CFDE Information Portal

CFDE Workbench

Information PortalData Portal

Home

CF Programs

CFDE Centers

Partnerships

Training & Outreach

Publications

Webinars

About

CFDE Workbench

CFDE Associated and Common Fund Programs’ Landmark Publications

CentersDCCsLandmarkR03s

Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma'ayan A. 2025. GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets. Gigascience. 14:giaf025. https://www.doi.org/10.1093/gigascience/giaf025

LINCS

John Erol Evangelista, Daniel J.B. Clarke, Zhuorui Xie, Stephanie Olaiya, Heesu Kim, Giacomo B. Marino, Anna Byrd, Shivaramakrishna Srinivasan, Sumana Srinivasan, Mano R. Maurya et al.,. 2025. The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs. Biorxiv. . https://www.doi.org/doi.org/10.1101/2025.02.04.636535

Landmark

Center

DRC

Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME et al.,. 2025. Playbook workflow builder: Interactive construction of bioinformatics workflows. Plos Computational Biology. 21:e1012901. https://www.doi.org/10.1371/journal.pcbi.1012901

LINCS

Gjoni K, Pollard KS. 2024. SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. Bioinformatics (oxford, England). 40(6). https://www.doi.org/10.1093/bioinformatics/btae340

R03

Software

Machine Learning

Computer Simulation

Computational Biology

Humans

Mutagenesis

AI-READI Consortium. 2024. AI-READI: rethinking AI data collection, preparation and sharing in diabetes research and beyond. Nature Metabolism. . https://www.doi.org//10.1038/s42255-024-01165-x

Landmark

Bridge2AI

Li X, Zhou Chen Y, Kalia A, Zhu H, Liu LP, Hassoun S. 2024. An Ensemble Spectral Prediction (ESP) model for metabolite annotation. Bioinformatics (oxford, England). 40(8). https://www.doi.org/10.1093/bioinformatics/btae490

R03

Metabolomics

Algorithms

Neural Networks, Computer

Machine Learning

Metabolome

Beaven E, Kumar R, An JM, Mendoza H, Sutradhar SC, Choi W, Narayan M, Lee YK, Nurunnabi M. 2024. Potentials of ionic liquids to overcome physical and biological barriers. Advanced Drug Delivery Reviews. 204:115157. https://www.doi.org/10.1016/j.addr.2023.115157

R03

Administration, Cutaneous

Biological Barrier

Ionic Liquid

Ionic Liquids

Local Delivery

Noninvasive Delivery

Drug Delivery Systems

Systemic Delivery

Humans

Fisher JL, Wilk EJ, Oza VH, Gary SE, Howton TC, Flanary VL, Clark AD, Hjelmeland AB, Lasseigne BN. 2024. Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates. Febs Open Bio. 14(5):803-830. https://www.doi.org/10.1002/2211-5463.13796

R03

Gene Expression Profiling

Cancer

Drug Repositioning

Glioblastoma

Animals

Glioblastoma

Gene Expression Regulation, Neoplastic

Gene Signature

Mice

Brain Neoplasms

Transcriptomic Signature

Xenograft Model Antitumor Assays

Transcriptome

Antineoplastic Agents

Neoplasms

Cell Line, Tumor

Drug Repurposing

Humans

Diwan R, Gaytan SL, Bhatt HN, Pena-Zacarias J, Nurunnabi M. 2024. Liver fibrosis pathologies and potentials of RNA based therapeutics modalities. Drug Delivery And Translational Research. 14(10):2743-2770. https://www.doi.org/10.1007/s13346-024-01551-8

R03

Animals

Liver Cirrhosis

Rna

Lipid Nanoparticle

Rna Therapeutics

Mrna

Nanoparticles

Drug Delivery Systems

Sirna

Humans

Liver Fibrosis

Liu YA, Aboud O, Dahabiyeh LA, Bloch O, Fiehn O. 2024. Metabolomic characterization of human glioblastomas and patient plasma: a pilot study. F1000research. 13:98. https://www.doi.org/10.12688/f1000research.143642.3

R03

Glioblastoma

Biomarker

Pilot

Adult

Female

Untargeted Metabolomics

Metabolomics

Brain Neoplasms

Neoplasm Recurrence, Local

Humans

Male

Glioblastoma

Biomarkers, Tumor

Pilot Projects

Biogenic Amines

Middle Aged

Feasibility

Aged

Metabolome

MoTrPAC Study Group, Lead Analysts, MoTrPAC Study Group. 2024. Temporal dynamics of the multi-omic response to endurance exercise training. Nature. 629(8010):174-183. https://www.doi.org/10.1038/s41586-023-06877-w

