Projekt

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Harnessing Phylogenetic Variation Among Genetic Loci to Unravel Species Phylogenies, Lateral Gene Transfer, and Recombination Hotspots

Gesuchsteller/in Dessimoz Christophe
Nummer 150654
Förderungsinstrument SNF-Förderungsprofessuren
Forschungseinrichtung
Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Centre Intégratif de Génomique Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Genetik
Beginn/Ende 01.09.2015 - 31.08.2019
Bewilligter Betrag 1'540'725.00
Alle Daten anzeigen

Alle Disziplinen (6)

Disziplin
Genetik
Informatik
Mathematik
Zoologie
Molekularbiologie
Methoden der Epidemiologie und der Präventivmedizi

Keywords (15)

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

Lay Summary (Französisch)

Lead
L'histoire évolutive des gènes est souvent modélisée à l'aide d'arbres. Or, même si l'on considère un groupe d'espèces fixe, les arbres induits pour chaque famille de gène peuvent varier considérablement. Ce projet cherche à mieux caractériser cette hétérogénéité par le développement de nouvelles méthodes statistiques et computationnelles. Ces avancées seront utilisées pour éclairer des questions ouvertes sur l'origine des espèces, sur les transfers de gènes latéraux, et sur les points chauds de recombinaison.
Lay summary

Les arbres phylogénetiques sont utilisés à travers tous les domaines du vivant pour représenter des relations évolutives entres espèces et gènes. Ils jouent un rôle important non seulement en biologie évolutive, mais aussi en génomique fonctionnelle, biologie développementale, oncologie, ou encore en épidémiologie. Cependant, les caractères moléculaires des génomes ne découlent pas nécessairement tous d'un arbre unique, à cause de duplication de gènes, recombinaison, assortiment incomplet des espèces, transfert de gène latéraux, etc. Sous le paradigme actuel, ces différences sont souvent ignorées, ce qui peut conduire à des estimations d'arbres incomplètes, biaisées, ou excessivement confiantes. Ce projet a pour but de mieux modéliser cette hétérogénéité, afin d'élucider des questions portant sur l'histoire évolutives des gènes et des espèces (en particulier les questions proches des origines de la vie sur terre), de détecter des séquences contaminées dans des échantillons d'ADN, d'identifier des transferts de gènes latéraux entres espèces, et de caractériser des évènements de réassortiments dans les virus.

