orcid publication

Species- and strain-level assessment usingrrnlong-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects

orcid publication

Microbial enterotypes beyond genus level: Bacteroides species as a predictive biomarker for weight change upon controlled intervention with arabinoxylan oligosaccharides in overweight subjects

orcid publication

Gut microbiota profiles in critically ill patients, potential biomarkers and risk variables for sepsis

orcid publication

Infusion of donor feces affects the gut-brain axis in humans with metabolic syndrome

orcid publication

Bacteroides uniformis combined with fiber amplifies metabolic and immune benefits in obese mice

orcid publication

Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fiber Supplementation in Women and Men

orcid publication

Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice

orcid publication

Holdemanella biformis improves glucose tolerance and regulates GLP‐1 signaling in obese mice

orcid publication

Editorial: Remodeling Composition and Function of Microbiome by Dietary Strategies-Functional Foods Perspective

orcid publication

The microbiota composition drives personalized nutrition: Gut microbes as predictive biomarkers for the success of weight loss diets

orcid publication

Gut bless you: The microbiota-gut-brain axis in irritable bowel syndrome

orcid publication

Assessment of human microbiota stability across longitudinal samples using iteratively growing-partitioned clustering

orcid publication

Intestinal microbiota is modified in pediatric food protein–induced enterocolitis syndrome

orcid publication

Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects

orcid publication

Editorial: Contribution of the maternal microbiome to offspring health

orcid publication

Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM)

project

Development of HPC and AI-Based Tools for Large-Scale Spatial Transcriptomics and Single-Cell Data Integration

In today’s science, data processing technologies play an increasingly crucial role, driven by technological advances...

orcid publication

Novel dimensionality reduction method, Taelcore, enhances lung transplantation risk prediction

In this work, we present a new approach to predict the risk of acute cellular rejection (ACR)...

tool

CoMM-BIP

A Contrastive Multi-Modal learning model with Biologically Informed Priors!

tool

TaelCore

A Python library for dimensional reduction using topological auto-encoders

tool

 S²-PepAnalyst

Our web tool, S2-PepAnalyst, is designed to predict SSPs from input sequences or uploaded files (FASTA/FA/TXT)...

research line

Topological Machine Learning

Exploring topological and geometric approaches to unveil robust patterns in high-dimensional multi-omics data.

research line

Application of Deep Learning to Biomedical Image Analysis

research line

Development of Computational Tools for Spatial Transcriptomics Data Analysis

research line

Application of Machine Learning for Cancer Biomarker Discovery

orcid publication

The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons

orcid publication

Pluripotency factors regulate the onset of Hox cluster activation in the early embryo

orcid publication

Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T cells reveal Long Range Dysregulation of Key Inflammatory Pathways mediated by disease-associated Susceptibility Loci

orcid publication

HDAC6 regulates expression of the oncogenic driver EWSR1-FLI1 through theEWSR1promoter in Ewing sarcoma

orcid publication

Evidence for a role of phenotypic mutations in virus adaptation

orcid publication

Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

orcid publication

RNA-seq, bioinformatic identification of potential MicroRNA-Like Small RNAs in the edible mushroom Agaricus bisporus and experimental approach for their validation

orcid publication

Cell survival enabled by leakage of a labile metabolic intermediate

orcid publication

reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics

orcid publication

Single‐cell multi‐omics analysis of COVID‐19 patients with pre‐existing autoimmune diseases shows aberrant immune responses to infection

orcid publication

COVID-19 progression and convalescence in common variable immunodeficiency patients show dysregulated adaptive immune responses and persistent type I interferon and inflammasome activation

orcid publication

Human Papillomavirus-Encoded microRNAs as Regulators of Human Gene Expression in Anal Squamous Cell Carcinoma: A Meta-Transcriptomics Study

orcid publication

Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus

tool

mstatspop

Genome Variability Analyses of multiple populations: Calculation and estimation of variability statistics and neutrality tests.

orcid publication

Statistical Properties of New Neutrality Tests Against Population Growth

orcid publication

Mining the pig genome to investigate the domestication process

orcid publication

Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests

orcid publication

A Genomic Perspective on Wild Boar Demography and Evolution

orcid publication

Polygenic adaptation of rosette growth in Arabidopsis thaliana

orcid publication

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region

orcid publication

Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22

orcid publication

Primers for 22 candidate genes for ecological adaptations in Brassicaceae

orcid publication

Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A-lyrata

orcid publication

Birth-and-death evolution of the Cecropin multigene family in Drosophila

orcid publication

A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism

orcid publication

Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions

orcid publication

Positive selection versus demography: Evolutionary inferences based on an unusual haplotype structure in Drosophila simulans

orcid publication

Mlcoalsim: Multilocus Coalescent Simulations

orcid publication

Population genetic inference using a fixed number of segregating sites: a reassessment

orcid publication

Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana

orcid publication

Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination

orcid publication

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

orcid publication

Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions in Arabidopsis thaliana

orcid publication

Population history in Arabidopsis halleri using multilocus analysis

orcid publication

Optimal Neutrality Tests Based on the Frequency Spectrum

orcid publication

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

orcid publication

Evolutionary study of a potential selection target region in the pig

orcid publication

Neutrality Tests for Sequences with Missing Data

orcid publication

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

orcid publication

Worldwide genetic relationships of pigs as inferred from X chromosome SNPs

orcid publication

Population genomics from pool sequencing

orcid publication

Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

orcid publication

MsPar: A parallel coalescent simulator

orcid publication

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

orcid publication

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

orcid publication

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly

orcid publication

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome

orcid publication

On genetic differentiation between domestic pigs and Tibetan wild boars

orcid publication

A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids

orcid publication

A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig

orcid publication

Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes

orcid publication

Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS

orcid publication

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

orcid publication

Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis

orcid publication

Improving bioinformatics analysis of large sequence datasets parallelizing tools for population genomics

orcid publication

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

orcid publication

The neutral frequency spectrum of linked sites

orcid publication

Genetic diversity and selection signatures of the beef ‘Charolais de Cuba’ breed

orcid publication

Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations

orcid publication

The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon

orcid publication

The Site Frequency/Dosage Spectrum of Autopolyploid Populations

orcid publication

Pervasive selection pressure in wild and domestic pigs

orcid publication

Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections

orcid publication

The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle

orcid publication

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

orcid publication

Transposable element polymorphisms improve prediction of complex agronomic traits in rice

orcid publication

Copy number variation on ABCC2-DNMBP loci impacts the diversity and composition of the gut microbiota in pigs

orcid publication

Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects

orcid publication

Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology

orcid publication

Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs

orcid publication

Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)

orcid publication

A General Framework for Neutrality Tests Based on the Site Frequency Spectrum

orcid publication

Crash of a population of the marine heterotrophic flagellate Cafeteria roenbergensis by viral infection

orcid publication

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

orcid publication

New insights into the diversity of marine picoeukaryotes