CFDE Associated and Common Fund Programs’ Landmark Publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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