e-mail: jean-francois.flot@ulb.be

Research interests

Molecular approaches to species delimitation - Molecular systematics - Genome assembly - Experimental evolution - Genome evolution - Bioinformatics

Curriculum vitae

Selected publications

For a complete list see Google Scholar

Flot J-F (2010) SeqPHASE: a web tool for interconverting phase input/output files and fasta sequence alignments. Molecular Ecology Resources 10, 162-166.

This article presents a computer programme facilitating the inference of haplotype sequences from genotypes in a population of individuals.

Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton. BMC Evolutionary Biology 10, 372.

In this article I introduce a new graphical approach to species delimitation using haplowebs, i.e. haplotype networks on which sequences found co-occurring in heterozygous individuals are connected with curves. This approach bases itself on allele sharing to delineate species and therefore does not require species to be monophyletic (hence it is not affected by incomplete lineage sorting).

Flot J-F, Blanchot J, Charpy L, et al. (2011) Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecology 11, 22.

This article presents another type of haploweb (tree-based instead of network-based) and its application to species delimitation in corals.

Flot J-F, Hespeels B, Li X, et al. (2013) Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500, 453-457.

Available biological and paleontological data suggest that bdelloid rotifers have been reproducing in a purely asexual fashion for tens of million years, but this hypothesis remains controversial. This article presents the highly unusual genome structure of bdelloids and interprets it as the result of ameiotic evolution.

Flot J-F, Bauermeister J, Brad T, et al. (2014) Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Molecular Ecology 23, 1405-1417.

This article uses haplowebs and phylogenetic trees to delineate amphipod species inhabiting the underground of the Mangalia region of Romania (including Movile Cave, a rare example of chemoautotrophic ecosystem analogous to the those found on oceanic ridges) and analyses their symbioses with sulphur-oxidizing bacteria of the genus Thiothrix.

Flot J-F (2015) Species delimitations’s coming of age. Systematic Biology 64, 897-899.

The article introduces a special issue of Systematic Biology focused on new molecular approaches to species delimitation.

Flot J-F, Marie-Nelly H, Koszul R (2015) Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Letters 589, 2966-2974.

This article reviews recent the advances and perspectives offered by 3C (chromosome conformation capture) in the field of genome sequencing.

Debortoli N, Li X, Eyres I, et al. (2016) Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex. Current Biology 26, 723-732.

This article (whose first author was a PhD student I co-supervised in Namur) reports that bdelloid rotifers of the genus Adineta exchange DNA both within and between species. As signatures of exchanges are scattered among genomic regions evolving asexually, these exchanges are better explained by horizontal gene transfers than by meiotic sex.

Schwager EE, Sharma PP, Clarke T et al. (2017) The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biology 15, 62.

This article demonstrates that spiders and scorpions probably share an ancient, ancestral whole-genome duplication.

Dellicour S, Flot J-F (2018) The hitchhiker's guide to single-locus species delimitation. Molecular Ecology Resources 18, 1234-1246.

This article provides a comparative benchmark of single-locus approaches to species delimitation (namely ABGD, GMYC, bGMYC, PTP, bPTP and haplowebs) under various simulated conditions.

Borko Š, Collette M, Brad T, Zakšek V, Flot J-F et al. (2019) Amphipods in a Greek cave with sulphidic and non-sulphidic water: phylogenetically clustered and ecologically divergent. Systematics and Biodiversity 17, 558–572.

This article (stemming partly from the MSc thesis of co-first author Martin Collette) investigates the morphology and ecology of the three Niphargus species present in the sulfidic cave of Melissotrya near Larissa in Greece (including the description of a new species, N. gammariformis).

Limasset A, Flot J-F, Peterlongo P (2020) Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 36, 1374-1381.

In this article we introduce a novel graph-based approach to short-read correction and demonstrate that it is more accurate than state-of-the-art k-mer spectrum-based approaches.

Spöri Y, Flot J-F (2020) HaplowebMaker and CoMa: two web tools to delimit species using haplowebs and conspecificity matrices. Methods in Ecology and Evolution 11, 1434-1438.

This article (from the MSc and PhD research of first author Yann Spöri) introduces the two web-based programs https://eeg-ebe.github.io/HaplowebMaker/ and https://eeg-ebe.github.io/CoMa/.

Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F (2021) Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms. BMC Bioinformatics 22, 303.

This article (from the PhD research of first author Nadège Guiglielmoni) explores computational strategies to obtain properly collapsed genome assemblies for diploid, heterozygous species.

Ramírez-Portilla C, Baird AH, Cowman PF, Quattrini AM, Harii S, Sinniger F, Flot J-F (2022) Solving the coral species delimitation conundrum. Systematic Biology 71, 461–475.

This article, from the PhD thesis of first author Catalina Ramírez-Portilla, examines coral morphospecies that are not reciprocally monophyletic in mitochondrial DNA phylogenies and are for this reason often assumed to hybridize. In the case of tabular Acropora from Okinawa (Japan) that fall in this category, it demonstrates that they are actually «good» species (i.e. clearly distinguished using morphology, cross-breeding tests and patterns of allele sharing at nuclear loci), with no evidence for ongoing hybridization.

