Grants

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

Precise operations on droplets embedded in intelligent microfluidic architectures for applications in medical diagnostics and biological research.
Foundation for Polish Science (FNP): First TEAM.
PI: Piotr Korczyk.

Deciphering biochemical signaling to inform more effective therapeutic strategies.
Foundation for Polish Science (FNP): First TEAM.
PI: Michał Komorowski.

Detecting signalling aberrations in cancer cells.
National Science Center (NCN): Preludium 12 grant.
PI: Karol Nienałtowski.

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

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

Analysis of hydrodynamic interactions between single molecules using optical tweezers.
National Science Center (NCN): Preludium 10 grant, 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 Center (NCN): Opus 9 grant, 2016–2019.
PI: Michał Komorowski.

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

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

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 Center (NCN): Sonata Bis 4 grant, 2015–2018.
PI: Piotr Korczyk.

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

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

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

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

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

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

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

Inter- and intracellular signaling in innate immune response: experimental and mathematical analysis.
National Science Center (NCN): OPUS 2 grant, 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 grant, 2009–2013.
PI: Tomasz Lipniacki.

Multiparameter and information theoretic models of biochemical signal transduction – modeling and inference.
Foundation for Polish Science (FNP): HOMING Plus grant, 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 Center (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 Center (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 Center (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

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.
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 evolutions 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 Aligment Search Tool) and how to use genome databases and clustering tools.
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)