Nombre de documents

27

Christian BAUDET


Research Interests

My research interests are mainly linked with Bioinformatics and Computational Biology.

My past research includes works related to Strucutural Bioinformatics, Trimming Procedures for EST sequencing projects and study of Genome Rearrangement Problems.

During my postdoc, I explored methods for detecting genomic rearrangement breakpoints, cophylogeny reconciliation and theoretical computer science problems related to distance between pairs of trees: rSPR (rooted Subtree Prune and Regraft) distance and its closely related problem MAF (Maximum Agreement Forest).

Currently, I have a position at the Bioinformatics Platform "Gilles Thomas" of the Centre Léon Bérard, a Cancer Research Center located at Lyon, France.

Here you can access my Curriculum Vitae (full version in english or short version in french)

Background

In December 2003, I received my Engineer degree in Computer Engineering from the University of Campinas (Unicamp).

During my studies, from January 2002 to June 2003, I had the opportunity of working as programmer at the Computational Biology Research Group located at Embrapa Informática Agropecuária. In this group, I actively participated on the implementation of several softwares, for visualization of protein parameters, which form the suite STING.

In July 2003, I was recruited as Analyst Developer at Scylla Bioinformatics, one of the first private companies strictly linked to the Bioinformatics area 
in Brazil. Working with all aspects of the development cycle (analysis of user requirements, design of system and database, code implementation, test, documentation and maintenance) I was responsible for the development of systems for:

- EST Sequecing Project Management
- Whole Genome Sequecing Project Management
- Marker Assisted Selection System

My contract with Scylla Bioinformatics ended in January 2009.

In 2004, I joined the Computer Science Master program of the Institute of Computing at the University of Campinas. My master dissertation involved the EST trimming procedure developed at Scylla Bioinformatics for the EST Sequencing Project Management system. In December 2006, I presented my dissertation before a jury to obtain my Master Degree.

In 2006, I joined the Computer Science PhD program in the same 
institute. The research developed during my thesis involved two genome rearrangement problems:

- Enumeration of Traces for the Sorting by Signed Reversals Problem
- Detection of genomic rearrangement breakpoints.

Part of this work was developed during a PhD Sandwich program, which was funded by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), a Brazilian governmental institution. The program started in March 2009 and ended in May 2010 and took place at the UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive (LBBE) with the Baobab-Bamboo team, a CNRS-INRIA-UCBL team.

To obtain my PhD degree, I presented my thesis before a jury in December 2010.

After obtaining my PhD degree, I rejoined the Baobab-Bamboo team in a Post-doc position that started at January 2011. Since then, I’m working with three main topics:

- Detection of genome rearrangement breakpoints
- Algorithms for cophylogeny reconciliation
- Phylogenetic tree distances 

Software

Coala - COevolution Assessment by a Likelihood-free Approach

Despite an increasingly vaster literature on cophylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Many of the most used algorithms do the host-parasite reconciliation analysis using an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host-switch. All known event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. The main problem with this approach is that the cost of the events strongly influence the reconciliation obtained.

To deal with this problem, we developed an algorithm, called Coala, for estimating the frequency of the events based on an approximate Bayesian computation approach.

Official webpage


Eucalypt - EnUmerator of Coevolutionary Associations in PoLYnomial-Time delay

Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tree using event-based maximum parsimony.

Eucalypt is a polynomial-delay algorithm for enumerating all optimal reconciliations for a pair of host and parasite trees.

Official webpage


Cassis : Detection of genomic rearrangement breakpoints

The package Cassis implements methods for precise detection of genomic rearrangement breakpoints.

Official webpage


BD2006Trimmer - Perl Script for EST sequence trimming

Perl script developed during my Master dissertation.

