Below appears the students and postdocs I (co-)advised over the years. The links where any exists should be up-to-date. If they are not, please, drop me a message (see Contact).
Current PhD students
Nicolas Homberg, co-advised with Christine Gaspin, funded by an Inra-Inria PhD grant
Current PhD students in co-supervision with another country
Gabriela Torres Montanaro, co-advised with Ariel M. Silber, University of São Paulo, Brazil, with funds by FAPESP, Brazil
Current postdocs
Scheila G. Mucha, funded by Inria
Ex-PhDs, sandwich PhDs, visiting PhDs, or postdocs
Nadia Pisanti, PhD defended in 2001, co-advised with Fabrizio Luccio, later came back as postdoc for 9 months, currently Associate Professor at the Department of Computer Science of the University of Pisa, Italy
Sébastien Provencher, postdoc for 2 years starting from 2001, currently high school teacher in Canada
Laurent Marsan, PhD defended in 2002, co-advised with Maxime Crochemore, currently Associate Professor at IUT Versailles
Estela Maris Rodrigues, PhD defended in 2003, co-advised with Yoshiko Wakabayashi, currently Associate Professor at Mackenzie University, São Paulo, Brazil
Philippe Blayo, PhD defended in 2003 at the Université de Marne-la-Vallée, co-advised with Maxima Crochemore
Julien Allali, PhD defended in 2004, co-advised with Maxime Crochemore, currently Associate Professor at the LABRI, University of Bordeaux
Raquel Tavares, postdoc for 2 years, currently Associate Professor at University Lyon 1
Susana Vinga, Lisbon, Portugal, PhD defended in 2005, advisor: Jonas de Almeida, currently Associate Professor at the INESC-IST, Lisbon
Jeane C. B. de Melo, PhD defended in 2005, co-advised with Kátia Guimarães, University of Pernambuco, Brazil, currently Associate Professor at the Federal Agricultural University of Recife
Said Sadique Adi, PhD defended in 2005, co-advised with Carlos Eduardo Ferreira, University of São Paulo, Brazil, currently Associate Professor at the Universidade Federal de Mato Grosso do Sul, Brazil
Pierre Peterlongo, PhD defended in 2006, co-advised with Maxime Crochemore and Nadia Pisanti, currently CR2 in the GenScale INRIA Project-Team, Rennes
Eric Tannier, postdoc for one year starting June 2003, currently CR1 in the Beagle INRIA Project-Team, Lyon
Patricia Thébault, postdoc for two years starting September 2005, currently Associate Professor at University of Bordeaux
Cinzia Pizzi, postdoc for one year until Dec. 2007, currently Associate Professor at Padova University, Italy
Vincent Lacroix, PhD defended in 2007, University of Lyon 1, CNRS BDI scholarship, was postdoc at Centre de Regulació Genòmica for 14 months before doing 9 months of postdoc back in the team; currently Associate Professor in Erable
Paulo Gustavo Fonseca, postdoc for one year after part of his PhD done in the team and defended in 2008, currently Associate Professor at INESC-ID, Instituto Superior Técnico, Lisbon
Claire Lemaitre, PhD defended in 2008, University of Lyon 1, co-advised with Christian Gautier, currently CR2 in the GenScale INRIA Project-Team, Rennes
Marc Deloger, PhD defended in 2009, University of Lyon 1, co-advised with Cristina Vieira, currently bioinformaticien at the Bioinformatics Platform of Gustave Roussy
Marília Dias Vieira Braga, PhD Defended in 2009, AlBan and University of Lyon I, co-advised with Eric Tannier, currenly Associate Researcher at the Genome Informatics group, Bielefeld University, Germany
Ludovic Cottret, PhD defended in 2009, University of Lyon 1, co-advised with Hubert Charles, INSA Lyon, currently IR INRA, Toulouse
Augusto Vellozo, postdoc for two years from 2008, currently Researcher at TecSinapse, Brazil
Amélie Véron, postdoc for two years from 2008, currently Project manager at Complex Systems Modeler at The CoSMo Company, Lyon
