The Gen3 data platform is used as the basis for many data repositories and enables research on large and diverse datasets. The list below includes publications that discuss data commons or meshes that leverage Gen3, include analyses that were performed on or made possible by a Gen3 system, or reference datasets that are now stored on a Gen3 system. If you see we are missing your paper please let us know by submitting this form.
Adams, Clare IM, et al. "Environmental DNA metabarcoding describes biodiversity across marine gradients." ICES Journal of Marine Science 80.4 (2023): 953-971. View Article
Adams, Meredith CB, et al. "NIH HEAL Clinical Data Elements (CDE) implementation: NIH HEAL Initiative IMPOWR network IDEA-CC." Pain Medicine (2023): pnad018. View Article
Ahalt, Stan, et al. "Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research." Journal of the American Medical Informatics Association 30.7 (2023): 1293-1300. View Article
Baughan, Natalie, et al. "Sequestration methodology in practice through evaluation of joint demographic distributions of 54,185 patients in the Medical Imaging and Data Resource Center (MIDRC) data commons." Medical Imaging 2023: Imaging Informatics for Healthcare, Research, and Applications. Vol. 12469. SPIE, 2023. View Article
Bailey, Sarah, et al. "Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics." Molecular Ecology Resources (2023). View Article
Byers, Alexa K., et al. "Whole genome sequencing of Penicillium and Burkholderia strains antagonistic to the causal agent of kauri dieback disease (Phytophthora agathidicida) reveals biosynthetic gene clusters related to antimicrobial secondary metabolites." Molecular Ecology Resources (2023). View Article
Chapman, Katie, et al. "Scholarly Data Share 2.0: Granular Access to Research Data." Practice and Experience in Advanced Research Computing. 2023. 177-180. View Article
Chen, Weijie, et al. "Machine learning with multimodal data for COVID-19." Heliyon (2023). View Article
Dahlquist, Jacklyn M., Sarah C. Nelson, and Stephanie M. Fullerton. "Cloud-based biomedical data storage and analysis for genomic research: Landscape analysis of data governance in emerging NIH-supported platforms." Human Genetics and Genomics Advances 4.3 (2023). View Article
Drukker, Karen, et al. "Toward fairness in artificial intelligence for medical image analysis: identification and mitigation of potential biases in the roadmap from data collection to model deployment." Journal of Medical Imaging 10.6 (2023): 061104-061104. View Article
Duncan, Jamie. "Data protection beyond data rights: Governing data production through collective intermediaries." Internet Policy Review 12.3 (2023): 1-22. View Article
Foote, Andrew D., et al. "“Type D” killer whale genomes reveal long-term small population size and low genetic diversity." Journal of Heredity 114.2 (2023): 94-109. View Article
French, Rebecca K., et al. "Host phylogeny shapes viral transmission networks in an island ecosystem." Nature Ecology & Evolution (2023): 1-10. View Article
Gamage, Thiranja P. Babarenda, et al. "Vision for the 12 LABOURS Digital Twin Platform." View Article
García-Closas, Montserrat, et al. "Moving Toward Findable, Accessible, Interoperable, Reusable Practices in Epidemiologic Research." American Journal of Epidemiology 192.6 (2023): 995-1005. View Article
Gorre, Naveena, et al. "MIDRC CRP10 AI interface—an integrated tool for exploring, testing and visualization of AI models." Physics in Medicine & Biology 68.7 (2023): 074002. View Article
Gorre, Naveena, et al. "User experience evaluation for MIDRC AI interface." Medical Imaging 2023: Imaging Informatics for Healthcare, Research, and Applications. Vol. 12469. SPIE, 2023. View Article
Guhlin, Joseph, et al. "Species-wide genomics of kākāpō provides tools to accelerate recovery." Nature Ecology & Evolution 7.10 (2023): 1693-1705. View Article
Higgins, David, et al. "Gabriella Miller Kids First Data Resource Center (KFDRC): Empowering discovery across germline and somatic variation in pediatric cancer." Cancer Research 83.7_Supplement (2023): 6576-6576. View Article
Le Duc, Huy. On-premise containerized, light-weight software solutions for Biomedicine. Diss. 2023. View Article
