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Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes.

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Publications

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Author(s): Cinta Pegueroles, Susana Iraola-Guzmán, Uciel Chorostecki, Ewa Ksiezopolska, Ester Saus, Toni Gabaldón
Published in: RNA Biology, Issue 16/3, 2019, Page(s) 320-329, ISSN 1547-6286
DOI: 10.1080/15476286.2019.1572438

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa

Author(s): Miguel A. Naranjo-Ortíz, Silvia Rodríguez-Píres, Rosario Torres, Antonieta De Cal, Josep Usall, Toni Gabaldón
Published in: Genome Announcements, Issue 6/17, 2018, ISSN 2169-8287
DOI: 10.1128/genomeA.00214-18

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

Author(s): Pedro González-Torres, Francisco Rodríguez-Mateos, Josefa Antón, Toni Gabaldón
Published in: mBio, Issue 10/1, 2019, ISSN 2150-7511
DOI: 10.1128/mBio.02494-18

Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal

Author(s): Toni Gabaldón, Cécile Fairhead
Published in: Current Genetics, Issue 65/1, 2019, Page(s) 93-98, ISSN 0172-8083
DOI: 10.1007/s00294-018-0867-z

Fungal evolution: major ecological adaptations and evolutionary transitions

Author(s): Miguel A. Naranjo‐Ortiz, Toni Gabaldón
Published in: Biological Reviews, 2019, ISSN 1464-7931
DOI: 10.1111/brv.12510

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

Author(s): Irene Julca, Marina Marcet-Houben, Pablo Vargas, Toni Gabaldón
Published in: BMC Biology, Issue 16/1, 2018, ISSN 1741-7007
DOI: 10.1186/s12915-018-0482-y

Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens

Author(s): Ewa Ksiezopolska, Toni Gabaldón
Published in: Genes, Issue 9/9, 2018, Page(s) 461, ISSN 2073-4425
DOI: 10.3390/genes9090461

Evolutionary and functional patterns of shared gene neighbourhood in fungi

Author(s): Marina Marcet-Houben, Toni Gabaldón
Published in: Nature Microbiology, Issue 4/12, 2019, Page(s) 2383-2392, ISSN 2058-5276
DOI: 10.1038/s41564-019-0552-0

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

Author(s): Verónica Mixão, Antonio Perez Hansen, Ester Saus, Teun Boekhout, Cornelia Lass-Florl, Toni Gabaldón
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
DOI: 10.3389/fgene.2019.00383

MICU1 Confers Protection from MCU-Dependent Manganese Toxicity

Author(s): Jennifer Wettmarshausen, Valerie Goh, Kai-Ting Huang, Daniela M. Arduino, Utkarsh Tripathi, Anja Leimpek, Yiming Cheng, Alexandros A. Pittis, Toni Gabaldón, Dejana Mokranjac, György Hajnóczky, Fabiana Perocchi
Published in: Cell Reports, Issue 25/6, 2018, Page(s) 1425-1435.e7, ISSN 2211-1247
DOI: 10.1016/j.celrep.2018.10.037

Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations

Author(s): Laia Carreté, Ewa Ksiezopolska, Emilia Gómez-Molero, Adela Angoulvant, Oliver Bader, Cécile Fairhead, Toni Gabaldón
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
DOI: 10.3389/fmicb.2019.00112

Genome Variation in the Model Halophilic Bacterium Salinibacter ruber

Author(s): Pedro González-Torres, Toni Gabaldón
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
DOI: 10.3389/fmicb.2018.01499

Relative timing of mitochondrial endosymbiosis and the “pre-mitochondrial symbioses” hypothesis

Author(s): Toni Gabaldón
Published in: IUBMB Life, Issue 70/12, 2018, Page(s) 1188-1196, ISSN 1521-6543
DOI: 10.1002/iub.1950

Hybridization and the origin of new yeast lineages

Author(s): Toni Gabaldón
Published in: FEMS Yeast Research, 2020, ISSN 1567-1356
DOI: 10.1093/femsyr/foaa040

Gene gain and loss across the metazoan tree of life

Author(s): Rosa Fernández, Toni Gabaldón
Published in: Nature Ecology & Evolution, Issue 4/4, 2020, Page(s) 524-533, ISSN 2397-334X
DOI: 10.1038/s41559-019-1069-x

Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

Author(s): Irene Julca, Marina Marcet-Houben, Fernando Cruz, Carlos Vargas-Chavez, John Spencer Johnston, Jèssica Gómez-Garrido, Leonor Frias, André Corvelo, Damian Loska, Francisco Cámara, Marta Gut, Tyler Alioto, Amparo Latorre, Toni Gabaldón
Published in: Molecular Biology and Evolution, Issue 37/3, 2019, Page(s) 730-756, ISSN 0737-4038
DOI: 10.1093/molbev/msz261

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

Author(s): Verónica Mixão, Toni Gabaldón
Published in: BMC Biology, Issue 18/1, 2020, ISSN 1741-7007
DOI: 10.1186/s12915-020-00776-6

HaploTypo: a variant-calling pipeline for phased genomes

Author(s): Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manu Molina, Toni Gabaldón
Published in: Bioinformatics, Issue 36/8, 2019, Page(s) 2569-2571, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz933

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

Author(s): Hrant Hovhannisyan, Ahmed Hafez, Carlos Llorens, Toni Gabaldón
Published in: Bioinformatics, Issue 36/3, 2019, Page(s) 925-927, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz626

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization

Author(s): Hrant Hovhannisyan, Ester Saus, Ewa Ksiezopolska, Alex J. Hinks Roberts, Edward J. Louis, Toni Gabaldón
Published in: Frontiers in Genetics, Issue 11, 2020, ISSN 1664-8021
DOI: 10.3389/fgene.2020.00404