Vipin K. Menon

The paper benchmarks five machine learning-based variant annotation methods for rare variant association testing across 350,377 UK Biobank participants, finding CADD provides best signal separation and GPN-MSA highest enrichment for loss-of-function intolerant genes.

The paper introduces pertTF, a transformer-based model for predicting genetic perturbation responses, showing improved performance in expression prediction and cell identity shifts across cellular contexts.

This study uses a knockout village framework to analyze how mutations in diabetes genes alter pancreatic beta cell development, revealing non-canonical cell fate shifts and identifying ISL1 as a key regulator.

The paper benchmarks multiple base editors and develops a model to predict editing efficiency, validating edits for disease-associated variants and identifying cancer-related SNVs.

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

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 measures tryptophan metabolites in fecal samples from healthy individuals and links them to bacterial abundance and predicted microbial sources.

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

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

Truvari improves structural variant comparison by preserving allelic diversity, reducing allele frequency inflation compared to other methods.

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