Download script 

 


Article dans une revue8 documents

  • Christian Baudet, Ulisses Dias, Zanoni Dias. Sorting by weighted inversions considering length and symmetry. BMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 19), pp.11. 〈10.1186/1471-2105-16-S19-S3〉. 〈hal-01316998〉
  • Christian Baudet, Béatrice Donati, Blerina Sinaimeri, Pierluigi Crescenzi, Christian Gautier, et al.. Cophylogeny Reconstruction via an Approximate Bayesian Computation. Systematic Biology, Oxford University Press (OUP), 2015, 64 (3), pp.416-431. 〈10.1093/sysbio/syu129〉. 〈hal-01092972〉
  • Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot. EUCALYPT: efficient tree reconciliation enumerator. Algorithms for Molecular Biology, BioMed Central, 2015, 10 (1), pp.11. 〈10.1186/s13015-014-0031-3〉. 〈hal-01092977〉
  • Christian Baudet, Zanoni Dias, Marie-France Sagot. Sampling solution traces for the problem of sorting permutations by signed reversals. Algorithms for Molecular Biology, BioMed Central, 2012, 7 (1), pp.18. 〈10.1186/1748-7188-7-18〉. 〈hal-00784400〉
  • Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, et al.. Cassis: detection of genomic rearrangement breakpoints.. Bioinformatics, Oxford University Press (OUP), 2010, 26 (15), pp.1897-8. 〈10.1093/bioinformatics/btq301〉. 〈hal-00681095〉
  • Goran Neshich, Adauto Mancini, Michel Yamagishi, Paula Kuser, Renato Fileto, et al.. STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2005, Database issue, 33, pp.D269-D274. 〈10.1093/nar/gki111〉. 〈hal-01092988〉
  • Goran Neshich, Walter Rocchia, Adauto Mancini, Michel Yamagishi, Paula Kuser, et al.. Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2004, Web Server issue, 32, pp.W595-W601. 〈10.1093/nar/gkh480〉. 〈hal-01092990〉
  • Goran Neshich, Roberto Togawa, Adauto Mancini, Paula Kuser, Michel Yamagishi, et al.. STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2003, 31 (13), pp.3386 - 3392. 〈10.1093/nar/gkg578〉. 〈hal-01092995〉

Communication dans un congrès9 documents

  • Gustavo Galvão, Christian Baudet, Zanoni Dias. Sorting Signed Circular Permutations by Super Short Reversals. Robert Harrison ; Yaohang Li; Ion Măndoiu 11th International Symposium on Bioinformatics Research and Applications, Jun 2015, Norfolk, Virginia, United States. Springer International Publishing, Proceedings of the 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), 9096, pp.272-283, 2015, Bioinformatics Research and Applications. 〈http://grid.cs.gsu.edu/isbra15/〉. 〈10.1007/978-3-319-19048-8_23〉. 〈hal-01316993〉
  • Christian Baudet, Ulisses Dias, Zanoni Dias. Length and Symmetry on the Sorting by Weighted Inversions Problem. Sérgio Campos. 9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Horizonte, Brazil. Lecture Notes in Computer Science, 8826, pp.99 - 106, 2014, Advances in Bioinformatics and Computational Biology. 〈10.1007/978-3-319-12418-6_13〉. 〈hal-01092607〉
  • Ulisses Dias, Christian Baudet, Zanoni Dias. Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions. Jing Gao. Proceedings of the 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013), Sep 2013, Maryland, United States. pp.181--190, 2013, 〈http://dl.acm.org/citation.cfm?doid=2506583.2506614〉. 〈10.1145/2506583.2506614〉. 〈hal-00922670〉
  • Christian Baudet, Zanoni Dias. Partial enumeration of solutions traces for the problem of sorting by signed reversals. Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Aug 2011, Chicago, United States. ACM, pp.505--507, 2011, 〈10.1145/2147805.2147884〉. 〈hal-00748607〉
  • Christian Baudet, Zanoni Dias. An improved algorithm to enumerate all traces that sort a signed permutation by reversals. ACM. ACM Symposium on Applied Computing (SAC), Mar 2010, Sierre, Switzerland. pp.1521-1525, 2010, 〈10.1145/1774088.1774416〉. 〈hal-00748579〉
  • Christian Baudet, Zanoni Dias. Chronological order of reversal events on Rickettsia genus. Proceedings of the International Symposium on Biocomputing, Feb 2010, Calicut, Kerala, India. ACM, pp.1:1--1:5, 2010, 〈10.1145/1722024.1722026〉. 〈hal-00748584〉
  • Eduardo Tanaka, Marcio Juliato, Christian Baudet, Miguel Galves, Thiago Coelho, et al.. Desenvolvimento de um teclado virtual com diversos layouts e varreduras. V Congresso Ibero-americano de Informática na Educação Especial (CIIEE2005), Jul 2005, Montevideo, Uruguay. pp.141 - 161, 2005, 〈http://www.capacidad.es/ciiee05/index.htm〉. 〈hal-01093636〉
  • Marcio Juliato, Eduardo Tanaka, Christian Baudet, Miguel Galves, Thiago Coelho, et al.. TFlex: Um Simulador de Teclado com Múltiplos Modos de Varredura. VI Simpósio sobre Fatores Humanos em Sistemas Computacionais (IHC 2004), Dec 2004, Curitiba, Brazil. 2004. 〈hal-01093638〉
  • Marcio Juliato, Eduardo Tanaka, Christian Baudet, Miguel Galves, Thiago Coelho, et al.. TFLEX: Proposta de Simulador de Teclado com Diferentes Varreduras e Layouts. VII Congreso Iberoamericano de Informática Educativa (RIBIE 2004), Oct 2004, Monterrey, Mexico. 1, pp.630 - 639, 2004. 〈hal-01093641〉

