Publications and communications of Denis Baurain

Cornet, L., Lupo, V., Declerck, S., & Baurain, D. (10 January 2024). Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks. Applied Microbiology, 4 (1), 124-132. doi:10.3390/applmicrobiol4010009

Mittelheiser, L., Baurain, D., & Frederich, B. (22 November 2023). Diversity, distribution and evolution of colour patterns in three reef fish families [Paper presentation]. Indo-Pacific Fish Conference.

Cornet, L., Durieu, B., Baert, F., D'hooge Elisabeth, Collignon, D., Meunier, L., Lupo, V., Cleenwerck, I., Daniel, H.-M., Rigouts, L., Sirjacobs, D., Declerck, S., Vandamme, P., Wilmotte, A., Baurain, D., & Becker, P. (September 2023). The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics [Paper presentation]. ECCO XLI – 2023, Bruxelles, Belgium.

Jabri, H., Krings, S., Fall, P. A., Baurain, D., Daube, G., & Taminiau, B. (10 August 2023). Microbiota Profiling on Veterinary Faculty Restroom Surfaces and Source Tracking. Microorganisms, 11 (8), 2053. doi:10.3390/microorganisms11082053

Mittelheiser, L., Baurain, D., & Frederich, B. (30 May 2023). Comparative study of the color pattern evolution in three reef fish families [Poster presentation]. Zoology 2023, Leiden, Netherlands.

Cornet, L., Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Benoit Durieu, Ilse Cleenwerck, Heide-Marie Daniel, Leen Rigouts, Stéphane Declerck, Peter Vandamme, Wilmotte, A., Lupo, V., Baurain, D., & Pierre Becker. (2023). The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics [Paper presentation]. ICCC15.

Meunier, L., Baurain, D., & Cornet, L. (2023). AMAW: automated gene annotation for non-model eukaryotic genomes. F1000Research, 12, 186. doi:10.12688/f1000research.129161.1

Cornet, L., Durieu, B., Baert, F., D'hooge, E., Colignon, D., Meunier, L., Lupo, V., Cleenwerck, I., Daniel, H.-M., Rigouts, L., Sirjacobs, D., Declerck, S., Vandamme, P., Wilmotte, A., Baurain, D., & Becker, P. (28 December 2022). The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics. GigaScience, 12. doi:10.1093/gigascience/giad022

Baurain, D. (25 November 2022). Au-delà de l’Ancien Testament... Les données de
 séquences génétiques [Paper presentation]. Colloque annuel de la SRSL : Nombres, images et autres données, Liège, Belgium.

Mittelheiser, L., Baurain, D., & Frederich, B. (22 September 2022). Diversity and evolution of color patterns in the goatfishes (Syngnathiformes, Mullidae) [Paper presentation]. Zoology 2022.

Cornet, L., & Baurain, D. (September 2022). A guided tour into genomic contamination detection [Poster presentation]. Reconstructing the human past: using ancient and modern genomics, Heidelberg, Germany.

Cornet, L., Cleenwerck, I., Praet, J., Léonard, R., Vereecken, N. J., Michez, D., Smagghe, G., Baurain, D., & Vandamme, P. (28 June 2022). Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity. mSystems, 7 (3), 0150021. doi:10.1128/msystems.01500-21

Mittelheiser, L., Baurain, D., & Frederich, B. (15 March 2022). Patrons de coloration chez les rougets (Mullidae) : une diversification aléatoire ? [Paper presentation]. 8ème Rencontres de l'Ichtyologie en France.

Corato, A., Le, T. T., Baurain, D., Jacques, P., Remacle, C.* , & Franck, F.*. (23 February 2022). A Fast-Growing Oleaginous Strain of Coelastrella Capable of Astaxanthin and Canthaxanthin Accumulation in Phototrophy and Heterotrophy. Life (Basel, Switzerland), 12 (3), 334. doi:10.3390/life12030334
* These authors have contributed equally to this work.

Cornet, L., & Baurain, D. (21 February 2022). Contamination detection in genomic data: more is not enough. Genome Biology, 23 (1), 60. doi:10.1186/s13059-022-02619-9

Léonard, R., Sauvage, E., Lupo, V., Perrin, A., Sirjacobs, D., Charlier, P., Kerff, F., & Baurain, D. (18 February 2022). Was the last bacterial common ancestor a monoderm after all? Genes, 13. doi:10.3390/genes13020376

Lupo, V., Mercuri, P., Frère, J.-M., Joris, B., Galleni, M., Baurain, D.* , & Kerff, F.*. (2022). An Extended Reservoir of Class-D Beta-Lactamases in Non-Clinical Bacterial Strains. Microbiology Spectrum, 10 (2), 0031522. doi:10.1128/spectrum.00315-22
* These authors have contributed equally to this work.

Cornet, L., D'Hooge, E., Magain, N., Stubbe, D., Packeu, A., Baurain, D.* , & Becker, P.*. (2021). The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach. Microbial Genomics. doi:10.1099/mgen.0.000707
* These authors have contributed equally to this work.

Bertrand, A., Detry, E., Nouet, C., Hanikenne, M., & Baurain, D. (2021). The rhizosphere microbiota of the zinc and cadmium hyperaccumulators Arabidopsis halleri and Noccaea caerulescens is highly convergent in Prayon (Belgium). ORBi-University of Liège. https://orbi.uliege.be/handle/2268/304726. doi:10.21203/rs.3.rs-968648/v1

Leleu, M., Van Vlierberghe, M., Ball, S., Cenci, U., & Baurain, D. (28 May 2021). Chlamydiales implication in the evolution of Archaeplastida: Testing the Ménage à Trois Hypothesis [Paper presentation]. Séminaire hebdomadaire de l'UGSF.

Sévéno, J., Sirjacobs, D., Witkowski, A., Gastineau, Baurain, D., Lejeune, P., Gobert, S., Badawi, M., Leignel, V., & Mouget, J.-L. (14 May 2021). Comparison of epiphytic diatom communities on turf and Padina sp. during blue Haslea blooms in the Ligurian Sea and the Adriatic Sea [Paper presentation]. 7th Conference of the International Society for Applied Phycology, virtual platform, Japan.