MoTrPAC

Acetylation

Physical Endurance

Rats

Mitochondria

Female

Time Factors

Non-alcoholic Fatty Liver Disease

Proteome

Transcriptome

Blood

Multiomics

Lipidomics

Cardiovascular Diseases

Animals

Humans

Male

Endurance Training

Internet

Organ Specificity

Epigenome

Phosphorylation

Ubiquitination

Wounds And Injuries

Inflammatory Bowel Diseases

Proteomics

Databases, Factual

Metabolome

Physical Conditioning, Animal

Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B et al.,. 2024. SenNet recommendations for detecting senescent cells in different tissues. Nature Reviews Molecular Cell Biology. . https://www.doi.org/10.1038/s41580-024-00738-8

Landmark

SenNet

Fisher JL, Clark AD, Jones EF, Lasseigne BN. 2024. Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. Bmc Pharmacology & Toxicology. 25(1):5. https://www.doi.org/10.1186/s40360-023-00727-1

R03

Network Biology

Drug

Male

Sex

Adverse Events

Drug Targets

Gene Expression

Gene-regulatory

Gene Expression Regulation

Liver

Sex-biased

Female

Humans

Pharmacovigilance

Shahneh MRZ, Strobel M, Vitale GA, Geibel C, Abiead YE, Garg N, Wagner B, Forchhammer K, Aron A, Phelan VV et al.,. 2024. ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization. Journal Of The American Society For Mass Spectrometry. 35(11):2564-2578. https://www.doi.org/10.1021/jasms.4c00061

R03

Weiskittel TM, Cao A, Meng-Lin K, Lehmann Z, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Yong Ung C et al.,. 2023. Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms. Pharmaceuticals (basel, Switzerland). 16(5). https://www.doi.org/10.3390/ph16050752

R03

Systems Pharmacology

Gene Dependency

Systems Biology

Takata N, Miska JM, Morgan MA, Patel P, Billingham LK, Joshi N, Schipma MJ, Dumar ZJ, Joshi NR, Misharin AV et al.,. 2023. Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis. Nature Communications. 14(1):4129. https://www.doi.org/10.1038/s41467-023-39672-2

Metabolomics

Eye

Gene Expression Regulation

Mice

Retina

Glycolysis

Lactic Acid

Morphogenesis

Energy Metabolism

Mammals

Animals

Roy AL, Conroy RS, Taylor VG, Mietz J, Fingerman IM, Pazin MJ, Smith P, Hutter CM, Singer DS, Wilder EL. 2023. Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program. Molecular Cell. 83(3):335-342. https://www.doi.org/10.1016/j.molcel.2022.12.025

Landmark

4DN

Genome

United States

Cell Nucleus

Genomics

Upchurch S, Palumbo E, Adams J, Bujold D, Bourque G, Nedzel J, Graham K, Kagda MS, Assis P, Hitz B et al.,. 2023. RNAget: an API to securely retrieve RNA quantifications. Bioinformatics (oxford, England). 39(4). https://www.doi.org/10.1093/bioinformatics/btad126

GTEx

Genome

Rna

Sequence Analysis, Rna

Genomics

Software

Afrin H, Esquivel SV, Kumar R, Zahid MI, Oporeza B, Rahman MF, Boland T, Nurunnabi M. 2023. beta-Glucan-Mediated Oral Codelivery of 5FU and Bcl2 siRNA Attenuates Stomach Cancer. Acs Applied Materials & Interfaces. 15(27):32188-32200. https://www.doi.org/10.1021/acsami.3c03528

R03

Rna, Small Interfering

Animals

Fluorouracil

Stomach Cancer

Stomach Specific

Oral Biologics

Oral Local Delivery

Mice

Mice, Inbred C57bl

Stomach Neoplasms

Beta-glucans

Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A. 2023. PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. Peerj. 11:e14927. https://www.doi.org/10.7717/peerj.14927

LINCS

Phenotype

Animals

Gene Expression

Unsupervised Learning

Mice

Gene Ontology

Molecular Sequence Annotation

Rna-seq

Druggable Genome

Transcriptomics

Mammals

Humans

Gene Function Predictions

Kumar R, Huda MN, Habib A, Nafiujjaman M, Woo HJ, Kim T, Nurunnabi M. 2023. Carbon Coated Iron-Cobalt Nanoparticles for Magnetic Particle Imaging. Acs Applied Bio Materials. 6(8):3257-3265. https://www.doi.org/10.1021/acsabm.3c00354