Rodriguez Jimenez A, Guiglielmoni N, Goetghebuer L, Dechamps E, George IF, Flot J-F (2022) Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains. BMC Genomics 23, 618.

In this article, PhD student Ana Rodriguez Jimenez assembled complete circular genomes of five strains of sponge-isolated Vagococcus fluvialis bacteria and compared them with previously sequenced strains of the same species from other environments, revealing putative signature of symbiosis.

Bizic M, Brad T, Ionescu D, Barbu-Tudoran L, Zoccarato L, Aerts JW, Contarini P-E, Gros O, Volland JM, Popa R, Ody J, Vellone D, Flot J-F, Tighe S, Sarbu SM (2023) Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species. ISME Journal 17, 340-353.

In this article we assembled the complete circular genome of a Thiovulum strain from Movile Cave in Romania, described it as a new species candidate and compared its genome with those of closely related marine species of the same genus.

Malek-Hosseini MJ, Flot J-F, Fatemi Y, Babolimoakher H, Kuntner M, Diripasko OA, Jelić D, Bogutskaya NG (2023) The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi & Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters. Subterranean Biology 46, 97-127.

Here we describe a new species of cave fish from a sulfidic cave in Iran. Surprisingly, this species is found there in two morphological distinct forms (with and without mental disc), a spectacular example of 
intraspecific polymorphism.

Silva FE, Luna LW, Batista R, Röhe F, Gubili C, Farias IP, Hrbek T, Valsecchi J, Ribas CC, McDevitt AD, Dellicour S, Flot J, Boubli JP (2024) Impact of Quaternary Amazonian river dynamics on the diversification of uakari monkeys (genus Cacajao). Journal of Biogeography jbi.14844.

This article investigates the biogeography of a primate genus primarily associated with seasonally flooded forests in central and western Amazonia and shows that its diversification is heavily inluenced by river dynamics.

Faure R, Lavenier D, Flot J-F (2024) HairSplitter: haplotype assembly from long, noisy reads. Peer Community Journal 4, e96.

HairSplitter, from the PhD thesis of first author Roland Faure, is a groundbreaking approach to assemble noisy reads in a very accurate fashion, allowing to discriminate haplotypes in diploid organisms as well viral or microbial strains in metagenome assemblies even when the divergence between the sequences is much lower than the error rate of the reads.

Spöri Y, Flot J-F (2024) Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story. Briefings in Bioinformatics 25, bbae367.

This article (from the PhD thesis of first author Yann Spöri) shows how the Haxe programming language can be used to generate and maintain, from a single code, both a web version of a tool (for beginners and non-bioinformaticians) and a command-line version suited for advanced users and high-throughput applications. The web version (as well as the downloadable command-line version) can then be hosted very simply and for free on e.g. GitHub Pages (e.g https://eeg-ebe.github.io/SeqPHASE).

Team

Ginevra Lilli, Yann Spöri, Fabio Stoch and all MSc students)

1. 
   

Lab technicians

Esra Kaymak (2015-2016, shared with the group of Olivier Hardy)

Sandra Cervantes Arango (2017); now PhD student at the University of Oulu (http://www.oulu.fi/pyhajarvilab)

Florence Rodriguez (2019-present)

Postdoctoral researchers

Eulalia Banguera Hinestroza (2016-2019); now executive director of the Corporación para la Investigación en Ciencias Marinas, Manejo de Recursos y Tecnología (https://www.cimartec.org)

Antoine Limasset (2017-2018); now tenured research scientist at CNRS (http://www.cnrs.fr/)

Raoul Tuekam Kayo (2018-2019); now Assistant Professor at the University of Bamenda (http://uniba.cm/)

Fabio Stoch: 2021-present

Felipe Silva: 2021-present

PhD students

Nicolas Debortoli (2012-2018, co-supervised with Karine Van Doninck); formerly R&D Director at e-biom (http://e-biom.com); now bioinformatician in a research institute (https://www.narilis.be/facilities/namur-molecular-tech)

Alessandro Derzelle (2014-present, co-supervised with Karine Van Doninck)

Fabio Stoch (2016-2021), now postdoc in EEG group

Dieter Weber (2016-2022); now researcher at the Musée National d'Histoire Naturelle de Luxembourg (https://www.mnhn.lu)

Catalina Ramírez Portilla (2017-2023, co-supervised with Thomas Wilke)

Ana Rodriguez Jimenez (2017-2022, co-supervised with Isabelle George); now Senior Consultant in Life Sciences & Public Policy at Alcimed (https://www.alcimed.com/fr/)

Nadège Guiglielmoni (2018-2021, co-supervised with Romain Koszul), now postdoc at the University of Cologne (http://sex-lab.org)

Yann Spöri (2019-present, co-supervised with Simon Dellicour)

Claire Chauveau (2020-present, co-supervised with Serban Sarbu)

Hugo Ducret (2021-present, co-supervised with Marc Kochzius)

Roland Faure (2021-present, co-supervised with Dominique Lavenier)

