Xiaoxu Yang

The paper identifies genetic variants associated with placental abnormalities in stillbirths by analyzing exome sequencing data from placental and fetal samples.

The paper benchmarks sequencing methods to recover mosaic variants in human brain tissue and introduces RIVER to enhance variant detection across methods.

BulkMonSTR detects mosaic STR mutations in bulk sequencing data with improved precision and F1 scores compared to existing methods.

The paper uses genomic mosaicism to study clonal dynamics of trunk neural crest-derived ganglia, finding conserved developmental patterns across species.

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

This paper introduces UDSeq, a duplex sequencing protocol for accurate somatic mutation detection with low DNA input and high coverage, achieving a low error rate and enabling cross-species profiling.

CREPE is a computational tool that designs and evaluates primers for large-scale PCR, achieving over 90% successful amplification for acceptable primers.

This study identifies somatic mutations in ALS genes in the motor cortex of sporadic ALS patients, particularly in excitatory neurons, suggesting a role in disease initiation.

This study identifies cell type-specific enhancers by analyzing cis and trans activities using ChIP-STARR-seq in two human cell lines.

The paper uses mosaic variant barcodes to analyze clonal dynamics in human forebrain cell types, revealing lineage relationships and clonal spread patterns.

This study identifies 69 mutated genes in malformations of cortical development using multiomic profiling of 317 brain resections and single-cell sequencing.

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

The paper assesses the transmission of de novo mutations from sperm to blastocysts in couples undergoing IVF and finds predictable but slightly under-transmitted mutations based on sperm mutational abundance.

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

The paper analyzes sperm mosaic mutations in healthy males, finding that many are stable over time and pose a lifelong transmission risk to offspring.

This study identifies somatic SNVs in non-cancerous human brain tissues and establishes best practices for detecting low-frequency variants.

MosaicBase is a database of postzygotic mosaic variants in noncancer diseases and asymptomatic individuals, revealing distinct genomic features of disease-causing variants.

The paper quantifies autism recurrence risk by detecting paternal sperm mosaicism through single molecule genotyping and whole genome sequencing.

The paper profiles somatic L1Hs insertions in Rett patients and healthy controls, finding increased insertions in the brain and altered genomic patterns linked to MECP2 dysfunction.

The paper identifies and characterizes two types of postzygotic single-nucleotide mosaicisms in healthy individuals using whole-genome sequencing across multiple organs.