Léonard, R., Leleu, M., Van Vlierberghe, M., Cornet, L., Kerff, F., & Baurain, D. (05 May 2021). ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies. PeerJ, 9, 11348. doi:10.7717/peerj.11348

Cornet, L., Magain, N., Baurain, D., & Lutzoni, F. (2021). Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: a case study with Cyanobacteria and cyanolichens. Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2021.107100

Córdoba Jacoste, F. J., Perez, E., Van Vlierberghe, M., Bertrand, A., Lupo, V., Cardol, P., & Baurain, D. (2021). De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes, 12 (6). doi:10.3390/genes12060842

Cornet, L., Ahn, A.-C., Wilmotte, A., & Baurain, D. (2021). ORPER: A Workflow for Constrained SSU rRNA Phylogenies. Genes, 12 (11). doi:10.3390/genes12111741

Di Franco, A., Baurain, D., Glöckner, G., Melkonian, M., & Philippe, H. (2021). Lower statistical support with larger datasets: insights from the Ochrophyta radiation. Molecular Biology and Evolution. doi:10.1093/molbev/msab300

Gain, G.* , Vega de Luna, F.* , Córdoba Jacoste, F. J., Perez, E., Degand, H., Morsomme, P., Thiry, M., Baurain, D., Pierangelini, M., & Cardol, P. (2021). Trophic state alters the mechanism whereby energetic coupling between photosynthesis and respiration occurs in Euglena gracilis. New Phytologist. doi:10.1111/nph.17677
* These authors have contributed equally to this work.

Lupo, V., Van Vlierberghe, M., Vanderschuren, H., Kerff, F., Baurain, D., & Cornet, L. (2021). Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics. Frontiers in Microbiology, 12, 755101. doi:10.3389/fmicb.2021.755101

Van Vlierberghe, M., Di Franco, A., Philippe, H., & Baurain, D. (2021). Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project. BMC Research Notes, 14 (1), 306. doi:10.1186/s13104-021-05717-2

Van Vlierberghe, M., Philippe, H., & Baurain, D. (2021). Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. BMC Research Notes, 14 (1), 143. doi:10.1186/s13104-021-05553-4

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (27 November 2020). Chlamydiales implication in the evolution of Archaeplastida: Testing the Ménage à Trois Hypothesis [Paper presentation]. Journée André Verbert.

Baurain, D. (2020). Modern Perl for Biologists II | Deeper Concepts. (ULiège - Université de Liège, INFO0953-1 Scripting interfaces for biological software and databases).

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (14 October 2020). Chlamydiales implication in the evolution of Archaeplastida: Testing the Ménage à Trois Hypothesis [Paper presentation]. ByteMAL 2020.

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (14 October 2020). Chlamydiales implication in the evolution of Archaeplastida [Poster presentation]. ByteMAL 2020.

Baurain, D. (2020). Modern Perl for Biologists I | The Basics. (ULiège - Université de Liège, INFO0953-1 Scripting interfaces for biological software and databases).

Baurain, D. (06 March 2020). Making a living out of publicly available genomic data: a juicy but risky business [Paper presentation]. Molecular Bacteriology, Liège, Belgium.

Baurain, D. (2020). Evolution génétique de l'homme moderne [Paper presentation]. U3A - Section Sciences et Nature, Liège, Belgium.

Baurain, D. (2020). L'Arbre du Vivant [Paper presentation]. Darwin Day 2020, Liège, Belgium.

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (07 February 2020). Chlamydiales implication in the evolution of Archaeplastida [Paper presentation]. InBioS day.

Meunier, L., Tocquin, P., Cornet, L., Sirjacobs, D., Leclère, V., Pupin, M., Jacques, P., & Baurain, D. (2020). Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects. Bioinformatics, 36 (15), 4345-4347. doi:10.1093/bioinformatics/btaa517

Zanatta, F.* , Engler, R.* , Collart, F.* , Broennimann, O., Mateo, R. G., Papp, B., Muñoz, J., Baurain, D., Guisan, A.* , & Vanderpoorten, A.*. (2020). Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities. Nature Communications, 11, 5601. doi:10.1038/s41467-020-19410-8
* These authors have contributed equally to this work.

Bertrand, A., Detry, E., Nouet, C., Hanikenne, M., & Baurain, D. (28 November 2019). Impact of the sequencing coverage in metagenetic and metagenomic studies [Poster presentation]. Advances in Computational Biology 2019 Conference.

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (28 November 2019). Chlamydiales implication in the evolution of Archaeplastida [Poster presentation]. Advances in Computational Biology, Barcelone, Spain.

Tamisier, L., Colson, C., Maclot, F., Zhang, P., Wang, X., Francis, F., Baurain, D., & Massart, S. (29 October 2019). Experimental evolution of Barley yellow dwarf virus in cultivated and wild Poaceae species [Poster presentation]. International Advances in Plant Virology 2019.

Ahn, A.-C., Cornet, L., Beets, K., Lara, Y., Durieu, B., Javaux, E., Baurain, D., & Wilmotte, A. (18 October 2019). Biodiversity of Cyanobacteria and associated microbiome in the BCCM/ULC Culture Collection [Poster presentation]. 2019 Symposium of the Belgian Society for Microbiology, Bruxelles, Belgium.

Leleu, M., Van Vlierberghe, M., Cenci, U., Ball, S., & Baurain, D. (04 September 2019). Chlamydiales implication in the evolution of Archaeplastida [Poster presentation]. XIV ème ICES, Lille, France.

Van Vlierberghe, M., & Baurain, D. (02 September 2019). Endosymbiosis and kleptoplastidy in the evolution of complex algae [Paper presentation]. ICES 2019 - 14th International Colloquium in Endocytobiology and Symbiosis, Lille, France.

Van Vlierberghe, M., & Baurain, D. (2019). AUTOMATED BIOINFORMATICS TO EVALUATE THE RELATIVE CONTRIBUTION OF ENDOSYMBIOSIS AND KLEPTOPLASTY IN THE EVOLUTION OF COMPLEX RED ALGAE [Paper presentation]. 7th European Phycological Congress (EPC7), Zagreb, Croatia.

Wilmotte, A., Beets, K., Simons, V., Lara, Y., Durieu, B., Cornet, L., & Baurain, D. (27 August 2019). BCCM/ULC : genomic research on Polar cyanobacteria. European Journal of Phycology, 54 (sup1), 31-117. doi:10.1080/09670262.2019.1626627

Sévéno, J., Sirjacobs, D., Lejeune, P., Baurain, D., Gobert, S., Badawi, M., Leignel, V., & Mouget, J.-L. (August 2019). Blue Haslea blooms in natural environment First investigations in Revellata bay, Corsica, France [Poster presentation]. EPC7 - 7th European Phycological Congress, Zagreb, Croatia.

Ahn, A.-C., Beets, K., Lara, Y., Durieu, B., Simons, V., Cornet, L., Baurain, D., & Wilmotte, A. (13 June 2019). Cyanobacteria of Polar Regions: Focus of the BCCM/ULC Culture Collection [Poster presentation]. ECCO 2019 XXXVIII Annual Meeting of the European Culture Collections' Organisation, Turin, Italy.

