Vinay Viswanadham

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Hybrid transcriptome assembly and annotation of Japanese macaque prefrontal cortex

The paper presents a hybrid transcriptome assembly and annotation of Japanese macaque prefrontal cortex using short- and long-read RNA sequencing data.

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

This study identifies a core gene program underlying Tfh cell differentiation using a multi-scale network systems approach, revealing a novel role for IL-12 in regulating Tfh precursor differentiation.

Rare Germline Variants in Immune and Drug Target Genes Among Cancer Exceptional Responders

This study identifies rare germline variants in immune and drug target genes that are enriched in cancer exceptional responders compared to typical patients, suggesting potential biomarkers for improved treatment outcomes.

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection

The paper identifies a sequencing artifact in Illumina NovaSeq 6000 two-color chemistry that causes T>G substitutions, affecting low-VAF somatic variant detection.

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

Systematic artifacts from Illumina two-color chemistry confound variant identification and actionability in clinical panels

This study identifies systematic T>G sequencing artifacts in Illumina two-color chemistry that can create false pathogenic variants and inflate tumor mutational burden in clinical panels.

Timing the onset of homologous recombination deficiency before breast cancer diagnosis

The paper estimates the timing of homologous recombination deficiency (HRD) onset in breast cancers using HRDTimer, finding HRD occurs years before diagnosis in different subtypes.

Tissue specificity and chromosomal alterations shape divergent immune programs in HRD tumors

This study identifies two immune archetypes in HRD tumors—immune-inflamed and immune-evasive—linked to chromosomal instability and lineage, informing biomarker-driven therapies.

High-resolution detection of copy number alterations in single cells with HiScanner

HiScanner detects high-resolution copy number alterations in single cells, outperforming existing methods and revealing distinct CNA patterns in neurons and oligodendrocytes.

Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures

The paper identifies mutational signatures SBS26 and SBS54 in MMRD tumors that correlate with immune checkpoint blockade response and survival, suggesting their use as prognostic biomarkers.

Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex

The paper uses somatic mutations to analyze lineage divergence in human cortical regions, finding late divergence of neuronal cell types and regional inhomogeneities in progenitor proliferation.

Linked-read analysis identifies mutations in single-cell DNA sequencing data

The paper introduces LiRA, a method to distinguish true mutations from artifacts in single-cell DNA sequencing data by phasing somatic variants with germline variants.

A Bayesian approach for correcting Tn5 transposition bias in ATAC-seq footprinting

The paper corrects Tn5 transposition bias in ATAC-seq to improve footprinting accuracy by using existing tools and a novel global occupancy estimate.