R03

Magnetic Nanoparticles

Metal Nanoparticles

Ironu2212cobalt Nanoparticles

Iron

Magnetic Phenomena

Cobalt

Nanoparticles

Mpi

Carbon

Bioimaging

Animals

Esquivel SV, Bhatt HN, Diwan R, Habib A, Lee WY, Khatun Z, Nurunnabi M. 2023. beta-Glucan and Fatty Acid Based Mucoadhesive Carrier for Gastrointestinal Tract Specific Local and Sustained Drug Delivery. Biomolecules. 13(5). https://www.doi.org/10.3390/biom13050768

R03

Drug Carriers

Gastrointestinal Tract

Animals

Mucoadhesive

Docosahexaenoic Acids

Stomach Specific

Fatty Acids

Mice

Local Delivery

Oral Medicine

Drug Delivery Systems

U03b2-glucan

Beta-glucans

Higgins D, Thibert JP, Mattioni M, DiGiovanna J, Grossman RL, Farrow BK, Wenger E, Volchenboum S, Carroll RJ, Haendel MA et al.,. 2023. Gabriella Miller Kids First Data Resource Center (KFDRC): Empowering discovery across germline and somatic variation in pediatric cancer. Cancer Research. 7_Supplement(83):6576. https://www.doi.org/10.1158/1538-7445.AM2023-6576

Landmark

Kids First

Bhatt HN, Pena-Zacarias J, Beaven E, Zahid MI, Ahmad SS, Diwan R, Nurunnabi M. 2023. Potential and Progress of 2D Materials in Photomedicine for Cancer Treatment. Acs Applied Bio Materials. 6(2):365-383. https://www.doi.org/10.1021/acsabm.2c00981

R03

Nanostructures

Phototherapy

Graphenes

Photochemotherapy

Solid Tumor

Boron Nitride

Molybdenum Disulfide

Photothermal Therapy

Graphite

Neoplasms

Humans

Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A. 2023. Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Research. 51(W1):W168-W179. https://www.doi.org/10.1093/nar/gkad393

LINCS

Search Engine

Internet

Gene Library

Proteins

Databases, Factual

Software

Williams AS, Wilk EJ, Fisher JL, Lasseigne BN. 2023. Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. Cancer Reports (hoboken, N.j.). 6(9):e1874. https://www.doi.org/10.1002/cnr2.1874

R03

Cancer Model

Glioblastoma

Patient-derived Xenograft

Glioblastoma

Cell Line

Gene Expression

Xenograft Model Antitumor Assays

Preclinical Model

Transcriptome

Cell Line, Tumor

Heterografts

Humans

Rodriguez EP, Li Y, Vaniya A, Shih PM, Fiehn O. 2023. Alternative Identification of Glycosides Using MS/MS Matching with an In Silico-Modified Aglycone Mass Spectra Library. Analytical Chemistry. 95(28):10618-10624. https://www.doi.org/10.1021/acs.analchem.3c00957

R03

Sugars

Ions

Glycosides

Chromatography, High Pressure Liquid

Chromatography, Liquid

Spectrometry, Mass, Electrospray Ionization

Tandem Mass Spectrometry

Tissue Distribution

Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A. 2023. lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database : The Journal Of Biological Databases And Curation. 2023. https://www.doi.org/10.1093/database/baad009

LINCS

Rna, Long Noncoding

Animals

Clustered Regularly Interspaced Short Palindromic Repeats

Knowledge

Cell Line

Mice

Databases, Factual

Humans

Prieto LI, Sturmlechner I, Graves SI, Zhang C, Goplen NP, Yi ES, Sun J, Li H, Baker DJ. 2023. Senescent alveolar macrophages promote early-stage lung tumorigenesis. Cancer Cell. 41(7):1261-1275.e6. https://www.doi.org/10.1016/j.ccell.2023.05.006

R03

Aging

Cyclin-dependent Kinase Inhibitor P16

Macrophages, Alveolar

Tumor Microenvironment

Cell Transformation, Neoplastic

Cellular Senescence

Lung

Mice

Lung Neoplasms

Cytotoxic Tu00a0cells

Alveolar Macrophages

Senolytic

Animals

Humans

Kong F, Keshet U, Shen T, Rodriguez E, Fiehn O. 2023. LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers. Analytical Chemistry. 95(46):16810-16818. https://www.doi.org/10.1021/acs.analchem.3c02263