Meunier, L., Jacques, P., & Baurain, D. (14 March 2019). Natural products: what is the biosynthetic potential of unicellular eukaryotes? [Poster presentation]. VIZBI 2019 (Visualising Biological Data), Heidelberg, Germany.

Tamisier, L., Colson, C., Maclot, F., Zhang, P., Francis, F., Baurain, D., & Massart, S. (28 January 2019). Experimental evolution of Barley yellow dwarf virus in cultivated and wild Poaceae species [Paper presentation]. 17emes Rencontres de Virologie Végétale, Aussois, France.

Demoulin, C.* , Lara, Y.* , Cornet, L., François, C., Baurain, D., Wilmotte, A., & Javaux, E. (2019). Cyanobacteria evolution: Insight from the fossil record. Free Radical Biology and Medicine, 140, 206-223. doi:10.1016/j.freeradbiomed.2019.05.007
* These authors have contributed equally to this work.

Di Franco, A., Poujol, R., Baurain, D., & Philippe, H. (2019). Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evolutionary Biology, 19 (1), 21. doi:10.1186/s12862-019-1350-2

Vassaux, A., Meunier, L., Vandenbol, M., Baurain, D., Fickers, P., Jacques, P., & Leclère, V. (2019). Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnology Advances. doi:10.1016/j.biotechadv.2019.107449

Wilmotte, A., Beets, K., Santoro, M., Simons, V., Lara, Y., Durieu, B., Javaux, E., Jacques, P., Cornet, L., & Baurain, D. (18 December 2018). BCCM/ULC: a collection of cyanobacteria linking Poles to Space [Paper presentation]. The FRS-FNRS Contact Group “Astrobiology: from stars and planets to extreme life”, in collaboration with the EOS ET-HOME project, Liège, Belgium.

Bertrand, A., Detry, E., Nouet, C., Baurain, D., & Hanikenne, M. (08 November 2018). Microbial diversity in the rhizosphere of plant metal hyperaccumulators [Paper presentation]. Journées thématiques de l'AFEM (Association Francophone d'Ecologie Microbienne).

Santoro, M., Beets, K., Simons, V., Lara, Y., Durieu, B., Javaux, E., Jacques, P., Cornet, L., Baurain, D., & Wilmotte, A. (11 October 2018). The BCCM/ULC collection of cyanobacteria in the spotlight at ULiège [Poster presentation]. Journée conjointe du Centre Inter Universitaire de Biologie Marine (CIBIM), de l’Ecole doctorale Biodiversité, Ecologie, Evolution auprès du FNRS et des collèges doctoraux d’Océanologie et de Biologie des organismes et Ecologie, Liège, Belgium.

Wilmotte, A., Santoro, M., Beets, K., Lara, Y., Durieu, B., Simons, V., Silva-Stenico, E., De Fiore, M., Cornet, L., & Baurain, D. (October 2018). Ex-situ conservation and exploration of polar cyanobacteria in the BCCM/ULC Collection [Poster presentation]. BSM 2018 Annual Symposium "Microbes in the spotlight", Brussels, Belgium.

Durieu, B., Baurain, D., Wilmotte, A., & Lara, Y. (19 June 2018). Cold Adaptation Strategy of the Antarctic Cyanobacterium P. priestleyi ULC007 [Poster presentation]. Polar 2018, Where the Poles come together, Open Science Conference, Davos, Switzerland.

Durieu, B., Lara, Y., Stelmach Pessi, I., Lambion, A., Verleyen, E., Baurain, D., & Wilmotte, A. (19 June 2018). Biogeography of Cyanobacteria in Antarctic Mats and Implication for Conservation [Paper presentation]. Polar 2018, Where the Poles come together, Open Science Conference, Davos, Switzerland.

Wilmotte, A., Beets, K., Simons, V., Lara, Y., Durieu, B., Cornet, L., Baurain, D., & Laughinghouse IV, H. (June 2018). Ex-situ Conservation of Polar Cyanobacteria in the BCCM/ULC Collection [Poster presentation]. POLAR 2018 'Where the Poles come together', Davos, Switzerland.

Naomé, A., Maciejewska, M., Calusinska, M., Martinet, L., Anderssen, S., Adam, D., Tenconi, E., Deflandre, B., Coppieters, W., Karim, L., Hanikenne, M., Baurain, D., Delfosse, P., van Wezel, G., & Rigali, S. (May 2018). Complete Genome Sequence of Streptomyces lunaelactis MM109T, Isolated from Cave Moonmilk Deposits. Genome Announcements, 6 (21), 00435-18. doi:10.1128/genomeA.00435-18

Córdoba Jacoste, F. J., Perez, E., Van Vlierberghe, M., Baurain, D., & Cardol, P. (March 2018). Generation of a comprehensive transcriptomic and proteomic resource for the photosynthetic eukaryote Euglena gracilis [Paper presentation]. Applied Bioinformatics in Life Sciences (2nd edition).

Lara, Y., Beets, K., Simons, V., Durieu, B., Cornet, L., Santoro, M., Laughinghouse IV, H., Javaux, E., Baurain, D., & Wilmotte, A. (March 2018). Polar cyanobacteria in the BCCM/ULC collection : diversity and characterization [Poster presentation]. COST Life Origin Final Workshop, Bertinoro, Italy.

Lara, Y., Durieu, B., Pessi, I., Cornet, L., Baurain, D., Javaux, E., & Wilmotte, A. (March 2018). The survival toolkit of the Antarctic cyanobacterium Phormidesmis priestleyi ULC007 [Paper presentation]. COST Life Origin Final Workshop, Bertinoro, Italy.

Adam, D., Maciejewska, M., Naomé, A., Martinet, L., Coppieters, W., Karim, L., Baurain, D., & Rigali, S. (2018). Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits. Antibiotics, 7(2) (28), 10.3390/antibiotics7020028. doi:10.3390/antibiotics7020028

Córdoba Jacoste, F. J., Perez, E., Baurain, D., & Cardol, P. (2018). Generation of a transcriptomic and proteomic resource for the photosynthetic eukaryote Euglena gracilis [Poster presentation]. European Congress on Photosyntesis Research.

Córdoba Jacoste, F. J., Perez, E., Van Vlierberghe, M., Baurain, D., & Cardol, P. (2018). Generation of a comprehensive transcriptomic and proteomic resource for the photosynthetic eukaryote Euglena gracilis [Poster presentation]. Sfphi2018: Journées de la Société Française de Photosynthèse.

