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SysFate

Systems Biology of cell Fate decisions

Marco Antonio Mendoza

Laboratory of Systems Biology

ISSB laboratory; UMR 8030

Génomique Métabolique

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PRODUCT
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Our laboratory study cell fate decisions from a systems biology perspective, i.e. by aiming to understand their transitions from the reorganization of complex regulatory wires defining their biological state.

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Our ambition is focused on enhancing our understanding of cell fate transitions in a variety of biological systems by the reconstruction of the gene regulatory networks that are reorganized during these transition events. At term we aim to provide a comprehensive view of the gene regulatory wires defining each of the cell/tissue types in an organism, thus representing a landmark catalog for the future therapeutic developments in regenerative medicine.

In this context, we follow the innovation engine strategy of Systems biology; i.e. We address biological questions with the help of novel technological developments and bioinformatics.

From big-data functional genomics to the reconstruction of  regulatory programs defining biological systems

With the democratization of sequencing technologies, the major challenge of the present genomics era does not reside anymore in data acquisition, but rather in having computational solutions for interrogating billions of data points from several datasets in a comparative manner such that their embedded information might provide means to describe biological systems.
Over the years, our team addressed these questions through the development of a universal quality control strategy for ChIP-seq and related datasets (Mendoza-Parra et al; NAR 2013), which has been applied to certify > 100,000 public datasets and more recently by the release of a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multidimensional data integration.

 

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The innovation engine strategy in Systems biology

Main research projects:

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ABOUT

n° Citations: 2695; h-index: 20; i10-index: 26 (December 2024)

2024

  • Salim Megat, Christine Marques, Marina Hernan Godoy, Chantal Sellier, Geoffrey Stuart-Lopez, Sylvie Dirrig-Grosch, Charlotte Gorin, Aurore Brunet, Mathieu Fischer, Celine Keime, Pascal Kessler, Marco Antonio Mendoza-Parra, Sonja W Scholz, Luigi Ferrucci, Albert Ludolph, Bryan Traynor, Adriano Chio, Luc Dupuis, Caroline Rouaux; CREB3 gain of function variants protect against ALS; October 11th 2024; BioRxiv

 

2023

2022

2021

 

​2020

 

2019

2018

 

2017

2016

 

 

 

 

 

2015

 

 

2014

 

 

 

2013

 

 

 

2012

 

2011

 

 

 

 

2009

 

non-peer-reviewed articles

 

  • Marco Antonio Mendoza, 2001, Les Phytases : Structure, Caractérisation et Applications, www.123bio.net/revues/

Publications

FEATURED

Software

TETRAMER

qcComparator

POLYPHEMUS

NGS-QC Generator

MeDiChISeq

MULTILAYER

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Epimetheus

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qcChromStater

LOGIQA

Networks

BJ fibroblast stepwise tumorigenesis transformation
Malysheva et al; Genome Medicine. 2016
Master regulatory networks 
MEFs to iPS cells reprogramming
TETRAMER
tumorigenic transformation driven by conditioned medium from senescent cells
TETRAMER
retinoids action on neuronal/endodermal cell fate acquisiton
Mendoza-Parra et al; Genome Research. 2016
B-lymphoma to primary macrophage transdifferentiation 
TETRAMER
CONTACT

Open positions

we are always interested in working with scientists sensitive to the topics we drive in the lab. Interested master or PhD candidate applicants as well as postdoctoral scientists could directly contact us:
Current open positions:
- PhD student position.
-EU-funded engineer position in Bioinformatics (Single-cell transcriptomic).
DEMO
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