S. Ramakrishnan

Resolving inflammatory bowel disease risk variants to genes and cell types

This study identifies 619 IBD risk signals, resolves 81 high-confidence variants, and prioritizes 664 candidate effector genes using GWAS, eQTL, and exome sequencing.

Exome sequencing directly implicates 68 genes in inflammatory bowel disease

This study uses exome and genome sequencing to identify 68 genes directly associated with inflammatory bowel disease, providing clearer genetic insights and therapeutic targets.

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

A single cell framework identifies functionally and molecularly distinct multipotent progenitors in adult human hematopoiesis

This study identifies new functionally and molecularly distinct multipotent progenitors in adult human hematopoiesis using multiomic single cell analyses and functional assays.

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time

The paper investigates convergent evolution of plant prickles, finding that mutations in a cytokinin gene repeatedly cause prickle loss across species.

S-nitrosylation of EZH2 at C329 and C700 interplay with PRC2 complex assembly, methyltransferase activity, and EZH2 stability to regulate endothelial functions

Single-Molecule Morphology of Topologically Digested Olympic Networks

The paper studies the structure and topology of kinetoplast DNA (kDNA) networks by sequencing and analyzing their morphology after partial digestion with restriction enzymes.

Regulation of shelterin proteins TERF2IP and TRF2 by H3K4me3-p65 axis drives hyperglycemia dependent endothelial senescence

This study shows hyperglycemia increases TERF2IP and TRF2 via H3K4me3-p65 axis, driving endothelial senescence through p53 and p21 upregulation.

Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using In vitro Platform for Improving Insulin Therapy

The paper develops a method to quantify first and second phase insulin secretion dynamics using an insulin-nanoluc luciferase reporter system, validated through genetic and small-molecule screening.

Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer

This paper develops a platform for analyzing integral membrane proteins and lipids in intact membranes using native mass spectrometry, showing how lipid binding and membrane composition affect protein function.

Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells

This study shows that ECM proteins differentially affect morphology, proliferation, and drug sensitivity in primary but not metastatic pancreatic cancer cells, with transcriptomic changes in primary cells.

Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

This paper establishes Physalis as a new Solanaceae model system by presenting chromosome-scale genomes and identifying genetic factors influencing floral traits and the Inflated Calyx Syndrome.

Aldosterone mediates potassium-induced kidney fibrosis through tubular and mesenchymal mineralocorticoid receptor activation

This study shows high dietary potassium worsens kidney fibrosis in mice by activating MR in tubular and mesenchymal cells, mediated by aldosterone.

Increasing triacylglycerol formation and lipid storage by unsaturated lipids protects renal proximal tubules in diabetes

This study shows that unsaturated lipids reduce renal damage in diabetes by increasing lipid storage and protecting against ER stress in proximal tubular cells.

Molecular Determinants of Complexin Clamping in Reconstituted Single-Vesicle Fusion

The paper identifies molecular mechanisms by which Complexin clamps SNARE assembly in single-vesicle fusion, showing its role in delaying fusion and enhancing clamping through specific structural interactions.

Racial differences in androgen metabolism and receptor signaling in prostate cancer

This study identifies racial differences in androgen metabolism and receptor signaling in prostate cancer, showing African American men use an alternative pathway for DHT biosynthesis associated with disease progression.

Patient derived models of bladder cancer amplify tumor specific gene expression compared to surgical specimen while maintaining gene expression of molecular subtype and epithelial mesenchymal transition markers

This study compares gene expression profiles of patient-derived models (PDMs) with surgical specimens of bladder cancer, finding PDXs most similar to original tumors while maintaining EMT and molecular subtype markers.

Lung Bronchial Epithelial Cells are HIV Targets for Proviral Genomic Integration

This study shows HIV infects and integrates into lung bronchial epithelial cells, establishing latency and contributing to obstructive lung diseases in HIV-positive individuals.

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor

The paper identifies a plasmid-encoded ter operon in Klebsiella pneumoniae that functions as a microbiome-dependent gut fitness factor, enhancing colonization in the presence of specific gut microbiota.