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List of works by Toni Gabaldón

2x genomes--depth does matter

scientific article (publication date: 2010)

A metabolic scenario for the evolutionary origin of peroxisomes from the endomembranous system

scientific article

A midzone-based ruler adjusts chromosome compaction to anaphase spindle length.

scientific article published on 10 March 2011

A phylogenomics approach for selecting robust sets of phylogenetic markers

scientific article (publication date: April 2014)

Acquisition of prokaryotic genes by fungal genomes

article

Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication.

scientific article

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

An anaerobic mitochondrion that produces hydrogen

scientific article

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

scientific article

Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest

scientific article

Apolipoprotein L2 contains a BH3-like domain but it does not behave as a BH3-only protein

scientific article published on 5 June 2014

Assigning duplication events to relative temporal scales in genome-wide studies

scientific article published on 11 November 2010

Automatic Prediction of the Genetic Code

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

scientific article

Big data and other challenges in the quest for orthologs

scientific article

Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis.

scientific article published in August 2018

Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

scientific article published on 10 January 2022

Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition

article

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

scientific article published on 17 May 2021

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors

scientific article published on 19 May 2022

Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin

scientific article

Comparative Genomics-Based Prediction of Protein Function

Comparative genomics of emerging pathogens in the Candida glabrata clade

scientific article

Comparative transcriptomics of early dipteran development

scientific article

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode

scientific article published on 2 January 2012

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

scientific article

Computational approaches for the prediction of protein function in the mitochondrion

scientific article published on 26 July 2006

Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum

scientific article published on 14 December 2015

Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes

scientific article

Coronavirus Disease 2019 (COVID-19): Emerging and Future Challenges for Dental and Oral Medicine

scientific article published on 28 May 2020

Correction to: The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

scientific article published in 2021

Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest ⬇️

scientific article published on 11 September 2020

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

scientific article published on 5 December 2016

Correction: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

scientific article published on 14 July 2016

Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

scientific article published on 30 July 2015

CycADS: an annotation database system to ease the development and update of BioCyc databases

scientific article

DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death

scholarly article by J Díez et al published 12 April 2010 in Cell Death & Differentiation

Differential expression of fungal genes determines the lifestyle of Plectosphaerella strains during Arabidopsis thaliana colonization

scientific article published on 28 July 2020

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

scientific article published on 25 June 2015

Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter

scientific article published on 12 August 2020

Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast

article published in 2017

Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium

scientific article published on 08 December 2020

ETE: a python Environment for Tree Exploration

scientific article published in 2010

Echinocandin-Induced Microevolution of Candida parapsilosis Influences Virulence and Abiotic Stress Tolerance

scientific article published in 2018

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

scientific article published on 4 April 2017

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

scientific article

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

scientific article published on 22 April 2011

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

scientific article published on 01 February 2020

Evolution of proteins and proteomes: a phylogenetics approach.

scientific article published in January 2005

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization

scientific article

Evolution of spliceosomal introns following endosymbiotic gene transfer

scientific article

Evolution of the Peroxisomal Proteome

scientific article published on 01 January 2018

Evolution of the ferritin family in vertebrates

Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens

scientific article published on 19 September 2018

Evolutionary and functional patterns of shared gene neighbourhood in fungi

scientific article published on 16 September 2019

Evolutionary considerations on the origin of peroxisomes from the endoplasmic reticulum, and their relationships with mitochondria

scientific article published on 17 May 2014

Evolutionary genomics of yeast pathogens in the Saccharomycotina.

scientific article published on 3 August 2016

Evolutionary histories of expanded peptidase families in Schistosoma mansoni

scientific article published in 2011

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

scientific article

FUNGALOXPHOS: an integrated database for oxidative phosphorylation in fungi

scientific article

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

scientific article

From Endosymbiont to Host-Controlled Organelle: the Hijacking of Mitochondrial Protein Synthesis and Metabolism

From Saccharomyces cerevisiae to Candida glabratain a few easy steps: important adaptations for an opportunistic pathogen

scientific article published on 16 September 2010

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

scientific article

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism

scientific article

Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans

scientific article published on 08 April 2020

Functional and evolutionary implications of gene orthology.

scientific article

Fungal evolution: cellular, genomic and metabolic complexity

scientific article published on 17 April 2020

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

scientific article published on 01 December 2019

Fungal evolution: major ecological adaptations and evolutionary transitions

scientific article published on 25 April 2019

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

scientific article

Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

scientific article

Gene gain and loss across the metazoan tree of life

scientific article published on 28 January 2020

Genetically encodable bioluminescent system from fungi

article published in the Proceedings of the National Academy of Sciences of the United States of America

Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii)

scientific article published on 03 December 2019

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

scientific article published in 2019

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa.

scientific article

Genome Variation in the Model Halophilic Bacterium

article published in 2018

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

scientific article

Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies

scientific article

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

scientific article

Genome sequence of the olive tree, Olea europaea

scientific article

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum

scientific article published on 5 January 2016

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

scientific article

Genome, Transcriptome, and Functional Analyses of Penicillium expansum Provide New Insights Into Secondary Metabolism and Pathogenicity ⬇️

scientific article

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

scientific article

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

article published in 2019

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.).

