[DMANET] PhD and postdoc open positions (Rennes and Paris, France)

Doctoral and postdoctoral positions on methods and algorithms to
calculate biomolecular structures in the framework of the Distance
Geometry Problem (DGP).

A doctoral and a postdoctoral (14 months) position are currently open in
the framework of the international ANR project multiBioStruct in
collaboration with Taiwan (https://anr.fr/Project-ANR-19-CE45-0019).
This project intends to develop novel computational approaches for the
identification of biomolecular structures by exploiting new experimental
data and by employing methods belonging to the DGP class. The project
stands on rigid basis given by more than 10 years of previous research
activities, which have already confirmed the validity of the approach on
a set of small globular protein conformations. Our current aim is extend
its domain of applicability to larger molecules, as well as to more
complex biological systems. This extension will require, for example,
(i) the developments of Machine Learning (ML) techniques; (ii) the
conception of novel efficient strategies for global and combinatorial
optimization; and (iii) the implementation of software tools capable of
finding exact or approximated solutions to the given problems.

The project's consortium includes three French teams that have been
collaborating on this topic since more than 10 years: IRISA (Rennes),
Institut Pasteur (Paris) and Ecole Polytechnique (Palaiseau).
Additionally, the project has two international partners in Taiwan: two
Academia Sinica's teams located in Taipei. The two PhD and postdoc
candidates are expected to actively work in this highly international
and highly multi-disciplinary environment, and to interact with all the
partners of the consortium.

We seek motivated candidates with a strong background in informatics,
with good programming skills in low-level programming languages (C,
C++). Some practice in Java and multi-threading are appreciable. The
candidates need to have a great interest in biological applications.
Previous knowledge and experience on biological problems is a plus.

The PhD candidate will be recruited at IRISA, University of Rennes 1.
The position is open from February 2021, for a 3-year period (standard
time length for PhDs in France).

The postdoc research will be recruited at Institut Pasteur, Paris. The
position is open from December 2020, for 14 months.

If you're interested in one of the two positions, please don't hesitate
to contact us and to send us your curriculum vitae accompanied with a
motivation letter.

Contacts (please send an email to both addresses, for both open positions) :
- Antonio Mucherino (antonio.mucherino@irisa.fr)
- Therese Malliavin (therese.malliavin@pasteur.fr)

References

Malliavin TE, Mucherino A, Lavor C, Liberti L.
Systematic exploration of protein conformational space using a Distance
Geometry approach.
J Chem Inf Model 59, 4486-4503 (2019).

Mucherino A, Lin J-H.
An efficient exhaustive search for the Discretizable Distance Geometry
Problem with interval data.
IEEE Conference Proceedings, Federated Conference on Computer Science
and Information Systems (FedCSIS19),
Workshop on Computational Optimization (WCO19),
Leipzig, Germany, 135-141 (2019).

Worley B, Delhommel F, Cordier F, Malliavin T, Bardiaux B, Wolff N,
Nilges M, Lavor C, Liberti L.
Tuning interval Branch-and-Prune for protein structure determination.
Journal of Global Optimization 72:109-127 (2018).

Liberti L, Lavor C, Maculan N, Mucherino A,
Euclidean Distance Geometry and applications.
SIAM Review 56:3-69 (2014).

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