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Computational Systems Biology of Cancer

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M2_E28b_Computational_SysBio_Cancer_schedule_2021

Master in Life Science, ENS
Bio-M2_E28b | Computational Systems Biology of Cancer (Curie/Mines/ENS)
Year and Semester : M2+(PhD and Postdocs) | S1
Where : Institut Curie, Paris (first week) - Biology Department, ENS (2nd week)
Duration : 1 week including Saturday morning which is devote to a career workshop +1 week of computational projects
First and last day of class : E28 : September 26th-30th, 2022 | E28b : October 3rd-7th, 2022
Maximum class size : E28 : 15 students | E28b : 12 students

Coordination

Denis Thieffry, IBENS.
Emmanuel Barillot, Institut Curie
Inna Kuperstein, Institut Curie

Credits

3 ECTS for IMaLiS students (+ 3 ECTS of computational projects)

Keywords

Cancer | Systems biology | Computational biology | Genomics | Proteomics | Tissue imaging | Machine learning.

Course prerequisites

M1 level knowledge of genetics, genomics, and cellular and molecular biology for the course.
Bases of shell scripts, python or R programming for the computational project.

Course objectives and description

Aims The objective of the course is to promote better integration of computational approaches into biological and clinical labs and to clinics. We aim to help participants to improve interpretation and use of multi-scale data that nowadays are accumulated in any biological or medical lab.
This year, the course will particularly focus on multi model data integration in cancer research and in clinics. We will review current methods and tools for the analysis and interpretation of big data, along with concrete applications related to cancer. In particular, we will emphasize the role of machine learning methods for understanding the heterogeneity of tumours and applications in personalised treatment schemes development.
Themes : Speakers will expose various approaches for omics, imaging, and clinical data analysis, as well as interpretation combining signalling networks together with multi-scale datasets. They will further cover drug sensitivity prediction algorithms, biomarkers and cancer drivers identification, patient stratification approaches, as well as application of mathematical modelling and image analysis in cancer with focus on AI/ML approaches.
Organisation : The course (granting 3 ECTS for IMaLiS students) is organized at Institut Curie (Paris) over a full week, including Saturday morning, which is devote to a career workshop.
IMaLiS M2 students (exclusively) can further apply for a week-long computational project (granting 3 ECTS, resp. D. Thieffry), based on the content of the article presented during the first week.

Assessment

• The evaluation is based on the oral presentation of an article related to the topics of the course. Article assignment is organised before the start of the course, while the presentations take place in the afternoons during the course week.
The evaluation of the projects is based on the production of a computational notebook (in python and/or R) and on an oral presentation at the end of the week.

Course material

The schedule and all slides will be made available on Institut Curie’s training website (https://training.institut-curie.org/).

Suggested readings in relation with the module content

Barillot E, Calzone L, Hupe P, Vert J-P, Zinovyev A (2013). Computational Systems Biology of Cancer. CRC Press.