Ashley D. Sanders

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

This study shows that STING acts as a genome-integrity checkpoint in epithelial cells, independent of interferon, and its loss leads to chromosomal instability and tumor development.

This study identifies IBD type-associated EGC activation signatures and reveals TNF/IFN-γ-driven necroptosis of activated enteric glia in inflammatory bowel diseases.

This study integrates multi-omic and multimodal data from IBD patients to identify molecular, histopathological, and clinical features associated with inflammatory bowel diseases.

This study identifies cell type-specific molecular consequences of mosaic structural variants in hematopoietic stem and progenitor cells across aging.

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.

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

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

This paper introduces scNOVA, a method to analyze somatic structural variants in single-cell multiomics data, revealing their functional impacts on gene regulation and cancer pathways.

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 uses Strand-seq data to correct and construct full-length chromosomes by determining scaffold order and orientation without overlapping sequences.

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.

This paper introduces scTRIP, a method to detect structural variations in single cells, revealing new SV classes and mutational processes in cancer samples.

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

This paper introduces an integrative phasing strategy to generate dense and accurate whole-chromosome haplotypes using Strand-seq and long-read sequencing technologies.