Nimisha Chaturvedi

Accurate Variant Classification in Tumour-Only Genomic Data Using Interpretable Tabular Models

This paper presents a workflow using XGBoost, LightGBM, and TabNet to classify variants in tumour-only data, showing improved accuracy across ancestries and tumour types.

Accel-Align: A Fast Sequence Mapper and Aligner based on the Seed-Embed-Extend Method

Accel-Align introduces a new sequence aligner using seed-embed-extend methodology, achieving 3-12x speed improvements over existing aligners without sacrificing accuracy.

Genomics of Human Respiratory Syncytial Virus Vaccine Attenuation

The paper identifies mutations frequent in HRSV vaccine candidates and rare in wild-type genomes that may contribute to vaccine attenuation.

Pervasive adaptation of hepatitis C virus to interferon lambda polymorphism across multiple genotypes

This study identifies associations between IFN-lambda polymorphism and HCV variation across multiple genotypes and ancestries, showing viral adaptation to host immune pressure.

HIV Peptidome-Wide Association Study Reveals Patient-Specific Epitope Repertoires Associated with HIV Control

This paper develops a peptidome-wide association study to identify HIV epitopes linked to viral load, revealing patient-specific epitope repertoires that explain HLA-related variation in HIV control.

Human genomics of acute liver failure due to hepatitis B virus infection: an exome sequencing study in liver transplant recipients

This study uses exome sequencing to investigate genetic factors contributing to acute liver failure from HBV infection in liver transplant recipients but finds no causal variants.

Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes

The paper shows that correcting for population stratification in host and pathogen genomes reduces false positives and negatives in association analyses.

Genetic factors and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

This study identifies age, sex, and genetic variants as key predictors of variability in humoral immune responses to pathogens and vaccines.

Sequence Alignment Through the Looking Glass

This study analyzes how sequence aligners use modern processors and finds they underutilize hardware, identifying bottlenecks for future aligner design.

Heterozygous gene truncation delineates the human haploinsufficient genome

The paper estimates that 10.8% of human genes are haploinsufficient based on truncating variants in 11,546 individuals.