Alice Salussolia (2021-present, co-supervised with Fabio Stoch)

Mohammed Tawfeeq (2021-present, co-supervised with Thomas Verdebout)

Sophie-Luise Heidig (2021-present, co-supervised with Danny Ionescu and Wim Vranken)

Antoine Houtain (2021-2024, co-supervised with Karine Van Doninck)

Stephen Bergacker (2022-present, co-supervised with Marc Kochzius)

Ginevra Lilli (2022-2024, co-supervised with Isabelle George)

Dina Mae Rañises (2023-present, co-supervised with Karine Van Doninck)

Helena Willard (2023-present, co-supervised with Jaap Kaandorp)

Olivier Collard (2024-present)

Ninon Lecoquierre (2024-present), co-supervised with Hidetaka Furuya and Wen-Juan Ma

Khaoula El Mchachti (2024-present), co-supervised with Charles Van der Henst

MSc students

Yann Spöri (2017)

Emilie Berns (2017-2018, co-supervised with Frédéric Sinniger)

Martin Collette (2017-2018)

Grégory Philippart (2017-2018, co-supervised with Philippe Grosjean)

Giula Puntin (2017-2018, co-supervised with David M. Baker)

Hisham Shaikh (2018-2019, co-supervised with Keren Maor-Landaw, Madeleine van Oppen and Geoffrey McFadden)

Ursula Swaelus (2018-2019)

Stephen Bergacker (2019-2020)

Pierrot Van der Aa (2019-2020)

Jessica Ody (2019-2020)

Jenny Arrendsdorff (2019-2020)

Juliana Vanegas Gonzalez (2020-2021, co-supervised with Catalina Ramirez-Portilla, James Tan and Zainudin Bachok)

Dina Mae Rañises (2020-2022, co-supervised with Machel Malay and Mark Vermeij)

Olivier de Thier (2022-2023, co-supervised with Roland Faure)

Erwan Denné (2022-2023, co-supervised with Marc Kochzius and Stephen Bergacker)

Maryeme Benounou (2023-2024, co-supervised with Mohammed M.Tawfeeq)

Khaoula El Mchachti (2023-2024, co-supervised with Charles Van der Henst)

Md. Khayrul Hasan (2023-2024, co-supervised with Dina Rañises and Mohammed M.Tawfeeq)

Galia Jbilou (2023-2024, co-supervised with Claire Chauveau)

Maxime Mees (2023-present, co-supervised with Felipe Innes Silva)

Tristan Permentier (2023-2024, co-supervised with Hugo Decret)

Sara Loutani (2024-present, co-supervised with Charles Van der Henst and Adam Valček)

Kevin Madrigal Ferrer (2024-present, co-supervised with Ikhwanuddin Abdulla)

Jeanny Magana (2024-present), co-supervised with Dina Mae Rañises

Paola Sidgwick (2024-present, co-supervised with Felipe Ennes Silva)

Claire de Walque (2024-present, co-supervised with Felipe Ennes Silva)

Interns and visiting researchers

Stephen Bergacker (2016-2017, 12 months)

Antoine Limasset (2016, 3 months)

Catalina Ramírez Portilla (2016, 1 month)

Yann Spöri (2016, 3 months)

René Desneux (2017, 1 month)

Max Le Bouder (2018, 2 months)

Haena Kwak (2018, 1 month)

Jinkyung Shin (2018, 1 month)

Magali Verplancke (2019, 2 months)

Kenneth Sandoval (2019, 2 months)

Juan Antonio Ruiz Santiesteban (2019, 1 month)

Antoine Vicario (2019-2020, 6 months)

Claire Chauveau (2019-2020, 12 months)

Nelle Meyers (2019-2020, 12 months)

Nicolas Jacqmin (2019-2020, 12 months)

Ksenia Juravel (2020, 2 weeks)

Anne Guichard (2020, 1 month)

Kathryn Stankiewicz (2020, 1 month)

Roland Faure (2020, 5 months)

Yihe Zhao (2020, 2 months)

Samantha Rush (2020-2021, 6 months)

David Baland (2020-2021, 6 months)

Capucine Lentze (2020-2021, 6 months)

Soren Temara (2020-2021, 6 months)

Tiana Renard (2021, 1 month)

Haena Kwak (2022, 2 months)

Yukyung Kim (2022, 2 months)

Joohee Park (2022, 2 months)

Sebastian Guzman (2022, 2 months)

Silvia Adrián (2022, 2 weeks)

Germain Agazzi (2023, 6 months)

Roxane Gris (2023, 2 months)

Caroline Deflandre (2023, 2 months)

Maxime Keller (2023, 2 months)

Aabha Deshpande (2023, 2 months)

María Conejero (2023, 2 weeks)

Dorien Aerts (2023, 1 month)

Olivier Collard (2023, 4 months)

Ninon Lecoquierre (2023-2024, 12 months)

Seda Mirzoyan (2024, 1 month)

Elisabeth Mansouri (2024, 2 months)

Maud Januarius (2024, 2 months)

Alberto Rock (2024, 1 month)

Martin Joly (2024, 2 months)