Publications and communications of Luc Cornet

Christodoulou, M., Savora, H., Cornet, L., & Wilmotte, A. (08 March 2024). BCCM/ULC public collection of cyanobacteria: A tool for microbial research and innovation [Poster presentation]. Belgian Society of Microbiology Annual Symposium 2024: Milestones in Microbiology, Brussels, Belgium.

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

Christodoulou, M., Vaz, M., Beets, K., Savora, H., Cornet, L., & Wilmotte, A. (14 November 2023). Insights into the biological and chemical diversity of cyanobacteria from the BCCM/ULC collection [Paper presentation]. Annual Meeting on Plant Ecology and Evolution (AMPEE7) Small is beautiful, even in Botany, Liège, Belgium.

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.

Picone Dorian, Luchena, M., Cornet, L., Becker, P., Wilmotte, A., & Vaz, M. (September 2023). Evaluation of the bioactive potential of polar cyanobacterial strains from BCCM/ULC [Poster presentation]. ECCO XLI – 2023, Bruxelles, Belgium.

Pardo-De la Hoz, C. J., Magain, N., Piatkowski, B., Cornet, L., Dal Forno, M., Carbone, I., Miadlikowska, J., & Lutzoni, F. (2023). Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria. Systematic Biology. doi:10.1093/sysbio/syad008

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

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

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

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

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

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

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

Syed-Shan-e-Ali, Z., Mehta, D., Cornet, L., & Vanderschuren, H. (30 January 2020). Full-length sequencing of extrachromosomal circular DNA using CIDER-Seq [Paper presentation]. Circular DNA in normal development and disease, Berlin, Germany.

Mehta, D., Cornet, L., Hirsch-Hoffmann, M., Syed-Shan-e-Ali, Z., & Vanderschuren, H. (2020). Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq. Nature Protocols, 15 (5), 1673-1689. doi:10.1038/s41596-020-0301-0

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

Syed-Shan-e-Ali, Z., Cornet, L., Mehta, D., & Vanderschuren, H. (November 2019). CIDER-Seq: An efficient tool to study plant-geminivirus recombinant eccDNAs [Paper presentation]. 9th International Geminivirus Symposium and 7th ssDNA Comparative Virology Workshop (IGS 2019), Davis, United States.

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.

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

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.

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

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.

Syed-Shan-e-Ali, Z., Cornet, L., Mehta, D., Patrignanic, A., & Vanderschuren, H. (28 October 2018). A Novel Method of Capturing and Sequencing Rolling Circle-Replicating Helitron Transposons [Paper presentation]. International plant epi / genetics symposium, Angers, France.

Syed-Shan-e-Ali, Z., Cornet, L., Comadira, G., Bawin, T., & Vanderschuren, H. (16 October 2018). Combining BAC and PacBio sequencing to resolve cassava mosaic disease resistance locus CMD2 [Paper presentation]. SASBi/SAGS congress 2018, Clarens, South Africa.

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.

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.

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.

Cornet, L. (2018). Genomics, Metagenomics and Phylogenomics of Cyanobacteria [Doctoral thesis, ULiège - Université de Liège]. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/218280

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

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.

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

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.

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.

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.

Dehant, V., Kabamba Baludikay, B., Beghin, J., Breuer, D., Claeys, P., Cornet, Y., Cornet, L., Debaille, V., EL Atrassi, F., François, C., De Keyser, J., Gillman, C., Goderis, S., Hidaka, Y., Honing, D., Hublet, G., Javaux, E., Karatekin, O., Maes, L., ... Wilquet, V. (June 2016). PLANET TOPERS: Planets, Tracing the Transfer, Origin, Preservation, and Evolution of their ReservoirS. Origins of Life and Evolution of the Biosphere, DOI 10.1007/s11084-016-9488. doi:10.1007/s11084-016-9488-z

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.

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.

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.

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

Cornet, L., Gerrienne, P., Meyer-Berthaud, B., & Prestianni, C. (01 September 2012). A Middle Devonian Callixylon (Archaeopteridales) from Ronquières, Belgium. Review of Palaeobotany and Palynology, 183, 1-8. doi:10.1016/j.revpalbo.2012.07.004

Cornet, L., Gerrienne, P., Meyer-Berthaud, B., & Prestianni, C. (21 June 2012). Un Callixylon (Archaeopteridales) du Dèvonien moyen de Belgique [Paper presentation]. Agora paleobotanica, Lyon, France.

Cornet, L., Gerrienne, P., & Meyer-Berthaud, B. (2010). Etude de spécimens de progymnospermes «type Callixylon » de Ronquières (Dévonien moyen, Belgique). In Miscellanea palaeontologica 2010.