Adam M. Phillippy

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

AniAnns annotates tandem repeat arrays by leveraging high ANI between repeat units, improving annotation accuracy and speed across plant and animal genomes.

The paper investigates mutation and recombination patterns in human acrocentric chromosome short arms using multiple sequencing technologies and a four-generation pedigree.

The paper presents a high-accuracy T2T rhesus macaque genome assembly, identifies subtelomeric repeats as a challenge, and reveals new genomic features and functional elements in these regions.

The paper introduces Verkko-Fillet, a tool for refining genome assemblies, and applies it to produce a telomere-to-telomere giraffe genome.

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper identifies rDNA sequence variants associated with human traits using UK Biobank data, finding enrichment in body size traits within the 28S rRNA Expansion Segment 15L region.

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

The paper introduces TTT, an algorithm that resolves assembly graph tangles in genomes, improving the accuracy of complex regions in reference assemblies.

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

This study presents genome assemblies and analyses of macaques to explore genetic variation, population history, and evolutionary differences between species and humans.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

The paper investigates epigenetic regulation of rDNA arrays, showing DNA methylation controls their activity and inheritance across generations.

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.

Parsnp 2.0 improves scalability and control for multiple genome alignment of microbial datasets, reducing memory and runtime while maintaining accuracy.

ModDotPlot provides a fast, interactive, alignment-free visualization of genomic repeats, outperforming existing methods in speed and accuracy.

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

This study characterizes the genome and single-cell transcriptome of Hydractinia, revealing that its stem cells use a conserved gene toolkit shared with all animals.