Search anything and hit enter
  • Teams
  • Members
  • Projects
  • Events
  • Calls
  • Jobs
  • publications
  • Software
  • Tools
  • Network
  • Equipment

A little guide for advanced search:

  • Tip 1. You can use quotes "" to search for an exact expression.
    Example: "cell division"
  • Tip 2. You can use + symbol to restrict results containing all words.
    Example: +cell +stem
  • Tip 3. You can use + and - symbols to force inclusion or exclusion of specific words.
    Example: +cell -stem
e.g. searching for members in projects tagged cancer
Search for
Count
IN
OUT
Content 1
  • member
  • team
  • department
  • center
  • program_project
  • nrc
  • whocc
  • project
  • software
  • tool
  • patent
  • Administrative Staff
  • Assistant Professor
  • Associate Professor
  • Clinical Research Assistant
  • Full Professor
  • Graduate Student
  • Lab assistant
  • Non-permanent Researcher
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
  • Group Leader
  • Head of Facility
  • Head of Operations
  • Head of Structure
  • Honorary President of the Departement
  • Labex Coordinator
Content 2
  • member
  • team
  • department
  • center
  • program_project
  • nrc
  • whocc
  • project
  • software
  • tool
  • patent
  • Administrative Staff
  • Assistant Professor
  • Associate Professor
  • Clinical Research Assistant
  • Full Professor
  • Graduate Student
  • Lab assistant
  • Non-permanent Researcher
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
  • Group Leader
  • Head of Facility
  • Head of Operations
  • Head of Structure
  • Honorary President of the Departement
  • Labex Coordinator
Search
Go back
Scroll to top
Share

About

The Biomics Platform is the C2RT structure at Institut Pasteur for Next Generation Sequencing and includes both short and long-read technologies.

Our mission is to facilitate scientific discovery within Pasteur Institute’s network and academic research institutes. Biomics accepts both service and collaborative projects and works closely with the C3BI and DSI to provide data analysis solutions and data storage for researchers. Please contact us for pricing and turnaround times.

Our website, https://biomics.pasteur.fr, allows you to:

  • Submit a new projet
  • Ask questions (price, delay time, grants…)
  • Monitor the progress of your project
  • Information on the services provided

Here are some examples of what we propose (Procaryotes, Eukaryotes and Viruses):

  1. Technology: Short-Reads (Illumina), Long-Reads (PacBio et Nanopore)
  2. DNA-Seq: Sequencing de novo and targeted
  3. RNA-Seq: Transcriptomic Analysis
  4. Métagenomic: Targeted sequencing studies (16S, 18S, ITS) or random (Shotgun)
  5. Bioinformatics: NGS data analysis (Variant, Assembly, Methylation study…)

Biomics and its staff of experts work hard for the successful and timely processing of all samples and requests. If you are unsatisfied with our service or have a suggestion on how we can improve please do not hesitate to contact us: Reclamation / Suggestions

Members

Marc Monot
Head of Facility
Head
Hugo Varet
Research Engineer
Laurence Ma
Technician
Odile Sismeiro
Research Engineer
Laure Lemee
Technician
Laurence Motreff
Technician
Rachel Legendre
Research Engineer
Thomas Cokelaer
Research Engineer
Catherine Dauga
Permanent Researcher
Imène Najjar
Project Manager
Sophia Achaibou
Undergraduate Student
Juliana Pipoli Da Fonseca
Research Engineer
Cédric Fund
Technician
Annie Etienne
Administrative Staff
Saliha Azebi
Research Engineer
Valérie Briolat
Research Engineer

Projects

project
Ongoing
5 Members

Entamoeba histolytica – bacterium interaction and the role of this interaction in intestinal pathogenesis

Nancy Guillen (PI)

Amoebiasis, a global medical problem, is a parasitic infection of the intestines caused by the protozoan Entamoeba histolytica. The consortium AMOEBAC, headed by Dr Serge Ankri (Technion Israel Institute of Technology, Israel) aims to […]
project
Completed
7 Members

Evolution of the Pathogenicity Locus of C. difficile

Bruno Dupuy (PI)

The major virulence factors of Clostridium difficile are toxins A and B. These toxins are encoded by tcdA and tcdB genes, which form a pathogenicity locus (PaLoc) together with three additional genes that have been […]
project
Ongoing
2 Members

Escherichia coli transcriptomic analysis upon OmrA or OmrB overexpression

Jean-Yves Coppee (PI)

OmrA and OmrB are two small regulatory RNAs (sRNAs) conserved in enterobacteria. Their transcription is activated by the EnvZ-OmpR two-component system and their levels therefore increase in response to an increase in osmolarity. They […]
project
Ongoing
3 Members

Intracellular membrane proliferation in E. coli

Jean-Yves Coppee (PI)

Overproduction of membrane proteins in the E. coli strains generally induce cell death. The multiple mutant C43 (DE3) derivative of BL21 (DE3) strain was selected to resist this overproduction. In this mutant,  the membrane […]
project
Ongoing
21 Members

Protected: Pasteur Human Genome

Thomas Bourgeron (PI)

