[SocBiN] Fwd: Post-doc position on Inference of RNA structure and function from sequence data at ENS

[Arne Elofsson]

Yours

Arne

-----------------------------------------
  Arne Elofsson                  Science for Life Laboratory
  Tel:+46-(0)70 695 1045   Stockholm University
  http://bioinfo.se/               Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
  Twitter:   https://twitter.com/arneelof
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751


---------- Forwarded message ---------
From: Simona Cocco <simona.cocco at phys.ens.fr>
Date: Tue, Dec 29, 2020 at 5:13 PM
Subject: Post-doc position on Inference of RNA structure and function from
sequence data at ENS
To: Remi Monasson <remi.monasson at phys.ens.fr>


Dear colleagues,
I am writing to advertise a post-doctoral opening on statistical physics
and  inference for biological data.
Please forward this announcement to potential candidates.

Best wishes,
Simona Cocco


*Postdoc position on  *

*Inference of RNA structure and function from sequence data *



Laboratory of Physics of the Ecole Normale Supérieure,

under the supervision of Simona Cocco and Rémi Monasson



*Context and project:*
 RNA, long recognized as a crucial intermediate in the fundamental  biological
process of production of proteins from genetic material (DNA) is also
involved in many catalytic and enzymatic processes.

In this context, a fundamental question is to relate the sequence of RNA
molecule to its structural and functional properties. The sequence content
must encode the 3D conformation of RNA (and alternative
conformations e.g. resulting from binding to a ligand), In addition,
the sequence
is subject to functional constraints due to the need to achieve catalytic
activity and specific interactions with other molecules or
chemical species (RNA, proteins, DNA, ions..). RNAs designed by nature and
obtained by sequencing many evolutionary distinct organisms can be used to
unveil the constraints acting on RNA. Combining this sequence data
available in databases such as RFAM with statistical physics and
computational methods will allow us to reconstruct the landscape associated
to a given function and structure. Our approach will also be tested on
well-controlled RNA sequence data obtained from in vitro selection (selex).
In turn, we will exploit the reconstructed landscapes to design new RNA
sequences, whose structural and functional properties will be
experimentally tested. The latter scope is part of the currently very
active field of design in material sciences, chemistry and biomedicine.


*Practical information:*

This post-doc is funded  by the ANR Decrypted for 18 months and
should start in Spring 2021. The recruited postdoc will work in
collaboration with Simona Cocco and Rémi Monasson, in the Statistical
Physics and Inference for Biology group in the Laboratory of Physics of the
Ecole Normale Supérieure. She/he will also benefit from the collaboration
with Bruno Sargueil (CiTCoM, Paris Descartes University ) and Yann Ponty (LIX,
Ecole Polytechnique ).



*How to apply:*

The candidate should have a PhD (or have it completed before the start
of the position) in a relevant field, and a strong experience in
theoretical physics, statistical physics or bioinformatic and machine
learning. To apply, please send a CV and a cover letter describing your
interests and previous work to simona.cocco at phys.ens.fr and
remi.monasson at phys.ens.fr



*Bibliography:*

[1]Inverse Statistical Physics of Protein Sequences: A Key Issues Review. S.
Cocco, C. Feinauer, M. Figliuzzi, R. Monasson, M. Weigt. Reports on
Progress in Physics 81, 032601 (2018).
<http://www.phys.ens.fr/~monasson/Articles/a107.pdf>

[2] Direct-Coupling Analysis of nucleotide coevolution facilitates RNA
secondary and tertiary structure prediction E. De Leonardis, S. Lutz, S.
Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt Nucleic Acid Research, doi:
10.1093/nar/gkv932 (2015)
<http://www.phys.ens.fr/~monasson/Articles/a97.pdf> (supplemental text
<http://www.phys.ens.fr/~monasson/Articles/a97-si1.pdf> and supplemental
figures <http://www.phys.ens.fr/~monasson/Articles/a97-si2.pdf>)

[3] 3D RNA and Functional Interactions from Evolutionary Couplings.
Weinreb, C., Riesselman, A.J., Ingraham, J.B., Gross, T., Sander, C. and
Marks, D.S. Cell 165(4), pp. 963–975 (2016).

[4]  An evolution-based model for designing chorismate mutase enzymes

W.P. Russ, M. Figliuzzi, C. Stocker, P. Barrat-Charlaix, M. Socolich, P.
Kast, D. Hilvert, R. Monasson, S. Cocco, M. Weigt, R. Ranganathan Science
369, 6502 (2020) <http://www.phys.ens.fr/~monasson/Articles/a125.pdf>
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