Main Page

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).