Cornet, L., Bertrand, A., Hanikenne, M., Javaux, E., Wilmotte, A., & Baurain, D. (2018). Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures. Microbial Genomics, 4. doi:10.1099/mgen.0.000212

Cornet, L., Meunier, L., Van Vlierberghe, M., Léonard, R., Durieu, B., Lara, Y., Misztak, A., Sirjacobs, D., Javaux, E., Philippe, H., Wilmotte, A., & Baurain, D. (2018). Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLoS ONE, 13 (7), 0200323. doi:10.1371/journal.pone.0200323

Cornet, L., Wilmotte, A., Javaux, E., & Baurain, D. (2018). A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria). BMC Research Notes, 11 (1), 435. doi:10.1186/s13104-018-3543-y

Maciejewska, M., Całusińska, M., Cornet, L., Adam, D., Pessi, I. S., Malchair, S., Delfosse, P., Baurain, D., Barton, H., Carnol, M., & Rigali, S. (2018). High-throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits. Antibiotics, 7(2) (28). doi:10.3390/antibiotics7020027

Joris, M., Schloesser, M., Baurain, D., Hanikenne, M., Muller, M., & Motte, P. (21 July 2017). Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors. Nucleic Acids Research, 45 (16), 9547-9557. doi:10.1093/nar/gkx638

Lara, Y., Durieu, B., Renard, M., Beets, K., Stelmach Pessi, I., Cornet, L., Simons, V., Baurain, D., Javaux, E., Jacques, P., & Wilmotte, A. (2017). The BCCM/ULC collection to conserve the biodiversity and study the secondary metabolites of Antarctic cyanobacteria. In A. Van de Putte (Ed.), Book of abstracts: XIIth SCAR Biology Symposium, Leuven, Belgium, 10-14 July 2017 (pp. 244). SCAR.

Martinet, L., Maciejewska, M., Adam, D., Naomé, A., Carnol, M., Barton, H., Smargiasso, N., De Pauw, E., Hanikenne, M., Baurain, D., & Rigali, S. (24 May 2017). Streptomyces from Moonmilk, an Untapped Source of New Bioactive Compounds [Poster presentation]. International symposium on the biology of Actinomycetes, Jeju, South Korea.

Léonard, R., Sirjacobs, D., Sauvage, E., Kerff, F., & Baurain, D. (11 May 2017). ToRQuEMaDA: Tool for retrieving queried eubacteria, metadata and dereplicating assemblie [Poster presentation]. PhD Student Day 2017, Liège, Belgium.

Lara, Y., Durieu, B., Cornet, L., Verlaine, O., Rippka, R., Stelmach Pessi, I., Misztak, A., Joris, B., Javaux, E., Baurain, D., & Wilmotte, A. (2017). Draft genome sequence of the axenic strain Phormidesmis priestleyi ULC007, a cyanobacterium isolated from Lake Bruehwiler (Larsemann Hills, Antarctica). Genome Announcements, 01546-16. doi:10.1128/genomeA.01546-16

Córdoba Jacoste, F. J., Perez, E., Baurain, D., & Cardol, P. (2017). Analysisi of Euglena gracilis proteome under mixotrophic conditions [Paper presentation]. Current trends in membrane protein biophysics.

Córdoba Jacoste, F. J., Perez, E., Baurain, D., & Cardol, P. (2017). Analysis of Euglena gracilis proteome under mixotrophic conditions [Paper presentation]. Proteomic Bioinformatics, Cambridge, United Kingdom.

Crasson, O., Courtade, G., Léonard, R., Aachmann, F., Legrand, F., Parente, R., Baurain, D., Galleni, M., Sorlie, M., & Vandevenne, M. (2017). Human chitotriosidase: Catalytic domain or carbohydrate binding module, who's leading HCHT's biological function. Scientific Reports, 7 (1). doi:10.1038/s41598-017-02382-z

Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., & Philippe, H. (2017). Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology and Evolution, 1 (9), 1370-1378. doi:10.1038/s41559-017-0240-5

Maciejewska, M., Adam, D., Naomé, A., Martinet, L., Tenconi, E., Calusinska, M., Delfosse, P., Hanikenne, M., Baurain, D., Compère, P., Carnol, M., Barton, H., & Rigali, S. (2017). Assessment of the Potential Role of Streptomyces in Cave Moonmilk Formation. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.01181

Mauroy, A., Taminiau, B., Nezer, C., Ghurburrun, E., Baurain, D., Daube, G., & Thiry, E. (2017). High-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication. Archives of Virology, 16 (4), 1019-1023. doi:10.1007/s00705-016-3179-y

Philippe, H., Vienne, D. M. D., Ranwez, V., Roure, B., Baurain, D., & Delsuc, F. (2017). Pitfalls in supermatrix phylogenomics. European Journal of Taxonomy, 283, 1-25. doi:10.5852/ejt.2017.283

Rodriguez, A., Burgon, J. D., Lyra, M., Irisarri, I., Baurain, D., Blaustein, L., Gocmen, B., Kunzel, S., Mable, B. K., Nolte, A. W., Veith, M., Steinfartz, S., Elmer, K. R., Philippe, H., & Vences, M. (2017). Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Molecular Phylogenetics and Evolution, 115, 16-26. doi:10.1016/j.ympev.2017.07.009

Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Queinnec, E., Ereskovsky, A., Lapebie, P., Corre, E., Delsuc, F., King, N., Worheide, G., & Manuel, M. (2017). A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Current Biology. doi:10.1016/j.cub.2017.02.031

Lara, Y., Durieu, B., Renard, M., Stelmach Pessi, I., Cornet, L., Simons, V., Baurain, D., Javaux, E., Jacques, P., & Wilmotte, A. (16 November 2016). The BCCM/ULC collection to conserve the biodiversity and study the secondary metabolites of Polar cyanobacteria [Poster presentation]. BIOFORUM 2016, Liège, Belgium.

Tocquin, P., Naomé, A., Jourdan, S., Anderssen, S., Hiard, S., van Wezel, G., Hanikenne, M., Baurain, D., & Rigali, S. (2016). PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/203998. doi:10.1101/084780

Becker, P., SZTERNFELD, P., ANDJELKOVIC, M., ANTHONISSEN, R., VERSCHAEVE, L., HENDRICKX, M., Renard, M., Lara, Y., Durieu, B., Simons, V., Laughinghouse, H. D., Cornet, L., Baurain, D., & Wilmotte, A. (28 October 2016). The BCCM/ULC collection to conserve the biodiversity and explore the applied potential of Polar cyanobacteria [Poster presentation]. Symposium “Microbiome and Host Metabolism", Brussels, Belgium.