R03

Chen F, Wang X, Jang SK, Quach BC, Weissenkampen JD, Khunsriraksakul C, Yang L, Sauteraud R, Albert CM, Allred NDD et al.,. 2023. Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nature Genetics. 55(2):291-300. https://www.doi.org/10.1038/s41588-022-01282-x

R03

Biology

Tobacco Use

Drug Repositioning

Polymorphism, Single Nucleotide

Genetic Predisposition To Disease

Genome-wide Association Study

Transcriptome

Humans

Amadori L, Calcagno C, Fernandez DM, Koplev S, Fernandez N, Kaur R, Mury P, Khan NS, Sajja S, Shamailova R et al.,. 2023. Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. Nature Cardiovascular Research. 2(6):550-571. https://www.doi.org/10.1038/s44161-023-00278-y

LINCS

Morgan EW, Dong F, Annalora AJ, Murray IA, Wolfe T, Erickson R, Gowda K, Amin SG, Petersen KS, Kris-Etherton PM et al.,. 2023. Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation. International Journal Of Tryptophan Research : Ijtr. 16:11786469231182510. https://www.doi.org/10.1177/11786469231182510

Metabolomics

Microbiome

Metabolomics

Indole

Aryl Hydrocarbon Receptor

Tryptophan Metabolism

Homeostasis

Kynurenine Pathway

Wilk EJ, Howton TC, Fisher JL, Oza VH, Brownlee RT, McPherson KC, Cleary HL, Yoder BK, George JF, Mrug M et al.,. 2023. Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion. Molecular Medicine (cambridge, Mass.). 29(1):67. https://www.doi.org/10.1186/s10020-023-00664-z

R03

Drug Repositioning

Adpkd

Trpp Cation Channels

Gene Expression

Pkd

Polycystic Kidney, Autosomal Dominant

Mice

Tolvaptan

Drug Repurposing

Lincs

Drug Prioritization

Polycystic Kidney Disease

Signature Reversion

Polycystic Kidney Diseases

Kidney

Animals

Humans

Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A. 2023. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Research. 51(W1):W213-W224. https://www.doi.org/10.1093/nar/gkad399

LINCS

Rna-seq

Internet

Cell Line

Proteomics

Pseudogenes

Humans

Software

Bittremieux W, Levitsky L, Pilz M, Sachsenberg T, Huber F, Wang M, Dorrestein PC. 2023. Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal Of Proteome Research. 22(2):625-631. https://www.doi.org/10.1021/acs.jproteome.2c00632

R03

Mass Spectrometry

Metabolomics

Mass Spectrometry

Metabolomics

Open Source

Proteomics

Python

Proteomics

Machine Learning

Software

Flanary VL, Fisher JL, Wilk EJ, Howton TC, Lasseigne BN. 2023. Computational Advancements in Cancer Combination Therapy Prediction. Jco Precision Oncology. 7:e2300261. https://www.doi.org/10.1200/PO.23.00261

R03

Drug Discovery

Retrospective Studies

Meta-analysis As Topic

Neoplasms

Humans

Machine Learning

Fame RM, Kalugin PN, Petrova B, Xu H, Soden PA, Shipley FB, Dani N, Grant B, Pragana A, Head JP et al.,. 2023. Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution. Nature Communications. 14(1):3720. https://www.doi.org/10.1038/s41467-023-39326-3

Metabolomics

Male

Blood-brain Barrier

Biological Transport

Mice

Prealbumin

Thyroid Hormones

Choroid Plexus

Brain

Animals

Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins SL, Ahooyi TM, Bologa CG, Yang JJ, Binder JL et al.,. 2023. Toxicology knowledge graph for structural birth defects. Communications Medicine. 3(1):98. https://www.doi.org/10.1038/s43856-023-00329-2

Kids First

LINCS

IDG

SPARC

Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A. 2023. Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. Aging Cell. 22(6):e13809. https://www.doi.org/10.1111/acel.13809

LINCS

Neoantigens

Gene Expression Profiling

Omics Integration

Car T-cell Therapy

Biomarkers

Cellular Senescence

Cell Line

Immunotherapy

Bioinforatics

Aging

Aged

Humans

Antibody Drug Conjugates

Pruvost M, Patzig J, Yattah C, Selcen I, Hernandez M, Park HJ, Moyon S, Liu S, Morioka MS, Shopland L et al.,. 2023. The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. Cell Reports. 42(8):112848. https://www.doi.org/10.1016/j.celrep.2023.112848

Metabolomics

Chromatin

Oligodendroglia

Progenitors

Nuclear Lamina

Myelin

Brain

Cells, Cultured

Nucleus

Epigenetics

Myelin Sheath

Chromatin

Transcriptome

Cp: Neuroscience

Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C et al.,. 2023. SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. Biomolecules. 13(6). https://www.doi.org/10.3390/biom13060895

