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Faculty of Biology and Medicine

Department of Ecology and Evolution

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Dr. David Dylus

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Publications

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In Press | 2020 | 2019 | 2018 | 2017 | 2016 |

In Press

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.

Dylus D., Altenhoff A., Majidian S., Sedlazeck F.J., Dessimoz C. Nature biotechnology. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AB990544B7BE]

2020

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test

Dylus David, Pillonel Trestan, Opota Onya, Wüthrich Daniel, Seth-Smith Helena M. B., Egli Adrian, Leo Stefano, Lazarevic Vladimir, Schrenzel Jacques, Laurent Sacha et al., 2020/11/24. Frontiers in Microbiology, 11. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_347E9A7AF57F]

How to build phylogenetic species trees with OMA.

Dylus D., Nevers Y., Altenhoff A.M., Gürtler A., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 511. Peer-reviewed.

[DOI][Pmid][serval:BIB_D8D72D90D99B]

2019

preview resource BIB_D405BD0232C3.P001

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.

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

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_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_5D37F76F22D0.P001

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution.

Dylus D.V., Czarkwiani A., Blowes L.M., Elphick M.R., Oliveri P., 2018. Genome Biology, 19 (1) p. 26. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_5D37F76F22D0]

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]

2016

preview resource BIB_82CD43EFE497.P001

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]

preview resource BIB_0DF2817F232A.P001

Skeletal regeneration in the brittle star Amphiura filiformis.

Czarkwiani A., Ferrario C., Dylus D.V., Sugni M., Oliveri P., 2016. Frontiers in Zoology, 13 p. 18. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_0DF2817F232A]

preview resource BIB_E453F764B1F8.P001

Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.

Dylus D.V., Czarkwiani A., Stångberg J., Ortega-Martinez O., Dupont S., Oliveri P., 2016. Evodevo, 7 p. 2. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E453F764B1F8]

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