Robert S. Fulton

The paper develops Nanopore-HiChIP to map enhancer hubs and shows they buffer allelic regulatory variation through kinetic compensation, preserving balanced transcriptional output.

The paper presents a human panepigenome map of DNA methylation, revealing epigenomic diversity across populations and highlighting the role of genetic variation in CpG presence and absence.

This paper uses long-read cDNA sequencing to identify novel transcripts and spliceosome-mutant-enriched isoforms in AML and MDS, providing a resource for improving short-read RNA-seq analyses.

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 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.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

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

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

The paper identifies intermediate methylation regions in normal cells as epimutation hotspots in cancer, showing they are prone to clonal epimutations in leukemia and other cancers.

This study uses linked-read sequencing to phase somatic mutations in multiple myeloma, extending haplotype blocks and revealing phasing patterns in key mutated genes.

This study identifies high-quality neoantigens in follicular lymphoma patients using WES and RNA-Seq, and initiates a clinical trial of personalized neoantigen vaccines combined with PD-1 blockade.

This paper develops species-specific single-cell T cell receptor sequencing (scTCRseq) for dogs, enabling analysis of T cell repertoires in cancer immunotherapy trials.

This study uses ultra-deep exome sequencing to identify recurrent mutations in classical Hodgkin lymphoma HRS cells, demonstrating its utility for analyzing genomic variants in large patient cohorts.

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

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 identifies a GRCh38 reference sequence change that prevents detection of U2AF1 mutations and provides a modified reference to address this issue.

This paper presents a domestic cat whole exome sequencing resource, demonstrating its effectiveness in identifying known and novel disease-associated variants across various breeds.

The paper uses exome sequencing and scRNA-seq to identify donor and recipient immune cells in kidney transplants and finds distinct transcriptional profiles in donor macrophages and T cells.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

Exome sequencing in Finnish populations identifies rare trait-associated alleles with higher frequencies and geographical clustering, revealing 30 novel associations with quantitative traits.

This paper links subclonal mutations to transcriptional profiles in AML using integrated single-cell RNA-sequencing and whole genome sequencing.

The paper identifies somatic mutations with prognostic effects in ER+ breast cancer using genomic data from multiple cohorts.