R03

Gene Expression Profiling

Spatial Gene Regulation

Cellular Niche

Artificial Intelligence

Deep Learning

Spatial Transcriptomics

Transcriptome

Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L et al.,. 2022. Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. Scientific Reports. 12(1):20791. https://www.doi.org/10.1038/s41598-022-19710-7

R03

Wdr62 Protein, Mouse

Cilia

Mice

Databases, Factual

Cell Cycle Proteins

Nerve Tissue Proteins

Mice, Knockout

Ciliopathies

Gene Knockout Techniques

Animals

Kumar R, Islam T, Nurunnabi M. 2022. Mucoadhesive carriers for oral drug delivery. Journal Of Controlled Release : Official Journal Of The Controlled Release Society. 351:504-559. https://www.doi.org/10.1016/j.jconrel.2022.09.024

R03

Gastric Cancer

Oral Delivery

Drug Carriers

Gastrointestinal Tract

Administration, Oral

Inflammatory Bowel Disease

Excipients

Mucoadhesive Polymer

Oral Medicine

Drug Delivery Systems

Colon

Humans

Srivastava H, Lippincott MJ, Currie J, Canfield R, Lam MPY, Lau E. 2022. Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners. Plos Computational Biology. 18(11):e1010702. https://www.doi.org/10.1371/journal.pcbi.1010702

R03

Rna, Messenger

Gene Expression Regulation

Proteomics

Proteome

Transcriptome

Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH et al.,. 2022. Making Common Fund data more findable: catalyzing a data ecosystem. Gigascience. 11. https://www.doi.org/10.1093/gigascience/giac105

LINCS

HMP

IDG

Ecosystem

Metadata

Financial Management

Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A. 2022. DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. Bmc Bioinformatics. 23(1):76. https://www.doi.org/10.1186/s12859-022-04590-5

LINCS

IDG

Drug Repositioning

Machine Learning

Gene Library

Search Engine

Text Mining

Transcriptomics

Drug Repurposing

Transcriptome

Software

Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML et al.,. 2022. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research. 50(W1):W697-W709. https://www.doi.org/10.1093/nar/gkac328

LINCS

Metadata

Transcriptome

Search Engine

Srivastava H, Pozzoli M, Lau E. 2022. Defining the Roles of Cardiokines in Human Aging and Age-Associated Diseases. Frontiers In Aging. 3:884321. https://www.doi.org/10.3389/fragi.2022.884321

R03

Cardiokine

Aging

Endocrine

Secretome

Hipsc

Heart

Proteomics

Transcriptomics

Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma'ayan A. 2022. Transforming L1000 profiles to RNA-seq-like profiles with deep learning. Bmc Bioinformatics. 23(1):374. https://www.doi.org/10.1186/s12859-022-04895-5

LINCS

Gene Expression Profiling

Rna-seq

Generative Adversarial Networks

Gene Expression Translation

Deep Learning

L1000

Rna-seq

Transcriptome

Humans

Surles-Zeigler MC, Sincomb T, Gillespie TH, de Bono B, Bresnahan J, Mawe GM, Grethe JS, Tappan S, Heal M, Martone ME. 2022. Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Frontiers In Neuroinformatics. 16:819198. https://www.doi.org/10.3389/fninf.2022.819198

SPARC

Sparc

Anatomical Terms

Ontologies

Peripheral Nervous System (pns)

Interlex

Hammond DE, Simpson DM, Franco C, Wright Muelas M, Waters J, Ludwig RW, Prescott MC, Hurst JL, Beynon RJ, Lau E. 2022. Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals. Molecular & Cellular Proteomics : Mcp. 21(7):100252. https://www.doi.org/10.1016/j.mcpro.2022.100252

R03

Protein Turnover

Proteolysis

Heavy Water

Lysine

Mice

Proteostasis

Amino Acids

Stable Isotope Labeling By Amino Acids

Protein Degradation

Proteome

Isotope Labeling

Animals

Lachmann A, Xie Z, Ma'ayan A. 2022. blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinformatics (oxford, England). 38(8):2356-2357. https://www.doi.org/10.1093/bioinformatics/btac076

LINCS

Algorithms

Probability

Gene Expression Profiling

Software

Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA Jr et al.,. 2022. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods. 19(2):134-136. https://www.doi.org/10.1038/s41592-021-01339-5

