HarshaVardhan Doddapaneni

This study examines microbiome and immune changes in astronauts after short and long-duration spaceflights, finding stable gut and oral microbiomes but transient skin microbiome shifts and immune activation.

This study analyzes a diverse glioma cohort to show ancestry influences on survival, somatic alterations, and mutational processes in diffuse gliomas.

This study evaluates somatic variant calling in normal tissues using single-cell RNA and ATAC sequencing, showing Monopogen outperforms other tools in accuracy and sensitivity.

This study analyzes multi-omics data from two spaceflight missions to identify molecular changes in immune, skeletal, and vascular systems, providing insights for mitigating health risks during space travel.

The paper introduces DRAGEN, a scalable mosaic variant caller that detects low VAF variants with high accuracy and efficiency, and presents a benchmark for low-VAF variants.

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

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

This paper introduces a qPCR-based assay to assess rRNA depletion efficiency in RNA-Seq libraries pre-sequencing, showing strong correlation with post-sequencing rRNA rates.

This study analyzes RSV evolutionary dynamics across pre-pandemic, pandemic, and post-pandemic periods in Houston, finding reduced diversity during the pandemic and increased non-synonymous mutations in RSV/B.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

This study uses whole-genome sequence data from diverse participants to identify novel genetic loci associated with brain structural volumes, highlighting the importance of diverse cohorts in uncovering genetic architecture.

This paper presents a probe-based capture enrichment method to obtain full-length genomes of RSV and HuNoV from clinical samples, achieving high completeness and improving variant tracking.

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

The paper analyzes intra-host RSV genetic variation using short-read sequencing, finding low variation but differences between genomic and transcriptomic data.

This study performs genome sequencing in Parkinson's disease patients and finds genetic variants in 3.4% for LRRK2 and 10.1% for GBA, with 82% of patients willing to share variants with relatives.

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

The paper presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

The paper presents a high-quality, complete reference genome for Cryptosporidium parvum using Oxford Nanopore and Illumina reads, enabling comprehensive genomic studies.

This study identifies 35 genes associated with circulating lipid levels using rare coding variants from 170,000 exomes across multiple ancestries.

This study identifies major sources of transcriptomic variation in human intestinal organoids, showing that culture methods like substrate and format have large effects compared to experimental manipulations.

This study develops an oligonucleotide capture sequencing method to generate SARS-CoV-2 genomic and transcriptome sequences from clinical samples, revealing differential transcriptional activity and ORF10 expression.

The paper presents the first genome sequence for a thysanopteran insect, providing insights into its biology and evolution as a crop pest.

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

This paper genomically characterizes 261 pediatric cancer patient-derived xenograft models to guide rational clinical trial design and drug development.

The paper reports exome sequencing of 457 ASD families, identifying 10.4% with known ASD genes and 3.4% with possibly associated variants, and provides statistical support for 34 ASD risk genes using the TADA framework.

The paper presents the milkweed bug genome and comparative analyses to study molecular evolution and feeding ecology in Hemiptera.

The paper reports the sequencing and manual annotation of the Gerris buenoi genome, identifying gene expansions linked to adaptations for aquatic life.