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

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

John Erol Evangelista et al.
The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
Temporal dynamics of the multi-omic response to endurance exercise training.
FEATURED

Temporal dynamics of the multi-omic response to endurance exercise training.

MoTrPAC Study Group et al.
Temporal dynamics of the multi-omic response to endurance exercise training.

CFDE Associated and Common Fund Programs’ Landmark Publications

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The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
John Erol Evangelista et al. | bioRxiv | Published: 2025
Playbook workflow builder: Interactive construction of bioinformatics workflows.
Clarke DJB et al. | PLoS computational biology | Published: 2025
Multimodal cell maps as a foundation for structural and functional genomics.
Schaffer LV et al. | Nature | Published: 2025
The Somatic Mosaicism across Human Tissues Network.
Coorens THH et al. | Nature | Published: 2025
The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data
Taha Mohseni Ahooyi et al. | bioRxiv | Published: 2025
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets
Marino GB et al. | GigaScience | Published: 2025
AI-READI: rethinking AI data collection, preparation and sharing in diabetes research and beyond.
AI-READI Consortium et al. | Nature metabolism | Published: 2024
An Ensemble Spectral Prediction (ESP) model for metabolite annotation.
Li X et al. | Bioinformatics (Oxford, England) | Published: 2024
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.
Gjoni K et al. | Bioinformatics (Oxford, England) | Published: 2024
Potentials of ionic liquids to overcome physical and biological barriers.
Beaven E et al. | Advanced drug delivery reviews | Published: 2024
Liver fibrosis pathologies and potentials of RNA based therapeutics modalities.
Diwan R et al. | Drug delivery and translational research | Published: 2024
SenNet recommendations for detecting senescent cells in different tissues
Suryadevara V et al. | Nature Reviews Molecular Cell Biology | Published: 2024
Evidence-Based Recommendations for Tablet Recordings From the Bridge2AI-Voice Acoustic Experiments.
Awan SN et al. | Journal of voice : official journal of the Voice Foundation | Published: 2024
Temporal dynamics of the multi-omic response to endurance exercise training.
MoTrPAC Study Group et al. | Nature | Published: 2024
Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes.
Fisher JL et al. | BMC pharmacology & toxicology | Published: 2024
Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates.
Fisher JL et al. | FEBS open bio | Published: 2024
Social Determinants of Health and Limitation of Life-Sustaining Therapy in Neurocritical Care: A CHoRUS Pilot Project.
Kwak GH et al. | Neurocritical care | Published: 2024
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.
Shahneh MRZ et al. | Journal of the American Society for Mass Spectrometry | Published: 2024
The Somatic Mosaicism across Human Tissues (SMaHT) Network, a SMART Investment?
Hubler ZML et al. | Clinical chemistry | Published: 2024
Metabolomic characterization of human glioblastomas and patient plasma: a pilot study.
Liu YA et al. | F1000Research | Published: 2024
Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico.
Williams AS et al. | Cancer reports (Hoboken, N.J.) | Published: 2023
Alternative Identification of Glycosides Using MS/MS Matching with an In Silico-Modified Aglycone Mass Spectra Library.
Rodriguez EP et al. | Analytical chemistry | Published: 2023
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.
Marino GB et al. | Database : the journal of biological databases and curation | Published: 2023
Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution.
Fame RM et al. | Nature communications | Published: 2023
Senescent alveolar macrophages promote early-stage lung tumorigenesis.
Prieto LI et al. | Cancer cell | Published: 2023
LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers.
Kong F et al. | Analytical chemistry | Published: 2023
Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms.
Weiskittel TM et al. | Pharmaceuticals (Basel, Switzerland) | Published: 2023
Enrichr-KG: bridging enrichment analysis across multiple libraries.
Evangelista JE et al. | Nucleic acids research | Published: 2023
Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing.
Chen F et al. | Nature genetics | Published: 2023
Computational Advancements in Cancer Combination Therapy Prediction.
Flanary VL et al. | JCO precision oncology | Published: 2023
Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis.
Amadori L et al. | Nature cardiovascular research | Published: 2023
Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation.
Morgan EW et al. | International journal of tryptophan research : IJTR | Published: 2023
Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils.
Bittremieux W et al. | Journal of proteome research | Published: 2023
RNAget: an API to securely retrieve RNA quantifications.
Upchurch S et al. | Bioinformatics (Oxford, England) | Published: 2023
beta-Glucan-Mediated Oral Codelivery of 5FU and Bcl2 siRNA Attenuates Stomach Cancer.
Afrin H et al. | ACS applied materials & interfaces | Published: 2023
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.
Marino GB et al. | Nucleic acids research | Published: 2023
Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion.
Wilk EJ et al. | Molecular medicine (Cambridge, Mass.) | Published: 2023
PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices.
Lachmann A et al. | PeerJ | Published: 2023
Carbon Coated Iron-Cobalt Nanoparticles for Magnetic Particle Imaging.
Kumar R et al. | ACS applied bio materials | Published: 2023
beta-Glucan and Fatty Acid Based Mucoadhesive Carrier for Gastrointestinal Tract Specific Local and Sustained Drug Delivery.
Esquivel SV et al. | Biomolecules | Published: 2023
Gabriella Miller Kids First Data Resource Center (KFDRC): Empowering discovery across germline and somatic variation in pediatric cancer.
Higgins D et al. | Cancer Research | Published: 2023
The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina.
Pruvost M et al. | Cell reports | Published: 2023
Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells.
Deng EZ et al. | Aging cell | Published: 2023
Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.
Takata N et al. | Nature communications | Published: 2023
SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes.
Meng-Lin K et al. | Biomolecules | Published: 2023
Potential and Progress of 2D Materials in Photomedicine for Cancer Treatment.
Bhatt HN et al. | ACS applied bio materials | Published: 2023
Toxicology knowledge graph for structural birth defects.
Evangelista JE et al. | Communications medicine | Published: 2023
Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program.
Roy AL et al. | Molecular cell | Published: 2023
Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging.
Han Y et al. | American journal of physiology. Heart and circulatory physiology | Published: 2022
Transforming L1000 profiles to RNA-seq-like profiles with deep learning.
Jeon M et al. | BMC bioinformatics | Published: 2022
Modular and mechanistic changes across stages of colorectal cancer.
Rahiminejad S et al. | BMC cancer | Published: 2022
Connecting high-resolution 3D chromatin organization with epigenomics.
Feng F et al. | Nature communications | Published: 2022
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
Kropiwnicki E et al. | BMC bioinformatics | Published: 2022
Mucoadhesive carriers for oral drug delivery.
Kumar R et al. | Journal of controlled release : official journal of the Controlled Release Society | Published: 2022
Gene and drug landing page aggregator.
Clarke DJB et al. | Bioinformatics advances | Published: 2022
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation.
Lachmann A et al. | Bioinformatics (Oxford, England) | Published: 2022
Tissue registration and exploration user interfaces in support of a human reference atlas.
Borner K et al. | Communications biology | Published: 2022
Getting Started with LINCS Datasets and Tools.
Xie Z et al. | Current protocols | Published: 2022
Genetic diversity fuels gene discovery for tobacco and alcohol use.
Saunders GRB et al. | Nature | Published: 2022
Considerations and challenges for sex-aware drug repurposing.
Fisher JL et al. | Biology of sex differences | Published: 2022
Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis.
Tetikol HS et al. | Nature communications | Published: 2022
Making Common Fund data more findable: catalyzing a data ecosystem.
Charbonneau AL et al. | GigaScience | Published: 2022
SigCom LINCS: data and metadata search engine for a million gene expression signatures.
Evangelista JE et al. | Nucleic acids research | Published: 2022
Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project.
Surles-Zeigler MC et al. | Frontiers in neuroinformatics | Published: 2022
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals.
Hammond DE et al. | Molecular & cellular proteomics : MCP | Published: 2022
Promoting validation and cross-phylogenetic integration in model organism research.
Cheng KC et al. | Disease models & mechanisms | Published: 2022
Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes.
Higgins K et al. | Scientific reports | Published: 2022
Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners.
Srivastava H et al. | PLoS computational biology | Published: 2022
Defining the Roles of Cardiokines in Human Aging and Age-Associated Diseases.
Srivastava H et al. | Frontiers in aging | Published: 2022
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser.
Petras D et al. | Nature methods | Published: 2022
Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape.
Mukund K et al. | Frontiers in immunology | Published: 2021
Machine Learning of Patient Characteristics to Predict Admission Outcomes in the Undiagnosed Diseases Network.
Amiri H et al. | JAMA network open | Published: 2021
The SPARC DRC: Building a Resource for the Autonomic Nervous System Community.
Osanlouy M et al. | Frontiers in physiology | Published: 2021
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository.
Powell CD et al. | Metabolites | Published: 2021
3D virtual reality vs. 2D desktop registration user interface comparison.
Bueckle A et al. | PloS one | Published: 2021
The NIH Somatic Cell Genome Editing program
Saha K et al. | Nature | Published: 2021
Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.
Sanford JA et al. | Cell | Published: 2020
GlyGen: Computational and Informatics Resources for Glycoscience.
York WS et al. | Glycobiology | Published: 2020
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
HuBMAP Consortium et al. | Nature | Published: 2019
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.
Keenan AB et al. | Cell systems | Published: 2018
Unexplored therapeutic opportunities in the human genome.
Oprea TI et al. | Nature Reviews Drug discovery | Published: 2018
H3Africa: current perspectives.
Mulder N et al. | Pharmacogenomics and personalized medicine | Published: 2018
The 4D nucleome project.
Dekker J et al. | Nature | Published: 2017
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.
Sud M et al. | Nucleic acids research | Published: 2016
High-throughput discovery of novel developmental phenotypes.
Dickinson ME et al. | Nature | Published: 2016
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.
GTEx Consortium et al. | Science (New York, N.Y.) | Published: 2015
The NIH Extracellular RNA Communication Consortium.
Ainsztein AM et al. | Journal of extracellular vesicles | Published: 2015
The Genotype-Tissue Expression (GTEx) project.
GTEx Consortium et al. | Nature genetics | Published: 2013
Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium et al. | Nature | Published: 2012
A framework for human microbiome research.
Human Microbiome Project Consortium et al. | Nature | Published: 2012
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The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
Consortium
About the CFDECF ProgramsCFDE CentersPartnershipsPilot Projects
Community
Workbench TutorialTraining & OutreachDocumentationGet QR CodesFunding Opportunities
Resources
Data & MetadataToolsChatbotUse CasesPublications
CFDE Workbench
Report a bug
The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
@CFDE Workbench 2025
This repository is under review for potential modification in compliance with Administration directives.