AlgoSB 2019: Mathematical and Computational Methods for Structured
RiboNucleic Acids
International Winter School in Algorithms in Structural Bioinformatics

14-18 JANUARY 2019
Centre International de Rencontres Mathématiques (CIRM), Marseille, France
https://algosb2019.sciencesconf.org/
*Registration deadline extended: 29 Oct 2018*
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We are pleased to announce the 6th edition of the Algorithms in
Structural Bioinformatics (AlgoSB) winter school. The aim of AlgoSB is
to introduce advanced methods in Structural Bioinformatics in the
largest sense, giving special attention to interdisciplinary approaches.
This year focus will be on computational methods for RNA structure
modelling.
The school will take place at Centre International de Rencontres
Mathématiques (CIRM), Marseille, France, located in Luminy in the
beautiful Calanques, from January 14 to 18, 2019.

Topics covered (in theory and practice):
* RNA 2D folding
* RNA folding kinetics
* RNA design
* Comparative folding
* 3D modeling and docking

Lectures are structured to provide a brief introduction to the topic of
the day and then proceed to advanced concepts  and methods, in
connection with real-life applications.

PROGRAM OVERVIEW
Each day consists of morning lectures by experts in the field, followed
by a practical session on participants laptops in the afternoon. The
topics of the classes include:

I   RNA 2D folding: Introduction and advanced thermodynamics-based
predictions
Ronny Lorenz - TBI, University of Vienna, Austria
Ivo Hofacker - TBI, University of Vienna, Austria
Main topics: Free-energy minimization; Partition-function based methods;
Statistical sampling; Enzymatic/chemical probing-guided predictions;
pseudoknots; basic 2D RNA-RNA interactions.

II   RNA folding kinetics and energy landscapes
Ronny Lorenz - TBI, University of Vienna, Austria
Juan Cortés - LAAS-CNRS, Toulouse, France
Frédéric Cazals - INRIA, Sophia-Antipolis, France
Charles Robert - LBT, IBPC, Paris, France
Main topics: Theoretical foundations of kinetic analysis; Advanced
sampling of approximated energy landscapes; Basin hopping graphs; Energy
Barrier estimation/Transition rates; Master equation resolution;
Co-transcriptional folding; Comparison of energy landscapes.

III  RNA design in theory and practice
Sven Findeiss - University of Leipzig, Germany
Main topics: Inverse folding; Ensemble defect optimization; Sequence
constraints; mRNA design; Programmatically-switching molecules; Design
of RNA sensors.

IV Comparative methods for structure analysis
Sebastian Will - TBI, University of Vienna, Austria
Main topics: Information-based methods; Simultaneous alignment/folding
of homologs; Covariance models; Genome-wide screens; Comparative
modeling; Structural indexing and clustering methods; Comparative
RNA-RNA interactions.

V  RNA-protein interactions and coarse-grained molecular dynamics for RNA
Isaure Chauvot de Beauchêne - CNRS & LORIA, University of Lorraine, France
Samuela Pasquali - Faculté de Pharmacie, Université Paris-Descartes, France
Main topics: RNA force fields; 3D coarse-grained molecular dynamics;
Atomistic simulation; Prediction/annotation of non-canonical modules;
Gradient-descent based methods; Macro-molecular docking; RNA-protein
interactions prediction;

VENUE
The Algorithms in Structural Bioinformatics school will take place on
the beautiful French mediterranean coastline, at the Centre
International de Rencontres Mathématiques (CIRM), Marseille, France,
located in Luminy.

AUDIENCE
The AlgoSB school is targeted towards PhD students, postdocs, and junior
researchers from public research institutions and industry, both in
France and internationally. This school is limited to 65 participants.
It is expected that all will stay for the whole duration of the school.

APPLICATION
To apply, visit our website
(https://algosb2019.sciencesconf.org/page/signup).
Please provide a short motivation letter (max. 2 pages) summarizing your
research interests and a short CV. You can enter this information
directly as plain text or provide links to pdfs. Application deadline:
October 15, 2018 -> October 29, 2018
Notifications: Nov 1st, 2018.

REGISTRATION (opens early Decembre 2018)
Registrations fees include housing at the CIRM, lunches and coffee breaks:
- 350 euros for academics at public research institutions and universities
- 500 euros for industry
Selected participants are requested to proceed to the payment by Jan 1st
2019.

Fees may be waived for deserving applicants unable to secure funding
(please notify us rather than refraining from participating).

AlgoSB 2019 organizers
 Yann Ponty, LIX, CNRS & Ecole Polytechnique, Palaiseau, France
 Andrea Tanzer, TBI, University of Vienna, Austria

Juan Cortès, LAAS-CNRS, Toulouse, France
Charles Robert, LBT-CNRS, IBPC, Paris, France
Frédéric Cazals, INRIA Sophia Antipolis - Mediterranee, France