Thèse1 document

  • Christian Baudet. Enumeração de traces e Identificação de Breakpoints : Estudo de aspectos da evolução.. Computer Science [cs]. UNICAMP (Université de Campinas), Brésil, 2010. Portuguese. 〈tel-01092714〉

Rapport9 documents

  • Christian Baudet, Miguel Galves, Zanoni Dias. Comparação de métodos para determinação de SNPs com medidas de confiabilidade. [Technical Report] 06-15, Instituto de Computação - UNICAMP. 2006. 〈hal-01092998〉
  • Paula Kuser, Jair De Siqueira Neto, Jorge Fernandez, Roberto Higa, Christian Baudet, et al.. Primeiro Curso STING Millennium Suite Chemogenomics: Ferramentas para Analisar Macromoleculares e Aplicações em Chemogenomics. [Technical Report] 26, Embrapa Informática Agropecuária. 2002. 〈hal-01093008〉
  • Paula Kuser, Christian Baudet, Adauto Mancini, Roberto Higa, Goran Neshich. Utilização do software GRASP para gerar arquivo de coordenadas com valores de potencial eletrostático.. [Technical Report] 24, Embrapa Informática Agropecuária. 2002. 〈hal-01093645〉
  • Paula Kuser, Christian Baudet, Roberto Higa, Goran Neshich. Curvatura da superfície de proteínas no Java Protein Dossier. [Technical Report] 38, Embrapa Informática Agropecuária. 2002. 〈hal-01093656〉
  • Roberto Higa, Christian Baudet, Esther De Freitas, Gabriela Dos Santos, Adauto Mancini, et al.. Experiência de utilização de XML no SMS. [Technical Report] 32, Embrapa Informática Agropecuária. 2002. 〈hal-01093648〉
  • Roberto Higa, Christian Baudet, Paula Kuser, Adauto Mancini, Goran Neshich. Apresentação gráfica de parâmetros protéicos utilizando o Java Protein Dossier. [Technical Report] 40, Embrapa Informática Agropecuária. 2002. 〈hal-01093659〉
  • Paula Kuser, Christian Baudet, Roberto Higa, Goran Neshich. Incorporação das propriedades rotâmeros e ocupância em métodos de análise estrutural de proteínas. [Technical Report] 34, Embrapa Informática Agropecuária. 2002. 〈hal-01093652〉
  • Roberto Higa, Christian Baudet, Adauto Mancini, Paula Kuser, Goran Neshich. Análise do grau de conservação de resíduos em proteínas com estrutura 3D resolvida utilizando o SMS. [Technical Report] 37, Embrapa Informática Agropecuária. 2002. 〈hal-01093654〉
  • Roberto Higa, Christian Baudet, Adauto Mancini, Amanda Mattiuz, Esther De Freitas, et al.. SMSLib - biblioteca C++ do Sting Millennium Suite. [Technical Report] 39, Embrapa Informática Agropecuária. 2002. 〈hal-01093658〉