Shankar Subramaniam

Spatial Landscape of Pregnancy-Associated Triple Negative Breast Cancer and Mammary Gland Involution

This study compares transcriptional differences between pre- and post-involution PA-TNBC tissues using spatial transcriptomics, identifying distinct inflammatory and chromatin remodeling patterns in post-involution tumors.

Spatially resolved tumor-microenvironment architecture defines therapeutic response in unresectable hepatoblastoma

This study identifies spatial tumor-microenvironment architectures in hepatoblastoma that correlate with therapeutic response using spatial transcriptomics and single-cell imaging.

Spatial context of cellular heterogeneity in triple-negative breast cancer reveals actionable subtypes

The paper identifies three TNBC subtypes based on spatial transcriptomics and cellular mapping, revealing distinct tumor microenvironment architectures and potential therapeutic targets.

Spatial landscape of pretransplant liver disease and post-transplant immune outcomes in children

The paper analyzes spatial molecular patterns in liver disease and transplant outcomes using single-cell RNA sequencing data from multiple conditions and post-transplant biopsies.

Differential peripheral immune dynamics underlie therapeutic response to chemotherapy and chemo-immunotherapy in triple-negative breast cancer

The paper identifies distinct immune states in TNBC patients based on treatment and response, linking peripheral immune dynamics to therapeutic outcomes.

BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data

BiomarkerKB integrates and standardizes biomarker data from multiple sources to enable structured exploration and discovery of biomarker-disease relationships.

Single-cell transcriptional landscape of muscle-derived stem/progenitor cells reveals hallmarks of aging and rejuvenation

The paper profiles murine muscle-derived stem/progenitor cells across age groups using single-cell transcriptomics and proteomics, revealing a transcriptional continuum of maturation and aging-related changes.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

The CFDE Workbench integrates metadata and processed data from Common Fund programs to enable FAIR and AI-ready cross-program knowledge discovery.

Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer

This study uses spatial transcriptomics to identify molecular and cellular differences between good and poor prognosis triple-negative breast cancer subtypes, revealing distinct gene signatures that could inform therapy.

Brain Organoids, Lessons from Fetal Neocortex Formation, and Rational Design for Quality Control

This paper discusses stages of neocortex formation in organoids, presents a guide for removing maldeveloped organoids, and introduces an imaging platform for automated quality control.

Integrated multiomics reveals inflammation-driven excessive erythrocytosis in subjects with Monge's disease

This study uses multiomics analysis to show that inflammation-driven NFκB activation under hypoxia causes excessive erythrocytosis in Monge's disease.

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.

A novel subtyping method for TNBC with implications for prognosis and therapy

This paper identifies three subtypes of TNBC based on transcriptomic profiles and cell-type composition, linking them to potential therapeutic targets and clinical outcomes.

Fundamental Limitations of Foundation Models in Single-Cell Transcriptomics

This study evaluates foundation models in single-cell transcriptomics and finds they underperform statistical models due to poor contextual encoding and information loss during tokenization.

Liver transplant rejection features memory cell priming, spatially differentiated networks and novel drug targets.

The paper identifies molecular and spatial features of early liver transplant rejection, including primed T-cells, immune synapse activation, and novel drug targets like proteasomal and HSP90 inhibitors.

The molecular chronology of mammary epithelial cell fate switching

The paper maps the molecular programs enabling basal-to-luminal fate switching in mammary epithelial cells using time-resolved single-cell epigenetic and transcriptomic analyses.

Tumor suppressor NME1/NM23-H1 modulates DNA binding of NF-κB RelA

This study identifies NME1 as a cofactor that enhances RelA's DNA binding to κB sites, promoting gene expression and suggesting that κB site clustering is necessary for transcription complex assembly.

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach

The paper introduces a cybernetic-inspired modeling framework to analyze the transcriptional regulation of the mammalian cell cycle, identifying functional network modules and predicting future cell cycles.

Methadone alters transcriptional programs associated with synapse formation in human cortical organoids

This study shows methadone exposure during early cortical development alters synapse-related transcriptional programs in human cortical organoids.

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

The paper introduces a web-based tool for collaborative analysis of mass spectrometry data, enabling remote inspection, visualization, and analysis of private and public datasets.

MetENP/MetENPWeb: An R package and web application for metabolomics enrichment and pathway analysis in Metabolomics Workbench

MetENP and MetENPWeb provide tools for metabolomics enrichment and pathway analysis using data from the Metabolomics Workbench.

Dedifferentiation and neuronal repression define Familial Alzheimer's Disease

This study identifies dedifferentiation and neuronal repression as key mechanisms in Familial Alzheimer's Disease using patient-derived neurons and multi-omics analysis.