Maciejewska, M.* , Adam, D.* , Martinet, L., Naomé, A., Całusińska, M., Delfosse, P., Carnol, M., Barton, H., HAYETTE, M.-P., Smargiasso, N., De Pauw, E., Hanikenne, M., Baurain, D., & Rigali, S. (2016). A Phenotypic and Genotypic Analysis of the Antimicrobial Potential of Cultivable Streptomyces Isolated from Cave Moonmilk Deposits. Frontiers in Microbiology. doi:10.3389/fmicb.2016.01455
* These authors have contributed equally to this work.

Baurain, D., Van Vlierberghe, M., Arnaud, D. F., & Philipe, H. (05 September 2016). Automated tools for the generation and interpretation of single gene trees at a broad taxonomic scale [Poster presentation]. ECCB 2016.

Wilmotte, A., Renard, M., Lara, Y., Durieu, B., Stelmach Pessi, I., Simons, V., Laughinghouse, H. D., Cornet, L., & Baurain, D. (September 2016). The BCCM/ULC collection to conserve and study the biodiversity of Polar cyanobacteria [Poster presentation]. 2Oth IAC Cyanophyte/Cyanobacteria Symposium, Innsbruck, Austria.

Wilmotte, A., Renard, M., Lara, Y., Cornet, L., Baurain, D., Waleron, M., & Waleron, K. (August 2016). The BCCM/ULC collection: a Biological Ressource Center to give access to the Antarctic cyanobacterial diversity [Poster presentation]. XXXIV SCAR Biennial Meetings and Open Science Conference 2016, Kuala Lumpur, Malaysia.

Baurain, D. (22 April 2016). HTC Bayesian Phylogenomics on the Zenobe Tier-1 supercomputer [Paper presentation]. CÉCI Scientific Day, Liège, Belgium.

Baurain, D., Wilmotte, A., & Frère, J.-M. (2016). Gram-Negative Bacteria: "Inner" vs. "Cytoplasmic" or "Plasma Membrane": A Question of Clarity rather than Vocabulary. Journal of Microbial and Biochemical Technology, 8 (4), 325-326. doi:10.4172/1948-5948.1000305

Kadri, N. K., Harland, C., Faux, P., Cambisano, N., Karim, L., Coppieters, W., Fritz, S., Mullaart, E., Baurain, D., Boichard, D., Spelman, R., Charlier, C., Georges, M., & Druet, T. (2016). Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. Genome Research, 26 (10), 1323-1332. doi:10.1101/gr.204214.116

Mouton, A., Espelta, J. M., Baurain, D., & Michaux, J. (2016). Using Next Generation Sequencing to characterize species diets: a study case with faeces of wild boar in the Spanish Pyrenees [Poster presentation]. Congenomics conference, Porto, Portugal.

Stelmach Pessi, I., De Carvalho Maalouf, P., Laughinghouse, H. D., Baurain, D., & Wilmotte, A. (2016). ON THE USE OF HIGH-THROUGHPUT SEQUENCING FOR THE STUDY OF CYANOBACTERIAL DIVERSITY IN ANTARCTIC AQUATIC MATS 1. Journal of Phycology, 52, 356–368. doi:10.1111/jpy.12399

Léonard, R., Baurain, D., Kerff, F., Sauvage, E., & Sirjacobs, D. (07 December 2015). On the LZ distance for dereplicating redundant prokaryotic genomes [Poster presentation]. 10th Benelux Bioinformatics Conference, Antwerp, Belgium.

Wilmotte, A., Renard, M., Kleinteich, J., Lara, Y., Cornet, L., Baurain, D., Silva-Stenico, M., Fiore, M., Laughinghouse, H. D., Puschkareva, E., & Elster, J. (07 September 2015). The BCCM/ULC culture collection to conserve, document and explore the polar cyanobacterial diversity [Poster presentation]. 6th Symposium on Polar and Alpine Microbiology, Ceske Budejovice, Czechia.

Lara, Y., Verlaine, O., Kleinteich, J., Stelmach Pessi, I., Rippka, R., Renard, M., Cornet, L., Baurain, D., & Wilmotte, A. (03 August 2015). Genome sequencing of an endemic filamentous Antarctic cyanobacterium [Poster presentation]. 15th International Symposium on Phototrophic Prokaryotes, Tubingen, Germany.

Wilmotte, A., Renard, M., Lara, Y., Cornet, L., Baurain, D., Waleron, M., & Waleron, K. (03 August 2015). The BCCM/ULC collection : a Biological Ressource Center for polar cyanobacteria [Poster presentation]. 15th International Symposium on Phototrophic Prokaryotes, Tubingen, Germany.

Crasson, O., Legrand, F., Léonard, R., Baurain, D., Galleni, M., & Vandevenne, M. (August 2015). The hidden face of the human macrophage chitotriosidase: taking a new look at this enzyme based on the biochemical and phylogenomic analysis of its chitin binding domain [Poster presentation]. Gordon Research Conferences : Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes, Andover MA, United States.

Baurain, D. (17 April 2015). Pinpointing the origin of plastids using phylogenomics [Paper presentation]. Invited Seminar at the University of Lille, Lille, France.

Gouy, R., Baurain, D., & Philippe, H. (2015). Rooting the tree of life: the phylogenetic jury is still out. Philosophical Transactions. Biological Sciences, 370 (1678), 20140329. doi:10.1098/rstb.2014.0329

Cornet, L., Javaux, E., Wilmotte, A., Hervé, P., & Baurain, D. (03 November 2014). A Phylogenomic analysis of the origin of plastids [Paper presentation]. IUAP Planet TOPERS meeting, Liège, Belgium.

Perez, E., Lapaille, M., Degand, H., Cilibrasi, L., Villavicencio-Queijeiro, A., Morsomme, P., Gonzalez-Halphen, D., Field, M. C., Remacle, C., Baurain, D., & Cardol, P. (November 2014). The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae. Mitochondrion, 19 Pt B, 338-349. doi:10.1016/j.mito.2014.02.001

Baurain, D. (23 October 2014). Evolution des eucaryotes : l'éclairage de la phylogénie moléculaire [Paper presentation]. Cours-conférence du Collège Belgique : Origine et évolution des eucaryotes, Bruxelles, Belgium.

Perez, E., Lapaille, M., Degand, H., Cilibrasi, L., Gilsoul, M., Morsomme, P., Field, M. C., Remacle, C., Cardol, P., & Baurain, D. (August 2014). Transcriptomics and Proteomics of a Secondary Green Alga [Poster presentation]. Protist 2014, Banff, Alberta, Canada.

