Team members / External members / Alumni and former members

Team members

Ricardo Andrade was a postdoc funded by the program Ciência Sem Fronteiras from the Brazilian Ministry of Research. He is now a postdoc funded by FAPESP with the Instituto de Matemática e Estatística (IME) of the University of São Paulo (USP), together also with ERABLE. He is interested in algorithms and computational biology. Clara Benoît-Pilven, who defended her PhD in December 2016, is currently an engineer in the team, funded by the Inserm. She works with Patrick Edery (Hospices Civils de Lyon) and Vincent Lacroix on NGS data and alternative splicing.
Hubert Charles is a professor in biology and biometry at the Insa-Lyon. He is interested in symbiosis and computational biology. Audric Cologne is a PhD student who started in September 2016. He is co-advised by Patrick Edery (Hospices Civils de Lyon) and Vincent Lacroix and works on NGS data and alternative splicing.
Pilu Crescenzi is a full professor of computer science at the University of Florence. He is interested in bioinformatics, theoretical computer science and computer science education. Mariana Ferrarini was a PhD student at the University of Lyon 1 and at Inria, co-advised by Arnaldo Zaha from the UFRGS, Brazil, and Marie-France Sagot. She defended her PhD on December 10, 2015. She was postdoc in the team and is now postdoc at UFRGS, together also with Erable. She is interested in symbiosis, metabolism and regulation.
Mattia Gastaldello is a PhD student co-advised by Tiziana Calamoneri from the University of Rome La Sapienza, and Marie-France Sagot. Mattia will share his time between Rome and Lyon. Christian Gautier was a full professor emeritus of biometry at the University of Lyon 1. He is interested in statistics and computational biology. He is now a permanent visitor of the team.
Alex di Genova is a PhD student at the University of Chile, Santiago, advised by Alejandro Maass and Eric Goles. He is interested in genomics and computational biology. He did a “sandwich PhD” of 18 months at the University of Lyon, advised by Marie-France Sagot. He is now back in Santiago, finishing his PhD. Roberto Grossi is a full professor of computer science at the University of Pisa. He is interested in algorithm design and analysis, data structures and computational biology.
Leandro Ishi Soares de Lima started his PhD with us in May 2015, with a scholarship funded by the program Ciência Sem Fronteiras from the Brazilian Ministry of Research. He is co-advised by Giuseppe Italiano, Vincent Lacroix, and Marie-France Sagot. He is interested in algorithm design and computational biology. Giuseppe Italiano is a Full Professor at the University of Rome Tor Vergata. His interests are in the design and analysis of algorithms for solving theoretical and applied problems, notably coming from biology, in graphs and massive data sets.
Vincent Lacroix is an associate professor in computational biology and statistics at the University of Lyon 1. He is interested in computational biology, metabolism, alternative splicing, and NGS. Alberto Marchetti-Spaccamela is a full professor in computer science at Sapienza University of Rome. He is interested in algorithm design and analysis, and complex networks.
Andrea Marino is a temporary researcher at the University of Pisa. He is interested mainly in graph algorithms and enumeration. Arnaud Mary is an associate professor in computer science and computational biology at the University of Lyon 1. He is interested in graph theory, algorithmics, and since joining us, in computational biology.
Carol Moraga Quinteros is a PhD student who started in September 2016. She is interested in small RNAs. Nadia Pisanti is a researcher (assistant professor) of computer science at the University of Pisa. She is interested in computational biology and algorithms.
Henri Taneli Pusa is a PhD student at the University of Lyon 1. He is interested in mathematics, computational biology and game theory. His scholarship is funded by the H2020-­MSCA-­ETN-­2014 project MicroWine. Marie-France Sagot is a director of research at Inria. She is interested in algorithm design and analysis, combinatorics, computational biology, and symbiosis.
Claire Sauer is our assistant, shared with another Inria Team. Alexander Schönhuth is a tenured Principal Investigator at the CWI in Amsterdam. His interests are at the interfaces of statistics, discrete mathematics and pattern recognition on the one hand, and molecular biology and biomedicine on the other hand.
Camille Sessegolo was a Master 2 student in bioinformatics at the University of Lyon 1 with Vincent Lacroix. She is since Sept 2017 a PhD student in the team. She is interested in NGS analysis and alternative splicing. Blerina Sinaimeri was a postdoc in combinatorics and computer science at Inria. She is now a Junior Researcher at Inria. She is interested in combinatorics, algorithm design and analysis, and computational biology.
Leen Stougie is researcher at the CWI, and a full professor in operations research at the Free University of Amsterdam. At the CWI, he is heading the Life Sciences and Health group. He is interested in combinatorics, algorithm design and complexity, and computational biology. Fabrice Vavre is a director of research at the CNRS. He is interested in the host-parasite relation.
André Veríssimo is a PhD student in computer science and computational biology co-advised by Susana Vinga and Marie-France Sagot. He is interested in genomics, and biological networks. André will be physically located at IDMEC, IST, Lisbon, Portugal, with however frequent, long stays in Lyon. Alain Viari is a director of research at Inria. He is interested in computational biology (proteomics, genomics, networks) and in algorithm design. He is Deputy Scientific Director at Inria in charge of the ICST for Life and Environmental Sciences.
Cristina Vieira-Heddi is a full professor in biology and biometry at the University of Lyon 1. She is interested in transposable elements. Laura Urbini is a PhD student in computer science and computational biology co-advised by Catherine Matias (Laboratoire de Probabilités et Modèles Aléatoires – UMR CNRS 7599, Université Paris Diderot) and Marie-France Sagot. She is interested in co-phylogeny.
Martin Wannagat was PhD student at the University of Lyon 1, France, and Inria, co-advised by Leen Stougie, Alberto Marchetti-Spaccamela (Sapienza University of Rome) and Marie-France Sagot. He is now engineer in the team, funded by Inria. He is interested in metabolism, symbiosis, and game theory. Irene Ziska was a Master 2 student at the Free University of Berlin doing her research-training period in Erable with Marie-France Sagot, in collaboration also with Susana Vinga from the IST at Lisbon, Portugal. From October 2017, she will be a PhD student in the team. She is interested in optimisation, metabolism, and species communities.

