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Denis Baurain

Professor of Bioinformatics

University of Liège
InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics
Sart Tilman, Quartier Vallée 1
Chemin de la Vallée 4, Bât. B22
4000 Liège
Belgium
+32 4 3663864

DETAILED INFORMATION

pUBLICATION LIST

Contents

Overview

UEP is part of PhytoSYSTEMS, the branch of the InBioS Research Unit at ULiège (University of Liège, Belgium) that groups all plant biologists and other researchers working on symbiotic associations involving microalgae. As suggested by its name, our lab is interested in inferring the evolutionary relationships among Eukaryotes using complete genome data. More generally, the goal of phylogenomics is to reconstruct the "Tree of Life", based on genetic similarities observed between extant organisms. This also includes elucidating the emergence of the three domains, i.e., Bacteria, Archaea and Eukaryotes. Owing to the complexity of the evolutionary processes that have led to the current biodiversity and the massive number of sequences considered during tree inference, phylogenomics requires sophisticated statistical methods and models, and thus significant computing resources.

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Research

Our lab is specialised in comparative genomics, phylogenomics and metagenomics of microbial organisms (both prokaryotes and eukaryotes, including Cyanobacteria and algae) and multicellular land plants and animals, while also active in the development and benchmarking of bioinformatics software tools. Current research lines can be organized as follows:

1. Algal origins and evolution

One focus is the origin and evolution of photosynthetic eukaryotic lineages. Eukaryotes are extremely diverse but 95% of them are unicellular (the so-called "protists"). While plants and animals correspond to small branches of the Tree of Life, most eukaryotic supergroups host a myriad of photosynthetic organisms, collectively called "algae". Plants and algae conduct photosynthesis in plastids, organelles ultimately derived from an endosymbiotic cyanobacterium. As current algae are dispersed in the eukaryotic diversity, the origin of their plastids is intriguing. Clearly, multiple events of organelle transfer are required to explain the observed distribution of plastids. Having demonstrated that the preferred scenario for the origins of complex red plastids (the Chromalveolate hypothesis) was incorrect, we proposed the Rhodoplex hypothesis to replace it. Now, our work tries to further develop this alternative scenario, notably by studying Euglena as a model of a complex green alga that might have emerged through kleptoplasty rather than endosymbiosis.

2. Cyanobacterial diversity and evolution

During the last decade, we have been developing genomics, metagenomics and phylogenomics of Cyanobacteria, not only because of their central role in the origin of plastids, but also for their own interest. Indeed, they are the only bacteria able to perform oxygenic photosynthesis, and those further able to fix atmospheric nitrogen are among the most autonomous and successful organisms on Earth. In a recently funded project, we investigate nutritional strategies in new genomes and metagenomes of basal Cyanobacteria and close outgroups to better understand the origin of oxygenic photosynthesis.

basal-cyano-team-mar-2025

© Denis Baurain

The BASAL Team meets Prof. Jimmy Saw (The George Washington University) in March 2025. The team led by Luc Cornet is a joint venture between UPE and BCCM/ULC. From left to right, Marie Harmel, Louise Hambücken, Luc Cornet, Jimmy Saw, Edi Sudianto and Sandeep Chakraborty.

3. Animal evolution

On the animal side, we were notably involved in the genome of the coelacanth in connection with the emergence of tetrapods, the largest dated phylogeny of jawed vertebrates, and the (ongoing) debate about the possible positions of sponges and comb jellies with respect to the origin of metazoans. Now, we are transitioning from "pure" phylogenomics aimed at recovering uncertain relationships to evolutionary studies integrating morpho-ecological data.

4. Evolution of complex protein families

At the single-gene level, we have demonstrated expertise with the phylogenetic analysis and nomenclature reassessment of complex protein families, possibly spanning the three domains of life, e.g., SR splicing factors, P-Type ATPases, class-D beta-lactamases, and muramyl ligases. These careful and time-consuming studies increasingly concern the genes determining the cell wall architecture in Bacteria and Archaea. In a somewhat related line, we have also been involved in natural product discovery from genomic data, not only in Cyanobacteria but Actinobacteria and "protist" lineages too.

5. Software and database development

Finally, our research activities also cover methodological bioinformatics, especially in the context of contamination of genomic data by foreign sequences, an issue that is unavoidable both in metagenomics and when sequencing Cyanobacteria, which often coexist with a diverse bacterial community. All our software packages and studies are published according to FAIR principles.


Lupo et al. 2021 - https://doi.org/10.3389/fmicb.2021.755101

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Teaching

Prof. Denis Baurain has a dual background in Software Engineering and Plant Molecular Biology. He teaches courses to various groups of students in Biology, Biochemistry, Bioinformatics and Veterinary Medicine. These teachings range from entry-level Biology to practical Computer Programming. More specialized courses include Protistology (e.g., algae, fungi) and Phylogenetic Methods. From 2016 to 2022, he was the Head of the Department of Life Sciences.

COURSE LIST

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Software and Databases

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Selected (FAIR) Supplementary Materials

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High-Performance Computing

For resource-demanding bioinformatic analyses, UEP has access to high-performance computing capacities, including PhytoSYSTEMS' durandal computing cluster, but also clusters hosted by the universities of the Fédération Wallonie-Bruxelles. Those larger machines are operated by the CÉCI (Consortium des Équipements de Calcul Intensif). The lab also owns durandal-2, which is the largest computing node of ULiège's cluster (nic5), and aida, a dual-GPU machine dedicated to protein modelling.

