Ravi Iyengar

An Implantable Poly(pro-curcumin) Film for Local, Long-Lasting Neuroprotection After Spinal Cord Injury

This paper introduces an implantable poly(pro-curcumin) film that provides long-lasting neuroprotection after spinal cord injury by locally delivering curcumin, improving locomotor recovery and reducing inflammation.

predicTox: An integrated database of clinical risk frequencies and human gene expression signatures for cardiotoxic drugs

The paper introduces predicTox, a database integrating clinical risk scores and gene expression data to identify genomic variants and pathways linked to drug-induced cardiotoxicity.

Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

The paper presents a multi-modal atlas of human kidney disease, identifying cellular and spatial mechanisms of injury resolution or failure and linking them to clinical outcomes.

MBCO PathNet: Integration and visualization of networks connecting functionally related pathways predicted from transcriptomic and proteomic datasets

MBCO PathNet integrates and visualizes functionally related pathways from transcriptomic and proteomic data using ontologies, providing pie charts, bar diagrams, heatmaps, and timelines.

Multiscale mapping of transcriptomic signatures for cardiotoxic drugs

The paper identifies cardiotoxic drug signatures using bulk transcriptomics and integrates them with genomic and single-cell data to predict toxicity mechanisms.

Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine

The paper uses ontologies to integrate clinical, pathological, and molecular kidney data for precision medicine analysis.

Central Nervous System axonal regeneration by spatially targeted drug combinations

This study identifies a four-drug combination that promotes axonal regeneration in the optic nerve of rats by targeting subcellular processes, leading to functional recovery.

Spinal Cord Injury regulates circular RNA expression in axons

The paper identifies SCI-induced changes in axonal RNA, including circular RNAs, and shows that reducing ADAR1 promotes axonal outgrowth.

An atlas of healthy and injured cell states and niches in the human kidney

The paper creates a high-resolution cellular atlas of healthy and injured kidney cell states and niches using single-cell and spatial technologies, identifying molecular signatures and pathways related to kidney injury.

Boldine modulates glial transcription and functional recovery in a murine model of contusion spinal cord injury

Boldine improves locomotor function and reduces glial activation in a mouse model of spinal cord injury by modulating calcium signaling and gene expression.

A reference tissue atlas for the human kidney

The paper constructs a reference tissue atlas of the human kidney using multi-omics data to identify cell types, pathways, and genes across nephron segments and interstitium.

Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration

The paper identifies extracellular histones as new inhibitors of CNS axonal regeneration, showing they induce growth cone collapse and can be reversed by activated protein C.

Predicting Individual Cell Division Events from Single-Cell ERK and Akt Dynamics

The paper uses single-cell imaging and machine learning to predict cell division from ERK and Akt activity dynamics in MCF10A cells, finding ERK alone predicts division with AUC=0.74.

Protein structure-based gene expression signatures

This paper introduces structural gene expression signatures (sGES) derived from protein structure features, showing their utility in identifying robust biological signatures across datasets and experimental platforms.

The human ApoE4 variant reduces functional recovery and neuronal sprouting after incomplete spinal cord injury in male mice

This study shows that the ApoE4 variant in mice leads to worse recovery and reduced neuronal sprouting after spinal cord injury compared to ApoE3.

A tissue- and organ-based cell biological atlas of obesity-related human genes and cellular pathways

The paper constructs a tissue- and organ-based subcellular-function atlas of obesity-related genes and pathways using publicly available datasets and integration methods.

Wilms tumor 1 promotes memory flexibility

This study identifies WT1 as a transcriptional repressor that decreases memory strength and promotes memory flexibility by regulating synaptic plasticity and learning outcomes.

Systems therapeutics analyses identify genomic signatures defining responsiveness to allopurinol and combination therapy for lung cancer

The paper identifies genomic signatures predicting allopurinol and combination therapy responses in lung cancer using TCGA, CCLE, and patient-derived tumor data.

Lack of dynamic balance between vesicle transport and microtubule growth in neurite outgrowth enables formation of dystrophic bulbs

The paper uses simulations and experiments to show that imbalances between higher-level subcellular processes like vesicle transport and microtubule growth lead to dystrophic bulb formation in neurite outgrowth.

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes

The paper develops an ontology to model subcellular processes and their interactions to predict whole cell functions from omics data.

A Comparison of mRNA Sequencing with Random Primed and 3’-Directed Libraries

This study compares 3-DGE and conventional mRNAseq, finding similar gene expression results with 3-DGE offering cost savings and scalability.

Fragile dynamics enable diverse genomic determinants to influence arrhythmia propensity

The paper identifies fragile physiological dynamics of ion channel kinetics associated with genomic determinants of arrhythmias and validates this relationship using RNA sequencing.

Clinically-weighted transcriptomic signatures for protein kinase inhibitor associated cardiotoxicity

The paper develops clinically-weighted transcriptomic signatures to predict protein kinase inhibitor-associated cardiotoxicity using mRNA sequencing and elastic net regression.

Chaotic propagation of spatial cytoskeletal instability modulates integrity of podocyte foot processes

The paper uses 3-D microscopy and dynamical models to show that spatially-specific actin cytoskeleton regulation in podocytes leads to chaotic foot process instability and glomerular pathophysiology.