Shaojie Zhang

The paper introduces ms2, a suite of algorithms for efficiently computing matching statistics and SMEMs in compressed pangenome indexes, achieving significant speedups over existing methods.

This paper develops efficient algorithms for detecting long exact matches between genome assemblies in compressed space and sublinear time, revealing novel structural variations in centromeres.

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

The paper introduces algorithms for constructing RLBWT-based compressed full text indexes in compressed space, reducing memory usage for large-scale pangenome analysis.

This paper introduces SLAB, an algorithm for identifying haplotype block cores using PBWT, and applies it to UK Biobank data to detect selection signals.

The paper introduces HP-PBWT, a parallel PBWT algorithm for efficient haplotype matching in large biobank datasets, achieving significant speed-ups in both IO-included and IO-excluded benchmarks.

Recomb-Mix improves local ancestry inference accuracy in admixed populations by integrating existing methods with a graph collapsing trick, outperforming current approaches in diverse scenarios.

This paper introduces Dynamic μ-PBWT, a memory-efficient data structure for dynamic updates of haplotype panels, supporting efficient queries and reducing memory usage compared to existing methods.

This paper defines haplotype matches in pangenome graphs and provides efficient algorithms for querying them using GBWT and related data structures.

The paper introduces ROH-DICE, a method to identify ROH diplotypes in UK Biobank, finding associations between clustered ROHs and diseases like autoimmune disorders and haemochromatosis.

FastRecomb efficiently estimates population-specific genetic maps from large biobank-scale genotyping data, achieving state-of-the-art performance at 10k resolution.

The paper introduces the MPSC problem as an alternative to the LS model for haplotype threading, enabling efficient haplotype reconstruction on large panels.

RaPID-Query enables fast and accurate genealogical search by identifying IBD segments between a query and a large database, achieving low error rates and quick processing times.

The paper introduces Syllable-PBWT, a space-efficient data structure for haplotype long-match queries, reducing memory use by over 100 times compared to existing methods.

This study identifies a mutation in Trim71 that causes congenital hydrocephalus by impairing stem cell differentiation through repression of Lsd1 mRNA translation.

The paper introduces mcPBWT, an algorithm for efficiently scanning composite haplotype patterns in PBWT data, identifying crossover events and gene-conversion tracts.

The paper introduces d-PBWT, a dynamic version of the PBWT data structure, enabling efficient insertion and deletion of haplotypes while maintaining PBWT functionality.

The paper infers genealogical history and social behaviors from IBD segments in UK Biobank data, revealing population-scale genetic connections and regional family preferences.

This study uses EpiGo-KRAB to introduce H3K9me3 at specific loci and shows it forms heterochromatin-like domains without widespread gene repression.

The paper develops a CRISPR-based system to image epigenetic modification effects on genome organization in living cells and shows it induces genomic relocation and H3K9me3 decoration.

This paper clusters RNA 3D loop structures to discover new structural motifs and variants, identifying both known and potential novel functional motifs.

CLAN improves duplex read mapping in crosslinked RNA sequencing by enhancing sensitivity and alignment accuracy.

The paper uses CRISPR-Sirius to track chromosomal loci dynamics in living cells and finds cell cycle-dependent changes in DNA contortion and movement.

RaPID detects identity by descent in large biobank-scale cohorts using a randomized positional BWT approach, achieving linear scaling and high accuracy.