Wilmotte, A., Stelmach Pessi, I., De Carvalho, P., Laughinghouse, H. D., & Baurain, D. (August 2014). Unveiling biogeographic patterns of Antarctic cyanobacteria by 454 pyrosequencing [Poster presentation]. XXX111 SCAR Biennial Meetings and Open Science Conference 2014’, Auckland, New Zealand.

Mauroy, A., Taminiau, B., Nezer, C., Ghurburrun, E., Baurain, D., Daube, G., & Thiry, E. (July 2014). High throughput sequencing analysis reveals genetic variability and selection pressure in different murine norovirus genomic regions during in vitro replication [Poster presentation]. International Union of Microbiological Societies (IUMS 2014) – XIVth International Congress of Bacteriology and Applied Microbiology, XIVth International Congress of Mycology, XVIth International Congress of Virology, Montréal, Canada.

Cornet, L., Javaux, E., Wilmotte, A., Philippe, H., & Baurain, D. (24 June 2014). A Phylogenomic analysis of the origin of plastids [Paper presentation]. ESF-EMBO Symposium Biology of Platsids, Pultusk, Poland.

Perez, E., Degand, H., Morsomme, P., Remacle, C., Cardol, P., & Baurain, D. (06 May 2014). Mitochondrial Proteomics of a Secondary Green Alga [Poster presentation]. PhytoSystems Day.

Baurain, D. (2014). Denis BAURAIN – Portfolio pédagogique. (ULiège - Université de Liège).

Mauroy, A., Taminiau, B., Nezer, C., Ghurburrun, E., Baurain, D., Daube, G., & Thiry, E. (March 2014). L'analyse par séquençage à haut débit révèle la variabilité génétique et la pression de sélection dans différentes régions génomiques du norovirus murin durant sa réplication in vitro [Paper presentation]. XVIe Journées Francophones de Virologie, Paris, France.

Petersen, J., Ludewig, A.-K., Michael, V., Bunk, B., Jarek, M., Baurain, D., & Brinkmann, H. (February 2014). Chromera velia, Endosymbioses and the Rhodoplex Hypothesis - Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles and Haptophytes (CASH Lineages). Genome Biology and Evolution, 6 (3), 666-684. doi:10.1093/gbe/evu043

Hanikenne, M., & Baurain, D. (07 January 2014). Origin and evolution of metal P-type ATPases in Plantae (Archaeplastida). Frontiers in Plant Science, 4, 544. doi:10.3389/fpls.2013.00544

Di Franco, A., Hanikenne, M., & Baurain, D. (09 December 2013). Identifying losses and expansions of selected gene families in incomplete genomic datasets [Poster presentation]. 8th Benelux Bioinformatics Conference, Bruxelles, Belgium.

Stelmach Pessi, I., de Carvalho Maalouf, P., Laughinghouse IV, H. D., Baurain, D., & Wilmotte, A. (November 2013). Assessment of bioinformatic pipelines for the analysis of 454 pyrosequencing data using artificial cyanobacterial communities [Poster presentation]. Microbial Diversity for Science and Industry, Brussels, Belgium.

Baurain, D. (18 April 2013). Computers As Genomic Time Machines for Meeting our Ancestors [Paper presentation]. Bioforum 2013, Liège, Belgium.

Amemiya, C. T., Alfoldi, J., Lee, A. P., Fan, S., Philippe, H., Maccallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J. J., Robinson, M., Dorrington, R. A., Gerdol, M., Aken, B., Biscotti, M. A., Barucca, M., ... Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496 (7445), 311-6. doi:10.1038/nature12027

Demoulin, V., Cornet, L., Delbruyère, E., & Baurain, D. (2013). The unusual Gasteromycetes Lycogalopsis solmsii belongs to the gomphoid-phalloid group. Acta Mycologica, 48 (1), 13-20. doi:10.5586/am.2013.002

Roure, B., Baurain, D., & Philippe, H. (January 2013). Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets. Molecular Biology and Evolution, 30 (1), 197-214. doi:10.1093/molbev/mss208

Baurain, D. (20 September 2012). L'évolution des Eucaryotes [Paper presentation]. Miniconférence de la Société Royale des Sciences de Liège, Liège, Belgium.

Baurain, D. (19 June 2012). Evolutionary analysis of a complex multigene family by semi-automated mining of public sequence databases [Paper presentation]. Systems Biology Workshop of the Greater Region University, Lultzhausen, Luxembourg.

Perez, E., Degand, H., Morsomme, P., Remacle, C., Cardol, P., & Baurain, D. (June 2012). Mitochondrial Proteomics of a Secondary Green Alga [Poster presentation]. Systems Biology Workshop of the Greater Region University, Lultzhausen, Luxembourg.

Califice, S.* , Baurain, D.* , Hanikenne, M., & Motte, P. (February 2012). A Single Ancient Origin for Prototypical Serine/Arginine-Rich Splicing Factors1[W][OA]. Plant Physiology, 158 (2), 546-560. doi:10.1104/pp.111.189019
* These authors have contributed equally to this work.

Durkin, K., Cambisano, N., Ahariz, N., Fasquelle, C., Karim, L., Sartelet, A., Baurain, D., Drogemüller, C., Leeb, T., Coppieters, W., Georges, M., & Charlier, C. (May 2011). Molecular dissection of the color-sided phenotype in cattle reveals a novel mechanism of chromosome evolution involving circular shuttling intermediates. Chromosome Research, 19 (S1), 18.

Karim, L.* , Takeda, H.* , Lin, L.* , Druet, T.* , Arias, J. A. C., Baurain, D., Cambisano, N., Davis, S. R., Farnir, F., Grisart, B., Harris, B. L., Keehan, M. D., Littlejohn, M. D., Spelman, R. J., Georges, M.* , & Coppieters, W.*. (2011). Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics, 43 (5), 405-13. doi:10.1038/ng.814
* These authors have contributed equally to this work.

Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011). Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology, 9 (3), 1000602. doi:10.1371/journal.pbio.1000602

Baurain, D., Brinkmann, H., Petersen, J., Rodriguez-Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A. J., Burger, G., Lang, B. F., & Philippe, H. (July 2010). Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Molecular Biology and Evolution, 27 (7), 1698-709. doi:10.1093/molbev/msq059

Baurain, D., Brinkmann, H., Petersen, J., Rodriguez-Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A. J., Burger, G., Lang, B. F., & Philippe, H. (July 2010). A phylogenomic falsification of the chromalveolate hypothesis [Poster presentation]. Annual Meeting of the Society for Molecular and Biology and Evolution - SMBE 2010, Lyon, France.

