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Faculty of Biology and Medicine

Department of Ecology and Evolution

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Dessimoz Group - Computational Evolutionary Biology and Genomics

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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

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2020 | 2019 | 2018 | ...

2020

New genome assembly of the barn owl (Tyto alba alba).

Ducrest A.L., Neuenschwander S., Schmid-Siegert E., Pagni M., Train C., Dylus D., Nevers Y., Warwick Vesztrocy A., San-Jose L.M., Dupasquier M. et al., 2020/03. Ecology and evolution, 10 (5) pp. 2284-2298. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_83891497D9E8]

Genomic encryption of digital data stored in synthetic DNA.

Grass R.N., Heckel R., Dessimoz C., Stark W.J., 2020/02/21..

[DOI][Pmid][serval:BIB_43671755DDDE]

Identifying orthologs with OMA: A primer.

Zahn-Zabal M., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 27. Peer-reviewed.

[DOI][Pmid][serval:BIB_B7D7E8705809]

2019

Structural variant calling: the long and the short of it.

Mahmoud M., Gobet N., Cruz-Dávalos D.I., Mounier N., Dessimoz C., Sedlazeck F.J., 2019/11/20. Genome biology, 20 (1) p. 246. Peer-reviewed.

[DOI][Pmid][serval:BIB_2D7AE4E0971F]

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 1; peer review: 1 approved with reservations]

Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias, 2019/10/29. F1000Research.

[DOI][serval:BIB_EF5C14AC5C45]

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., 2019/10/01. Molecular biology and evolution, 36 (10) pp. 2157-2164. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_A36FE75880A9]

iHam and pyHam: visualizing and processing hierarchical orthologous groups.

Train C.M., Pignatelli M., Altenhoff A., Dessimoz C., 2019/07/15. Bioinformatics, 35 (14) pp. 2504-2506. Peer-reviewed.

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

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]

preview resource BIB_6469004280EE.P001

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]

Enabling semantic queries across federated bioinformatics databases.

Sima A.C., Mendes de Farias T., Zbinden E., Anisimova M., Gil M., Stockinger H., Stockinger K., Robinson-Rechavi M., Dessimoz C., 2019/01/01. Database, 2019. Peer-reviewed.

[DOI][Pmid][serval:BIB_ED991CD0F569]

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]

preview resource BIB_D4984F5E8391.P001

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]

preview resource BIB_DA9EB0198996.P001

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]

VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links

Mendes de Farias Tarcisio, Stockinger Kurt, Dessimoz Christophe, 2019. Lecture Notes in Computer Science pp. 607-625. Peer-reviewed.

[DOI][serval:BIB_B5FCAC161AA9]

Semantic Integration and Enrichment of Heterogeneous Biological Databases.

Sima A.C., Stockinger K., de Farias T.M., Gil M., 2019. Methods in molecular biology, 1910 pp. 655-690. Peer-reviewed.

[DOI][Pmid][serval:BIB_3D396F44C44D]

2018

preview resource BIB_F6316B688D65.P001

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]

preview resource BIB_6DAC1269D35C.P001

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]

preview resource BIB_FC0F04688D1D.P001

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]

preview resource BIB_D31584E0556C.P001

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]

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Phd thesis

Publications (1)

preview resource BIB_D24577D3A885.P001

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)

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

How to apply

christophe.dessimoz[@]unil.ch

Biophore - CH-1015 Lausanne
Switzerland
Tel. +41 21 692 41 60
Fax +41 21 692 41 65

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