High performance computing; Lateral gene transfer; Gene evolution; Computational Biology; Phylogenomics; Endosymbiosis; Mixture model; Influenza evolution; Phylogenetics; Molecular Evolution; Tree of Life; Parasitic worms; Statistical modelling; Recombination; Bioinformatics
Jiang Yuxiang, Oron Tal Ronnen, Clark Wyatt T., Bankapur Asma R., D’Andrea Daniel, Lepore Rosalba, Funk Christopher S., Kahanda Indika, Verspoor Karin M., Ben-Hur Asa, Koo Da Chen Emily, Penfold-Brown Duncan, Shasha Dennis, Youngs Noah, Bonneau Richard, Lin Alexandra, Sahraeian Sayed M. E., Martelli Pier Luigi, Profiti Giuseppe, Casadio Rita, Cao Renzhi, Zhong Zhaolong, Cheng Jianlin, Altenhoff Adrian, et al. (2016), An expanded evaluation of protein function prediction methods shows an improvement in accuracy, in Genome Biology
, 17(1), 184.
Zimmer Fabian, Harrison Peter W., Dessimoz Christophe, Mank Judith E. (2016), Compensation of dosage-sensitive genes on the chicken Z chromosome, in Genome Biol Evol
Glover Natasha M., Redestig Henning, Dessimoz Christophe (2016), Homoeologs: What Are They and How Do We Infer Them?, in Trends in Plant Science
, 21(7), 609-621.
Victor Sojo, Dessimoz Christophe, Pomiankowski Andrew, Lane Nick (2016), Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life, in Mol Biol Evol
Robinson Oscar, Dylus David, Dessimoz Christophe (2016), Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web, in Mol Biol Evol
Altenhoff Adrian M, Boeckmann Brigitte, Capella-Gutierrez Salvador, Dalquen Daniel A, DeLuca Todd, Forslund Kristoffer, Huerta-Cepas Jaime, Linard Benjamin, Pereira Cécile, Pryszcz Leszek P, Schreiber Fabian, da Silva Alan Sousa, Szklarczyk Damian, Train Clément-Marie, Bork Peer, Lecompte Odile, von Mering Christian, Xenarios Ioannis, Sjölander Kimmen, Jensen Lars Juhl, Martin Maria J, Muffato Matthieu, Gabaldón Toni, Lewis Suzanna, Thomas Paul (2016), Standardized benchmarking in the quest for orthologs, in Nature Methods
, 13, 425-430.
Phylogenetic trees are used throughout biology to represent evolutionary relationships among species and genes. They play an important role well beyond the field of evolutionary biology, such as in functional genomics, in developmental biology, in oncology or in epidemiology. However, the molecular characters of genomes do not necessary all share a single tree, e.g., due to duplication, recombination, incomplete lineage sorting, lateral gene transfer, etc. In the current paradigm, these potential phylogenetic differences are often ignored, which can result in incomplete, biased, and overconfident inference.In this project, we want to embrace this phylogenetic variation to elucidate long-standing questions on species phylogenies (in particular, ones close to the origins of life), to identify contaminants in DNA samples, to uncover lateral gene transfer between parasitic worms and their hosts, and to identify reassortment events in flu viruses.To these ends, a substantial portion of our efforts will be directed toward the development of new methods and software tools for inferring the nature and extent of phylogenetic variation underlying multiple genetic loci. Focal point of the project is a new method that simultaneously solves the problems of partitioning genetic loci into clusters having common evolutionary histories, and of inferring these histories. This will require progress in statistical modelling, computational optimisation, benchmarking, and visualisation tools.Given the pervasiveness of phylogenetic trees across all of biosciences, this project will yield tools and advances that impact a broad community of researchers worldwide, and strengthen Switzerland's standing in phylogenomics.