Igor Nor, postdoc for 2 years starting from 2008, currently Senior researcher at Hewlett-Packard Laboratories, Haifa, Israel
Yves-Pol Deniélou, PhD defended in 2010, University of Grenoble, co-advised with Alain Viari, currently theatre actor and author
Nuno Mendes, PhD defended in 2011, IST at Lisbon-Portugal and University of Lyon I, co-advised with Ana Teresa Freitas, worked with Software Engineer at Findmore Consulting, Portugal, and currently with Practio
Alexandra Carvalho, PhD defended in 2011, IST, Lisbon, Portugal, co-advised with Arlindo Oliveira, currently Associate Professor at Instituto de Telecomunicações, Instituto Superior Técnico (IST), Lisbon, Portugal
Vicente Acuña, PhD defended in 2010, then postdoc for 18 months, currently Scientist at the Center for Mathematical Modeling (CMM) at the University of Chile, Santiago, Chile
Alexandre Freire, USP, São Paulo, Brazil, PhD defended in Brazil, supervisor: Carlos Eduardo Ferreira, sandwich PhD CNPq scholarship, currently Associate Professor at USP-Leste
Patricia Simões, PhD defended in 2012, FCT, University of Lyon I, co-advised with Sylvain Charlat, currently Research Assistant, Hospices Civils de Lyon
Matteo Brilli, postdoc for 2 years from 2010, currently Researcher at Bio Computing Project (BiP), Italy
Lilia Brinza, postdoc for 8 months starting from 2012, currently Bioinformatics manager at MaaT Pharm, Lyon
Janice Kielbassa, postdoc for 2 years starting from, currently engineer at Centre de Recherche en Cancérologie Lyon, CRCL
Paulo Vieira Milreu, PhD defended in 2012, University of Lyon I, co-advised with Vincent Lacroix and Christian Gautier, currently Researcher at TecSinapse, Brazil
Gustavo Sacomoto, PhD defended in 2014, University of Lyon I, then postdoc for one year, co-advised with Pierluigi Crescenzi, University of Florence, Italy, and Vincent Lacroix, currently Researcher at Google Paris
Pierre-Antoine Rollat-Farnier, PhD defended in 2014, University of Lyon I, co-advised with Laurence Mouton and Fabrice Vavre, currently IR CHU Lyon
Cecília Klein, PhD defended in 2014, University of Lyon I, co-advised with Ana Tereza de Ribeiro Vasconcelos, currently postdoc at the CRG, Barcelona, Spain
Beatrice Donati, PhD defended in 2015, University of Lyon I, co-advised with Pierluigi Crescenzi, University of Florence, Italy
Blerina Sinaimeri, postdoc from 2012 to 2015, now Inria Junior Researcher in the Erable Team
Susan Higashi, PhD defended in 2014, University of Lyon I, co-advised with Christian Gautier and Stefano Colella, then postdoc in the team for one year, currently working for a private company on software development
Christian Baudet, visiting PhD student from University of Campinas, Brazil, and then postdoc from 2011 to 2014; currently engineer at Centre Léon Bérard, Lyon, France
Laurent Bulteau, postdoc from 2014 to 2015, now Junior Researcher at CNRS, University of Marne-la-Vallée, France
Delphine Parrot, postdoc from 2014 to 2016, now postdoc at GEOMAR Centre for Marine Biotechnology, Kiel, Germany
Mariana Galvão Ferrarini, PhD defended in December 2015, co-advised with Arnaldo Zaha, Federal University of Rio Grande do Sul, then postdoc in the team for 1 year
Scheila G. Mucha, UFRGS, Porto Alegre, Brazil, PhD defended in Brazil, supervisor: Arnaldo Zaha, sandwich PhD Capes-Cofecub scholarship
Martin Wannagat, PhD defended in July 2016, University of Lyon 1, co-advised with Leen Stougie and Alberto Marchetti-Spaccamela, then postdoc in the team for 3 months, now engineer for 2 years funded by Inria
Alice Julien Laferrière, PhD defended in December 2016, co-advised with Susana Vinga and Vincent Lacroix
Laura Urbini, PhD defended in October 2017, co-advised with Catherine Matias