Lapaille, M., Escobar-Ramirez, A., Degand, H., Baurain, D., Rodriguez-Salianas, E., Coosemans, N., Boutry, M., Gonzalez-Halphen, D., Remacle, C., & Cardol, P. (July 2010). Atypical subunit composition of the chlorophycean mitochondrial F1FO ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme. Molecular Biology and Evolution, 27 (7), 1630-1644. doi:10.1093/molbev/msq049

Baurain, D. (20 April 2010). On the origin of chlorophyll c-containing algae: A phylogenomic falsification of the chromalveolate hypothesis [Paper presentation]. Biowissenschaftliches Zentrum Invited Seminar, Cologne, Germany.

Baurain, D., & Philippe, H. (2010). Current approaches to phylogenomic reconstruction. In G. Caetano-Anollés (Ed.), Evolutionary Genomics and Systems Biology (pp. 17-41). Hoboken, United States - New Jersey: Wiley-Blackwell. doi:10.1002/9780470570418.ch2

Caiment, F., Charlier, C., Hadfield, T., Cockett, N., Georges, M.* , & Baurain, D.*. (2010). Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing. Genome Research, 20 (12), 1651-62. doi:10.1101/gr.108787.110
* These authors have contributed equally to this work.

Hiard, S., Charlier, C., Coppieters, W., Georges, M., & Baurain, D. (2010). Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Research, 38 (Database), 640-D651. doi:10.1093/nar/gkp926

Lapaille, M., Escobar-Ramírez, A., Degand, H., Baurain, D., Thiry, M., Perez, E., Boutry, M., Gonzalez-Halpen, D., Remacle, C., & Cardol, P. (2010). F1FO ATP synthase mutants in Chlamydomonas: Stability and oligomycin resistance mediated by atypical Asa7 protein; interaction between chloroplastic and mitochondrial bioenergetics. Biochimica et Biophysica Acta. Bioenergetics, 1797 (Supplement 1), 29. doi:10.1016/j.bbabio.2010.04.104

Lapaille, M., Escobar-Ramirez, A., Degand, H., Baurain, D., Thiry, M., Perez, E., Boutry, M., Gonzalez-Halphen, D., Remacle, C., & Cardol, P. (2010). F1FO ATP synthase mutants in Chlamydomonas: Stability and oligomycin resistance mediated by atypical Asa7 protein; interaction between chloroplastic and mitochondrial bioenergetics [Poster presentation]. 16th European Bioenergetics Conference, Warsaw, Poland.

Fourré, F., & Baurain, D. (2009). A reduction method for noisy Boolean networks. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/80182.

Hiard, S., Charlier, C., Coppieters, W., Georges, M., & Baurain, D. (December 2009). Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates [Poster presentation]. BBC09, the fifth Benelux Bioinformatics Conference, Liège, Belgium.

Baurain, D., Hiard, S., Coppieters, W., Charlier, C., & Georges, M. (29 September 2009). Patrocles: a database of polymorphic miR-mediated gene regulation in vertebrates [Paper presentation]. La face cachée des microRNA, Liège, Belgium.

Califice, S., Baurain, D., Hanikenne, M., & Motte, P. (05 February 2009). Origin and evolution of SR proteins in Eukaryotes [Poster presentation]. High throughput technologies for alternative splicing, Valencia, Spain.

Hiard, S., Baurain, D., Coppieters, W., Tordoir, X., Charlier, C., & Georges, M. (July 2008). Patrocles: a database of polymorphic miRNA-mediated gene regulation [Poster presentation]. XX International Congress of Genetics, Berlin, Germany.

Hiard, S., Baurain, D., Coppieters, W., Tordoir, X., Charlier, C., & Georges, M. (03 March 2008). Patrocles: a database of polymorphic miRNA-mediated gene regulation [Paper presentation]. EADGENE miRNAs workshop and miRNAs in Health and Disease 2 / Satellite Course "A primer in miRNA biology", Liège, Belgium.

Teich, R., Zauner, S., Baurain, D., Brinkmann, H., & Petersen, J. (July 2007). Origin and distribution of Calvin cycle fructose and sedoheptulose bisphosphatases in Plantae and complex algae: A single secondary origin of complex red plastids and subsequent propagation via tertiary endosymbioses. Protist, 158 (3), 263-276. doi:10.1016/j.protis.2006.12.004

Baurain, D., Brinkmann, H., & Philippe, H. (January 2007). Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors? Molecular Biology and Evolution, 24 (1), 6-9. doi:10.1093/molbev/msl137

Brinkmann, H., Baurain, D., & Philippe, H. (2007). Phylogenomics: how far back in the past can we go? In R. Pudritz, P. Higgs, ... J. Stone (Eds.), Planetary Systems and the Origins of Life (pp. 149-177). Cambridge, United Kingdom: Cambridge University Press.

Baurain, D., Brinkmann, H., & Philippe, H. (22 December 2006). Phylogénomique des lignées photosynthétiques [Paper presentation]. Inauguration de l'EDT Plant Science, Louvain-la-neuve, Belgium.

Philippe, H., Brinkmann, H., & Baurain, D. (March 2006). Animal evolution — A fully-resolved phylogenomic tree argues against the Cambrian explosion hypothesis [Poster presentation]. First Phylogenomics Conference, Saint-Adèle, Québec, Canada.

Philippe, H., Brinkmann, H., & Baurain, D. (20 February 2006). The animal phylogeny and the fundamental importance of taxon sampling [Paper presentation]. UdeM Centre Robert Cedergren Monday Seminar, Montréal, Québec, Canada.

Delsuc, F., Baurain, D., & Philippe, H. (2006). Vertebrate origins: does the tunic make the man? MS. Medecine Sciences, 22 (8-9, AUG-SEP), 688-690. doi:10.1051/medsci/20062289688

Baurain, D., Beiko, R. G., & Ragan, M. A. (04 November 2005). Assessing the effects of compositional heterogeneity on phylogenomic analyses [Paper presentation]. 2nd annual Robert Cedergren Bioinformatics Colloquium, Montréal, Québec, Canada.

Bacha, S., & Baurain, D. (26 August 2005). Application of the Lempel-Ziv complexity to the alignment-free sequence comparison of protein families [Paper presentation]. Genomics and Computational Biology Group Meeting, Institute for Molecular Bioscience (IMB), Brisbane, Queensland, Australia.

Baurain, D. (2005). Le darwinisme peut-il tout expliquer ? [Paper presentation]. Réunion mensuelle Mensa BE (Liège), Liège, Belgium.

Bacha, S., & Baurain, D. (April 2005). Application of Lempel-Ziv complexity to alignment-free sequence comparison of protein families [Poster presentation]. Benelux Bioinformatics Conference 2005, Ghent, Belgium.

