Irene Gallego Romero

The paper uses a massively parallel reporter assay to study the regulatory effects of variant pairs in enhancers, finding non-additive effects and context-dependent interactions.

The paper uses sequence-to-function models to predict the functional impact of archaic hominin introgression in Papuan individuals, identifying genes associated with introgressed haplotypes.

This study shows that a recent lifestyle shift to agriculture in Bornean Punan people rapidly alters their transcriptome and DNA methylation, resembling agriculturalists more than their foraging relatives.

This paper shows that differences in power and linkage disequilibrium affect eQTL portability across ancestries and introduces a method to correct for these factors.

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

The paper introduces a method to add new marsupial genomes to existing vertebrate whole-genome alignments, improving phylogenetic coverage for comparative genomic analysis.

The paper investigates the regulatory effects of Neanderthal and Denisovan introgression in Papuan populations using a massively parallel reporter assay, finding differential activity in immune-related genes.

This study identifies eQTLs and environmental influences on immune cell diversity in Indonesian populations, highlighting the role of ancestry and environment in shaping immunity.

The paper identifies dunnart-specific enhancers and promoters in craniofacial development, showing divergence in regulatory landscapes between marsupials and placental mammals.

The paper tests regulatory potential of conserved enhancers in thylacine and wolf to assess functional convergence over 160 million years of evolution, finding limited evidence of convergent divergence.

The paper analyzes variant classification disparities between European-like and non-European-like genetic ancestries and shows that MAVE data can reduce these disparities in VUS reclassification.

The paper analyzes RNA-seq data from public databases and finds significant underrepresentation of non-European populations, highlighting biases in population descriptors.

The paper analyzes alternative splicing variation across 115 Indonesian samples to identify genetic variants influencing splicing, finding over 1,000 differential splicing events and 6,000 sQTLs with some ancestry-specific effects.

The paper presents a de novo transcriptome and improved genome assembly for the fat-tailed dunnart, providing valuable genomic resources for marsupial research.

The paper analyzes RNA-seq data from whole blood of Indonesians to identify pathogens, finding Flaviviridae and Plasmodium as predominant, with distinct microbiome profiles compared to Mali and UK cohorts.

The paper evaluates genetic diversity in chimpanzee transcriptomic data and finds that most samples have Western chimpanzee ancestry, with limited genetic diversity compared to wild populations.

This study compares transcriptomic responses to Plasmodium falciparum and P. vivax infections in Indonesian patients to African and South American studies, finding shared and unique pathways.

The paper identifies Indonesia-specific eQTLs and methylQTLs linked to local ancestry and archaic introgression, showing their impact on gene regulation and hematological traits.

The paper identifies Denisovan introgression in Papuan genomes that influences immune-related processes and regulatory elements, with experimental validation of functional impacts.

The paper analyzes DNA methylation and gene expression in Indonesian populations to show genetic ancestry, environmental influences, and immune-related differences across regions.

The paper compares chromatin accessibility and transcription factor binding in human and chimpanzee induced pluripotent stem cells, finding widespread conservation and suggesting the pluripotent state is evolutionarily constrained.

The paper examines regulatory variation in iPSCs and differentiated cells, finding lower individual variation in iPSCs and identifying shared chromatin regions for some cell type-specific QTLs.

This study compares regulatory differences in iPSCs and finds that genetic variation, not cell type of origin, primarily drives these differences.

The paper generates a panel of chimpanzee iPSCs and compares their regulatory variation with somatic cells and human iPSCs, finding reduced species-specific differences in iPSCs.

The paper quantifies how RNA degradation affects gene expression measurements and shows that a linear model controlling for RNA Integrity Number (RIN) can correct for these effects.