External members

Laurent Jacob is a Junior Researcher at the CNRS. He is interested in statistics for biology. He is an external member of ERABLE. Susana Vinga is a researcher at the Instituto Superior Técnico at Lisbon. She is an external member of ERABLE.

Alumni and former members (from 2011 on)

Vicente Acuña was a PhD student advised by Marie-France Sagot and Christian Gautier funded by Conycit and the team. He defended in June 2010. He was then postdoc in the team. He is interested in algorithms and computational biology. He is now Scientist at the Centro de Modelamiento Matemático (CMM) of the University of Chile, Santiago. Christian Baudet was a postdoc at the LBBE-UCBL-CNRS. He is interested in algorithm design and analysis, and in computational biology. He has now a position at the Centre Léon-Bérard at Lyon, France.
Etienne Birmelé is an associate professor at the University of Évry who spent one year of delegation in our team, funded by the ERC AdG SISYPHE. He will be as of October 2013 full professor at the University of Paris 5. Florence Bouheddi was the project-team’s assistant until December 2015.
Matteo Brilli was a postdoc in bioinformatics at Inria. After a postdoc at the Fondazione Edmund Mach in the Trento area, Italy, he is now senior postdoc at the University of Padova, Italy. Lilia Brinza was a postdoc in computational biology and statistics at Inria. She is interested in regulation, networks, and symbiosis. She has now works at Maat Pharma, in Lyon.
Émilie Chautard was a post-doc in computational biology at Inria and Inserm, co-advised by Didier Auboeuf from the Centre de Recherche en Cancérologie Lyon (CRCL) and by Vincent Lacroix. She is interested in RNA-seq, alternative splicing, protein interactions and cancer. She now has a position at Sanofi-Lyon. Marina da Graça was our assistant from September 2015 to August 2017, shared with another Inria Team.
Beatrice Donati was a PhD student jointly at the University of Florence, University of Lyon 1, France, and Inria, co-advised by Pierluigi Crescenzi and Marie-France Sagot. She defended in November 2014. She is interested in computational biology, algorithms and complexity. She is now postdoc at the University of Florence, Italy. Pierre-Antoine Rollat-Farnier was a PhD student in computational biology at the University of Lyon 1 and at the INRIA, co-advised by Laurence Mouton, Fabrice Vavre and Marie-France Sagot. He defended in November 2014. He currently holds a 3-years position at the Hospices Civils of Lyon.
Alexandre Freire was a “sandwich” PhD from the University of São Paulo (USP), Brazil, who spent one year with the team, co-advised by Carlos Eduardo Ferreira (USP) and Marie-France Sagot. After a postdoc at the University of Campinas (UNICAMP), Brazil, he is now Assistant Professor at the University of São Paulo (USP), São Paulo, Brazil. Susan Higashi was a PhD student in computational biology at the University of Lyon 1 and at Inria, advised by Christian Gautier and Stefano Colella. She was interested in algorithm design, computational biology, and small RNAs. She is now Software Engineer at Amadeus.
Alice Julien Laferrière defended in December 2016 her PhD in computational biology, funded by the BacHBerry project) and co-advised by Susana Vinga (IDMEC, IST, Lisbon), Vincent Lacroix, and Marie-France Sagot. She is interested notably on metabolic networks. Janice Kielbassa was a postdoc in computational biology and statistics at Inria. She is interested in NGS data analysis. She works now at the Centre de Recherche en Cancérologie Lyon (CRCL).
