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Christian Baudet

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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](http://www.ic.unicamp.br/~baudet/CV/baudet_cv.pdf) or short version [in french](http://www.ic.unicamp.br/~baudet/CV/baudet_cv_short_fr.pdf))** Background ---------- In December 2003, I received my Engineer degree in Computer Engineering from the University of Campinas ([Unicamp](http://www.unicamp.br/unicamp/?language=en)). During my studies, from January 2002 to June 2003, I had the opportunity of working as programmer at the [Computational Biology Research Group](http://www.nbi.cnptia.embrapa.br/) located at [Embrapa Informática Agropecuária](http://www.cnptia.embrapa.br/). In this group, I actively participated on the implementation of several softwares, for visualization of protein parameters, which form the suite [STING](http://www.nbi.cnptia.embrapa.br/SMS/). In July 2003, I was recruited as Analyst Developer at [Scylla Bioinformatics](http://www.scylla.com.br/index-en.html), 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) EST Sequecing Project Management ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Whole Genome Sequecing Project Management ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) 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](http://www.ic.unicamp.br/en) 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Enumeration of Traces for the Sorting by Signed Reversals Problem ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) 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](http://www.capes.gov.br/)), 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](http://lbbe.univ-lyon1.fr/)) with the [Baobab-Bamboo team](https://team.inria.fr/bamboo/en), 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Detection of genome rearrangement breakpoints ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Algorithms for cophylogeny reconciliation ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Phylogenetic tree distances Software -------- **[Coala - COevolution Assessment by a Likelihood-free Approach](http://coala.gforge.inria.fr/)**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](http://coala.gforge.inria.fr/) --- [**Eucalypt - EnUmerator of Coevolutionary Associations in PoLYnomial-Time delay**](http://eucalypt.gforge.inria.fr/)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](http://eucalypt.gforge.inria.fr/) --- [**Cassis : Detection of genomic rearrangement breakpoints**](http://pbil.univ-lyon1.fr/software/Cassis/)The package Cassis implements methods for precise detection of genomic rearrangement breakpoints. [Official webpage](http://pbil.univ-lyon1.fr/software/Cassis/) --- [**BD2006Trimmer - Perl Script for EST sequence trimming**](http://www.ic.unicamp.br/~baudet/BD2006Trimmer/bd2006trimmer.zip)Perl script developed during my Master dissertation. [Download script](http://www.ic.unicamp.br/~baudet/BD2006Trimmer/bd2006trimmer.zip)
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](http://www.ic.unicamp.br/~baudet/CV/baudet_cv.pdf) or short version [in french](http://www.ic.unicamp.br/~baudet/CV/baudet_cv_short_fr.pdf))** Background ---------- In December 2003, I received my Engineer degree in Computer Engineering from the University of Campinas ([Unicamp](http://www.unicamp.br/unicamp/?language=en)). During my studies, from January 2002 to June 2003, I had the opportunity of working as programmer at the [Computational Biology Research Group](http://www.nbi.cnptia.embrapa.br/) located at [Embrapa Informática Agropecuária](http://www.cnptia.embrapa.br/). In this group, I actively participated on the implementation of several softwares, for visualization of protein parameters, which form the suite [STING](http://www.nbi.cnptia.embrapa.br/SMS/). In July 2003, I was recruited as Analyst Developer at [Scylla Bioinformatics](http://www.scylla.com.br/index-en.html), 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) EST Sequecing Project Management ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Whole Genome Sequecing Project Management ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) 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](http://www.ic.unicamp.br/en) 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Enumeration of Traces for the Sorting by Signed Reversals Problem ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) 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](http://www.capes.gov.br/)), 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](http://lbbe.univ-lyon1.fr/)) with the [Baobab-Bamboo team](https://team.inria.fr/bamboo/en), 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: ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Detection of genome rearrangement breakpoints ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Algorithms for cophylogeny reconciliation ![-](http://lbbe.univ-lyon1.fr/squelettes-dist/puce.gif) Phylogenetic tree distances Software -------- **[Coala - COevolution Assessment by a Likelihood-free Approach](http://coala.gforge.inria.fr/)**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](http://coala.gforge.inria.fr/) --- [**Eucalypt - EnUmerator of Coevolutionary Associations in PoLYnomial-Time delay**](http://eucalypt.gforge.inria.fr/)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](http://eucalypt.gforge.inria.fr/) --- [**Cassis : Detection of genomic rearrangement breakpoints**](http://pbil.univ-lyon1.fr/software/Cassis/)The package Cassis implements methods for precise detection of genomic rearrangement breakpoints. [Official webpage](http://pbil.univ-lyon1.fr/software/Cassis/) --- [**BD2006Trimmer - Perl Script for EST sequence trimming**](http://www.ic.unicamp.br/~baudet/BD2006Trimmer/bd2006trimmer.zip)Perl script developed during my Master dissertation. [Download script](http://www.ic.unicamp.br/~baudet/BD2006Trimmer/bd2006trimmer.zip)

