Computer Programming

Bioinformatics Webinars Series


Marco Antonio Mendoza-Parra - Nanotumor copartner
Head of the team SysFate at Genoscope, Evry – France


Kristine Schauer - Nanotumor WP2 Leader
Group leader at Institute Gustave Roussy, Paris – France

Patrick Schultz - Nanotumor Co-coordinator
Head of the "Transcription Co-Activators" team at IGBMC, Illkirch – France




Jacky G. Goetz - Nanotumor Coordinator
Head of the "GoetLab for Tumor Biomechanics" at CRBS, Strasbourg France

Administrative contact:

Florent Colin
Nanotumor project manager, GoetzLab, CRBS, Strasbourg – France

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Over the last years, our understanding of physiological phenomena like cell differentiation, or their aberrant counterpart, tumorigenesis, has been enhanced by major progress on data acquisition at different granularity levels, from the ultrastructure of molecules to the organization of cells and tissues. For instance, major efforts in high resolution cryo- Electron Microscopy (EM) to visualize single molecules in their native states allow to reveal the three-dimensional organization of macromolecular complexes. Similarly, the combination of molecular biology strategies with massive parallel sequencing interrogates protein-DNA interactions involved in transcription regulation and , DNA 3-dimensional organization. The combination of cell imaging with molecular biology labelling strategies and spatial proteomics is opening the window to a molecular characterization of the cellular context, which as a whole is responsible to define cell identity as well as tissue substructure organization.

At each of these levels, the amount of data collected as well as their complexity, requires sophisticated bioinformatics solutions. We need to distinguish meaningful biological readouts from technical noise on the one hand, and summarize and integrate them into a condensed output for enhanced comprehension on the other hand. Indeed, the transition of biology into a data science requests for major investments in algorithm developments. Pipe-lines need to be designed for the granularity level at which the data has been acquired, but also providing means for interconnecting data at different levels. As part of the following Bioinformatics webinar series, we aim at getting the analytical perspective provided by major scientist leading bioinformatics developments at different levels of granularity. We expect that this event will contribute to the training of the new generations of quantitative biologists.

Marco A. Mendoza-Parra & Kristine Schauer

Speakers at a glance

Click on pictures for details

Anthony Mathelier
NCMM - Norway


"Cis-regulatory disruption
in Cancer"


Michael Habeck
Jena Univ. Hospital - Germany

Etienne Baudrier
iCube - France

Valentina Boeva
ETH Zürich - Switzerland

Benoit Naegel
iCube - France

Laura Cantini
IBENS - France

Macha Nikolsky
CBiB - France

Charles Kervran
INRIA - France

"Integration of heterogenous data in structural biology"

"Single cell Omics
and Cancer"


"Spatial Omics in
an intracellular context"


Julio Saez-Rodriguez
EMBL - Germany

"Leveraging Biological Knowledge to Extract Disease Mechanisms from Spatial & Multi-omics data"

"Deep Learning application in
biological imaging segmentation"


"Intratumoral transcriptional heterogeneity in cancer"

"A.I. application to
3D Cryo-tomogram"


December 3, 2021 - 1pm CET


Anthony Mathelier, PhD
Group Leader

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Computational Biology &
Gene Regulation Team

Centre for Molecular Medicine Norway (NCMM)

"Insights into the interplay between
transcription factor binding and cis-regulatory disruptions in cancers"


January 21, 2022 - 1pm CET

"The rise of deep learning in image analysis and
its application for segmentation in
biological imaging"


Benoit Naegel, PhD
Full Professor - Team Co-leader

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IMAGeS Team - Images, Modeling, Learning, Geometry and Statistics

The Engineering, Computer and Imaging Sciences Laboratory (iCube)


Etienne Baudrier, PhD
Associate Professor

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IMAGeS Team - Images, Modeling, Learning, Geometry and Statistics

The Engineering, Computer and Imaging Sciences Laboratory (iCube)


February 11, 2022 - 1pm CET

Laura Cantini.jpg

Laura Cantini, PhD
Permanent Researcher - CNRS

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Computational Systems Biology Team, part of the Computational Biology Center (CBC)
Institute of Biology of the
École Normale Supérieure (IBENS)

"Single Cell Omics and Cancer"
[Final Title to come]


March 11, 2022 - 1pm CET


Michael Habeck, PhD Professor

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Max Planck Institute for
Biophysical Chemistry (MPI-BPC)
Jena University Hospital (MSCJ)

"Integration of heterogeneous data
in structural biology"
[Final title to come]


April 15, 2022 - 1pm CET


Macha Nikolsky, PhD
Research Director - Head

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Computational Biology and
Bioinformatics team (IGBC)
Bordeaux Bioinformatics Center (CBiB)
Partner Investigator at FHU SMART

"Spatial Omics in an Intracellular Context"
[Final Title to come]


May 13, 2022 - 1pm CET


Valentina Boeva, PhD Assistant Professor

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Computational Epi-Genetics of Cancer (BoevaLab)
Dept. of Computer Science
at ETH Zürich


"Deciphering shared intratumor transcriptional heterogeneity of human tumors"


June 10, 2022 - 1pm CET


Charles Kervran, PhD
Team Leader



Inria Rennes,  UMR 144-CNRS,
Institut Curie, PSL University

"AI approaches to find molecules in a
3D cryo-tomogram"
[Final Title to come]


July 8, 2022 - 1pm CET


Julio Saez-Rodriguez, PhD
Team Leader - Professor

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Faculty of Medicine of
Heidelberg University
Director of the Institute of Computational Biomedicine
Group Leader at the
EMBL- Heidelberg University

"Leveraging Biological Knowledge 
to Extract Disease Mechanisms 
from Spatial & Multi-omics data"