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<header class="entry-header"> Dear all, <br>
<br>
Our PhD offer remains available, do not hesitate to apply!<br>
<br>
<h1 class="entry-title">Job Offer – Search engine for genomic
sequencing data</h1>
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<div class="clearfix entry-content">
<p>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 <a
href="https://www.ncbi.nlm.nih.gov/sra" moz-do-not-send="true">Sequence
Read Archive</a> 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”). </p>
<p>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. </p>
<p>In the framework of the broader <a
href="https://www.cesgo.org/seqdigger/" moz-do-not-send="true">SeqDigger
ANR project</a>, 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.</p>
<h3>Required skills </h3>
<p>Candidates must have strong interest and expertise in
algorithmics, data structures and C++ implementation. </p>
<p>Knowledge in genomics and biology will be highly appreciated
but is not a prerequisite. </p>
<h3>Practical information </h3>
<p>The recruited PhD student will work in the <a
href="https://team.inria.fr/genscale/" moz-do-not-send="true">GenScale</a>
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 (<a
href="https://www.ebi.ac.uk/" moz-do-not-send="true">EBI</a>,
<a href="https://www.techfak.uni-bielefeld.de/~stoye/"
moz-do-not-send="true">Bielefeld University</a>, …). Short
stays at EBI, Cambridge, are expected. </p>
<p><strong>Remuneration</strong>: net salary approx 1600€ per
month.</p>
<p>Starting date is flexible. PhD could start as early as
possible.</p>
<p>Informal enquiries are encouraged. Please contact <a
href="https://www.cesgo.org/seqdigger/job-offer-search-engine-for-genomic-sequencing-data/"
moz-do-not-send="true">pierre.peterlongo@inria.fr</a></p>
<p>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</p>
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