Grants

• Current

• Past

• TEAM 2009–2013

• Coordination of innate immune response in infected cell population: experiment and mathematical modeling.
  National Science Centre (NCN): Opus 15, 2019–2021
  PI: Tomasz Lipniacki.

• Development of new methods for measuring fluid viscosity and interphase pressure using microfluidic devices.
  National Science Centre (NCN): Preludium 15, 2019–2021
  PI: Damian Zaremba.

• Electrospun conducting hydrogel nanomaterials for neural tissue engineering.
  Foundation for Polish Science (FNP): First Team, 2019–2021.
  PI: Filippo Pierini.

• Injectible cell scaffolds in tissue engineering.
  National Centre for Research and Development (NCBiR): Lider 9, 2018–2021.
  PI: Paweł Nakielski.

• Stimuli-responsive chiral nematic liquid crystal hydrogel implants by electrospinning technique.
  National Science Centre (NCN): Sonata 10, 2016–2019.
  PI: Filippo Pierini.

• Design, construction and optimization of a combined Atomic Force Microscope and Optical Tweezers instrument for single molecules and nanomaterials characterization.
  National Centre for Research and Development (NCBiR): Lider 7, 2017–2020.
  PI: Filippo Pierini.

• The effect of shear flow on fibrin clot structure and fibrin-platelets interactions.
  Foundation for Polish Science (FNP): Homing.
  PI: Izabela Piechocka.

• Digital operations on droplets embedded into smart microfluidic architectures for applications in medical diagnostics and biological research.
  Foundation for Polish Science (FNP): First Team.
  PI: Piotr Korczyk.

• Deciphering biochemical signalling to inform more efficient therapeutic strategies.
  Foundation for Polish Science (FNP): First Team.
  PI: Michał Komorowski.

• Detecting signalling aberrations in cancer cells.
  National Science Centre (NCN): Preludium 12, 2017–2019.
  PI: Karol Nienałtowski.

• Non-standard parabolic problems in description of biological processes.
  National Science Centre (NCN): OPUS 11, 2017–2019.
  PI: Bogdan Kaźmierczak.

• Blood clotting in contact with nanofibers.
  National Science Centre (NCN): Sonata 10, 2016–2019.
  PI: Paweł Nakielski.

• Analysis of hydrodynamic interactions between single molecules using optical tweezers.
  National Science Centre (NCN): Preludium 10, 2016–2019.
  PI: Krzysztof Zembrzycki.

• Multi-scale dynamics of signal transduction: dissecting the MAPK pathway.
  Wiener Wissenschafts-, Forschungs- und Technologiefonds (WWTF Austria) grant "Mathematics and..." , 2015–2018.
  co-PI: Tomasz Lipniacki.

• Dynamics of STAT1, STAT3, and STAT5 phosphorylation in breast cancer cell lines: a systematic theoretical and experimental analysis.
  National Science Centre (NCN): Opus 9, 2016–2019.
  PI: Michał Komorowski.

• Innate immune response to RSV infection, role of non-structural proteins. Experiments and modeling of signal transduction and among cells communication.
  National Science Centre (NCN): Harmonia 6, 2015–2018.
  PI: Tomasz Lipniacki.

• Mechanisms controlling cell fate decisions in response to stress. Experimental and theoretical analysis.
  National Science Centre (NCN): Opus 7, 2015–2018.
  PI: Tomasz Lipniacki.

• European Molecular Biology Organisation (EMBO): Installation Grant, 2013–2016/2018.
  PI: Michał Komorowski.

• The study of hydrodynamic interactions of droplets in complex microfluidic structures. The analysis of algorithms encoded in the architecture of microchannels enabling dosing of the reactants with arbitrary precision.
  National Science Centre (NCN): Sonata Bis 4, 2015–2018.
  PI: Piotr Korczyk.

• Hydrogel noanofilaments for biomedical application.
  National Science Centre (NCN): Preludium 9, 2016–2018.
  PI: Sylwia Pawłowska.

• Innate immune signalling: optimal microfluidic protocols, prediction and control.
  Marie Curie Actions: Career Integration Grant, 2013–2017.
  PI: Michał Komorowski.

• Stochastic phenotype switching in growing and dividing bacteria.
  National Science Centre (NCN): Preludium 7, 2015–2017.
  PI: Joanna Jaruszewicz–Błońska.

• Regulation of the RAF/MEK/ERK cascade involving RAF isoforms.
  National Science Centre (NCN): Preludium 6, 2014–2017.
  PI: Paweł Kocieniewski.

• Dynamics of micro and nano objects suspended in fluids.
  National Science Centre (NCN): OPUS 2, 2012–2016.
  PI: Tomasz Kowalewski.

• Formation of spatial heterogeneities on the plasma membrane and their impact on cell signaling.
  National Science Centre (NCN): Preludium 5, 2014–2016.
  PI: Marek Kochańczyk.