Baurain, D., & Demoulin, V. (03 February 2005). Why does the red algal plastid lineage lack plastocyanin? [Paper presentation]. International Society for Evolutionary Protistology (ISEP) Conference XV, Melbourne, Victoria, Australia.

Cardol, P., Gonzalez-Halphen, D., Reyes-Prieto, A., Baurain, D., Matagne, R.-F., & Remacle, C. (February 2005). The mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the genome sequencing project [letter to the editor]. Plant Physiology, 137 (2), 447-459. doi:10.1104/pp.104.054148

Hanikenne, M., Krämer, U., Demoulin, V., & Baurain, D. (2005). A comparative inventory of metal transporters in the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschizon merolae. Plant Physiology, 137 (2), 428-446. doi:10.1104/pp.104.054189

Fourré, F., Baurain, D., & Barbason, H. (December 2004). From protein interaction to cell population dynamics: A theoretical framework combining Boolean networks with Markov processes illustrated in an ovarian carcinoma [Poster presentation]. Bioforum 2004, Liège, Belgium.

Baurain, D. (26 October 2004). Condensé de biologie moléculaire à l'usage des biomathématiques et de la bioinformatique [Paper presentation]. Analyse par ondelettes des séquences d’ADN : les mathématiques à la croisée de la biochimie, Liège, Belgium.

Baurain, D. (December 2003). La recherche appliquée privilégiée. Espace de Libertés: Magazine du Centre d'Action Laïque, Document 11, p. 28-30.

Baurain, D., Dinant, M., Coosemans, N., & Matagne, R.-F. (March 2003). Regulation of the alternative oxidase Aox1 gene in Chlamydomonas reinhardtii. Role of the nitrogen source on the expression of a reporter gene under the control of the Aox1 promoter. Plant Physiology, 131 (3), 1418-1430. doi:10.1104/pp.013409

Baurain, D. (2003). Clonage, caractérisation et étude de la régulation transcriptionnelle du gène Aox1 encodant l'oxydase alternative chez Chlamydomonas reinhardtii [Doctoral thesis, ULiège - Université de Liège]. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/71086

Baurain, D., Renquin, L., Grubisic, S., Scheldeman, P., Belay, A., & Wilmotte, A. (April 2002). Remarkable conservation of internally transcribed spacer sequences of Arthrospira ("Spirulina") (Cyanophyceae, Cyanobacteria) strains from four continents and of recent and 30-year-old dried samples from Africa. Journal of Phycology, 38 (2), 384-393. doi:10.1046/j.1529-8817.2002.01010.x

Matagne, R.-F., & Baurain, D. (September 2001). A mutation in the GTPase domain of the large subunit rRNA is involved in the suppression of a -1T frameshift mutation affecting a mitochondrial gene in Chlamydomonas reinhardtii. Molecular Genetics and Genomics, 266 (1), 103-108. doi:10.1007/s004380100526

Remacle, C., Baurain, D., Cardol, P., & Matagne, R.-F. (July 2001). Mutants of Chlamydomonas reinhardtii deficient in mitochondrial complex I: Characterization of two mutations affecting the nd1 coding sequence. Genetics, 158 (3), 1051-60.

Baurain, D., Dinant, M., & Matagne, R.-F. (May 2001). Transcriptional regulation of the Chlamydomonas alternative oxidase (Aox1) gene studied with a reporter gene construct [Poster presentation]. Bioforum 2001, Liège, Belgium.

Dinant, M.* , Baurain, D.* , Coosemans, N., Joris, B., & Matagne, R.-F. (April 2001). Characterization of two genes encoding the mitochondrial alternative oxidase in Chlamydomonas reinhardtii. Current Genetics, 39 (2), 101-108. doi:10.1007/s002940000183
* These authors have contributed equally to this work.

Baurain, D., & Wilmotte, A. (13 March 2001). Analyse de séquences d'ITS de souches d'Arthrospira provenant de quatre continents [Paper presentation]. Séminaire de Botanique, Liège, Belgium.

Baurain, D., Matagne, R.-F., & Dinant, M. (May 2000). The alternative oxidase genes and their expression in Chlamydomonas [Poster presentation]. 9th International Conference on the Cell and Molecular Biology of Chlamydomonas, Nordwijkerhout, Netherlands.

Remacle, C., Baurain, D., Colin, M., & Matagne, R.-F. (2000). Isolation and characterization of respiratory NADH:ubiquinone oxidoreductase (complex I) mutants in Chlamydomonas reinhardtii. Archives of Physiology and Biochemistry, 108 (Supplement 1), 10.

Scheldeman, P., Baurain, D., Bouhy, R., Muhling, M., Whitton, B. A., Belay, A., & Wilmotte, A. (15 March 1999). Arthrospira ('Spirulina') strains from four continents are resolved into only two clusters, based on amplified ribosomal DNA restriction analysis of the internally transcribed spacer. FEMS Microbiology Letters, 172 (2), 213-22. doi:10.1016/S0378-1097(99)00017-8

Baurain, D., Scheldeman, P., Renquin, L., Bouhy, R., & Wilmotte, A. (1999). Characterization of Arthrospira / Spirulina strains: Molecular Aspects.

Baurain, D., Belay, A., & Wilmotte, A. (May 1998). Molecular systematics of Arthrospira ('Spirulina') strains based on rRNA sequence analysis [Poster presentation]. Bioforum 1998, Liège, Belgium.

Baurain, D., Dinant, M., Loppes, R., & Matagne, R.-F. (May 1998). Genetic manipulations in Chlamydomonas reinhardtii: Use of the antisense strategy to inhibit the alternative oxidase [Poster presentation]. Bioforum 1998, Liège, Belgium.

Baurain, D., Dinant, M., Loppes, R., & Matagne, R.-F. (1998). Role of alternative oxidase (AOX) in Chlamydomonas reinhardtii: Isolation and characterization of transgenic clones carrying an antisense Aox construct. Archives of Physiology and Biochemistry, 106, 3.

Dinant, M., Baurain, D., & Matagne, R.-F. (1998). Characterization of a cDNA encoding the mitochondrial alternative oxidase (AOX) in Chlamydomonas reinhardtii and assays of AOX inactivation by the antisense strategy. In I. M. Møller, P. Gardeström, K. Glimelius, ... E. Glaser (Eds.), Plant Mitochondria: From Gene to Function (pp. 441-444). Leiden, Netherlands: Backhuys Publishers.

Baurain, D. (February 1992). VGA-MAC : Visualiser des images de MAC en VGA. PC Micro-Informatique, 59, p. 31-5.