Bioinformatics

Several groups are involved in the development of bioinformatic tools for the simulation and the analysis of genome structure, gene expression and proteomics data.

Autoclass@IJM: a Web interface for the Bayesian classification of heterogeneous data in biology
developed by Fiona Achcar, Denis Mestivier and Jean-Michel Camadro,  from the Computational Modelling and Biomathematics and Mitochrondria, Metals and Oxidative Stress teams at the Institut Jacques Monod.

AutoClass@IJM offers a computational resource with a web interface to AutoClass, a powerful unsupervised Bayesian classification system developed by the Ames Research Center at NASA. AutoClass has many powerful features with broad applications in biological sciences: (i) it determines the number of classes automatically, (ii) it allows the user to mix discrete and real valued data, (iii) it handles missing values.
End users upload their data sets through our web interface; computations are then queued in our cluster server. To help with the analysis of the Autoclass outputs, a CDT file that can be read by JavaTreeview-like software is provided.

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VIRAPOPS: a Forward Simulator Dedicated to Rapidly Evolved Viral Populations
dveloped by Anne Vanet and Michel Petitjean, groupes Molecular Oncology and Ovarian Pathologies at the Institut Jacques Monod and Computational approaches applied to pharmacological profiling, at Molécules thérapeutiques in silico.

Several global public health problems are due to RNA viruses (HIV, Flu, H5N1, HBC, SARS ....). Understand their mechanisms of action and describe their population becomes a vital necessity. Their capacity to mutate allows rapid selection of drug resistances: some active viral proteins may have up to 30% of their positions mutated. These combinations of mutations are possible through primary mutations compensated by secondary mutations, and avoiding synthetic lethal groups (lethal group of mutations, mutation with no effect when alone).
Yet, conventional population simulators are not able to model selection pressures on groups of mutations genetically linked. Moreover, primary and secondary infections are numerous and can succeed in cascade taking place in a seronegative or positive patient. It is to stage these different scenarios that we wanted to develop VIRAPOPS a forward simulator dedicated to RNA viruses, easy to use and answering questions related to these highly specific populations.

This program can be downloaded there:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

VIRAPOPS has been published in:
Petitjean, M., Vanet, A. (2014) VIRAPOPS: A forward simulator dedicated to rapidly evolved viral population, Bioinformatics, 30, 578-80
Abstract

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Furthermore, the Scientific Club BioInfo brings together scientists from the Institut Jacques Monod and from neighboring research institutes who want to develop their bioinformatics skills in analyzing high-troughput sequencing data.
They meet every Friday between 10 and 11am.

Contact: Virginie Orgogozo,  +33 (0)1 57 27 80 43,  orgogozo@ijm.univ-paris-diderot.fr.
Find out more and see the schedule...

All the Scientific Clubs at the Institut Jacques Monod...

Last modified 31 August 2017

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