Direktlink auf Lay Summary Letzte Aktualisierung: 28.03.2016

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Gearing up to handle the mosaic nature of life in the quest for orthologs
Forslund Kristoffer, Pereira Cecile, Capella-Gutierrez Salvador, da Silva Alan Sousa, Altenhoff Adrian, Huerta-Cepas Jaime, Muffato Matthieu, Patricio Mateus, Vandepoele Klaas, Ebersberger Ingo, Blake Judith, Fernández Breis Jesualdo Tomás, Boeckmann Brigitte, Gabaldón Toni, Sonnhammer Erik, Dessimoz Christophe, Lewis Suzanna, Altenhoff Adrian, Bello Carla, Blake Judith, Boeckmann Brigitte, Briois Sébastien, Capella-Gutierrez Salvador, Chalstrey Edward, et al. (2018), Gearing up to handle the mosaic nature of life in the quest for orthologs, in Bioinformatics, 34(2), 323-329.
RecPhyloXML - a format for reconciled gene trees
Duchemin Wandrille, Gence Guillaume, Chifolleau Anne-Muriel Arigon, Arvestad Lars, Bansal Mukul S, Berry Vincent, Boussau Bastien, Chevenet Françcois, Comte Nicolas, Davín Adrián A, Dessimoz Christophe, Dylus David, Hasic Damir, Mallo Diego, Planel Rémi, Posada David, Scornavacca Celine, Szöllősi Gergely, Zhang Louxin, Éric Tannier, Daubin Vincent (2018), RecPhyloXML - a format for reconciled gene trees, in Bioinformatics, bty389.
GOATOOLS: A Python library for Gene Ontology analyses
Klopfenstein D. V., Zhang Liangsheng, Pedersen Brent S., Ramírez Fidel, Vesztrocy Alex Warwick, Naldi Aurélien, Mungall Christopher J., Yunes Jeffrey M., Botvinnik Olga, Weigel Mark, Dampier Will, Dessimoz Christophe, Flick Patrick, Tang Haibao (2018), GOATOOLS: A Python library for Gene Ontology analyses, in Scientific Reports, 8, 10872.
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Piližota Ivana, Train Clément-Marie, Altenhoff Adrian, Redestig Henning, Dessimoz Christophe (2018), Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome, in Bioinformatics.
Prioritising candidate genes causing QTL using hierarchical orthologous groups
Warwick Vesztrocy Alex, Dessimoz Christophe, Redestig Henning (2018), Prioritising candidate genes causing QTL using hierarchical orthologous groups, in Bioinformatics, 34(17), 612-619.
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
Altenhoff Adrian M., Glover Natasha M., Train Clément-Marie, Kaleb Klara, Warwick Vesztrocy Alex, Dylus David, de Farias Tarcisio M., Zile Karina, Stevenson Charles, Long Jiao, Redestig Henning, Gonnet Gaston H., Dessimoz Christophe (2018), The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces, in Nucleic Acids Research, 46, D477-D485.
Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.
Suchan Tomasz, Espíndola Anahí, Rutschmann Sereina, Emerson Brent C, Gori Kevin, Dessimoz Christophe, Arrigo Nils, Ronikier Michał, Alvarez Nadir (2017), Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study., in Molecular phylogenetics and evolution, 114, 189-198.
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.
Train Clément-Marie, Glover Natasha M, Gonnet Gaston H, Altenhoff Adrian M, Dessimoz Christophe (2017), Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference., in Bioinformatics (Oxford, England), 33(14), 75-82.
Comparative genomics reveals contraction in olfactory receptor genes in bats.
Tsagkogeorga Georgia, Müller Steven, Dessimoz Christophe, Rossiter Stephen J (2017), Comparative genomics reveals contraction in olfactory receptor genes in bats., in Scientific reports, 7(1), 259-259.
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Jeffares Daniel C, Jolly Clemency, Hoti Mimoza, Speed Doug, Shaw Liam, Rallis Charalampos, Balloux Francois, Dessimoz Christophe, Bähler Jürg, Sedlazeck Fritz J (2017), Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast., in Nature communications, 8, 14061-14061.
The Gene Ontology Handbook
Dessimoz Christophe, Škunca Nives (2017), The Gene Ontology Handbook, Springer, New York.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
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, Skunca Nives, Dessimoz Christophe, Dogan Tunca, Hakala Kai, Kaewphan Suwisa, Mehryary Farrokh, Salakoski Tapio, Ginter Filip, Fang Hai, Smithers Ben, Oates Matt, Gough Julian, Törönen Petri, Koskinen Patrik, Holm Liisa, Chen Ching-Tai, Hsu Wen-Lian, Bryson Kevin, Cozzetto Domenico, Minneci Federico, Jones David T, Chapman Samuel, Bkc Dukka, Khan Ishita K, Kihara Daisuke, Ofer Dan, Rappoport Nadav, Stern Amos, Cibrian-Uhalte Elena, Denny Paul, Foulger Rebecca E, Hieta Reija, Legge Duncan, Lovering Ruth C, Magrane Michele, Melidoni Anna N, Mutowo-Meullenet Prudence, Pichler Klemens, Shypitsyna Aleksandra, Li Biao, Zakeri Pooya, ElShal Sarah, Tranchevent Léon-Charles, Das Sayoni, Dawson Natalie L, Lee David, Lees Jonathan G, Sillitoe Ian, Bhat Prajwal, Nepusz Tamás, Romero Alfonso E, Sasidharan Rajkumar, Yang Haixuan, Paccanaro Alberto, Gillis Jesse, Sedeño-Cortés Adriana E, Pavlidis Paul, Feng Shou, Cejuela Juan M, Goldberg Tatyana, Hamp Tobias, Richter Lothar, Salamov Asaf, Gabaldon Toni, Marcet-Houben Marina, Supek Fran, Gong Qingtian, Ning Wei, Zhou Yuanpeng, Tian Weidong, Falda Marco, Fontana Paolo, Lavezzo Enrico, Toppo Stefano, Ferrari Carlo, Giollo Manuel (2016), An expanded evaluation of protein function prediction methods shows an improvement in accuracy., in Genome biology, 17(1), 184-184.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
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.
Compensation of dosage-sensitive genes on the chicken Z chromosome
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, 075-075.
Homoeologs: What Are They and How Do We Infer Them?
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.
Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life
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, 164-164.
Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web
Robinson Oscar, Dylus David, Dessimoz Christophe (2016), Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web, in Mol Biol Evol, 080-080.
Standardized benchmarking in the quest for orthologs
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.
Clustering genes of common evolutionary history.
Gori Kevin, Suchan Tomasz, Alvarez Nadir, Goldman Nick, Dessimoz Christophe, Clustering genes of common evolutionary history., in Molecular biology and evolution, msw038.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Dr. Manuel Gil, University of Zurich Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Prof. Nadir Alvarez, DEE, UNIL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Dr. Nick Goldman, EMBL-EBI Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Prof. Ioannis Xenarios, Vital-IT, Swiss Institute of Bioinformatics and UNIL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
Dr. Nick Lane, University College London Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Belgrade BioInformatics Conference 2018 Vortrag im Rahmen einer Tagung Spectral signature of gene family trees 22.06.2018 Belgrade, Serbien De Oliveira Martins Leonardo;
Center for Advanced Modeling Science Day Vortrag im Rahmen einer Tagung Big Data Comparative Genomics 17.11.2017 Lausanne, Schweiz Dessimoz Christophe;
Annual debate of the Linnaean Society of London Vortrag im Rahmen einer Tagung Debate on Big Data 16.11.2017 London, Grossbritannien und Nordirland Dessimoz Christophe;
BC2 conference Vortrag im Rahmen einer Tagung Spectral signature of gene family tree 13.09.2017 Basel, Schweiz De Oliveira Martins Leonardo; Dessimoz Christophe;
Life in Numbers 3 Vortrag im Rahmen einer Tagung Integrating genomes via fine-grained orthology 31.08.2017 Wädenswil, Schweiz Dessimoz Christophe;
ISMB/ECCB Vortrag im Rahmen einer Tagung OMA algorithm 2.0:
more robust to asymmetric evolutionary rates 
and more scalable hierarchical orthologous group inference 25.07.2017 Prague, Tschechische Republik Train Clément; Dessimoz Christophe; Glover Natasha;
SMBE Symposium on Evolution of Gene Families Vortrag im Rahmen einer Tagung Relating genes and their functions across many species:
Going whole HOG 07.06.2017 Los Angeles, Vereinigte Staaten von Amerika Glover Natasha; Dessimoz Christophe;
Departmental seminar Einzelvortrag Making the most of noisy, 
low-quality genomes 19.04.2017 Tokyo, Japan Dessimoz Christophe;
Departmental Seminar Einzelvortrag Gene Ontology:
biases, pitfalls, remedies 14.04.2017 Kobe, Japan Dessimoz Christophe;
ECCB 2016 Vortrag im Rahmen einer Tagung Automated filtering of multiple sequence alignments frequently worsens phylogenetic inference 06.09.2016 The Hague, Niederlande Dessimoz Christophe;
C3BI seminar series, Institut Pasteur, Paris (F) Einzelvortrag Hierarchical Orthologous Groups: a unifying and scalable framework for large-scale gene evolution 12.05.2016 Paris, Frankreich Dessimoz Christophe;
RECOMB Comparative Genomics Vortrag im Rahmen einer Tagung Hierarchical Orthologous Groups a unifying and scalable framework for large-scale gene evolution 05.10.2015 Frankfurt, Deutschland Dessimoz Christophe;


