Avi Ma’ayan

Perturb-Seqr integrates multiple Connectivity Mapping datasets to enable drug and target discovery by searching for gene expression signatures of drug and gene perturbations.

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

This study shows that miR-206 regulates Purkinje neuron firing dynamics and sensorimotor gating in mice, linking it to schizophrenia-related behaviors.

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

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

ChEA-KG constructs a human transcription factor regulatory network using gene set enrichment analysis and provides an interactive web interface for network exploration and analysis.

The paper introduces a gene set foundation model trained on diverse gene sets to predict gene functions, achieving superior performance compared to existing methods.

RummaGEO automatically mines gene sets from GEO RNA-seq studies for human and mouse, enabling signature search and metadata analysis.

The paper shows that transient Notch activation converts human pluripotent stem cell-derived cardiomyocytes into Purkinje fiber-like cells with altered electrophysiology and gene expression.

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

Rummagene extracts and provides access to gene sets from PMC publications for search and analysis, revealing trends and enabling functional predictions.

The paper presents a LINCS Microenvironment perturbation dataset cataloging transcriptional, proteomic, epigenomic, and phenotypic responses of MCF10A cells to six ligands, enabling integrative analysis of molecular and phenotypic changes.

The paper constructs a reproductive toxicity knowledge graph (ReproTox-KG) to link birth defects, drugs, and genes, identifying potential molecular mechanisms for drug-induced birth defects.

iLINCS provides a web-based platform for analyzing omics signatures of diseases and cellular perturbations through integrative analytics and visualization tools.

The paper describes the development of a metadata federation system for NIH Common Fund data to improve discoverability without data movement.

The paper analyzes CPTAC phosphoproteomics data to identify kinase activity differences between tumor and normal tissues across cancers and develops a web portal for querying kinase activity scores and associated data.

PrismExp improves gene function prediction by partitioning RNA-seq co-expression data into tissue-specific segments, outperforming cross-tissue approaches across multiple domains.

piNET is a web platform for analyzing and visualizing proteomics data, including PTMs, by connecting them to biological knowledge and LINCS signatures.

The paper predicts PKMYT1 as a potential therapeutic target for kidney cancer using bioinformatics tools.

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.

Signaling Pathways Project maps over 10,000 transcriptomic and ChIP-Seq experiments to signaling nodes and ranks node targets by meta-analysis (consensomes), validated against literature and bench assays.

The paper shows that hair follicle niche precursors are specified before niche formation and requires FGF20 from progenitors.

This study profiles proteomic changes across postnatal human cortical development, identifies age-related protein modules, and links them to RNA expression and genetic risk loci for intellectual disability.

BioJupies automates the creation of interactive Jupyter Notebooks for RNA-seq analysis, enabling users to generate reproducible reports from raw data to visualizations and differential expression analyses.

Elysium provides a cloud-based RNA-seq alignment service with a GUI, allowing users to upload FASTQ files and obtain aligned results without needing programming skills or Amazon credentials.

The paper develops ARCHS4, a resource that provides uniformly processed RNA-seq data from human and mouse, enabling easier integration and analysis.