[CPM-SPIRE-L] funded PhD position in computer science

[Camille Marchet]

Dear colleagues,

It would be deeply appreciated if you could forward this offer to your
students.

Best regards.


PhD position in computer science

Theoretical foundations of compressed data structures and k-mer membership

Institution: University of Lille, CRIStAL Laboratory, France
Duration: 36 months (full-time)
Application deadline: April 30 2025
Start date: fall 2025

Contact: camille.marchet at univ-lille.fr, simon.puglisi at helsinki.fi

------------------------------


We invite applications for a fully-funded PhD position in algorithm and
data structure design.

The successful candidate will investigate k-mer membership data
structures—i.e.,
highly efficient ways to store and query which k-length substrings appear
in a larger collection of strings. These data structures are fundamental in
analyzing large string databases (for example, collections of genomic
sequences), but also raise key combinatorial challenges. The investigation
will involve both design of new k-mer membership data structures and
also theoretical
lower bounds on their size.

Although these problems arise from genomics, this PhD thesis will emphasize
algorithm design and rigorous mathematical and algorithmic theory, rather
than biological applications.

Key research topics

   -

   Formal relationships between k-mer set sizes and classical
   compressibility measures (e.g., Burrows–Wheeler transform runs, grammars,
   LZ parses).
   -

   Lower bounds for storing and querying k-mer spectra.
   -

   Design (and possible implementation) of new k-mer membership data
   structures.
   -

   Advanced combinatorial models for highly repetitive or pangenomic string
   collections.
   -

   Possible extensions to succinct/compressed data structures in string
   processing (e.g., wavelet trees, rank/select indexes).

------------------------------

What we offer

   -

   Funding: 36-month PhD contract of University of Lille
   -

   International collaboration: As part of an international chair project,
   you will collaborate closely with Prof. Simon Puglisi (University of
   Helsinki, Finland) and his team, and benefit from funded exchange visits
   to Helsinki. This includes multi-week research stays.
   -

   Conference travel: The project budget supports attending and presenting
   at top-tier international conferences, workshops, and summer schools.

------------------------------

Candidate profile

   -

   Master’s degree (or equivalent) in Computer Science or Mathematics (with
   a strong algorithmic focus).
   -

   Solid background in theoretical computer science: data structures,
   string algorithms, combinatorics on words, complexity, or related areas.
   -

   Good programming skills are a plus but not mandatory.
   -

   Prior knowledge in bioinformatics is not a requirement.
   -

   We remain attentive to applications from minority candidates.
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