  • durandal (2013-2019) IBM/Lenovo Flex grid computer composed of 1 x440 node and 11 x240 nodes, for a total of 228 Intel Xeon cores, 2.9 TB RAM, and 162 TB storage
  • durandal-2 (2021) NEC HPC2224Ri-2 node with 128 AMD Rome cores, 2 TB RAM, and 18 TB SSD storage (part of the much larger nic5)
  • aida (2023) Supermicro SYS-740GP-TNRT server with 20 Intel Xeon cores, 256 GB RAM, 2 NVIDIA Tesla A100, and 7 TB SSD storage

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Lab Members

Postdocs

  • Dr. Luc Cornet (2025-today, Scient. Collab. lev. Research Associate) [website]
  • Dr. Edi Sudianto (2024-today)

PhD Students

  • Louise Hambücken (2024-today, with Dr. Luc Cornet)
  • Leandro Smacchia (2023-today, with Prof. Patrick Flammang and Dr. Jérôme Delroisse, UMONS)
  • Benoît Durieu (2017-today, with Dr. Annick Wilmotte)
  • Loïc Meunier (2015-today, with Prof. Philippe Jacques)
  • Mick Van Vlierberghe (2015-today, Teaching Assistant)

Master's Students

  • Mathieu Bruyneel (with Dr. Arnaud Vanden Broeck)
  • Luca Galet (with Prof. Nicolas Magain)
  • Bernard Georges (with Dr. Christophe Lambert, GSK)

Other Members

  • Rosa Gago (Lab Manager)
  • Marie Harmel (Bioinformatician)
  • Jerry Tshimanga Mutayi (Undergrad intern in Bioinformatics, HEH)

Scientific Collaborators

  • Dr. Henner Brinkmann
  • Dr. Louis Collet
  • Prof. Vincent Demoulin
  • Dr. Marie Leleu
  • Dr. Raphaël Léonard
  • Dr. Valérian Lupo

uep-team-dec-2018-v2

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Alumni

Postdocs

  • Dr. Damien Sirjacobs (2011-2025)
  • Dr. Alice Mouton (2014-2015)

PhD Students

  • Dr. Laurent Mittelheiser (2020-2025, with Prof. Bruno Frédérich)
  • Dr. Richard Gouy (2014-2024)
  • Dr. Valérian Lupo (2018-2022, with Dr. Frédéric Kerff)
  • Dr. Marie Leleu (2018-2022, with Prof. Steven Ball and Dr. Ugo Cenci, Université de Lille, France)
  • Dr. Raphaël Léonard (2014-2021, with Dr. Frédéric Kerff)
  • Dr. Luc Cornet (2012-2018, with Prof. Emmanuelle Javaux)
  • Dr. Emilie Perez (2010-2015, with Dr. Pierre Cardol)

Master's Students

  • 2024-2025
    - Romain Dumont de Chassart (with Prof. Per Alström, Uppsala University)
    - Yassine El Mehdi-Lamghari (with Prof. Keith Durkin)
    - Mai Abdelkader Abdelkader Elmezain (Erasmus Mundus Joint Master Degree in Marine Environment) 
    - Eline Junique
    - Harris-Barthélemy Vassart (with Prof. Claire Périlleux)
  • 2023-2024
    - Marie Harmel
    - Lydie Mahoro (HEPL)
    - Coralie Mullender
  • 2022-2023
    - Leandro Smacchia (with Prof. Marc Hanikenne)
  • 2021-2022
    - Célyne Roomans
  • 2020-2021
    - Agnieszka Misztak
  • 2018-2019
    - Marie-Catherine Bouquieaux (with Dr. Bernard Taminiau)
  • 2017-2018
    - Pierre-Marie Berthol (with Prof. Marc Hanikenne)
    - Jérôme Gillon (with Prof. Bernard Joris)
  • 2016-2017
    - Amandine Bertrand (with Dr. Tom Druet)
  • 2015-2016
    - Yoan Bouzin (Université de Rennes, France)
    - Catherine Colson (with Dr. Axel Mauroy)
    - The Anh Nguyen (University of Science and Technology of Hanoi, Vietnam)
  • 2014-2015
    - François Ancien (with Prof. Bernard Joris)
    - Loïc Meunier (with Dr. Annick Wilmotte)
    - Mick Van Vlierberghe (with Prof. Patrick Meyer)
  • 2013-2014
    - Arnaud Lavergne (with Dr. Bernard Peers)
    - Raphaël Léonard (with Dr. Eric Sauvage)
  • 2012-2013
    - Arnaud Di Franco

International Interns

  • 2021-2022
    - Carlos Alejandro Pérez Rojas (CIBNOR, La Paz, Mexico)
  • 2019-2020
    - Alexandros Syllas (Aristotle University of Thessaloniki, Greece)
  • 2014-2015
    - Madga Furmaniak (Medical University of Gdańsk, Poland)
    - Agnieszka Misztak (University of Gdańsk, Poland)

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Main Collaborators

  • Cell Wall: Dr. Frédéric Kerff (ULiège)
  • Cyanobacteria: Dr. Annick Wilmotte (ULiège and BCCM/ULC)
  • Euglena: Dr. Pierre Cardol (ULiège)
  • Phylogenomics: Prof. Hervé Philippe (CNRS Moulis, France)
  • Software and more: Dr. Luc Cornet (ULiège and BCCM/ULC)

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updated on 2/28/26

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