Riddhiman K. Garge

The paper develops a proteomics-based machine learning workflow to identify cell-type-specific protein complexes in mouse embryonic stem cells, revealing 3,986 complexes and 1,388 unique interactions specific to mESC.

The paper uses saturation genome editing to assess the functional impact of RAD51D and XRCC2 variants, showing high accuracy in distinguishing pathogenic from benign variants.

The paper introduces VIS-seq, an image-based method to assess variant effects on cellular phenotypes, revealing multidimensional variant impacts across different diseases.

The paper develops iPSC-SGE to assess variant effects in diverse genetic and cell contexts, identifying pathogenic variants and essential disease genes.

The paper uses saturation genome editing to evaluate BARD1 variants, resolving most variants of uncertain significance and confirming their role in tumor suppression.

This paper introduces Genome-Shuffle-seq, a method for generating and mapping structural variants in mammalian genomes, and demonstrates its application in mouse embryonic stem cells.

This study uses quantitative proteomics to analyze human and mouse gastruloids at four stages, revealing protein dynamics, discordance with transcriptomes, and gene networks linked to developmental defects.

This study induces human gastruloids with embryo-like structures using retinoic acid and shows they match E9.5 mouse embryos in developmental stage through single-cell RNA-seq and computational staging.

The paper systematically profiles protein dynamics in ale yeast during fermentation and repitching, identifying changes in ergosterol and isobutyraldehyde metabolism.

The paper uses deep mutational scanning to analyze CYP2C19 variants, revealing a tradeoff between substrate specificity and protein abundance.

This study engineers yeast to produce cholesterol, enabling functional expression of human opioid and other GPCRs, creating biosensors with measurable agonist responses and antagonist inhibition.

The paper analyzes the spatiotemporal gene expression patterns in the mouse oviduct across the estrous cycle and anteroposterior axis, finding stable transcriptional dynamics across the cycle.

This study identifies TUBB8 as the molecular target of benzimidazoles, revealing their mechanism of vascular disruption and potential clinical applications.

The paper replaces yeast genes with human orthologs to study functional divergence, finding that replaceability depends on divergence and expression patterns of human co-orthologs.

The paper presents experiment-matched datasets of RNAs, proteins, metabolites, and lipids in budding yeast during the cell cycle, revealing coordinated control of lipid metabolism.