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Center for Microbes, Development and Health - Computational Biologist/Engineer


The newly-created, multidisciplinary Center of Excellence directed by Prof. Philippe Sansonetti at Institut Pasteur of Shanghai, with support by the Chinese Academy of Sciences and the Shanghai Municipality, calls for applications by outstanding Computational Biologists/Engineers   

New-generation sequencing, bioinformatics and multi-omics have promoted the human microbiota to a position of driver of health and disease in case of dysbiosis. Major challenges remain in defining the frontiers of the symbiosis, its impact on development, physiology, health and disease, particularly the emerging post-modern, non-communicable, epidemics in industrialized regions and microbiota-related pathologies in low-income regions, such as susceptibility to infections and stunting.  

CMDH aims to establish causality links by combining basic and experimental research with clinical studies to open the way to prophylactic and therapeutic interventions.  

The Center is now developing capacities in new generation sequencing for bacterial metataxonomics, metagenomics, metatranscriptomics and the accompanying capacities in bioinformatics and big-data management. CMDH is thus actively seeking to recruit a computational biologist who will be in charge of this cutting-edge multi-omics platform.  

Call for a Computational Biologist/Engineer

Desired skills and experience  

- Education or training background in bioinformatics, biostatistics or related fields; 

- Familiar with Linux/Unix Shell working environment;  

- Strong programming skills (R, Python or perl); 

With confirmed experience sustained with publications in: 

- Metagenomics 16s analysis (e.g. phyloseq, QIIME, Mothur and/or Kraken 2);  

- (Meta-)transcriptomics analysis (e.g. Bowtie, samtools, bedtools, cufflinks, PIPE-CLIP); 

- Genomic assembly and annotation (Illumina+Nanopore), comparative genomics, phylogenomics, etc.  


Job environment  

The computational biologist will be in charge of the multi-omics platform and will work closely with the below units:     

  1.    The Experimental bacteriology laboratory (EBL) headed by Dr. Jean-Marc Collard   

EBL aims to decipher key ecological rules driving the maturation steps of the intestinal microbiota from the neonatal period to the age of 3 when it reaches its steady state.   In a developmental perspective, EBL will identify constraints, environmental clues, and individual/collective dynamics driving the stepwise construction of the gut bacterial ecosystem. On this basis, EBL will address the dynamics of constitution of dysbiosis seen as a stalled maturation process with possible consequences on disease programming later in life. To achieve these goals, EBL will develop an innovative combination of culturomics, metataxonomics and single cell analysis to deeply interrogate the construction of bacterial consortia and the resulting prokaryote-prokaryote episymbotic and exclusion events that support bacterial assembly. EBL scientists will work in close collaboration with other groups of the CMDH, developing microfluidic and organ-on-chip technologies, gnotobiology, omics and high-resolution photon microscopy.  

  2.    The Discovery and Molecular Characterization of Pathogens Unit (DMCP) headed by Dr. Nicolas Berthet

The first research axis of DMCP is the discovery and molecular characterization of pathogens from primary samples based on the use of different high throughput sequencing technologies. The second axis is the search for prognostic markers to anticipate the progression of precancerous lesions to malignancy for cervical cancer.  

  3.    The Microbial RNA Systems Biology Unit (MRSB) headed by Dr. Yanjie Chao 

Noncoding RNA is an essential component of life. MRSB previous research has discovered many important small noncoding RNAs in model bacterial pathogens, such as the 3’UTR-derived small RNAs. Using high-throughput RNA sequencing, transposon insertion sequencing and other systems-wide approaches, MRSB will study the RNA regulatory network in important human pathogens as well as commensal bacteria, e.g. Klebsiella pneumoniae. We hope to better understand how pathogenic and commensal bacteria control their gene expression to colonize the host, especially gene regulations mediated by RNA-binding proteins, noncoding RNAs, and novel small proteins.   

Women are strongly encouraged to apply. 

Deadline for Application: Open until position is filled. 

Application documents (CV, 3 recommendation letters, and application form) should be sent to Philippe Sansonetti <>, Emilie Carlot <> and Jody Shen <>.