Dessimoz Group - Computational Evolutionary Biology and Genomics

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

In Press | 2018 | 2017 | 2016 | 2015 | ...

In Press

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. Bioinformatics. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_F6316B688D65]

2018

Submit a Topic Page to PLOS Computational Biology and Wikipedia.

Mietchen D., Wodak S., Wasik S., Szostak N., Dessimoz C., 2018/05. PLoS computational biology, 14 (5) pp. e1006137. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_44F587EDD0AF]

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. 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.

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

2017

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.

[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]

A Gene Ontology Tutorial in Python.

Vesztrocy A.W., Dessimoz C., 2017. Methods in molecular biology, 1446 pp. 221-229. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_6D82D9E2A2D4]

2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y., Oron T.R., Clark W.T., Bankapur A.R., D'Andrea D., Lepore R., Funk C.S., Kahanda I., Verspoor K.M., Ben-Hur A. et al., 2016/09/07. Genome Biology, 17 (1) p. 184. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_3564C07C1354]

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

Robinson O., Dylus D., Dessimoz C., 2016/08. Molecular biology and evolution, 33 (8) pp. 2163-2166. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_82CD43EFE497]

Clustering Genes of Common Evolutionary History.

Gori K., Suchan T., Alvarez N., Goldman N., Dessimoz C., 2016/06. Molecular biology and evolution, 33 (6) pp. 1590-1605. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_36DE5D65E7A5]

Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.

Zimmer F., Harrison P.W., Dessimoz C., Mank J.E., 2016/04/25. Genome biology and evolution, 8 (4) pp. 1233-1242.

[URN] [DOI] [Pmid] [serval:BIB_7DFE950E8AB0]

Standardized benchmarking in the quest for orthologs.

Altenhoff A.M., Boeckmann B., Capella-Gutierrez S., Dalquen D.A., DeLuca T., Forslund K., Huerta-Cepas J., Linard B., Pereira C., Pryszcz L.P. et al., 2016. Nature Methods, 13 (5) pp. 425-430. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_E8F5620D5F4F]

Homoeologs: What Are They and How Do We Infer Them?

Glover N.M., Redestig H., Dessimoz C., 2016. Trends in Plant Science, 21 (7) pp. 609-621. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_59A0CA77B84B]

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y., Oron T.R., Clark W.T., Bankapur A.R., D'Andrea D., Lepore R., Funk C.S., Kahanda I., Verspoor K.M., Ben-Hur A. et al., 2016. Genome Biology, 17 (1) p. 184.

[DOI] [Pmid] [serval:BIB_0DA5AAECE9FC]

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

Sojo V., Dessimoz C., Pomiankowski A., Lane N., 2016. Molecular Biology and Evolution, 33 (11) pp. 2874-2884. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_6990F70049C3]

2015

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

Altenhoff Adrian M, Skunca Nives, Glover Natasha, Train Clément-Marie, Sueki Anna, Pilizota Ivana, Gori Kevin, Tomiczek Bartlomiej, Müller Steven, Redestig Henning et al., 2015. Nucleic acids research, 43 (Database issue) pp. D240--9.

[serval:BIB_0E374421DCD4]

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)

Interns & project students

Abraham Olaoye, CS summer intern
Oscar Robinson, CS summer intern
Jan Koch, Erasmus student
Clément-Marie Train, MSc project student

External collaborators

Raphaëlle Luisier