Section: Partnerships and Cooperations

International Research Visitors

Visits of International Scientists

• R. Giegerich

  • Institution: Bielefeld University (Germany)

  • 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))