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Next Generation Causal Analysis: Inspired by the Induction of Biological Pathways from Cytometry Data

Objective

Discovering the causal mechanisms of a complex system of interacting components is necessary in order to control it. Computational Causal Discovery (CD) is a field that offers the potential to discover causal relations under certain conditions from observational data alone or with a limited number of interventions/manipulations.

An important, challenging biological problem that may take decades of experimental work is the induction of biological cellular pathways; pathways are informal causal models indispensable in biological research and drug design. Recent exciting advances in flow/mass cytometry biotechnology allow the generation of large-sample datasets containing measurements on single cells, thus setting the problem of pathway learning suitable for CD methods.
CAUSALPATH builds upon and further advances recent breakthrough developments in CD methods to enable the induction of biological pathways from cytometry and other omics data. As a testbed problem we focus on the differentiation of human T-cells; these are involved in autoimmune and inflammatory diseases, as well as cancer and thus, are targets of new drug development for a range of chronic diseases. The biological problem acts as our campus for general novel formalisms, practical algorithms, and useful tools development, pointing to fundamental CD problems: presence of feedback cycles, presence of latent confounding variables, CD from time-course data, Integrative Causal Analysis (INCA) of heterogeneous datasets and others.

Three features complement CAUSALPATH’s approach: (A) methods development will co-evolve with biological wet-lab experiments periodically testing the algorithmic postulates, (B) Open-source tools will be developed for the non-expert, and (C) Commercial exploitation of the results will be sought out.

CAUSALPATH brings together an interdisciplinary team, committed to this vision. It builds upon the PI’s group recent important results on INCA algorithms.

Field of science

  • /medical and health sciences/health sciences/inflammatory diseases

Call for proposal

ERC-2013-CoG
See other projects for this call

Funding Scheme

ERC-CG - ERC Consolidator Grants

Host institution

PANEPISTIMIO KRITIS
Address
University Campus Gallos
74100 Rethimno
Greece
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 1 322 000
Principal investigator
Ioannis Tsamardinos (Prof.)
Administrative Contact
Eleni Karkanaki (Ms.)

Beneficiaries (2)

PANEPISTIMIO KRITIS
Greece
EU contribution
€ 1 322 000
Address
University Campus Gallos
74100 Rethimno
Activity type
Higher or Secondary Education Establishments
Principal investigator
Ioannis Tsamardinos (Prof.)
Administrative Contact
Eleni Karkanaki (Ms.)
KAROLINSKA INSTITUTET
Sweden
EU contribution
€ 402 000
Address
Nobels Vag 5
17177 Stockholm
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Hamilton Caroline (Mrs.)