Metabolomics

Mass Spectrometry

Data Visualization

Web Browser

Software

Borner K, Bueckle A, Herr BW 2nd, Cross LE, Quardokus EM, Record EG, Ju Y, Silverstein JC, Browne KM, Jain S et al.,. 2022. Tissue registration and exploration user interfaces in support of a human reference atlas. Communications Biology. 5(1):1369. https://www.doi.org/10.1038/s42003-022-03644-x

HuBMAP

Humans

Software

Xie Z, Kropiwnicki E, Wojciechowicz ML, Jagodnik KM, Shu I, Bailey A, Clarke DJB, Jeon M, Evangelista JE, V Kuleshov M et al.,. 2022. Getting Started with LINCS Datasets and Tools. Current Protocols. 2(7):e487. https://www.doi.org/10.1002/cpz1.487

LINCS

Drug Discovery

Disease

Gene Library

Bioinformatics

Web Application

Proteomics

Gene Sets Visualization

Signature Analysis

Databases, Factual

Transcriptome

Humans

Cheng KC, Burdine RD, Dickinson ME, Ekker SC, Lin AY, Lloyd KCK, Lutz CM, MacRae CA, Morrison JH, O'Connor DH et al.,. 2022. Promoting validation and cross-phylogenetic integration in model organism research. Disease Models & Mechanisms. 15(9). https://www.doi.org/10.1242/dmm.049600

R03

Research Resources

Technology

Validation

Model Organisms

Integration

Phylogeny

Human Diseases

Phenomics

Reproducibility Of Results

Omics

Animals

Biological Evolution

Humans

Saunders GRB, Wang X, Chen F, Jang SK, Liu M, Wang C, Gao S, Jiang Y, Khunsriraksakul C, Otto JM et al.,. 2022. Genetic diversity fuels gene discovery for tobacco and alcohol use. Nature. 612(7941):720-724. https://www.doi.org/10.1038/s41586-022-05477-4

R03

Tobacco Use

Sample Size

Multifactorial Inheritance

Europe

Risk Factors

Genetic Variation

Alcohol Drinking

Genetic Loci

Internationality

Genetic Predisposition To Disease

Transcriptome

Genome-wide Association Study

Humans

Rahiminejad S, Maurya MR, Mukund K, Subramaniam S. 2022. Modular and mechanistic changes across stages of colorectal cancer. Bmc Cancer. 22(1):436. https://www.doi.org/10.1186/s12885-022-09479-3

Metabolomics

Gene Expression Profiling

Computational Biology

Biomarkers, Tumor

Gene Expression Regulation, Neoplastic

Signal Transduction

Signaling Pathways

Gene Regulatory Networks

Biomarkers

Mtus1 Protein, Human

Colorectal Cancer

Colorectal Neoplasms

Neoplasm Staging

Stage-specific Networks

Crc Stages

Stage-unique Networks

Humans

Tumor Suppressor Proteins

Tetikol HS, Turgut D, Narci K, Budak G, Kalay O, Arslan E, Demirkaya-Budak S, Dolgoborodov A, Kabakci-Zorlu D, Semenyuk V et al.,. 2022. Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis. Nature Communications. 13(1):4384. https://www.doi.org/10.1038/s41467-022-31724-3

Kids First

Genome, Human

Data Analysis

Genomics

Sequence Analysis, Dna

High-throughput Nucleotide Sequencing

Humans

Software

Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma'ayan A. 2022. Gene and drug landing page aggregator. Bioinformatics Advances. 2(1):vbac013. https://www.doi.org/10.1093/bioadv/vbac013

LINCS

IDG

Fisher JL, Jones EF, Flanary VL, Williams AS, Ramsey EJ, Lasseigne BN. 2022. Considerations and challenges for sex-aware drug repurposing. Biology Of Sex Differences. 13(1):13. https://www.doi.org/10.1186/s13293-022-00420-8

R03

Computational Drug Repurposing

Pharmaceuticals

Male

Sex Differences

Drug Repositioning

Therapeutics

Sex Characteristics

Sex-aware

Female

Drug Repurposing

Review

Transcriptome

Neoplasms

Humans

Sex-bias

Han Y, Wennersten SA, Wright JM, Ludwig RW, Lau E, Lam MPY. 2022. Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging. American Journal Of Physiology. Heart And Circulatory Physiology. 323(3):H538-H558. https://www.doi.org/10.1152/ajpheart.00244.2022

