Avi Ma’ayan

Perturb-Seqr: Signature Search Engine Integrating Connectivity Mapping Resources

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: 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.

Cerebellar microRNA-206 tunes Purkinje neuron firing dynamics to control sensorimotor gating

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

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.

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.

ChEA-KG: Human Transcription Factor Regulatory Network with a Knowledge Graph Interactive User Interface

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.

A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets

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: Automatic Mining of Human and Mouse Gene Sets from GEO

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

Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes towards a Purkinje Fiber Fate

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.

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.

Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

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

A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses

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.

ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects

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.

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

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

Making Common Fund data more Findable: Catalyzing a Data Ecosystem

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

CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways

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: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression 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: a versatile web platform for downstream analysis and visualization of proteomics data

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

PKMYT1 is a computationally predicted target for kidney cancer

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

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

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

The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

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.

Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to its Formation and Is Progenitor Dependent

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

Temporal proteomic profiling of postnatal human cortical development

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: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud

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: RNA-seq Alignment in the Cloud

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.

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

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