WBA 2014 - Workshop in Bioinformatics and Algorithms

March 25 and 26, 2014

Auditorium of NUMEC (Núcleo de Apoio à Pesquisa em Modelagem Estocástica e Complexidade)
at the Institute of Mathematics and Statistics of the University of São Paulo - IME-USP

A meeting on the occasion of the visit to the University of São Paulo (USP) of the Bamboo Team under the leadership of Marie-France Sagot, INRIA Rhône-Alpes, France.

We are pleased to invite all the interested researchers to this informal meeting. The participants are welcome to attend the lectures as well as the Problem Session (with submissions on the spot). The meeting will focus on algorithmic aspects of problems arising in bioinformatics and combinatorial optimization.

Program

Date Time Activity
March 25
(Tuesday)
9:30-10:00 From Bamboo to Erable (Marie-France Sagot, INRIA & LBBE)
10:00-10:30 Precursor sets in metabolic networks (Martin Wannagat, INRIA & LBBE)
10:30-11:00 Mirinho: efficient precursor miRNA predictor (Susan Higashi, INRIA & LBBE)
11:00-11:30
== Coffee Break ==
11:30-12:00 Algorithms to tell stories (Paulo Vieira Milreu, Researcher at TecSinapse)
12:00-14:00
== Lunch ==
14:00-14:30 Sorting permutations by prefix and suffix versions of reversals and transpositions (Carla Negri Lintzmayer, IC-UNICAMP)
14:30-15:00 Convex recoloring of phylogenetic trees (Phablo F.S. Moura, IME-USP)
15:00-16:00
= Open Problem Session ==
(open to all participants who wish to present problems, to discuss ideas, and possibly start new collaborations)
16:00-16:20
== Coffee Break ==
16:20-17:40
== Group Work ==
20:00
== Dinner ==
March 26
(Wednesday)
9:30-10:00 Statistical methods in graphs with applications in biological data (André Fujita, IME-USP)
10:00-10:30 Algorithmic issues in cophylogenetic analysis (Blerina Sinaimeri, INRIA & LBBE)
10:30-11:00
== Coffee Break ==
11:00-11:30 Topological colored motifs in reaction graphs (Marco Aurélio Stefanes, UFMS)
11:30-12:00 Efficient algorithms to list st-paths (Gustavo Sacomoto, INRIA & LBBE)
12:00-14:00
== Lunch ==
14:00-16:00
== Group Work ==
16:00-16:20
== Coffee Break ==
16:20-xxxx
== Group Work ==

All activities will take place at the building of NUMEC, located next to the building (Bloco C) of Computer Science Department at IME-USP.

The talks will be given in the Auditorium of NUMEC (ground floor). For the group work, the participants may use the Auditorium as well as the ground floor of NUMEC. Another blackboard is available next to the Auditorium.

The Laboratory at the first floor may be used by the authorized participants (who have sent their photos to the organization) to connect to the network of IME (with their own notebooks). Eduroam is also available.

Abstracts of the Talks

Confirmed Participants

    Alexandre da Silva Freire, IC-UNICAMP, Campinas, Brazil
    Alice Julien-Laferriere, INRIA & LBBE University Claude Bernard, Lyon, France
    André Fujita, IME-USP, São Paulo, Brazil
    Blerina Sinaimeri, INRIA & LBBE University Claude Bernard, Lyon, France
    Carla Negri Lintzmayer, IC-UNICAMP, Campinas, Brazil
    Carlos Eduardo Ferreira, IME-USP, São Paulo, Brazil
    Catherine Matias, INRIA & LBBE University Claude Bernard, Lyon, France
    Cecília Klein, INRIA & LBBE University Claude Bernard, Lyon, France
    Christian Baudet, Postdoc at INRIA & LBBE University Claude Bernard, Lyon, France
    Cristina Fernandes, IME-USP, São Paulo, Brazil
    Florence Bouhedi, INRIA & LBBE University Claude Bernard, Lyon, France
    Gustavo Rodrigues Galvão, IC-UNICAMP, Campinas, Brazil
    Gustavo Sacomoto, Postdoc at INRIA & LBBE University Claude Bernard, Lyon, France
    Leandro Ishi Soares de Lima, Programmer at LEDES - FACOM/UFMS
    Marco Aurélio Stefanes, UFMS, Campo Grande, Mato Grosso do Sul, Brazil
    Mariana Galvão Ferrarini, INRIA & LBBE University Claude Bernard, Lyon, France
    Marie-France Sagot, INRIA & LBBE University Claude Bernard, Lyon, France
    Martin Wannagat, INRIA & LBBE University Claude Bernard, Lyon, France
    Paulo Vieira Milreu, Researcher at TecSinapse, Brazil
    Phablo F.S. Moura, IME-USP, São Paulo, Brazil
    Ricardo Andrade, INRIA & LBBE University Claude Bernard, Lyon, France
    Said Sadique Adi, UFMS, Campo Grande, Mato Grosso do Sul, Brazil
    Susan Higashi, INRIA & LBBE University Claude Bernard, Lyon, France
    Ulisses Dias, IC-UNICAMP, Campinas, Brazil
    Vicente Acuña, CMM Universidad de Chile, Santiago, Chile
    Yoshiko Wakabayashi, IME-USP, São Paulo, Brazil

Organization

Chair: Yoshiko Wakabayashi, USP || Combinatorics and Combinatorial Optimization Research Group || NUMEC
Co-chair: Marie-France Sagot, INRIA Rhône-Alpes, Université Claude Bernard, Lyon I
Alexandre da Silva Freire, IC-UNICAMP
Lourdes Vaz da Silva Netto, NUMEC-USP (lourdesv@ime.usp.br)

Support

IME-USP
and
Computer Science Graduate Program - IME-USP


Núcleo de Apoio à Pesquisa em Modelagem Estocástica e Complexidade (NUMEC)

Combinatorics and Combinatorial Optimization
Research Group - IME-USP


Last modified: Thu Mar 20 20:44:20 BRT 2014