Selber organisiert

Titel Datum Ort
1st Lausanne Computational Biology meeting 03.05.2016 Lausanne, Schweiz
8th Fisher Centre meeting 21.03.2016 London, Grossbritannien und Nordirland
7th Fisher Centre meeting 12.11.2015 London, Grossbritannien und Nordirland

Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Medienarbeit: Printmedien, Online-Medien Votre ADN peut-il être hacké? We Demain International 2018
Medienarbeit: Printmedien, Online-Medien 'Adversarial DNA' breeds buffer overflow bugs in PCs The Register International 2017
Medienarbeit: Radio, Fernsehen Journal du matin RTS Radio 1ère Westschweiz 2017
Medienarbeit: Radio, Fernsehen La Méthode Scientifique France Culture International 2017
Medienarbeit: Printmedien, Online-Medien L'ADN, clé USB de demain? Québec Science International 2017
Medienarbeit: Printmedien, Online-Medien L'ADN, une nouvelle arme pour les pirates informatiques? Le Temps Westschweiz 2017
Medienarbeit: Printmedien, Online-Medien Quand l'ADN se transforme en disque dur Le Figaro International 2017

Auszeichnungen

Titel Jahr
Sentinel of Science Award (awarded by Publons for top 1% of peer reviewers in the field of Biochemistry, Genetics and Molecular Biology) 2017
EMBO Young Investigator 2016

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
136461 The Million Protein, Thousand Species Tree(s) of Life 01.09.2011 Stipendien für fortgeschrittene Forschende

Abstract

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.
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