Molecular Evolution; Mixture model; Phylogenetics; Bioinformatics; Recombination; Computational Biology; Phylogenomics; Gene evolution; High performance computing; Homoeology; Statistical modelling; Tree of Life
Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N (2021), Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism., in
Genome Biol Evol, evab010.
Glover N, Sheppard S, Dessimoz C (2021), Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs., in
Genome Biol Evol, evab077.
Dessimoz C, Przytycka TM (2021), ISMB/ECCB 2021 proceedings, in
Bioinformatics (Oxford, England), 37(1), i7-i8.
Rossier Victor, Vesztrocy Alex Warwick, Robinson-Rechavi Marc, Dessimoz Christophe (2021), OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, in
Bioinformatics, btab219.
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Consortium QFO, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I (2021), Ten years of collaborative progress in the Quest for Orthologs., in
Mol Biol Evol, msab098.
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C (2021), Want to track pandemic variants faster? Fix the bioinformatics bottleneck, in
NATURE, 591(7848), 30-33.
Briand S, Dessimoz C, El-Mabrouk N, Lafond M, Lobinska G (2020), A generalized Robinson-Foulds distance for labeled trees, in
BMC Genomics, 21, 779.
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Farias Tarcisio Mendes de (2020), A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 3 approved], in
F1000Research, 21027.
Benton Richard, Dessimoz Christophe, Moi David (2020), A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor, in
eLife, 9, e62507.
Warwick Vesztrocy A, Dessimoz C (2020), Benchmarking gene ontology function predictions using negative annotations, in
Bioinformatics (Oxford, England), 36(1), 210-218.
Zahn-Zabal Monique, Dessimoz Christophe, Glover Natasha M. (2020), Identifying orthologs with OMA: A primer, in
F1000Research, 9, 27-27.
Dylus D, Pillonel T, Opota O, Wuethrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbie V, Dessimoz C, Greub G, Lebrand A (2020), NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test, in
FRONTIERS IN MICROBIOLOGY, 11(ARTN 59109), 591093.
Altenhoff AM, Train C-M, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova H-S, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C (2020), OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more., in
Nucleic Acids Res, 49(D1), D373-D379.
Zile Karina, Dessimoz Christophe, Wurm Yannick, Masel Joanna (2020), Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence, in
Genome Biology and Evolution, 12(8), 1355-1366.
FernándezR, GabaldonT, DessimozChristophe (2020), Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference, in Delsuc F, Galtier N, Scornavacca C (ed.), No commercial publisher | Authors open access book, France, 2.4:1-2.4:14.
Byma S, Dhasade A, Altenhoff A, Dessimoz C, Larus JR (2020), Parallel and scalable precise clustering, in
Parallel Architectures and Compilation Techniques - Conference Proceedings, PACT, 217-228, ACM, New York, NY, USA217-228.
Moi D, Kilchoer L, Aguilar PS, Dessimoz C (2020), Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes, in
PLOS COMPUTATIONAL BIOLOGY, 16(7), e1007553.
Shaw Liam P., Wang Alethea D., Dylus David, Meier Magda, Pogacnik Grega, Dessimoz Christophe, Balloux Françcois (2020), The phylogenetic range of bacterial and viral pathogens of vertebrates, in
Molecular Ecology, 15463.
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, for Orthologs Consortium Quest, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C (2020), The Quest for Orthologs benchmark service and consensus calls in 2020., in
Nucleic Acids Res, 48(W1), W538-W545.
Phylogenetic trees depict evolutionary relationships among biological entities, such as genes, individuals, and species. They are fundamental to evolutionary biology, and their relevance extends to all of biology, including epidemiology, comparative genomics, oncology, developmental biology, host-pathogen interactions.One major complication arises whenever the characters making up an entity do not all share a common evolutionary history-a phenomenon referred to as phylogenetic incongruence. For example, phylogenetic incongruence arises when, among the loci used to infer species phylogenies, there is presence of incomplete lineage sorting, hybridization, introgression, lateral gene transfer, duplication and losses, etc.In this SNSF professorship extension project, we will continue to develop process-agnostic, general-purpose phylogenetic inference methods, and we will use these advances to tackle long-standing biological questions complicated by multiple sources of phylogenetic incongruence. Specifically, we will (1) improve the scalability, usability, and interpretability of our emerging software tool treesignal, which models incongruence using a machine learning framework; (2) contribute toward resolution of the Avian Tree of Life by employing methods that side-step genome assembly and annotation and cope with multiple sources of incongruence (in particular incomplete lineage sorting and genome annotation artifacts); (3) investigate the functional consequences of allopolyploidization (hybridization followed by whole genome duplication) in crop genomics, with a special focus on upland cotton.If successful, the project could resolve highly contended phylogenies, and shed light on genes related through hybridisation, many of which have been neglected to date due to methodological limitations. Ultimately, we believe that process-agnostic analysis of incongruence among loci has the potential to become a routine step in phylogenetic analyses.