Publications

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Cophylogeny Reconstruction via an Approximate Bayesian Computation

Christian Baudet , Béatrice Donati , Blerina Sinaimeri , Pierluigi Crescenzi , Christian Gautier
Systematic Biology, 2015, 64 (3), pp.416-431. ⟨10.1093/sysbio/syu129⟩
Journal articles hal-01092972v1
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EUCALYPT: efficient tree reconciliation enumerator

Beatrice Donati , Christian Baudet , Blerina Sinaimeri , Pierluigi Crescenzi , Marie-France Sagot
Algorithms for Molecular Biology, 2015, 10 (1), pp.11. ⟨10.1186/s13015-014-0031-3⟩
Journal articles hal-01092977v1
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Sorting by weighted inversions considering length and symmetry

Christian Baudet , Ulisses Dias , Zanoni Dias
BMC Bioinformatics, 2015, 16 (Suppl 19), pp.11. ⟨10.1186/1471-2105-16-S19-S3⟩
Journal articles hal-01316998v1
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Sampling solution traces for the problem of sorting permutations by signed reversals

Christian Baudet , Zanoni Dias , Marie-France Sagot
Algorithms for Molecular Biology, 2012, 7 (1), pp.18. ⟨10.1186/1748-7188-7-18⟩
Journal articles hal-00784400v1

Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet , Claire Lemaitre , Zanoni Dias , Christian Gautier , Eric Tannier
Bioinformatics, 2010, 26 (15), pp.1897-8. ⟨10.1093/bioinformatics/btq301⟩
Journal articles hal-00681095v1
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STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database

Goran Neshich , Adauto L Mancini , Michel E. B. Yamagishi , Paula R. Kuser , Renato Fileto
Nucleic Acids Research, 2005, Database issue, 33, pp.D269-D274. ⟨10.1093/nar/gki111⟩
Journal articles hal-01092988v1
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Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

Goran Neshich , Walter Rocchia , Adauto L Mancini , Michel E. B. Yamagishi , Paula R. Kuser
Nucleic Acids Research, 2004, Web Server issue, 32, pp.W595-W601. ⟨10.1093/nar/gkh480⟩
Journal articles hal-01092990v1
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STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

Goran Neshich , Roberto C. Togawa , Adauto L Mancini , Paula R. Kuser , Michel E. B. Yamagishi
Nucleic Acids Research, 2003, 31 (13), pp.3386 - 3392. ⟨10.1093/nar/gkg578⟩
Journal articles hal-01092995v1
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Sorting Signed Circular Permutations by Super Short Reversals

Gustavo R Galvão , Christian Baudet , Zanoni Dias
11th International Symposium on Bioinformatics Research and Applications, Jun 2015, Norfolk, Virginia, United States. pp.272-283, ⟨10.1007/978-3-319-19048-8_23⟩
Conference papers hal-01316993v1
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Length and Symmetry on the Sorting by Weighted Inversions Problem

Christian Baudet , Ulisses Dias , Zanoni Dias
9th Brazilian Symposium on Bioinformatics, BSB 2014, Oct 2014, Belo Horizonte, Brazil. pp.99 - 106, ⟨10.1007/978-3-319-12418-6_13⟩
Conference papers hal-01092607v1
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Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions

Ulisses Dias , Christian Baudet , Zanoni Dias
Proceedings of the 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013), ACM Special Interest Group on Bioinformatics, Computational Biology, and Biomedical Informatics, Sep 2013, Maryland, United States. pp.181--190, ⟨10.1145/2506583.2506614⟩
Conference papers hal-00922670v1

Partial enumeration of solutions traces for the problem of sorting by signed reversals

Christian Baudet , Zanoni Dias
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Aug 2011, Chicago, United States. pp.505--507, ⟨10.1145/2147805.2147884⟩
Conference papers hal-00748607v1

Chronological order of reversal events on Rickettsia genus

Christian Baudet , Zanoni Dias
Proceedings of the International Symposium on Biocomputing, Feb 2010, Calicut, Kerala, India. pp.1:1--1:5, ⟨10.1145/1722024.1722026⟩
Conference papers hal-00748584v1