R03

Alternative Splicing

Aging

Male

Rna Splicing

Proteogenomics

Sex Difference

Mice

Female

Proteoforms

Alternative Splicing

Proteogenomics

Rna-binding Proteins

Aging

Animals

Feng F, Yao Y, Wang XQD, Zhang X, Liu J. 2022. Connecting high-resolution 3D chromatin organization with epigenomics. Nature Communications. 13(1):2054. https://www.doi.org/10.1038/s41467-022-29695-6

R03

Chromosomes

Chromatin

Gene Expression Regulation

Epigenomics

Regulatory Sequences, Nucleic Acid

Humans

Osanlouy M, Bandrowski A, de Bono B, Brooks D, Cassarà AM, Christie R, Ebrahimi N, Gillespie T, Grethe JS, Guercio LA et al.,. 2021. The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. Frontiers In Physiology. 12:693735. https://www.doi.org/10.3389/fphys.2021.693735

Landmark

SPARC

Fair

Sparc

Autonomic Nervous System

Computational Life Sciences

Data Annotation

Data Curation

Knowledge Management

Neural Mapping

Mukund K, Nayak P, Ashokkumar C, Rao S, Almeda J, Betancourt-Garcia MM, Sindhi R, Subramaniam S. 2021. Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. Frontiers In Immunology. 12:738073. https://www.doi.org/10.3389/fimmu.2021.738073

Metabolomics

Cell Differentiation

Cdc2

Sequence Analysis, Rna

Megakaryocyte

Immunity, Innate

Lymphopoiesis

Killer Cells, Natural

Receptors, Antigen, T-cell, Gamma-delta

Covid-19

Adult Multisystem Inflammatory Disease, Covid-19 Related

Cell Proliferation

Plasmablast

Mucosal-associated Invariant T Cells

Sars-cov-2

Single-cell Analysis

Humans

Aggregation

Neutrophils

Mdsc

Interferon Type I

Low-density Neutrophils

Immune-remodeling

T-lymphocytes

Systemic Inflammatory Response Syndrome

Thrombopoiesis

Bueckle A, Buehling K, Shih PC, Borner K. 2021. 3D virtual reality vs. 2D desktop registration user interface comparison. Plos One. 16(10):page. https://www.doi.org/10.1371/journal.pone.0258103

HuBMAP

Middle Aged

Male

User-computer Interface

Adult

Tissue And Organ Harvesting

Virtual Reality

Imaging, Three-dimensional

Young Adult

Female

Adolescent

Humans

Amiri H, Kohane IS, Undiagnosed Diseases Network. 2021. Machine Learning of Patient Characteristics to Predict Admission Outcomes in the Undiagnosed Diseases Network. Jama Network Open. 4(2):e2036220. https://www.doi.org/10.1001/jamanetworkopen.2020.36220

Landmark

UDN

Undiagnosed Diseases

Young Adult

Adult

Infant, Newborn

Female

Reproducibility Of Results

Roc Curve

Whole Genome Sequencing

Child

Retrospective Studies

Rare Diseases

Computer Simulation

Prospective Studies

Referral And Consultation

Humans

Area Under Curve

Male

Patient Admission

Triage

Middle Aged

Patient Selection

Infant

Child, Preschool

Adolescent

Machine Learning

Powell CD, Moseley HNB. 2021. The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. Metabolites. 11(3). https://www.doi.org/10.3390/metabo11030163

R03

Data Deposition

Data Validation

Python Package

Metabolomics Workbench

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M et al.,. 2020. GlyGen: Computational and Informatics Resources for Glycoscience. Glycobiology. 30(2):72-73. https://www.doi.org/10.1093/glycob/cwz080

Landmark

GlyGen

Computational Biology

Glycoinformatics/database

Structure

Polysaccharides

Function

Bioinformatics

Software

Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S et al.,. 2020. Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell. 181(7):1464-1474. https://www.doi.org/10.1016/j.cell.2020.06.004

Landmark

MoTrPAC

Middle Aged

Male

Physical Endurance

Animals

Child

Oxygen Consumption

Adult

Young Adult

Female

Exercise

Research Design

Adolescent

Humans

HuBMAP Consortium. 2019. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 574(7777):187-192. https://www.doi.org/10.1038/s41586-019-1629-x

Landmark

HuBMAP

Male

Models, Anatomic

Atlases As Topic

Female

Molecular Biology

Organ Specificity

International Cooperation

Biomedical Research

National Institutes Of Health (u.s.)

