[CPM-SPIRE-L] PhD offer: Search engine for genomic sequencing data

[Pierre Peterlongo]

Dear all,

Our PhD offer remains available, do not hesitate to apply!


  Job Offer – Search engine for genomic sequencing data

We are currently witnessing a deep knowledge revolution due to the 
availability of exponentially expanding DNA sequence databases. This is 
made possible by the continuous acceleration of DNA sequencing 
throughput. Sequencing data is accumulating faster than Moore’s Law, 
bringing fundamental new insights, conjecture, and understanding, with 
impacts in medicine, agronomy and ecology. Today, the Sequence Read 
Archive <https://www.ncbi.nlm.nih.gov/sra> raw data archive stores more 
than 10^16 nucleotides, in the form of short sequences (<1000 bp) which 
represent fragments from generally unknown genomic location (the “reads”).

Currently there exists no way to query this treasure of information. 
Today, it would be unthinkable to access the Internet without powerful 
search engines. However, this is precisely the current situation for raw 
read archives, where precious data sleep undisturbed in rarely-opened 
drawers. In this project we propose to develop a new scaling 
breakthrough, allowing users to directly query sequencing data on the 
fly in order to tap into the largest underexploited resource in life 
sciences.

In the framework of the broader SeqDigger ANR project 
<https://www.cesgo.org/seqdigger/>, we propose to design and propose new 
indexing schemes, scaling up very large DNA collection (assembled or 
not), and offering a way to query in real time input sequences of 
interest. The recruited PhD student will explore existing methods, 
mainly based on Bloom Filters, and will propose new algorithmic solutions.


      Required skills

Candidates must have strong interest and expertise in algorithmics, data 
structures and C++ implementation.

Knowledge in genomics and biology will be highly appreciated but is not 
a prerequisite.


      Practical information

The recruited PhD student will work in the GenScale 
<https://team.inria.fr/genscale/> team at Inria Rennes, France. She/he 
will work in close collaboration with the SeqDigger partners (Pasteur 
Institute Paris, CEA Genoscope, MIO) and external collaborators (EBI 
<https://www.ebi.ac.uk/>, Bielefeld University 
<https://www.techfak.uni-bielefeld.de/~stoye/>, …). Short stays at EBI, 
Cambridge, are expected.

*Remuneration*: net salary approx 1600€ per month.

Starting date is flexible. PhD could start as early as possible.

Informal enquiries are encouraged. Please contact 
pierre.peterlongo at inria.fr 
<https://www.cesgo.org/seqdigger/job-offer-search-engine-for-genomic-sequencing-data/>

Applicants should send a full CV, a cover letter explaining their 
motivation, experience, and achievements, at least 2 references with 
contact information, and their date of availability

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