scientific article published on 26 October 2020

Genomic history of the origin and domestication of common bean unveils its closest sister species

scientific article published on 29 March 2017

High variability of mitochondrial gene order among fungi

scientific article published on February 2014

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation

scientific article

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

scientific article

Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi

scientific article

Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins

scientific article published on 01 July 2021

Hybridization and emergence of virulence in opportunistic human yeast pathogens

scientific article published on 5 July 2017

Immunity and other defenses in pea aphids, Acyrthosiphon pisum ⬇️

scientific article published on 23 February 2010

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

scientific article published in 2019

Impact of the mitochondrial genetic background in complex III deficiency

scientific article

Inferring gene function from evolutionary change in signatures of translation efficiency

scientific article published on 3 March 2014

Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing

scientific article

Joining forces in the quest for orthologs

scientific article published on 29 September 2009

Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.

scientific article

Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host

scientific article

Large-scale assignment of orthology: back to phylogenetics?

scientific article published on 30 October 2008

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry

scientific article published on 3 February 2016

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes

scientific article published in September 2005

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

scientific article

Measuring guide-tree dependency of inferred gaps in progressive aligners ⬇️

scientific article published on February 23, 2013

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

scientific article published on 11 December 2010

Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans

article

Misidentification of genome assemblies in public databases: the case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications

scientific article

Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis.

scientific article published on 05 October 2016

Mitochondrial genome variability within the Candida parapsilosis species complex

article

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

scientific article

Oral microbiome in down syndrome and its implications on oral health

scientific article published on 30 December 2020

Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes

scientific article

Origin and evolution of the peroxisomal proteome

scientific article

Origin, diversification and substrate specificity in the family of NCS1/FUR transporters

scientific article published on 7 April 2015

PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes

scientific article published on 31 July 2013

Parental origin of the allotetraploid tobacco Nicotiana benthamiana

scientific article published on 12 December 2019

Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.

scientific article published on 21 April 2009

Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift

scientific article published on 28 August 2020

Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

scientific article published on 8 December 2017

Perceptions about postdocs

scientific article

Peroxisome diversity and evolution

scientific article

PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome

scientific article published in January 2010

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease

scientific article published on 28 November 2006

Peroxisomes in parasitic protists

scientific article

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

scientific article

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

scientific article published on 22 April 2007

Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates

scientific article published on 19 December 2012

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

scientific article published on 01 March 2020

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

scientific article published on 25 January 2018

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

scientific article

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi

scientific article

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

scientific article

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

scientific article

PhylomeDB: a database for genome-wide collections of gene phylogenies

scientific article

Predicting phenotypic traits of prokaryotes from protein domain frequencies

scientific article

Prediction of protein function and pathways in the genome era.

scientific article

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

scientific article published in July 2015

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

scientific article published on 13 February 2017

Reconstruction of the proto-mitochondrial metabolism

scientific article (publication date: August 2003)

Redundans: an assembly pipeline for highly heterozygous genomes

scientific article published on 29 April 2016

Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.

scientific article published on 13 December 2010

Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum

scientific article published on 8 September 2017

Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis

Secondary structure impacts patterns of selection in human lncRNAs

scientific article

Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

scientific article published on 02 May 2020

Selection of marker genes using whole-genome DNA polymorphism analysis ⬇️

scientific article published on 19 March 2012

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

scientific article published on 16 June 2015

Shaping the mitochondrial proteome

scientific article

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Structural analyses of a hypothetical minimal metabolism

scientific article published on October 2007

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

article

Systematic phenotyping of a large-scale Candida glabrata deletion collection reveals novel antifungal tolerance genes

scientific article (publication date: June 2014)

TACC3-TSC2 maintains nuclear envelope structure and controls cell division.

scientific article published on 15 March 2010

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

article

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

The Case of the Missing Ancient Fungal Polyploids

scientific article published on 26 September 2016

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

scientific article published on 22 May 2024

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

scientific article published on 30 October 2015

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

scientific article published on 30 October 2015

The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens

scientific article published on 18 August 2020

The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology

scientific article

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

scientific article

The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata

scientific article published on 17 December 2015

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

scientific article

The complete mitochondrial genome of the Giant Manta ray, Manta birostris.

scientific article published on 10 January 2014

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

scientific article published in 2021

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima ⬇️

scientific article

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

scientific article

The genome of melon (Cucumis melo L.).

scientific article

The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism

scientific article

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

scientific article

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

scientific article published on 14 May 2012

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

scientific article published on 23 July 2020

The human phylome

scientific article published on January 2007

The kinomes of apicomplexan parasites

scientific article published on 26 April 2012

The long non-coding RNA landscape of Candida yeast pathogens

scientific article published on 16 December 2021

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes

scientific article published in March 2010

The transposable element-rich genome of the cereal pest Sitophilus oryzae

scientific article published on 09 November 2021

The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome

scientific article

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

scientific article

Timing the origin of eukaryotic cellular complexity with ancient duplications

scientific article published on 26 October 2020

Toward community standards in the quest for orthologs ⬇️

scientific article (publication date: 15 March 2012)

Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).

scientific article

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

scientific article (publication date: 26 February 2013)

Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

scientific article published on 07 March 2022

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

scientific article published on 31 January 2019

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

Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation

scientific article

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees

scientific article

Trends in yeast diversity discovery ⬇️

scholarly article published in 2021

Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis

scientific article published on January 2013

Variation and evolution of biomolecular systems: searching for functional relevance

scientific article

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

scientific article published on 06 March 2016

Whole-Genome Sequencing Recommendations

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

scientific article

YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

nextPARS: Parallel probing of RNA structures in Illumina.

scientific article

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences

scientific article published on 19 May 2016

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

scientific article (publication date: August 2009)

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