel&nbsp;J</span>, <span class="pmbm">Komorowski&nbsp;M</span><br/>''Nature Communications'' <u>12</u>:4175 (2021) [https://doi.org/10.1038/s41467-021-24449-2 CrossRef] | [https://www.nature.com/articles/s41467-021-24449-2.pdf PDF]<br style="line-height: 100%; margin-bottom:16px">
* '''Super-spreading events initiated the exponential growth phase of COVID-19 with <i>R</i><sub>0</sub> 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'' <u>7</u>:200786 (2020) [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-PDF] [https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098/rsos.200786&file=rsos200786_review_history.pdf Correspondence]<br style="line-height: 100%; margin-bottom:16px">
* '''Quantitative determination of mechanical stability in the novel coronavirus spike protein'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Moreira RA</span>, <span class="nopmbm">Chwastyk M</span>, <span class="nopmbm">Baker JL</span>, <span class="nopmbm">Guzman HV</span>, <span class="pmbm">Poma AB</span><br style="line-height: 50%; margin-bottom:10px"/>''Nanoscale'' <u>12</u>:16409 (2020) [https://doi.org/10.1039/D0NR03969A CrossRef]<br style="line-height: 100%; margin-bottom:16px">
* '''Multifunctional platform based on electrospun nanofibers and plasmonic hydrogel: A smart nanostructured pillow for near-infrared light-driven biomedical applications'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Nakielski&nbsp;P</span>,  <span class="pmbm">Pawłowska&nbsp;S</span>, <span class="pmbm">Rinoldi&nbsp;C</span>, <span class="pmbm">Ziai&nbsp;Y</span>, <span class="nopmbm">De&nbsp;Sio&nbsp;L</span>, <span class="nopmbm">Urbanek&nbsp;O</span>, <span class="pmbm">Zembrzycki&nbsp;K</span>, <span class="pmbm">Pruchniewski&nbsp;M</span>, <span class="nopmbm">Lanzi&nbsp;M</span>, <span class="nopmbm">Salatelli&nbsp;E</span>, <span class="nopmbm">Calogero&nbsp;A</span>, <span class="pmbm">Kowalewski&nbsp;TA</span>, <span class="nopmbm">Yarin&nbsp;AL</span>, <span class="pmbm">Pierini&nbsp;F</span><br style="line-height: 50%; margin-bottom:10px"/>''ACS Applied Materials & Interfaces'' <u>12(49)</u>:54328–5434 (2020) [https://dx.doi.org/10.1021/acsami.0c13266 CrossRef] | [https://pubs.acs.org/doi/pdf/10.1021/acsami.0c13266 PDF]<br style="line-height: 100%; margin-bottom:16px">
* '''Ultraviolet light-assisted electrospinning of core–shell fully cross-linked P(NIPAAm-<i>co</i>-NIPMAAm) hydrogel-based nanofibers for thermally-induced drug delivery self-regulation'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Pawłowska&nbsp;S</span>, <span class="pmbm">Rinoldi&nbsp;C</span>, <span class="pmbm">Nakielski&nbsp;P</span>, <span class="pmbm">Ziai&nbsp;Y</span>, <span class="nopmbm">Urbanek&nbsp;O</span>, <span class="nopmbm">Li&nbsp;X</span>, <span class="pmbm">Kowalewski&nbsp;TA</span>, <span class="nopmbm">Ding&nbsp;B</span>, <span class="pmbm">Pierini&nbsp;F</span><br style="line-height: 50%; margin-bottom:10px"/>''Advanced Materials Interfaces'' 2000247 (2020) [https://doi.org/10.1002/admi.202000247 CrossRef] | [http://pmbm.ippt.pan.pl/publications/supplementary/Pawlowska-2020-AdvMaterInterfaces-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Pawlowska-2020-AdvMaterInterfaces-SuppMovie.mp4 SuppMovie-MP4]  [https://onlinelibrary.wiley.com/doi/10.1002/admi.202070064 CoverPicture]<br style="line-height: 100%; margin-bottom:16px">


<span style="display:none">
* '''Accounting for corner flow unifies the understanding of droplet formation<br/>in microfluidic channels'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Korczyk&nbsp;PM</span>, <span class="nopmbm">van Steijn&nbsp;V</span>, <span class="pmbm">Blonski&nbsp;S</span>, <span class="pmbm">Zaremba&nbsp;D</span>, <span class="nopmbm">Beattie&nbsp;DA</span>, <span class="nopmbm">Garstecki&nbsp;P</span><br style="line-height: 50%; margin-bottom:10px"/> ''Nature Communications'' <u>10</u>:2528 (2019) [https://doi.org/10.1038/s41467-019-10505-5 CrossRef] | [{{SERVER}}/publications/Korczyk-2019-NatCommun.pdf PDF] [{{SERVER}}/publications/supplementary/Korczyk-2019-NatCommun-SuppInfo.pdf SuppInfo-PDF]<br style="line-height: 100%; margin-bottom:16px">  
Image:TEAM-1.jpg|center|frame|link=|alt=Photo by Magdalena Wiśniewska-Krasińska|Bio-modeling members of our Laboratory, December 2009.
 
</span>
* '''The limited information capacity of cross-reactive sensors drives the evolutionary<br/>expansion of signaling'''<br style="line-height: 50%; margin-bottom:10px"/><span class="pmbm">Komorowski M</span>, <span class="nopmbm">Tawfik DS</span><br style="line-height: 50%; margin-bottom:10px"/>''Cell Systems'' <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] | [https://www.cell.com/action/showPdf?pii=S2405-4712%2818%2930480-0 PDF]<br style="line-height: 100%; margin-bottom:16px">
__NOTITLE__
 
* '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways'''<br style="line-height: 50%; margin-bottom:10px"/><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&nbsp;S</span>, <span class="nopmbm">Kimmel M</span>, <span class="nopmbm">Brasier AR</span>, <span class="pmbm">Lipniacki T</span><br style="line-height: 50%; margin-bottom:10px"/>''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]<br style="line-height: 100%; margin-bottom:16px">
 
* '''An information-theoretic framework for deciphering pleiotropic and noisy<br/>biochemical signaling'''<br style="line-height: 50%; margin-bottom:10px"/><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><br style="line-height: 50%; margin-bottom:10px"/>''Nature Communications'' <u>9</u>:4591 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/30389942 PubMed] [http://dx.doi.org/10.1038/s41467-018-07085-1 CrossRef] |&nbsp;[http://pmbm.ippt.pan.pl/publications/Jetka-2018-NatCommun.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Jetka-2018-NatCommun-SuppInfo.pdf SuppInfo-PDF]<br style="line-height: 100%; margin-bottom:16px">
 
* '''Single-material organic solar cells based on electrospun fullerene-grafted polythiophene nanofibers'''<br style="line-height: 50%; margin-bottom:10px"/><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><br style="line-height: 50%; margin-bottom:10px"/>''Macromolecules'' <u>50</u>(13):4972–81 (2017) [http://dx.doi.org/10.1021/acs.macromol.7b00857 CrossRef]<br style="line-height: 100%; margin-bottom:16px">
 
* '''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]
<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)].
__NOTOC__

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).

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