André Corvelo

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Lancet2 improves somatic variant calling with faster runtime and better performance, especially for InDels, using enhanced methods and machine learning.

This paper introduces an explainable boosting machine model to identify and filter variant artifacts caused by formalin-fixed paraffin embedding in cancer genomics.

The paper presents a chromosome-level genome assembly of the Hispid cotton rat, annotating 24,878 protein-coding genes and identifying genetic innovations.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

The paper identifies IL10RB as a key regulator of COVID-19 host susceptibility and severity through integrative analysis of genetic and transcriptomic data, and validates potential drug repositioning candidates.

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

This study identifies HPV integration hotspots in oropharyngeal cancers and shows their role in disrupting host gene expression and genomic stability.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

The paper analyzes single-nucleus transcriptomes from brain regions of COVID-19 patients to show increased neuroinflammation and microglial transcriptome changes, without evidence of viral brain tropism.

The paper introduces an updated version of the Lancet somatic variant caller that supports linked-reads sequencing data analysis by integrating barcodes and haplotype read assignments.

The paper identifies a pan-genome in the Mediterranean mussel with 25% of genes subject to presence/absence variation, suggesting an adaptive strategy for resilience and invasiveness.

taxMaps provides fast and accurate taxonomic classification of short-read metagenomic data with significantly reduced computational cost compared to BLASTn.

Lancet improves somatic variant calling accuracy, especially for indels, using colored DeBruijn graphs and local assembly across synthetic and real whole-genome sequencing data.