• Inter- and intracellular signaling in innate immune response: experimental and mathematical analysis.
  National Science Centre (NCN): OPUS 2, 2012–2015.
  PI: Tomasz Lipniacki.

• Estimation of the kinetic rates in the NF-κΒ signalling system.
  Polish Ministry of Science and Higher Education: Iuventus Plus, 2013–2015.
  PI: Michał Komorowski.

• Mechanistic aspects and spatial effects in cell signaling.
  Foundation for Polish Science (FNP): TEAM, 2009–2013.
  PI: Tomasz Lipniacki.

• Multiparameter and information theoretic models of biochemical signal transduction – modeling and inference.
  Foundation for Polish Science (FNP): HOMING Plus, 2011–2013.
  PI: Michał Komorowski.

• Application of electrospun nanofibrous mats as active wound dressing for prevention of post-traumatic brain damage (Zastosowanie elektroprzędzonych nanowłókien jako opatrunków aktywnych w zapobieganiu pourazowym zmianom w tkance mózgowej).
  National Center for Research and Development (NCBiR), 2010–2013.
  PI: Tomasz Kowalewski.

• Traveling waves in cylindrical domains (Fale biegnące w obszarach cylindrycznych). National Science Centre (NCN), 2010–2012.
  PI: Bogdan Kaźmierczak.

• Application of information theory-based computational methods for the analysis of signal transduction efficiency in neuronal networks (Zastosowanie metod komputerowych bazujących na teorii informacji do analizy efektywności transmisji sygnałów w sieciach neuronowych).
  National Science Centre (NCN), 2011–2012.
  PI: Janusz Szczepański.

• Efficient methods for generation of secure parameters of public key algorithms (Opracowanie wydajnych metod generowania bezpiecznych parametrów algorytmów klucza publicznego).
  National Science Centre (NCN): grant for a Ph.D. student, 2011–2012.
  PI: Janusz Szczepański.

Mechanistic aspects and spatial effects in cell signalling

within the TEAM Programme sponsored by the Foundation for Polish Science, 2009–2013

Concepts and objectives

The leading aim of the project is to identify and study the turning points in molecular pathways of immune response and cancer, in which the single cell fate, understood as a choice between apoptosis, senescence, proliferation, differentiation or cell cycle arrest, is decided. As a model molecular pathways we will consider these related to innate and adaptive immune response and cancer, in which we have expertise. The project will be realized both by means of numerical simulations and theoretical analysis.

TEAM in December 2009.

TEAM project laureates

Postdocs:

• Sławomir Błoński
• Piotr Szopa (till 31.01.2012)

Ph.D. Students:

• Michał Dyzma
• Joanna Jaruszewicz
• Paweł Kocieniewski

M.Sc. Students:

• Marta Bogdał
• Dominika Nowicka
• Jakub Pękalski (till 31.08.2011)
• Paweł Żuk (till 30.09.2011)

Financed topics

1. Theoretical modeling and experimental analysis of regulatory pathways connected with innate immune response. The candidates are expected to have laboratory experience or/and knowledge in the field of mathematical biology, stochastic processes and differential equations.
   
   
2. Evolution and co-evolution of genes (and their regulatory regions) related to IRF3 and NF-κB pathway. Such analysis will be helpful in analysis of crosstalk of IRF3 and NF-κB pathways. The evolution of genes is related to their biological importance, typically well conserved genes play key roles in the regulatory pathway. Transcription factors IRF3 and NF-κB play central role in innate immune responses. The student will have to learn BLAST (Basic Local Alignment Search Tool) and how to use genome databases and clustering tools.
   
   
3. Mutations of p53 pathways genes in various types of cancer. Various types of cancers are associated with specific mutations of p53, Mdm2, Akt, PTEN and other regulating genes. The students will have to search databases to find the mutations (or deletions) and analyze what is their potential impact on dynamics of p53 regulatory pathways we consider.

Team members

• Tomasz Lipniacki – principal investigator (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

• Bogdan Kaźmierczak (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

• Beata Hat-Plewińska (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

• Marek Kochańczyk (Jagiellonian University, Krakow, Poland)

• Aleksandra Nowicka (Institute of Theoretical Physics, PAS, Warsaw, Poland) – till 01.10.2011

External collaborators

• Mark Alber (Notre Dame University, US)

• Allan R. Brasier (University of Texas Medical Branch, Galveston, TX, US)

• James R. Faeder (University of Pittsburgh School of Medicine, US)

• William S. Hlavacek (Los Alamos National Laboratory, US)

• Marek Kimmel (Rice University and MD Anderson Cancer Center, Houston, TX, US)

• Vitaly Volpert (Université Claude Bernard - Lyon 1, France)

• Michael R.H. White (Liverpool University, UK)