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CFDE Associated and Common Fund Programs’ Landmark Publications

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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
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
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 Expression
Gene-regulatory
Gene Expression Regulation
Liver
Sex-biased
Female
Humans
Pharmacovigilance
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Cellular Senescence
Lung
Mice
Lung Neoplasms
Cytotoxic Tu00a0cells
Alveolar Macrophages
Senolytic
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
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
Artificial Intelligence
Deep Learning
Spatial Transcriptomics
Transcriptome
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
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
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
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
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
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
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
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
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
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
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
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
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, 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
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
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
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
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
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
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
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
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
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
Drug Discovery
Disease
Gene Library
Bioinformatics
Web Application
Proteomics
Gene Sets Visualization
Signature Analysis
Databases, Factual
Transcriptome
Humans
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
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
Landmark
SPARC
Sparc
Anatomical Terms
Ontologies
Peripheral Nervous System (pns)
Interlex
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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. 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
Report a bug
Consortium
About the CFDECF-DCCsData PortalPartnershipsFunding Opportunities
Ecosystem
Training & OutreachCentersDocumentationPublicationsR03sGet QR Codes
Assets
Data & MetadataToolsChatbotUse CasesVideo Tutorial
@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
About the CFDECF-DCCsData PortalPartnershipsFunding Opportunities
Ecosystem
Training & OutreachCentersDocumentationPublicationsR03sGet QR Codes
Assets
Data & MetadataToolsChatbotUse CasesVideo Tutorial
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