Roderic Guigó

The paper identifies widespread misannotations of vertebrate selenoprotein genes in public databases and introduces an improved homology-based tool for accurate prediction.

The paper uses long-read RNA-seq from diverse human populations to reveal ancestry bias in gene annotations and shows improved transcript discovery with personal genome assemblies.

The paper integrates phylogenomics and functional annotations to trace gene function evolution across species, revealing convergent adaptations in multicellular and terrestrial transitions.

The paper introduces CapTrap-seq, a long-read sequencing method for zebrafish, improving transcriptome accuracy by capturing full-length transcripts and novel spliced isoforms.

The paper identifies RNA-initiating sites at STRs and links them to gene expression, revealing regulatory roles and interactions with Alu repeats.

The paper introduces a method to estimate the relative localization of transcripts between the nucleus and cytosol using combined nuclear, cytosolic, and whole-cell RNA-seq data.

EPIraction creates an enhancer-gene interaction atlas using H3K27ac ChIP-Seq data and GWAS SNPs to annotate candidate target genes.

The paper introduces the BioGenome Portal, an open-source web platform for managing biodiversity genomics data, demonstrating its use in two projects.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

The paper introduces CapTrap-seq, a method for full-length RNA transcript sequencing, and shows it produces highly accurate transcript models in human tissues.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper identifies lncRNAs involved in Drosophila imaginal disc development and regeneration, showing that CR40469 is essential for wing regeneration and can be partially compensated by CR34335.

The paper develops a machine learning model to identify functional lncRNAs and validates SNHG6's role in hematopoietic differentiation and leukemia.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The paper introduces a fast non-parametric test for genetic associations with multiple traits, demonstrating its effectiveness in splicing QTL mapping and hippocampal subfield GWAS.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

The paper investigates day-night and seasonal gene expression variation across human tissues using GTEx data, finding unique patterns in different tissues and conserved clock gene differences across species.

The paper identifies a conserved transcriptional program across metazoan lineages that drives cell differentiation, independent of lineage-specific factors.

The paper identifies shared transcriptome alterations across neurodegenerative and psychiatric disorders using post-mortem brain samples.

The paper identifies weak CEBPA binding in humans as a cause of slower B cell transdifferentiation compared to mice, linked to Alu repeat expansions.

The paper shows that tissue-specific enhancers are mostly intronic and regulate genes involved in tissue-specific functions, while housekeeping genes are controlled by intergenic enhancers.

The paper introduces a paired-guide RNA CRISPR-Cas9 system to identify protein-coding and lncRNA genes involved in human B-cell to macrophage transdifferentiation, identifying 26 potential novel genes.

The paper identifies 916,360 conserved long-range RNA structures in the human transcriptome and shows their association with pre-mRNA processing.

The paper identifies and analyzes splicing quantitative trait loci (sQTLs) across multiple tissues using the GTEx dataset, revealing their role in splicing regulation and disease.

The paper tracks transcriptomic and epigenomic changes during human pre-B cell to macrophage transdifferentiation, finding coordinated chromatin state transitions and gene activation patterns.

PyHIST is a tool for segmenting and preprocessing histological images to prepare them for machine learning applications.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.