Bioinformatics and Biostatistics HUB

BIGSdb-Pasteur is the genomic-based strain taxonomy and nomenclature platform of Institut Pasteur, powered by the BIGSdb software developed at Oxford University. This web platform hosts collections of curated, open or private databases of bacterial […]

We present ePeak, a Snakemake-based pipeline for the identification and quantification of reproducible peaks from raw ChIP-seq, CUT&RUN and CUT&Tag epigenomic profiling techniques. It also includes a statistical module to perform tailored differential marking […]

Due to advances in high-throughput sequencing technologies, generating whole genome sequencing (WGS) data with high coverage depth (e.g. ≥ 500×) is now becoming common, especially when dealing with non-eukaryotic genomes. Such high coverage WGS […]

SHADE is a Shiny application for providing support to research teams in refining their experiments designs. In particular, SHADE was designed to help biologist with nested designs, raising awareness on common statistical biases. It […]

JolyTree implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain an estimation oƒ the […]

Going the extra mile in Gene Set Enrichment analysis: seeing the data with g-RITA Gene Set Enrichment Analysis (GSEA) is a powerful approach for interpreting OMIC data based on the functional annotation of genes. Such […]

BACNET is a Java based platform to develop website for multi-omics analysis. Our platform integrates different type of tools, the three most important being: A table tools for Heatmap drawing and manipulation. Genome viewer […]

JASS is a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface. The generation of joint […]

Goalign and Gotree are comand line tools aiming at manipulating multiple alignments and phylogenetic trees. They are implemented in Go language. Goalign aims at handling multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, […]

NGPhylogeny.fr is a Free, simple to use web service dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.

CRAW is a package which aim to compute and visualize the coverage of RNA seq experiments. The main feature of this tools is the coverage is computed on the both strands, and is centred […]

Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format. listeriomics.pasteur.fr The main purpose of the website is […]

Sequana is a Python framework designed to provide pipelines to analyse Next Generation Sequencing data sets. Sequana provides tools to access the sequence quality but also post-processing analysis such as depth of coverage or […]

BioServices is a Python package that provides access to many Bioinformatics Web Services (e.g., UniProt, KEGG, NCBI) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols). The primary […]

SynTView is a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic […]

DREAMTools aims at sharing code used in the scoring of DREAMchallenges that pose fundamental questions about system biology and translational medicine. For more information please visit the following links Source code: github.com/dreamtools Documentation: http://dreamtools.readthedocs.io

Summary COVID-19 represents a massive health threat for humans and has already caused huge economic problems all over the world. Profound knowledge of SARS-CoV-2 interaction with the host and the host immune response are […]

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In the JOBIM 2021 conference, we are launching a pilot project on gender speaking differences in academia. Through this evidence-based and mixed-method study, we intend to answer the following question: how to create the conditions for gender-equal expression in scientific conferences? Objective […]

This project is a part of the international Infect-Era program, AMOEBAC: Entamoeba histolytica-bacterium interaction and the role of this interaction in intestinal pathogenesis (http://www.infect-era.eu/2nd-call-2014) The aim of this investigation is to understand the induced […]

Entamoeba histolytica is a protozoan parasite and an amitochondriate pathogenic amoeba, which may cause dysentery and liver abscess in humans (i.e. amoebiasis). Differential pathogenicity is observed among E. histolytica strains: strain HM1:IMSS is virulent […]

Neonatal acquisition of ESBL-PE in the community of a Low-Income Country  Severe bacterial infections are a leading cause of neonatal deaths, with low income countries (LICs) bearing the highest burden. In LICs, neonatal bacterial […]

The Viral Host Range database (VHRdb) represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the […]

PHINDaccess is a twinning initiative aimed to serve as a lever for Omics research performance of the Institut Pasteur de Tunis (IPT), aspiring to raise its positioning as an excellence center in the field […]

CNF1 is a toxin that catalyzes the permanent activation of host RhoA, Rac1 and Cdc42 small GTPases by selective deamidation of a glutamine residue into a glutamic acid. This 1 dalton post-translational modification can […]

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Life science uses many different formats. They may be old, or with complex syntax and converting […]

[Version française]… Cocaine addiction (CocAdd) is a major public health issue affecting 3% of the worlwide population, without validated pharmacotherapy. Nicotinic acetylcholine receptors (nAChRs)have been repeatedly associated in Human and rodent response to cocaine. […]

The cornerstone of the ELIXIR Tools platform is the bio.tools ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources, which is developed through ELIXIR-EXCELERATE Work Package […]

Project context and summary : The phylogenetic position and status of “giant viruses”, formerly called NucleoCytoplasmic Large DNA viruses (NCLDV) or putative order Megavirales, are controversial. Many preliminary phylogenetic analyses have been published, but […]

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]

In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens  to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]

Listeriolysin S is a bacteriocin specifically produced in the intestine of orally infected mice and necessary for Listeria monocytogenes survival in this organ. In order to investigate whether this toxin might influence the composition […]

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Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]

The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]

High-throughput sequencing has revolutionized our abilities to track and characterize novel bacterial strains as they emerge and disseminate globally. Genome-based epidemiological typing systems provide ultimate resolution for strain discrimination. Genome sequences may also be […]

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

To perform the assembly of a bacterial genome from Illumina sequencing in order to submit it to the MicroScope/MaGe platform of Genoscope.

Hydrogen Deuterium eXchange followed by Mass Spectrometry (HDX-MS) is a recognized biophysical tool in structural biology capable of probing protein/ligand interactions, conformational changes, and protein folding and dynamics. The use of improved HDX-MS workflows […]

To perform assignment of 16S sequences to bacterial genera and statistical analysis of variations of bacterial populations collected from mice feces

The goal of this project is to set sequence analysis tools to evaluate the frequency of mutations within a pool of bacteriophage genomes sequenced by NGS.

fq2dna (FASTQ files to de novo assembly) is a command line tool to ease the de novo assembly oƒ archaea, bacteria or virus genomes ƒrom raw high-throughput sequencing (HTS) paired-end (PE) reads. Every data […]

ƒqCleanER (ƒastq Cleaning and Enhancing Routine) is a command line tool to ease the diƒƒerent standard preprocessing steps oƒ short high-throughput sequencing (HTS) reads. Eight standard HTS read processing steps can be carried out […]

The ARIAweb server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays […]

Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.

sequana_coverage is a standalone application that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in high throughput sequencing data. Thanks to HTML reports, is allows users to browse the detected […]

We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .

RΕQ is a program ƒor quickly estimating a conƒidence value at each branch oƒ a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures (e.g. Felsenstein 1985, Makarenkov et al. 2010, […]

Shiny Exploration tool for Transcriptomic Analysis

Comparative Gene Set Enrichment Analysis tool

Sustainable and comprehensive software distribution for the life sciences

This project aims at efficiently storing millions of unique molecular compounds along with some of their already calculated properties. The database named Chem-REST is able to deal with extensive sets of data: millions of […]

The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology. EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to […]

Integrated bash and R toolbox for linkage analysis using SLURM (TARS Cluster) that include (1) basic quality control of initial file structures, (2) quality control analysis and file preparation by the Alohomora software and […]

Comat is a R toolbox that provides quality control reports, matrix distances, permutation test, corrected p values and graphics for the 2 by 2 comparison of contingency matrices of same dimension in batches.

CRISPR polymorphism is a powerful tool to subtype Salmonella strains and is now used in routine for epidemiological investigations. This tool gets a CRISPR profile by identifying the presence of known spacers and direct […]

ToolDog is a program that generates tool description from a tool entry from https://bio.tools.