Mitchell Robert Vollger

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

The paper introduces rustybam, a Rust-based toolkit for alignment analysis, and SafFire, a visualization tool for genome comparisons, both available open source.

The paper analyzes HERV-K(HML-2) structural variation and coding capacity across human pangenomes using long-read sequencing, revealing polymorphic loci and incomplete representation in reference genomes.

IsoRanker uses long-read transcriptomics to prioritize non-coding variants in Mendelian conditions by detecting expression outliers, allelic imbalance, and NMD, leading to the identification of pathogenic variants in one individual.

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

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 study benchmarks nine short-read sequencing chemistries across seven sequencers using donor-specific assemblies to measure sequencing errors against sample-matched references, revealing platform-specific error profiles and highlighting the importance of donor-specific references for unbiased comparison.

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

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

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

This paper introduces DAF-seq, a method for single-molecule and single-cell chromatin fiber sequencing, enabling precise analysis of protein occupancy and chromatin accessibility.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

This study uses Fiber-seq to analyze TE regulatory potential in maize, revealing epigenetic patterns and gene interaction mechanisms.

This paper introduces FiberFold, a deep learning model that predicts haplotype-specific 3D chromatin organization using Fiber-seq data, revealing changes in TADs in a Mendelian disease.

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

This paper introduces fibertools, a toolkit for DNA-m6A detection and integration of long-read genetic and epigenetic data, achieving high accuracy and speed.

This study uses targeted Fiber-seq to analyze the chromatin impact of mosaic variants, showing that pathogenic DMPK CTG expansions disrupt regulatory elements and that base editing can alter chromatin accessibility.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.

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

mutyper assigns mutation types to SNP data using ancestral genome estimates and computes mutation spectra for individuals and populations.

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 identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

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 assesses SNVs within human segmental duplications, finding increased mutation rates and interlocus gene conversion, along with distinct mutational spectra.

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.

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 the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.