Mark Diekhans

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

SQANTI-browser converts SQANTI3 classifications into UCSC Genome Browser Track Hubs for visualizing and curating long-read transcriptomes with metadata and filtering capabilities.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

HMM-Flagger evaluates genome assemblies by detecting structural errors using read coverage modeling, showing improved accuracy in human assemblies.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

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

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 produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper analyzes single-cell long-read mRNA isoform regulation across mouse brain regions, cell types, and development, finding pervasive isoform variability and cell-type specific splicing patterns.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

The paper identifies high-confidence full-length human RNA isoform scaffolds using nanopore sequencing by improving 5' cap detection and 3' polyadenylation site identification.

AMELIE 2 improves Mendelian disorder diagnosis by matching patient phenotypes and genotypes to primary literature, achieving high accuracy and efficiency.