Tomàs Marquès‐Bonet

A sample-to-identification workflow to monitor animal and plant biodiversity using metabarcoding and real time analysis

The paper presents an eDNA workflow integrating metabarcoding and real-time analysis to improve biodiversity monitoring by overcoming limitations in sensitivity, taxonomic range, and processing time.

ProteoParc: A tool to generate protein reference databases for ancient and non-model organisms

ProteoParc generates custom protein reference databases for ancient and non-model organisms to improve peptide identification and ZooMS marker annotation in proteomics studies.

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

This study uses non-invasive fecal samples and chromosome 21 target capture sequencing to analyze bonobo population structure, identifying three subpopulations and river barriers influencing genetic differentiation.

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

This study uses non-invasive genomic sampling to analyze genetic diversity in wild gorillas, revealing population clusters and migration patterns, and predicts geographic origins with high accuracy.

Genomic resources for comparative analyses of obligate avian brood parasitism

The paper generates genome assemblies for ten brood parasitic bird species and their outgroups, enabling comparative genomic analyses of obligate brood parasitism evolution.

Palaeoproteomic insights into the deep roots of the cave bear lineage in Europe

This study uses palaeoproteomics to resolve the evolutionary placement of cave bears, finding Ursus dolinensis basal within the speloid lineage.

A phylogenetic protein-coding genome-phenome map of complex traits across 224 primate species.

Cross-species genome-phenome mapping in primates reveals thousands of protein-coding variants linked to the evolution of complex traits.

Unveiling the evolutionary history of European vipers and their venoms from a multi-omic approach

This study uses multi-omic data to uncover the evolutionary history and venom evolution in European vipers, revealing adaptive introgression and chromosomal rearrangements.

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

The paper analyzes the genomes of spider monkeys and northern muriquis to assess genetic diversity, load, and divergence, finding no alignment between genetic diversity and endangerment status, higher genetic load in wild populations, and divergence linked to environmental factors.

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

Local genetic adaptation to habitat in wild chimpanzees

This study identifies local genetic adaptation to habitat in wild chimpanzees, particularly to pathogens like malaria, using newly generated exomes.

Genomic signatures of island colonization in highly diverse primates

The paper compares genomic diversity, inbreeding, and genetic load between insular and mainland populations of three West African primates, finding lower diversity and higher inbreeding in island populations but no evidence of increased deleterious variation.

Screening great ape museum specimens for DNA viruses

The paper screens great ape museum specimens for DNA viruses, identifying multiple viruses and obtaining near-complete genomes, including high-coverage hepatitis B virus genomes.

Deep genetic substructure within bonobos

This paper identifies three genetically distinct bonobo populations with inferred geographic origins and estimates split times and effective population sizes, highlighting the need for conservation attention to substructure.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

Y chromosome sequence and epigenomic reconstruction across human populations

The paper uses long-read sequencing to generate and compare Y chromosome assemblies across haplogroups and assesses epigenetic modifications in human populations.

The landscape of tolerated genetic variation in humans and primates

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

A global catalog of whole-genome diversity from 233 primate species

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

Rare penetrant mutations confer severe risk of common diseases

The paper identifies rare variant polygenic risk scores as more effective than common variant polygenic risk scores in identifying individuals with outlier phenotypes in common human diseases and complex traits.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

This study sequenced the genomes of two Arabian leopards, revealing population decline, inbreeding, and purging of deleterious mutations, and highlights the need for more genetic data to inform conservation efforts.