Alaina Shumate

LiftOn improves genome annotation by integrating DNA and protein alignments, enabling accurate annotation transfer between closely and distantly related species.

CHESS 3 improves upon previous versions by using better algorithms and filtering to create a more accurate catalog of human genes and transcripts.

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 evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper improves transcriptome assembly by combining long and short reads using StringTie, achieving higher accuracy and transcript count than either method alone.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

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 T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

The paper presents a new reference genome, PR1, from a Puerto Rican individual, highlighting its completeness and annotations compared to existing genomes.

Liftoff maps genes between genome assemblies with high accuracy, achieving 99.9% gene mapping between human genome versions and 98.4% between human and chimpanzee genomes.

The paper assembles and annotates a population-specific Ashkenazi human reference genome, showing improved contiguity and completeness compared to GRCh38.

The paper presents an updated wheat genome assembly, Triticum 4.0, which includes 15.07 gigabases of sequence and over 5700 new genes, improving upon previous assemblies.

The paper compiles RNA sequencing data from 9,795 experiments to create a new human gene catalog, identifying novel genes and transcripts while highlighting extensive transcriptional noise.