Narayanan Raghupathy

A proteomic polygenic score to identify IL-18 driven inflammatory bowel disease

The paper develops a proteomic polygenic score to predict IL-18 levels and IBD risk, identifying ~30% of IBD patients as IL-18 High.

Anapc5 and Anapc7 as genetic modifiers of KIF18A function in fertility and mitotic progression

This study identifies Anapc5 and Anapc7 as genetic modifiers of KIF18A function in fertility and mitotic progression by analyzing mouse strain differences and cell line models.

Variation in histone configurations correlates with gene expression across nine inbred strains of mice

The paper examines how histone modifications vary across mouse strains and correlates these variations with gene expression, finding strong links between chromatin states and gene expression, but not DNA methylation.

Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data

The paper introduces GBRS, a method to reconstruct diploid genomes and quantify gene expression in multi-parent populations using RNA-Seq data without requiring genotype information.

scBASE: A Bayesian mixture model for the analysis of allelic expression in single cells

scBASE improves allelic expression analysis in single cells by classifying allelic states and pooling information across cells.

Reference trait analysis reveals correlations between gene expression and quantitative traits in disjoint samples

The paper introduces a reference trait analysis method to correlate complex traits with molecular features in disjoint samples, showing it outperforms TWAS in identifying associated transcripts.

The genome of C57BL/6J \"Eve\", the mother of the laboratory mouse genome reference strain

The paper generates a new de novo genome assembly for C57BL/6J Eve, addressing genetic drift in the reference strain and improving genomic accuracy.

Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes

The paper identifies genetic variants influencing metastability in mouse embryonic stem cells by analyzing gene expression and chromatin accessibility in 185 genetically diverse cells.

Hierarchical Analysis of Multi-mapping RNA-Seq Reads Improves the Accuracy of Allele-specific Expression

EMASE improves ASE estimation by hierarchically allocating multi-mapping RNA-Seq reads, showing better performance than standard methods in simulations and detecting ASE in F1 hybrid mice.