Peter Ebert

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

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.

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

The paper improves genome inference by introducing haplotype sampling and polishing workflows, enhancing variant detection in the 1000 Genomes Project cohort.

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.

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

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.

This study compares variant calling precision and recall of Oxford Nanopore and PacBio HiFi platforms across different sequence coverages.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

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.

The paper analyzes gaps and structural variants in phased human genome assemblies, identifying issues with contig ends, misorientations, and large-scale insertions and deletions.

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.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

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

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

SCIDDO detects differential chromatin domains from ChIP-seq data to simplify analysis of chromatin changes.

The paper compares DNase I-Seq, ATAC-Seq, and NOMe-Seq to identify assay-specific features and their impact on chromatin accessibility and gene expression prediction.

The paper identifies AHR and GLIS1 as key regulators of mesenchymal multipotency using temporal epigenomic and transcriptomic data from mouse bone marrow stromal cells.

The paper integrates single cell RNA-seq with bulk epigenomic data to identify distinct regulatory states in bidirectional promoters and their associations with structural features and TF binding.

The paper identifies partially methylated domains (PMDs) as widespread epigenomic features across human and mouse cells, showing cell-type specificity and links to gene expression, replication timing, and proliferation.

The paper predicts tissue-specific gene expression across species using epigenome data from reference organisms.

This paper introduces CoMIK, a discriminative method for comparing variable-length genomic sequences, showing improved classification performance and interpretability.

This paper introduces TEPIC, a method that combines open-chromatin data with TF binding affinities to predict gene expression, achieving results comparable to TF ChIP-seq.