Gunnar Klau was leader of the Life Sciences group at CWI in the Netherlands, and until early 2017 member of Erable. He is now Full Professor at the Heinrich Heine University of Düsseldorf in Germany. His main research interest is the design of discrete algorithms for problems in bioinformatics, in particular in the area of network analysis. Cecilia Klein was a PhD student at the University of Lyon 1 and at Inria, co-advised by Ana Tereza Vasconcelos and Marie-France Sagot. She defended her PhD in November 2013. She was then postdoc in the team. She is interested in computational biology. She is now postdoc at the Centre de Regulació Genòmica in Barcelona, Spain.
Hélène Lopez-Maestre was a PhD student in computational biology co-advised by Vincent Lacroix and Cristina Vieira. She is interested notably in transposable elements and NGS. She defended her PhD on February 15, 2017. She is now Engineer at the Centre Léon-Bérard, Lyon. Camille Marchet was an engineer at Inria funded by the Technological Development Actions (ADT). She is interested in computational biology, notably NGS. She is now a PhD student in the GenScale team at Inria.
Nuno Mendes was a PhD student at the University of Lyon 1 and at the Instituto Superior Técnico of Lisbon, Portugal, advised by Marie-France Sagot and Ana Teresa Freitas. He defended in June 2011. He was interested in small RNAs and regulation. He is now Software Engineer at Pentaho in Lisbon, Portugal. Paulo Milreu was a PhD student at the University of Lyon 1 and at the CNRS, advised by Vincent Lacroix, Christian Gautier and Marie-France Sagot. He defended in December 2012. He is interested in algorithms, computational biology, and metabolism. He is now working at TecSinapse to develop a bridge between the company and academia.
Igor Nor was a postdoc in computer science at the CNRS. He is now working at HP-Labs in Israel. Nina Paffoni was a Master 2 student in bioinformatics at the University of Lyon 1 with Blerina Sinaimeri and Stéphane Dray from the LBBE. She is interested in cophylogeny and ecology.
Delphine Parrot was a postdoc in biology and bioinformatics with a scholarship funded by the BacHBerry project. She is interested in microbial biology, symbiosis, metabolism and regulation. She is now postdoc in the Marine Natural Products Team at the Helmholtz Centre for Ocean Research in Kiel, Germany. Alexandra Popa was a PhD student in computational biology and statistics at the University of Lyon 1, advised by Christian Gautier and Dominique Mouchiroud. She defended in May 2011. She now works at CeMM Research Center for Molecular Medicine, Vienna, Austria.
Gustavo Sacomoto was a PhD student in computational biology jointly at the University of Florence, University of Lyon 1, France, and Inria, co-advised by Pierluigi Crescenzi, Vincent Lacroix and Marie-France Sagot. He defended his PhD on March 6th, 2014. He was then a postdoc in the team. He is now working at Google in Paris, France. Patricia Simões was a PhD student in bioinformatics at the University of Lyon 1, advised by Marie-France Sagot and Sylvain Charlat. She defended in March 2012. She was interested in symbiosis. She is now working at Inserm in Lyon.

Permanent link to this article: https://team.inria.fr/erable/en/team-members/