Yannis Nevers

I started my research path with a PhD at University of Strasbourg in France, from which I gratuated in 2018. There, I worked on orthology inference and the use of phylogenetic profiling to infer gene function. I joined the Dessimoz lab in 2019 to continue develloping innovative novel algorithmic method based on orthology inference and enact comparative genomics analysis. My main scientific interests lie in the understanding of all living species, reconstructing the evolution of their gene repertoire and how it relates to extant species phenotypes.


Research Interests

  • Comparative genomics
  • Orthology inference
  • Evolution of gene repertoire
  • Phylogenetic profiling
  • Genome annotation
  • Alternative Splicing
  • Genomic data quality

Publications

Peer-reviewed articles

  1. Novel approach combining transcriptional and evolutionary signatures to identify new multiciliation genes. A. Defosset, D. Merlat, L. Poidevin, Y. Nevers, A. Kress, O. Poch, O. Lecompte.

  2. Ten years of collaborative progress in the Quest for Orthologs. B. Linard, I. Ebersberger, S. Mcglynn, N. Glover, T. Mochizuki, M. Patricio, O. Lecompte, Y. Nevers, PD. Thomas, T. Gabaldón, E. Sonnhammer, C. Dessimoz, I. Uchiyama. Molecular Biology and Evolution. 2021. (doi: 10.1093/molbev/msab098)

  3. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. AM. Altenhoff , CM. Train , KJ. Gilbert , I. Mediratta , T. Mendes de Farias , D. Moi , Y. Nevers , HS. Radoykova , V. Rossier , A. Warwick Vesztrocy , NM. Glover , C. Dessimoz. Nucleic Acids Res. 2021 (doi: 10.1093/nar/gkaa1007)

  4. Proteome-scale detection of differential conservation patterns at protein and sub-protein levels with BLUR. A. Defosset, A. Kress, Y. Nevers, R. Ripp, JD. Thompson, O. Poch, O. Lecompte. Genome Biol Evol. 2020 (doi: 10.1093/gbe/evaa248.)

  5. The Quest for Orthologs benchmark service and consensus calls in 2020. AM.. Altenhoff, J. Garrayo-Ventas, S. Cosentino, D. Emms, NM. Glover, A. Hernández-Plaza, Y. Nevers, V. Sundesha, D. Szklarczyk, JM. Fernández, L. Codó, The Quest For Orthologs Consortium, JL. Gelpi, J. Huerta-Cepas, W. Iwasaki, S. Kelly, O. Lecompte, M. Muffato, MJ. Martin, S. Capella-Gutierrez, PD. Thomas, E. Sonnhammer, C. Dessimoz. Nucleic Acids Res. 2020 (doi: 10.1093/nar/gkaa308)

  6. New genome assembly of the barn owl (Tyto alba alba). AL. Ducrest, S. Neuenschwander, E. Schmid-Siegert, M. Pagni, C. Train, D. Dylus, Y. Nevers , A. Warwick Vesztrocy, LM. San-Jose, M. Dupasquier, C. Dessimoz, I. Xenarios, A. Roulin, J. Goudet. Ecol Evol. 2020

  7. OrthoInspector 3.0: open portal for comparative genomics. Y. Nevers, A. Kress, A. Defosset, R. Ripp, B. Linard, JD. Thompson, O. Poch, O. Lecompte. Nucleic Acids Research. Database Issue 2019. (doi: 10.1093/nar/gky1068)

  8. Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling. Y. Nevers, M. Prasad, L. Poidevin, K. Chennen, A. Allot, A. Kress, R. Ripp, H. Dollfus, O. Poch, O. Lecompte. Molecular Biology and Evolution 2017.(doi: 10.1093/molbev/msx146)

  9. MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers. A. Allot, K. Chennen, Y. Nevers, L. Poidevin, A. Kress, R. Ripp, JD. Thompson, O. Poch, O. Lecompte. J Med Internet Res. 2017. (doi: 10.2196/jmir.6676).

Preprints

  1. Protein length distribution is remarkably consistent across Life. Y Nevers, N Glover, C Dessimoz, O Lecompte. bioRXiv 2021 (doi.org/10.1101/2021.12.03.470944)

  2. How to build phylogenetic species trees with [version 1; awaiting peer review] D. Dylus, Y. Nevers, AM. Altenhoff, A. Gürtler, C. Dessimoz, NM. Glover F1000Research 2020 (doi.org/10.12688/f1000research.23790.1)

  3. A Linear-Time Solution to the Labeled Robinson-Foulds Distance Problem. S. Briand, C. Dessimoz, N. El-Mabrouk, Y. Nevers. bioRXiv 2020. (doi.org/10.1101/2020.09.14.293522)

Book chapter

  1. Orthology: Promises and Challenges. Y. Nevers,A. Defosset ,O. Lecompte. In: Pontarotti P. (eds) Evolutionary Biology—A Transdisciplinary Approach 2020. (doi.org/10.1007/978-3-030-57246-4_9)

Education

  • (2015 – 2018) PhD Thesis in Health and Life Sciences - Bioinformatics and System Biology University of Strasbourg, France. Dissertation: “Exploitation of evolutionary markers to explore genotype-phenotype relationships. Application to ciliopathies.”

  • (2013 - 2015) Life Sciences Master - Structural biology, bioinformatics and biotechnologies, University of Strasbourg, France.

  • (2010 - 2013) Life Sciences Bachelor - Biochemistry and molecular biology , University of Strasbourg, France.