Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness
- Amir Arastehfar, Farnaz Daneshnia, Hrant Hovhannisyan, …, Erika Shor, Toni Gabaldon, David S Perlin
- None, 10.1101/2023.06.15.545195
Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens
- Verónica Mixão, Juan Carlos Nunez-Rodriguez, Valentina Del Olmo, …, Teun Boekhout, Attila Gacser, Toni Gabaldón
- BMC Biol, 10.1186/s12915-023-01608-z
Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap
- Farnaz Daneshnia, João N de Almeida Júnior, Macit Ilkit, …, Arnaldo Lopes Colombo, Martin Hoenigl, Amir Arastehfar
- Lancet Microbe, 10.1016/s2666-5247(23)00067-8
Whole-genome sequencing confirms a persistent candidaemia clonal outbreak due to multidrug-resistant Candida parapsilosis
- Farnaz Daneshnia, Süleyha Hilmioğlu-Polat, Macit Ilkit, …, Cornelia Lass-Flörl, Toni Gabaldon, Amir Arastehfar
- J Antimicrob Chemother, 10.1093/jac/dkad112
Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies
- Irene Julca, Pablo Vargas, Irene Julca, …, Irene Julca, Pablo Vargas, Toni Gabaldón
- BMC Biol, 10.1186/s12915-023-01583-5
The little skate genome and the evolutionary emergence of wing-like fins
- Elisa de la Calle-Mustienes, Rafael D Acemel, Christina Paliou, …, Darío G Lupiáñez, Daniel S Rokhsar, José Luis Gómez-Skarmeta
- Nature, 10.1038/s41586-023-05868-1
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
- Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed, …, Jaume Perez-Sanchez, Toni Gabaldon, Carlos Llorens
- Genes (Basel), 10.3390/genes14020267
EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
- Marina Marcet-Houben, Ismael Collado-Cala, Diego Fuentes-Palacios, …, Andrés Garisoain-Zafra, Uciel Chorostecki, Toni Gabaldón
- J Mol Biol, 10.1016/j.jmb.2023.168013
How genomics can help biodiversity conservation
- Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, …, Robert M Waterhouse, Camila J Mazzoni, Jacob Höglund
- Trends Genet, 10.1016/j.tig.2023.01.005
Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
- Hrant Hovhannisyan, Antonio Rodríguez, Ester Saus, …, Ester Saus, Mario Vaneechoutte, Toni Gabaldón
- Front Cell Infect Microbiol, 10.3389/fcimb.2023.1093178
Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening
- Olfat Khannous-Lleiffe, Jesse R Willis, Ester Saus, …, Sergi Castellví-Bel, Toni Gabaldón, On Behalf Of The Criprev Consortium
- None, 10.3390/cancers15010120
Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata
- Marina Marcet-Houben, María Alvarado, Ewa Ksiezopolska, Ester Saus, Piet W J de Groot, Toni Gabaldón
- BMC Biol, 10.1186/s12915-022-01412-1
Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer
- Madison Snyder, Susana Iraola-Guzmán, Ester Saus, Toni Gabaldón
- None, 10.3390/cancers14163866
PerSVade: personalized structural variant detection in any species of interest
- Miquel Àngel Schikora-Tamarit, Toni Gabaldón
- Genome Biol, 10.1186/s13059-022-02737-4
On the Biology, Diversity and Evolution of Nucleariid Amoebae (Amorphea, Obazoa, Opisthokonta 1
- Toni Gabaldón, Eckhard Völcker, Guifré Torruella
- Protist, 10.1016/j.protis.2022.125895
Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla
- Saoirse Foley, Anna Vlasova, Marina Marcet-Houben, Toni Gabaldón, Veronica F Hinman
- Genomics, 10.1016/j.ygeno.2022.110431
Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus
- Maria Augusta C Horta, Jacob L Steenwyk, Matthew E Mead, …, Toni Gabaldón, Antonis Rokas, Gustavo H Goldman
- mBio, 10.1128/mbio.01519-22
Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens
- Miquel Àngel Schikora-Tamarit, Toni Gabaldón
- Biochem Soc Trans, 10.1042/bst20211123
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches
- L A Bugnon, A A Edera, S Prochetto, …, L E Di Persia, D H Milone, G Stegmayer
- Brief Bioinform, 10.1093/bib/bbac205
Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
- Hans Christoph Liedtke, Fernando Cruz, Jèssica Gómez-Garrido, …, Tyler Alioto, Toni Gabaldón, Ivan Gomez-Mestre
- DNA Res, 10.1093/dnares/dsac013
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors
- Jesse R Willis, Ester Saus, Susana Iraola-Guzmán, …, Julia Ponomarenko, Jochen Hecht, Toni Gabaldón
- NPJ Biofilms Microbiomes, 10.1038/s41522-022-00279-y
Multiple Hybridization Events Punctuate the Evolutionary Trajectory of Malassezia furfur
- Bart Theelen, Verónica Mixão, Giuseppe Ianiri, …, Thomas L Dawson, Toni Gabaldón, Teun Boekhout
- mBio, 10.1128/mbio.03853-21
Candidemia Among Coronavirus Disease 2019 Patients in Turkey Admitted to Intensive Care Units: A Retrospective Multicenter Study
