Laboratoire de Recherche en Informatique
- Bioinformatics
Team
Yann Ponty
Identity
Researches
During my PHD studies supervised by Alain
Denise, whose initial subject can be found here,
I try to model the statistical noise that is ubiquitous in the objects
of interest in biology. More specifically, I'm working on the impact
of such a phenomenon over genomic sequences analysis tools.
This leads me to study, both theorically through the use of enumerative
combinatorics tools, or experimentally through the design and implementation
of random generation algorithms, some discrete models properties.
Among these models, I am working on RNA secondary structures, weighted
context-free languages and some constrained random walks.
Publications
Teaching activities
2003-2004 : IUT d'Orsay
- C++/Algorithms course - First year
- Computer architecture and Microprogramming course - First year
- Student project (Minimal Web Browser).
Subject
2004-2005 : IUT d'Orsay
2005-2006 : IUT d'Orsay
- C++/Algorithms course - Second year
- Visual Basic/GUI design - First year
Software
GenRGenS
: A software dedicated to the random generation of sequences.
Supports different classes of models, including weighted context-free
grammars, Markov models, ProSITE
patterns, etc ...
[Web site] [Reference]-
DIAL:
A web server which performs three-dimensional alignment and motif search
for experimentally-determined 3D structures of RNA. Takes into account sequential, secondary structure (Determined using
RNAView),
and 3D backbone (Dihedral angles) similarities.
[Webserver] [Reference]
GenRWalks: A Java applet coded as a proof of concept of researches
(In collaboration with Mireille Bousquet-Mélou, see submitted article)
led on properties of uni-dimensional walks under various constraints.
Performs random generation and display of walks that are either unconstrained, positive or culminating on
the positive quarter plane, using various algorithmic approaches (Recursive, rejection, Boltzmann sampling ...).
Plus, it looks good ! ;)
[Applet page] [Reference]
 VARNA
: A lightweight Java Applet dedicated to the quick drawing of an RNA secondary structure.
VARNA is open-source and distributed under the terms of the GNU GPL license.
Automatically scales up and down to take the most out of
a limited space. Can draw multiple structures simultaneously. Accepts a wide range of documented and illustrated
options, and offers basic user interaction.
[Applet]
- Online bibliography of the Bioinformatics team (LRI, Orsay) - Restricted Access
- Online Conferences/CFP/Journals of the Bioinformatics team (LRI, Orsay) - Restricted Access
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