Alex di Genova, visiting PhD student, PhD defended in November 2017, advised by Alejandro Maass, CMM University of Chile, Santiago, and Eric Goles, University Adolfo Ibañez, Santiago, Chile
Mattia Gastaldello, PhD defended in February 2018, co-advised with Tiziana Calamoneri, Sapienza University of Rome, Italy
Gabriela Paludo, visiting PhD student, advised by Henrique Ferreira, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
Rafael Nahat, visiting PhD student, co-advised by Aldo Tonso and José Gregório Cabrera Gomez, University of São Paulo, Brazil
Henri Taneli Pusa, PhD defended in February 2019, co-advised with Alberto Marchetti-Spaccamela
Leandro Ishi Soares de Lima, PhD defended in April 2019, co-advised with Vincent Lacroix and Giuseppe Italiano
Ricardo Andrade, postdoc initially funded for two years by the Science without Frontiers program from Brazil, and then by Fapesp, Brazil, in the latter case co-advised with Roberto Marcondes Cesar Junior, USP, Brazil
Alex di Genova, postdoc for 2 years, from December 2017 until November 2019, funded by Inria
Carol Moraga Quinteros, PhD defended in November 2020, co-advised with Rodrigo Gutiérrez, Universidad Catolica de Chile, funded by Conicyt
Irene Ziska, PhD defended in November 2020, co-advised with Susana Vinga, funded by Inria
André Veríssimo, PhD defended in February 2021, co-advised with Susana Vinga (main advisor), Inesc-ID, IST, Lisbon, Portugal
Marianne Borderes, PhD defended in July 2021, co-advised with Susana Vinga, funded by ANRt, together with MaatPharma, and notably Lilia (Brinza) Boucinha and Emmanuel Prestat
Yishu Wang, PhD defended in October 2021, co-advised with Blerina Sinaimeri and Mário Figueiredo, IST, Lisbon, Portugal
Ex-students who remained in academia
Yoan Diekmann, pre-Master student, co-advised with Eric Tannier and Julien Allali; currently Research Associate at UCL, UK
Steffen Heyne, Erasmus student, co-advised with Julien Allali, currently postdoc at Max Planck Institute of Immunobiology and Epigenetics, Germany
Alexis Gambis, DEA University of Marne-la-Vallée defended in 2004, currently a filmmaker specialised in docu-fiction, New York, USA
Florence Cavalli, Master 2 University of Lyon 1, defended in 2006, co-advised with Cristina Vieira, currently postdoc at University of Toronto, Canada
Cyril Fournier, 4th year of BIM, Insa-Lyon, worked for 3 months in the team in 2013, currently looking again for an engineer position
Maria-Emilia Puig Lombardi, Master 1 of AgroParisTech, Paris, currently Research Engineer at Institut Curie, Paris
Hong Phong Pham, Master student ENS Lyon, defended in 2015, co-advised with Laurent Bulteau and Arnaud Mary, currently doing a PhD at the Université Paris-Sud
Gregoire Beaudoire, Master student ENS Computer Science Department Lyon
Irene Ziska, Master student Free University of Berlin
Yishu Wang, Master student ENS Computer Science Department Lyon
Eric Cumunel, Master student University Lyon 1
Nicolas Homberg, Master student Polytech Grenoble and Hochschule Offenburg, Germany
Ex-students (DESS/DEA/Master) who did not continue in academia
Gérald Balayssac, DEA
Stéphane Bizard, DEA
Laurent Canet, DEA, co-supervision with Maxime Crochemore and Julien Allali
Anne Cariou, 5th year École Vétérinaire Maison-Alfort
Frédéric Chataigner, DEA, co-supervision with Christian Choffrut
Sophie Créno, 5th year engineering school and DEA
Philippe Lamy, 4th year engineering school
Ludovic Le Botlan, 4th year engineering school
Sylvain Lhullier, DEA
Anne Marcel, DESS
Muriel Meites, DESS
Benoît Olivieri, DEA
Gregory Pageot, pre-Master student, University of Marne-la-Vallée, co-advised with Maxime Crochemore and Julien Allali
Cathy Philippe, DEA, co-supervision with Christine Gaspin and Thomas Faraut, INRA Toulouse
Eric Poiret, 4th year engineering school
Sébastien Wirth, 4th year university
Marina Zelwer, DEA
Juliet Ansel, Master