There is no excerpt because this is a protected post.
project
Ongoing
17 Members

CoSimmGen : Constitution of a prospective cohort of healthy and diseased individuals with an associated human biological resources collection for the purpose of studying of genetic, immunological and environmental factors in human diseases

Marie-Noelle Ungeheuer (PI)

Context : Studying physiopathology of human diseases, focused in particular on genetic, immunological and environmental factors necessitate to access to human cohorts of healthy and diseased individuals and the corresponding bioresources. The rarity of […]
project
Completed
4 Members

Pathogenomic analysis of high potential virulent strains of C. difficile

Bruno Dupuy (PI)

Clostridium difficile is increasingly associated with infections in hospitals and in the community, and hypervirulent types are emerging. Six research groups from 5 countries undertook this project, aiming to use genomic approaches to study […]

Transversal Project

Fighting Antibiotic Resistance

Antibiotics are highly efficient drugs to kill pathogenic bacteria with low side effects. For more than 70 years, the massive use of these miracle drugs has saved millions of human and animal lives. Unfortunately […]

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues. Inception program uses Integrative Biology, Social Science […]

Major Federating Program Microbes & Brain

Program general concept Can microbes influence the brain to maintain health or drive pathology? Will our understanding of the microbes and brain connection generate novel therapeutic approaches? The Major Federating Program Microbes & Brain […]

Institut Carnot Pasteur MS

The Carnot Label Carnot label is granted to public research structures, showing high level R&I competencies dedicated to fostering innovation with industrial partners. The Carnot Institutes (IC) are funded to conduct upstream research capable […]

Software

software
Completed
2 Members

Sequanix: a dynamic graphical interface for Snakemake workflows

Thomas Cokelaer (PI)

We designed a PyQt graphical user interface—Sequanix—aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable […]
software
Ongoing
6 Members

Sequana: a set of flexible NGS pipelines

Thomas Cokelaer (PI)

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 […]
software
Ongoing
8 Members

SARTools

Hugo Varet (PI)

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 […]
software
Ongoing
8 Members

SHAMAN: SHiny Application for Metagenomic ANalysis

Amine Ghozlane (PI)

SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]

Tools

tool
Completed
2 Members

checkMyIndex

Hugo Varet (PI)

checkMyIndex is an application whose goal is to help in finding a set of compatible indexes for a sequencing experiment. It has been developped using the R/Shiny environment and is freely available at https://checkmyindex.pasteur.fr/. […]
tool
Ongoing
4 Members

Clean-ngs

Bernd Jagla (PI)

A new adapter removal program for next generation sequencing Clean-ngs is available on GitHub: https://github.com/PF2-pasteur-fr/clean_ngs For more information contact Bernd Jagla  

Services

Training on the Agilent Bioanalyzer

A SPOC for using the Agilent Bioanalyzer Training sessions for the use of the Bioanalyzer, organized at the Transcriptome and Epigenome platform of the Biomics pole, are now replaced by a SPOC, available 24 […]

Pushing the Limit: A Complete Solution for Generating Stranded RNA-Seq Libraries from Picogram Inputs of Total Mammalian RNA

With challenging samples, like RNA isolated using laser capture microscopy, it is difficult to obtain 10 ng of starting material; additionally, rRNA depletion leads to sample loss, undermining robust library preparation. The new release surpasses […]

Index compatibility for sequencing

Illumina uses a green laser to sequence G/T and a red laser to sequence A/C. At each cycle at least one of two nucleotides for each color channel need to be read to ensure […]

Protocol for library construction available allowing to perform RNAseq from low input

The SMARTer Ultra Low Input RNA Kit for Sequencing – v3 incorporates Clontech’s patented SMART (Switching Mechanism at 5’ End of RNA Template) technology. This technology uses the template switching activity of reverse transcriptase […]

Single Cell

RNAseq is routinely used for the characterization of bulk transcriptome. Nevertheless, Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In collaboration with the Centre d’Immunologie […]

CHIPSeq

ChIPSeq is used for the analysis of the interactions between the genome and nucleic acids binding proteins like transcription factors or chromatin associated proteins. Starting from the IPs / inputs, the PF can perform […]

RNAseq

RNAseq is used for gene expression profiling of different populations of coding or non coding RNAs as well as for the annotation of the genome (exhaustive mapping of TSS, identification of splicing isoforms…). Several […]

Equipments

Sequencing Systems • Illumina • MiSeQ

Here is the list of type runs on MiSeq :List_runs_MiSeq  

BioAnalyzer • Agilent • Bioanalyzer 2100

Our Bioanalyzer 2100 is dedicated to the microfluidic  electrophoresis of nucleic acids (DNA, RNA). Depositing the samples is done on specific chips depending on the type of sample. Electrophoresis is fast and provided quantitative […]

Sequencing Systems • Illumina • HiSeq 2000

Illumina sequencing devices which are shared with other platforms of the Biomics Pole

Sequencing Systems • Illumina • Hiseq 2500 (1To)

Illumina sequencing devices which are shared with other platforms of the Biomics Pole

Fundings

Publications

Download