Single-cell Analysis

Aging

Health

Humans

United States

Mulder N, Abimiku A, Adebamowo SN, de Vries J, Matimba A, Olowoyo P, Ramsay M, Skelton M, Stein DJ. 2018. H3Africa: current perspectives. Pharmacogenomics And Personalized Medicine. 11:59-66. https://www.doi.org/10.2147/PGPM.S141546

Landmark

H3Africa

H3africa

Genomic Medicine

Training

Population Genetics

Disease

Precision Medicine

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A et al.,. 2018. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 6(1):13-24. https://www.doi.org/10.1016/j.cels.2017.11.001

Landmark

LINCS

Gene Expression Profiling

Bd2k

Information Storage And Retrieval

Data Integration

Transcriptome

Systems Pharmacology

Lincsprogram

Systems Biology

L1000

P100

Humans

Mema

Lincsproject

Gene Library

Systems Biology

National Health Programs

Computational Biology

Databases, Chemical

Mcf10a

National Institutes Of Health (u.s.)

Cataloging

United States

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J et al.,. 2018. Unexplored therapeutic opportunities in the human genome. Nature Reviews Drug Discovery. 17(5):317-332. https://www.doi.org/10.1038/nrd.2018.14

Landmark

IDG

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B et al.,. 2017. The 4D nucleome project. Nature. 549(7671):219-226. https://www.doi.org/10.1038/nature23884

Landmark

4DN

Chromosomes

Genome

Molecular Imaging

Information Dissemination

Cell Nucleus

Chromatin

Spatio-temporal Analysis

Models, Biological

Models, Molecular

Cell Line

Mice

Reproducibility Of Results

Genomics

Goals

Single-cell Analysis

Animals

Humans

Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS et al.,. 2016. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Research. 44(D1):D463-70. https://www.doi.org/10.1093/nar/gkv1042

Landmark

Metabolomics

Databases, Chemical

User-computer Interface

Mass Spectrometry

Metabolomics

Molecular Structure

Magnetic Resonance Spectroscopy

Reference Standards

Software

Animals

Humans

Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H et al.,. 2016. High-throughput discovery of novel developmental phenotypes. Nature. 537(7621):508-514. https://www.doi.org/10.1038/nature19356

Landmark

KOMP2

Embryo, Mammalian

Genes, Essential

Mutation

Phenotype

Polymorphism, Single Nucleotide

High-throughput Screening Assays

Imaging, Three-dimensional

Mice

Penetrance

Conserved Sequence

Mice, Inbred C57bl

Sequence Homology

Genes, Lethal

Mice, Knockout

Disease

Genome-wide Association Study

Animals

Humans

Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley CA, Kuo LS, Labosky PA, Lenzi R et al.,. 2015. The NIH Extracellular RNA Communication Consortium. Journal Of Extracellular Vesicles. 4:27493. https://www.doi.org/10.3402/jev.v4.27493

Landmark

ExRNA

Exrna

Extracellular Rna

Ercc

GTEx Consortium. 2015. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science (new York, N.y.). 348(6235):648-60. https://www.doi.org/10.1126/science.1262110

Landmark

GTEx

Rna, Untranslated

Sequence Analysis, Rna

Arhgap42 Protein, Human

Transcriptome

Tibial Arteries

Blood Pressure

Gtpase-activating Proteins

Disease

Genotype

Humans

Pilot Projects

Rna Splicing

Genetic Variation

Organ Specificity

Gene Regulatory Networks

Quantitative Trait Loci

Genome, Human

Multigene Family

Gene Expression Regulation

Alleles

Genome-wide Association Study

GTEx Consortium. 2013. The Genotype-Tissue Expression (GTEx) project. Nature Genetics. 45(6):580-5. https://www.doi.org/10.1038/ng.2653

Landmark

GTEx

Gene Expression Profiling

Gene Expression

Government Programs

Organ Specificity

Tissue Banks

Molecular Sequence Annotation

Consensus Development Conferences, Nih As Topic

Quantitative Trait Loci

United States

Genome-wide Association Study

Humans

Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486(7402):207-14. https://www.doi.org/10.1038/nature11234

Landmark

HMP

Male

Metagenomics

Rna, Ribosomal, 16s

Phenotype

Young Adult

Biodiversity

Adult

Bacteria

Metabolic Networks And Pathways

Metagenome

Female

Ecosystem

Health

Adolescent

Humans

Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature. 486(7402):215-21. https://www.doi.org/10.1038/nature11209

Landmark

HMP

Statistics As Topic

Male

Metagenomics

Rna, Ribosomal, 16s

Young Adult

Adult

Metagenome

Bacteria

Reference Standards

Female

Adolescent

Humans

CFDE Workbench

Consortium

Community

Resources

@CFDE Workbench 2025

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

Community

Resources

CFDE Workbench

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.