Dessimoz Group - Computational Evolutionary Biology and Genomics

Presentation

At the interface between biology and computer science, our laboratory seeks to better understand evolutionary and functional relationships between genes, genomes, and species.

For more information on our lab, please consult the page http://lab.dessimoz.org

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Publications

Publications | Masters and Phd thesis

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Publications

In Press | 2019 | 2018 | 2017 | ...

In Press

Advances and Applications in the Quest for Orthologs.

Glover N., Dessimoz C., Ebersberger I., Forslund S.K., Gabaldón T., Huerta-Cepas J., Martin M.J., Muffato M., Patricio M., Pereira C. et al. Molecular biology and evolution. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_A36FE75880A9]

2019

OMA standalone: orthology inference among public and custom genomes and transcriptomes.

Altenhoff A.M., Levy J., Zarowiecki M., Tomiczek B., Warwick Vesztrocy A., Dalquen D.A., Müller S., Telford M.J., Glover N.M., Dylus D. et al., 2019/07. Genome research, 29 (7) pp. 1152-1163. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_D405BD0232C3]

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.

Philippe H., Poustka A.J., Chiodin M., Hoff K.J., Dessimoz C., Tomiczek B., Schiffer P.H., Müller S., Domman D., Horn M. et al., 2019/06/03. Current Biology, 29 (11) pp. 1818-1826.e6. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_43B8702FAD67]

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.

Piližota I., Train C.M., Altenhoff A., Redestig H., Dessimoz C., 2019/04/01. Bioinformatics, 35 (7) pp. 1159-1166. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_6469004280EE]

Inferring Orthology and Paralogy.

Altenhoff A.M., Glover N.M., Dessimoz C., 2019. Methods in molecular biology, 1910 pp. 149-175. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_062874BB14CB]

Assigning confidence scores to homoeologs using fuzzy logic.

Glover N.M., Altenhoff A., Dessimoz C., 2019. PeerJ, 6 pp. e6231. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_D4984F5E8391]

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python.

Kaleb K., Vesztrocy A.W., Altenhoff A., Dessimoz C., 2019. F1000Research, 8 p. 42. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_DA9EB0198996]

2018

iHam & pyHam: visualizing and processing hierarchical orthologous groups.

Train C.M., Pignatelli M., Altenhoff A., Dessimoz C., 2018/12/03. Bioinformatics. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_8E5F2D47F9B1]

RecPhyloXML: a format for reconciled gene trees.

Duchemin W., Gence G., Arigon Chifolleau A.M., Arvestad L., Bansal M.S., Berry V., Boussau B., Chevenet F., Comte N., Davín A.A. et al., 2018/11/01. Bioinformatics, 34 (21) pp. 3646-3652. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_F6316B688D65]

Prioritising candidate genes causing QTL using hierarchical orthologous groups.

Warwick Vesztrocy A., Dessimoz C., Redestig H., 2018/09/01. Bioinformatics, 34 (17) pp. i612-i619. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_6DAC1269D35C]

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Altenhoff A.M., Glover N.M., Train C.M., Kaleb K., Warwick Vesztrocy A., Dylus D., de Farias T.M., Zile K., Stevenson C., Long J. et al., 2018/01/04. Nucleic acids research, 46 (D1) pp. D477-D485. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_FC0F04688D1D]

Gearing up to handle the mosaic nature of life in the quest for orthologs.

Forslund K., Pereira C., Capella-Gutierrez S., Sousa da Silva A., Altenhoff A., Huerta-Cepas J., Muffato M., Patricio M., Vandepoele K., Ebersberger I. et al., 2018. Bioinformatics, 34 (2) pp. 323-329. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_D31584E0556C]

Submit a Topic Page to PLOS Computational Biology and Wikipedia.

Mietchen D., Wodak S., Wasik S., Szostak N., Dessimoz C., 2018. PLoS Computational Biology, 14 (5) pp. e1006137. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_44F587EDD0AF]

2017

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Boeckmann Brigitte, Dylus David, Moretti Sebastien, Altenhoff Adrian, Train Clement-Marie, Kriventseva Evgenia, Bougueleret Lydie, Xenarios Ioannis, Privman Eyal, Gabaldon Toni et al., 2017/09/05. biorxiv.

[DOI] [serval:BIB_7579ACF1CAEA]

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.

Jeffares D.C., Jolly C., Hoti M., Speed D., Shaw L., Rallis C., Balloux F., Dessimoz C., Bähler J., Sedlazeck F.J., 2017/01/24. Nature communications, 8 p. 14061. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_0B9096E627F3]

Gene Ontology: Pitfalls, Biases, and Remedies.

Gaudet P., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 189-205. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_CBFCF5FD756A]

Primer on the Gene Ontology.

Gaudet P., Škunca N., Hu J.C., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 25-37. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_E02D84F1D7CD]

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

Suchan T., Espíndola A., Rutschmann S., Emerson B.C., Gori K., Dessimoz C., Arrigo N., Ronikier M., Alvarez N., 2017. Molecular Phylogenetics and Evolution, 114 pp. 189-198. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_1CBC34940B2F]

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Train C.-M., Glover N.M., Gonnet G.H., Altenhoff A.M., Dessimoz C., 2017. Bioinformatics, 33 (14) pp. i75-i82.

[URN] [DOI] [WoS] [serval:BIB_7D03376859BC]

Comparative genomics reveals contraction in olfactory receptor genes in bats.

Tsagkogeorga G., Müller S., Dessimoz C., Rossiter S.J., 2017. Scientific Reports, 7 (1) p. 259. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_66353CA228EE]

Phd thesis

Publications (1)

Progressive Multiple Sequence Alignment with Indel Evolution

Maiolo Massimo, 2019., Université de Lausanne, Faculté de biologie et médecine, Dessimoz Christophe (dir.).

[URN] [serval:BIB_D24577D3A885]

Group members

Group leader

Prof. Christophe Dessimoz

Staff & postdocs

Dr. Adrian Altenhoff, OMA Project Manager (based at ETH Zurich)
Dr. Tugce Bilgin Sonay
Dr. David Dylus (based on University of Lausanne)
Dr. Natasha Glover (based on University of Lausanne)
Dr. Tarcisio Mendes De Farias
Dr. Leornado De Oliveira (based on University of Lausanne)
Dr. Nives Škunca (based at ETH Zurich)

PhD students

Kevin Gori (based at EMBL-EBI, co-supervised by Dr. Nick Goldman)
Jessica Joaquim
Jeremy Levy, CoMPLEX student (based at UCL, co-supervised by Prof. Max Telford)
Steven Müller (based at UCL, co-supervised by Prof. Max Telford)
Ivana Piližota, Impact student (based at UCL, co-supervised by Dr. Henning Redestig, Bayer CropScience)
Bartlomiej Tomiczek (based at UCL, co-supervised by Prof. Max Telford)
Clément Train
Tom Watkins (based at Crick, co-supervised by Prof. Charles Swanton, CRUK)

Dessimoz Group - Computational Evolutionary Biology and Genomics

Presentation

Publications

Publications

Phd thesis

Publications (1)

Group members

Group leader

Staff & postdocs

PhD students

Interns & project students

External collaborators

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