Javier Mendoza‐Revilla

Immune context unmasks regulatory effects of Neanderthal and Denisovan introgression

The paper identifies regulatory effects of Neanderthal and Denisovan introgression in immune-related genes using a massively parallel reporter assay across different cell types.

A multispecies foundation model for genome function prediction, gene annotation and sequence design

NTv3 is a foundation model that predicts genome function, annotates genes, and designs DNA sequences across species, outperforming existing models in multiple tasks.

Annotating the genome at single-nucleotide resolution with DNA foundation models

The paper introduces SegmentNT, a DNA foundation model for genome annotation, achieving state-of-the-art performance in identifying 14 genic and regulatory elements across species.

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

The paper introduces the Nucleotide Transformer, a foundation model for genomics, showing it can predict molecular phenotypes from DNA sequences with transfer learning across tasks and organisms.

A Foundational Large Language Model for Edible Plant Genomes

This paper introduces a large language model for plant genomics that provides state-of-the-art predictions for regulatory annotations and variant prioritization, along with a benchmark dataset for deep learning methods.

Environmental and genetic drivers of population differences in SARS-CoV-2 immune responses

The paper identifies environmental and genetic factors influencing population differences in SARS-CoV-2 immune responses using single-cell RNA-sequencing data.

The genomic landscape of contemporary western Remote Oceanians

This study analyzes genome-wide data from 1,433 ni-Vanuatu individuals to trace their genetic ancestry and admixture history, revealing synchronous admixture events and social assortative mating patterns.

Clotting factor genes are associated with preeclampsia in high altitude pregnant women in the Peruvian Andes

This study identifies clotting factor genes PROZ, F7, and F10 on chromosome 13 as associated with preeclampsia in high-altitude Andean families.

Disentangling signatures of selection before and after European colonization in Latin Americans

This study identifies loci under selection in Latin American admixed populations, distinguishing between pre- and post-admixture selection, and finds signals related to immunity and energy metabolism.

Prediction Of Eye, Hair And Skin Color In Admixed Populations Of Latin America

The paper evaluates prediction accuracy for eye, hair, and skin pigmentation in admixed Latin Americans using genomic and phenotypic data, finding that Random Forest and regression perform best, and that pigmentation SNPs improve accuracy, especially for skin color.

Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance

The paper analyzes ancestry in Latin Americans using haplotype-based methods, finding widespread Converso ancestry and links between Native ancestry and facial features.