Subject: Efficient algorithms for RNA secondary structure alignment.
Funding: Dgar (Ecole Polytechnique)
R. Giegerich visited the Amib project-team for a
month. He taught dynamic-programming to the students of the Bibs master.
He initiated a collaboration on sparsification, an algorithmic technique that speeds up dynamic programming algorithm.
A comprehensive review on RNA structure alignment algorithms, to appear in a forthcoming book, was also written during his stay.
J. Waldispühl
Institution: McGill University (Canada)
Subject: RNA design and tertiary structure prediction.
Funding: Digiteo (Lri )
J. Waldispühl visited Amib for a month. He finalized a collaboration on RNA design (Y. Ponty, leading to [16] ),
established a new collaborative research (with A. Denise and Y. Ponty, on tertiary motifs), laid the foundations of a future X-UPSud exchange program, initiated a workshop on molecular interactions (with J. Bernauer), and started a PhD co-supervision (A. Soulé, co-supervised with J.-M. Steyaert and Y. Ponty).
X. Huang
Subject: Millisecond dynamics at atomic resolution by Markov State Models
Institution: Hong Kong University of Science and Technology (Hong-Kong)
A. Sim
Subject: Modeling RNA by hierarchical natural moves
Institution: Stanford University (USA) / A*STAR (Singapore)
L. Pereyaslavets
Subject: Critical assessment of non bonded part of force fields
Institution: Stanford University (USA)
Y. Okamoto
Subject: Protein folding, unfolding, and ligand docking by computer simulations
Institution: Nagoya University (Japan)
Internships
A. Martirosyan (March-Jul 2012)
Subject: A Dynamical Model for the Transmembrane Potential Regulation by pH
Institution:Cergy University (Pontoise)
Funding: Inria
Supervision:L. Paulevé and M. Régnier
B. Brancotte (March-July 2012)
Subject: Designing a framework to compare biological data ranking methods
Institution: Paris-Sud University (France)
Funding: Inria
Supervision: S. Cohen-Boulakia and A. Denise
Gh.Fievet (March-Sept 2012)
Subject: Improving MPAS software
Institution: Paris-Sud University (France)
Funding: Ecole Polytechnique
Supervision:J.M. Steyaert
J. Weaver (Jun-Aug 2012)
Subject: Efficient Motif Discovery and Evaluation
Institution: Massachusetts Institute of Technology (United States)
Funding: MIT France program
Supervision: Y. Ponty and M. Régnier
A. Menard (Jun-Aug 2012)
Subject: Extending JalView 's RNA interconnection with Varna
Institution: Université Paris-Sud
Supervision: Y. Ponty and J. Procter (Univ. Dundee, Scotland)
A. Soulé (Jun-Aug 2012)
Subject: Prediction of RNA-RNA interactions in yeast
Institution: Ecole Polytechnique
Supervision: Y. Ponty and J.-M. Steyaert
V. Arendt (Jun-Aug 2012)
Subject: Integrating RNA web services into JalView using Jabaws
Institution: Duke University (United States)
Funding: Google Summer of Code program
Supervision: Y. Ponty and J. Procter (Univ. Dundee, Scotland)
T. Coulmy & N. Duhamel (Jun-Jul 2012)
Subject: Average-case property analysis of workflows based on hypergraphs
Institution: Université Paris-Sud
Supervision: S. Cohen-Boulakia and Y. Ponty
F.K. Sheong (May-Aug 2012)
Subject: RNA structural design by docking and machine learning
Institution: The Hong Kong University of Science and Technology (Hong Kong, (China))
L. Uroshlev (Oct-Nov 2012)
Subject: Reference state for RNA KB potentials
Institution: IOGEN (Moscou, (Russia))
A. Bari (Oct 2012)
Subject: stress-inducible miRNAs
Institution:El Farabi University (Almaty, (Kazakhstan))
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