Shilpa Garg

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

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 fermented miso on the International Space Station and found it is possible, with unique microbial and sensory characteristics compared to Earth-based controls.

The paper introduces a method to reduce plasmid transformation multiplicity in yeast during electroporation, improving mono-transformation rates without reducing efficiency.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

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.

This study investigates how 3D chromatin architecture influences and is influenced by somatic structural variants in cancer, showing an interplay between chromatin structure and SV formation.

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

This paper introduces a method for chromosome-scale haplotype-resolved genome assembly using long reads and long-range data, achieving high accuracy and contiguity in three human genomes.

This paper develops dead-Cas9 base editors that enable large-scale genome editing in human cells by reducing DNA nicking, allowing editing of over 10,000 loci.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper introduces a pedigree-graph-based method for haplotype-aware de novo assembly of related individuals using Illumina and PacBio data, achieving chromosomal-scale phased assemblies with low coverage.

The paper introduces vg, a toolkit for creating and using variation graphs as genome references, improving read mapping and variant calling accuracy over linear references.

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

Re-aligning reads to both alleles gives WhatsHap the lowest PacBio switch error rates (full coverage: 0.24% real, 0.02% simulated) and better indel phasing than hapCUT and phASER.

This paper combines read-based phasing and genetic haplotyping to improve haplotype inference in related individuals, achieving higher accuracy and more phased variants than either method alone.