Team members / External members / Alumni and former members

Team members

Christian Gautier was 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. François Gindraud is a permanent Research Engineer at Inria. He is currently attached to ​Erable.
Roberto Grossi is Full Professor of computer science at the University of Pisa. He is interested in algorithm design and analysis, data structures and computational biology. Nicolas Homberg was a Master 2 student at the Institut Polytechnique of Grenoble working at Erable. He was interested in genome assembly. He is now an Inra-Inria PhD student co-supervised by Christine Gaspin from Inra Toulouse and Marie-France Sagot from Erable.
Giuseppe Italiano is Full Professor at the LUISS University in Rome. 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. Laurent Jacob is Junior Researcher at the CNRS. He is interested in developing statistical and machine learning methods to solve problems in molecular biology.
Vincent Lacroix is 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 Full Professor in computer science at Sapienza University of Rome. He is interested in algorithm design and analysis, and complex networks.
Maxime Mahout is a PhD student from the University of Paris-Saclay supervised by Sabine Peres. He is interested in metabolism. Arnaud Mary is 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.
Scheila Gabriele Mucha is a postdoc who started in December 2019. She is a biologist interested in small RNAs. Luca Nesterenko is a PhD student co-supervised by Laurent Jacob and Bastien Boussau (LBBE) in collaboration also with Philippe Veber (LBBE). He is interested in phylogeny and machine learning.
Sabine Peres is Full Professor in mathematical and computational biology at the University of Lyon 1. She is interested in mathematical modelling and computational methods of metabolism. Nadia Pisanti is Associate Professor of computer science at the University of Pisa. She is interested in computational biology and algorithms.
Solon Pissis is Principal Investigator at the CWI in Amsterdam. His interests are algorithms and data structures on sequences and trees for pattern matching, indexing, comparison, and finding regularities. Anouchka Ronceray is our assistant, shared with another Inria Team.
Marie-France Sagot (ecstatically eating a Brazilian ice-cream called Chicabon in the photograph) is Director of Research at Inria. She is interested in algorithm design and analysis, combinatorics, computational biology, and symbiosis.
Occasionally, she also very happily does baby-sitting for the children of the members of the team.
Blerina Sinaimeri was a postdoc in combinatorics and computer science at Inria. She is Junior Researcher at Inria in detachment, and is now Associate Professor at LUISS University in Rome. She is interested in combinatorics, algorithm design and analysis, and computational biology.
Leen Stougie is Principal Investigator at the CWI, and 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.

Johanna Trost is an intern at the LBBE and Erable. She is advised by Laurent Jacob. She is interested in evolution and machine learning.
Alain Viari is Director of Research at Inria. He is interested in computational biology (proteomics, genomics, networks) and in algorithm design. He was Deputy Scientific Director at Inria in charge of the ICST for Life and Environmental Sciences from 2012 until Jan 2018. Cristina Vieira-Heddi is Full Professor in biology and biometry at the University of Lyon 1. She is interested in transposable elements.
Antoine Villie is a PhD student supervised by Laurent Jacob. He is interested on machine learning methods for pangenomics.