An improved algorithm to enumerate all traces that sort a signed permutation by reversals

Christian Baudet , Zanoni Dias
ACM Symposium on Applied Computing (SAC), Mar 2010, Sierre, Switzerland. pp.1521-1525, ⟨10.1145/1774088.1774416⟩
Conference papers hal-00748579v1

Desenvolvimento de um teclado virtual com diversos layouts e varreduras

Eduardo H. Tanaka , Marcio R. Juliato , Christian Baudet , Miguel Galves , Thiago T. Coelho
V Congresso Ibero-americano de Informática na Educação Especial (CIIEE2005), Jul 2005, Montevideo, Uruguay. pp.141 - 161
Conference papers hal-01093636v1
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TFLEX: Proposta de Simulador de Teclado com Diferentes Varreduras e Layouts

Marcio R. Juliato , Eduardo H. Tanaka , Christian Baudet , Miguel Galves , Thiago T. Coelho
VII Congreso Iberoamericano de Informática Educativa (RIBIE 2004), Oct 2004, Monterrey, Mexico. pp.630 - 639
Conference papers hal-01093641v1
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TFlex: Um Simulador de Teclado com Múltiplos Modos de Varredura

Marcio R. Juliato , Eduardo H. Tanaka , Christian Baudet , Miguel Galves , Thiago T. Coelho
VI Simpósio sobre Fatores Humanos em Sistemas Computacionais (IHC 2004), Dec 2004, Curitiba, Brazil
Conference papers hal-01093638v1
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Enumeração de traces e Identificação de Breakpoints : Estudo de aspectos da evolução.

Christian Baudet
Computer Science [cs]. UNICAMP (Université de Campinas), Brésil, 2010. Portuguese. ⟨NNT : ⟩
Theses tel-01092714v1
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Comparação de métodos para determinação de SNPs com medidas de confiabilidade

Christian Baudet , Miguel Galves , Zanoni Dias
[Technical Report] 06-15, Instituto de Computação - UNICAMP. 2006
Reports hal-01092998v1

Utilização do software GRASP para gerar arquivo de coordenadas com valores de potencial eletrostático.

Paula R. Kuser , Christian Baudet , Adauto L Mancini , Roberto H. Higa , Goran Neshich
[Technical Report] 24, Embrapa Informática Agropecuária. 2002
Reports hal-01093645v1

Experiência de utilização de XML no SMS

Roberto H. Higa , Christian Baudet , Esther M. de Freitas , Gabriela F. dos Santos , Adauto L Mancini
[Technical Report] 32, Embrapa Informática Agropecuária. 2002
Reports hal-01093648v1

Análise do grau de conservação de resíduos em proteínas com estrutura 3D resolvida utilizando o SMS

Roberto H. Higa , Christian Baudet , Adauto L Mancini , Paula R. Kuser , Goran Neshich
[Technical Report] 37, Embrapa Informática Agropecuária. 2002
Reports hal-01093654v1

Apresentação gráfica de parâmetros protéicos utilizando o Java Protein Dossier

Roberto H. Higa , Christian Baudet , Paula R. Kuser , Adauto L Mancini , Goran Neshich
[Technical Report] 40, Embrapa Informática Agropecuária. 2002
Reports hal-01093659v1
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Primeiro Curso STING Millennium Suite Chemogenomics: Ferramentas para Analisar Macromoleculares e Aplicações em Chemogenomics

Paula R. Kuser , Jair L. de Siqueira Neto , Jorge H. Fernandez , Roberto H. Higa , Christian Baudet
[Technical Report] 26, Embrapa Informática Agropecuária. 2002
Reports hal-01093008v1

Incorporação das propriedades rotâmeros e ocupância em métodos de análise estrutural de proteínas

Paula R. Kuser , Christian Baudet , Roberto H. Higa , Goran Neshich
[Technical Report] 34, Embrapa Informática Agropecuária. 2002
Reports hal-01093652v1

Curvatura da superfície de proteínas no Java Protein Dossier

Paula R. Kuser , Christian Baudet , Roberto H. Higa , Goran Neshich
[Technical Report] 38, Embrapa Informática Agropecuária. 2002
Reports hal-01093656v1

SMSLib - biblioteca C++ do Sting Millennium Suite

Roberto H. Higa , Christian Baudet , Adauto L Mancini , Amanda R. Mattiuz , Esther M. de Freitas
[Technical Report] 39, Embrapa Informática Agropecuária. 2002
Reports hal-01093658v1