- Amir Arastehfar, Nevzat Ünal, Tuğrul Hoşbul, …, Toni Gabaldón, Macit Ilkit, M Hong Nguyen
- None, 10.1093/ofid/ofac078
Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus
- Ana Cristina Colabardini, Fang Wang, Zhengqiang Miao, …, Taicia Fill, Koon Ho Wong, Gustavo H Goldman
- PLoS Genet, 10.1371/journal.pgen.1010001
Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy
- A Arastehfar, M Marcet-Houben, F Daneshnia, …, E Shor, T Gabaldón, D S Perlin
- None, 10.1016/j.simyco.2021.100133
The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks
- Teun Boekhout, M Catherine Aime, Dominik Begerow, …, Sheng Sun, Duong Vu, Andrey Yurkov
- None, 10.1007/s13225-021-00475-9
Human albumin enhances the pathogenic potential of Candida glabrata on vaginal epithelial cells
- Marina Pekmezovic, Ann-Kristin Kaune, Sophie Austermeier, …, Toni Gabaldón, Mark S Gresnigt, Bernhard Hube
- PLoS Pathog, 10.1371/journal.ppat.1010037
Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata
- Ewa Ksiezopolska, Miquel Àngel Schikora-Tamarit, Reinhard Beyer, Juan Carlos Nunez-Rodriguez, Christoph Schüller, Toni Gabaldón
- Curr Biol, 10.1016/j.cub.2021.09.084
Origin and Early Evolution of the Eukaryotic Cell
- Toni Gabaldón
- Annu Rev Microbiol, 10.1146/annurev-micro-090817-062213
Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species
- Marina Marcet-Houben, Maria Villarino, Laura Vilanova, …, Josep Usall, Toni Gabaldón, Rosario Torres
- None, 10.3390/jof7060464
Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients
- Anaïs Hérivaux, Jesse R Willis, Toine Mercier, …, Agostinho Carvalho, Toni Gabaldón, Cristina Cunha
- Thorax, 10.1136/thoraxjnl-2020-216179
Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations
- Verónica Mixão, Eva Hegedűsová, Ester Saus, …, Andrea Cillingová, Jozef Nosek, Toni Gabaldón
- DNA Res, 10.1093/dnares/dsab006
Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species
- Jesse R Willis, Ester Saus, Susana Iraola-Guzmán, …, Julia Ponomarenko, Jochen Hecht, Toni Gabaldón
- None, 10.1080/20002297.2021.1897328
Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole
- Sofía Siscar-Lewin, Toni Gabaldón, Alexander M Aldejohann, Oliver Kurzai, Bernhard Hube, Sascha Brunke
- mBio, 10.1128/mbio.01128-21
Aspergillus fumigatus and aspergillosis: From basics to clinics
- A Arastehfar, A Carvalho, J Houbraken, …, C Lass-Flörl, D S Perlin, M Hoenigl
- None, 10.1016/j.simyco.2021.100115
Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi
- Miquel Àngel Schikora-Tamarit, Marina Marcet-Houben, Jozef Nosek, Toni Gabaldón
- Open Biol, 10.1098/rsob.200362
Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS
- Uciel Chorostecki, Jesse R Willis, Ester Saus, Toni Gabaldon
- Methods Mol Biol, 10.1007/978-1-0716-1307-8_4
A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome
- Olfat Khannous-Lleiffe, Jesse R Willis, Ester Saus, …, David Gozal, Nuria Farré, Toni Gabaldón
- None, 10.3390/microorganisms9030641
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells
- Marina Pekmezovic, Hrant Hovhannisyan, Mark S Gresnigt, …, Geraldine Butler, Toni Gabaldón, Bernhard Hube
- Nat Microbiol, 10.1038/s41564-021-00875-2
Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans
- Verónica Mixão, Ester Saus, Teun Boekhout, Toni Gabaldón
- Genetics, 10.1093/genetics/iyaa004
Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans
- Shelby J Priest, Marco A Coelho, Verónica Mixão, …, Sheng Sun, Toni Gabaldón, Joseph Heitman
- PLoS Genet, 10.1371/journal.pgen.1008871
Oral microbiome in down syndrome and its implications on oral health
- Jesse R Willis, Susana Iraola-Guzmán, Ester Saus, …, Jochen Hecht, Julia Ponomarenko, Toni Gabaldón
- None, 10.1080/20002297.2020.1865690
Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium
- Amir Arastehfar, Toni Gabaldón, Rocio Garcia-Rubio, …, Macit Ilkit, Cornelia Lass-Flörl, David S Perlin
- None, 10.3390/antibiotics9120877
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
- Marco Gerdol, Rebeca Moreira, Fernando Cruz, …, Tyler S Alioto, David Posada, Antonio Figueras
- Genome Biol, 10.1186/s13059-020-02180-3
Timing the origin of eukaryotic cellular complexity with ancient duplications
- Julian Vosseberg, Jolien J E van Hooff, Marina Marcet-Houben, …, Leny M van Wijk, Toni Gabaldón, Berend Snel
- Nat Ecol Evol, 10.1038/s41559-020-01320-z
Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
- Claude Rispe, Fabrice Legeai, Paul D Nabity, …, Xin Zhou, François Delmotte, Denis Tagu
- BMC Biol, 10.1186/s12915-020-00864-7