External members

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. Ricardo Andrade was a postdoc funded by the program Ciência Sem Fronteiras from the Brazilian Ministry of Research, and later 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. He is now working at BGene in Grenoble.
Christian Baudet was a postdoc at the LBBE-UCBL-CNRS. He is interested in algorithm design and analysis, and in computational biology. He now works at Rigshospitalet, Copenhagen, Denmark. Clara Benoît-Pilven, who defended her PhD in December 2016, was postdoc in the team, funded by the Inserm. She worked with Patrick Edery (Hospices Civils de Lyon) and Vincent Lacroix on NGS data and alternative splicing. She now is postdoc at the University of Helsinki in Finland.
Etienne Birmelé was a Full Professor at the University of Paris 5 until 2021 and is now a Full Professor at the University of Strasbourg who spent one year of delegation in our team, funded by the ERC AdG SISYPHE. Marianne Borderes started a PhD (funded by the ANRt) in February 2018, co-supervised by Marie-France Sagot and Susana Vinga (IST, Lisbon) together with Maat Pharma, and in particular with Lilia (Brinza) Boucinha.
Florence Bouheddi was the project-team’s assistant until December 2015. Laurent Bulteau was a postdoc in computer science and computational biology at Inria with a scholarship funded by the BacHBerry project. He is since 2015 a CNRS junior researcher at the University of Paris-Est Marne-la-Vallée, France.
Matteo Brilli was a postdoc in bioinformatics at Inria. After a postdoc at the Fondazione Edmund Mach in the Trento area, and at the University of Padova, Italy, he is now Assistant Professor at the University of Milan. Lilia Brinza was a postdoc in computational biology and statistics at Inria. She is interested in regulation, networks, and symbiosis. She now works at Evotec, in Lyon.
Hubert Charles is Full Professor in biology and biometry at the Insa-Lyon. He is interested in symbiosis and computational biology. 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.
Audric Cologne was a PhD student who started in September 2016 and defended in October 2019. He was co-advised by Patrick Edery (Hospices Civils de Lyon) and Vincent Lacroix and worked on NGS data and alternative splicing. He was then postdoc at Erable working on the same topics until early 2022. He is now Research Fellow at BioAster. Pilu Crescenzi is a Full Professor of computer science at Gran Sasso, Italy. He is interested in bioinformatics, theoretical computer science and computer science education.
Eric Cumunel was a Master 2 student at the University of Lyon working at Erable. He was then engineer at Erable funded by the ANR project Aster. He wass interested in metabolism and regulation. 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. 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 for one year after the PhD, and then went for a postdoc at UFRGS, Brazil. She is now postdoc in another team at the LBBE in Lyon. She is interested in symbiosis, metabolism and regulation.
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. Mattia Gastaldello was a PhD student co-advised by Tiziana Calamoneri from the University of Rome La Sapienza, and Marie-France Sagot. Mattia shared his time between Rome and Lyon. He defended his PhD in February 2018.
Alex di Genova was a PhD student at the University of Chile, Santiago, advised by Gonzalo Ruz and Alejandro Maass. He is interested in genomics and genome assembly. He did a “sandwich PhD” of 18 months at the Univ. of Lyon, advised by Marie-France Sagot. He defended his PhD in November 2017 and then came back in Lyon since December 2017 as postdoc until November 2019. He is since February 1st, 2020, postdoc at Rare Cancer Genomics, Lyon, France, and will soon be working at the Universidad de O’Higgins, Chile. 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 Microsoft in Ireland.
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 was interested notably on metabolic networks. She now works as Data Scientist and Bioinformatics Consultant at Soladis/Roche in Basel, Switzerland Janice Kielbassa was a postdoc in computational biology and statistics at Inria. She is interested in NGS data analysis. She then worked at the Centre de Recherche en Cancérologie Lyon (CRCL). For family reasons, she is now back in Germany.
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. 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 was co-advised by Giuseppe Italiano, Vincent Lacroix, and Marie-France Sagot. He was interested in algorithm design and computational biology. He defended in April 2019. He now works as Scientific Software Developer at EBI, UK, in the group of Zamin Iqbal.
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 Associate Professor at the University of Barcelona, Spain, while being team leader at Clarivate. 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 was until February 2018 Engineer at the Centre Léon-Bérard, Lyon. She has now a position at the Pasteur Institute in Paris.
Camille Marchet was an engineer at Inria funded by the Technological Development Actions (ADT). She is interested in computational biology, notably NGS. She did a PhD in the GenScale team at Inria and is now a CNRS Junior Researcher in Lille. Andrea Marino was a temporary researcher at the University of Pisa and is now Assistant Professor at the University of Florence, Italy. He is interested mainly in graph algorithms and enumeration.
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. After having held a position as Head of Lisbon Office Operations at Practio in Lisbon, Portugal, he is now working at Facebook in the US. 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 worked for a while at TecSinapse to develop a bridge between the company and academia, and has moved now to another company.
Carol Moraga Quinteros was a PhD student who started in September 2016. She defended in November 2020. She was interested in small RNAs. She currently is postdoc in another team at the LBBE. Igor Nor was a postdoc in computer science at the CNRS. He is now working at HP-Labs in Israel.
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 was then postdoc in the Marine Natural Products Team at the Helmholtz Centre for Ocean Research in Kiel, Germany, and is now working at Evotec. 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.
Henri Taneli Pusa was a PhD student at the University of Lyon 1. He was interested in mathematics, computational biology and game theory. His scholarship was funded by the H2020-­MSCA-­ETN-­2014 project MicroWine. He defended in February 2019. After a very nice and long trip to Latin America in a cargo boat, he had a postdoc position at the University of Luxembourg. He is now postdoc at the Aalto University, Finland. 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 position at the Hospices Civils of Lyon.
Claire Sauer was our assistant, shared with another Inria Team, until December 2019. 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 San Francisco, USA.
Alexander Schönhuth was a tenured Principal Investigator at the CWI in Amsterdam. He is now Professor at the University of Bielefeld, Germany. 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 was since Sept 2017 a PhD student in the team. She defended in 2021. She is interested in NGS analysis and alternative splicing, and now works in a company.
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. Laura Urbini was 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 defended in October 2017. She was then postdoc at the Centre Léon-Bérard at Lyon, France. For family reasons, she then moved to Geneva where she is now looking for a position.
Fabrice Vavre is a Director of Research at the CNRS. He is now director of the LBBE. Augusto Vellozo was postdoc in the team. He is now working at TecSinapse to develop a bridge between the company and academia.
André Veríssimo was a PhD student in computer science and computational biology co-advised by Susana Vinga and Marie-France Sagot. He was interested in genomics, and biological networks. André was physically located at IST, Lisbon, Portugal, with however stays in Lyon. He defended in February 2021. Yishu Wang did her Master 2 (ENS-Lyon Computer Science) internship with Blerina Sinaimeri and Marie-France Sagot and defended from February to June 2018. She then did a PhD with the same plus Mário Figueiredo (IST, Lisbon, Portugal) that she defended in October 2021. She was interested in graph theory and algorithms, combinatorics and cophylogeny. She is now Biomodeler at Novadiscovery.
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 at BGene in Grenoble. 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. Since October 2017, she was a PhD student in the team. She defended in November 2020. She was interested in optimisation, metabolism, and species communities. She is now working in a private company.

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