Lukowski, Michael, Andrew Prokhorenkov, and Robert L. Grossman. "Towards self-describing and FAIR bulk formats for biomedical data." PLOS Computational Biology 19.3 (2023): e1010944. View Article
Makar, Jana, et al. "NeSI 2022 Annual Review." (2023). View Article
Nault, Rance, et al. "A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data." Environmental Health Perspectives 131.6 (2023): 065001. View Article
Pandey, Akanksha, Rishabha Malviya, and Sunita Dahiya. "Risk Assessment in the Field of Oncology using Big Data." Big Data in Oncology: Impact, Challenges, and Risk Assessment. River Publishers, 2023. 355-409. View Article
Pearman, William S., et al. "Differences in density: taxonomic but not functional diversity in seaweed microbiomes affected by an earthquake." bioRxiv (2023): 2023-02. View Article
Papa, Yvan, et al. "Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)." G3 13.2 (2023): jkac315. View Article
Pomp, André, et al. "Using IoT Technology for the Skilled Crafts." Enterprise Information Systems: 24th International Conference, ICEIS 2022, Virtual Event, April 25–27, 2022, Revised Selected Papers. Vol. 487. Springer Nature, 2023. View Article
Stephens, Keri. "MIDRC Lends Medical Imaging Expertise to New Biomedical Data Program." AXIS Imaging News (2023). View Article
Te Aika, Ben, et al. "Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data." Molecular Ecology Resources (2023). View Article
Timoshevskaya, Nataliya, et al. "An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes." Cell reports 42.3 (2023). View Article
Waller, Stephanie J., et al. "Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae." bioRxiv (2023): 2023-06. View Article
Walsh, Brian, Jordan Lee, and Kyle Ellrott. "pfb_fhir: A utility to extract clinical data systems into a portable format." medRxiv (2023): 2023-06. View Article
Whitney, Heather M., et al. "Longitudinal assessment of demographic representativeness in the Medical Imaging and Data Resource Center Open Data Commons." arXiv preprint arXiv:2303.10501 (2023). View Article
Adams, Clare IM, et al. "Environmental DNA reflects common haplotypic variation." Environmental DNA (2022).View Article
Barnes, Craig, et al. "The Biomedical Research Hub: a federated platform for patient research data." Journal of the American Medical Informatics Association 29.4 (2022): 619-625. View Article
Baughan, Natalie, et al. "Sequestration of imaging studies in MIDRC: a multi-institutional data commons." Medical Imaging 2022: Image Perception, Observer Performance, and Technology Assessment. Vol. 12035. SPIE, 2022. View Article
Borges, Vânia, et al. "Implementation Solutions for FAIR Clinical Research Data Management." International Conference on Enterprise Information Systems. Cham: Springer Nature Switzerland, 2022. View Article
Evangelista, John Erol, et al. "SigCom LINCS: data and metadata search engine for a million gene expression signatures." Nucleic acids research 50.W1 (2022): W697-W709. View Article
Garcia-Closas, Montserrat, et al. "Moving towards FAIR practices in epidemiological research." arXiv preprint arXiv:2206.06159 (2022). View Article
Giger, Maryellen L. "Medical Physics and Artificial Intelligence (AI) of Image Interpretation." True Tales of Medical Physics: Insights into a Life-Saving Specialty. Cham: Springer International Publishing, 2022. 463-489. View Article
Hung, Ling-Hong, et al. "Accessible, interactive and cloud-enabled genomic workflows integrated with the NCI Genomic Data Commons." bioRxiv (2022): 2022-08. View Article
Liu, Tianming, Eliot Siegel, and Dinggang Shen. "Deep learning and medical image analysis for COVID-19 diagnosis and prediction." Annual review of biomedical engineering 24 (2022): 179-201. View Article
Lubbe, Pascale, et al. "Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)." Zoological Journal of the Linnean Society 196.4 (2022): 1451-1463. View Article
Miller, Allison K., et al. "Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis)." Journal of Heredity 113.4 (2022): 380-397. View Article
O'Hara, Thomas, et al. "Economical Utilization of Health Information with Learning Healthcare System Data Commons." Perspectives in Health Information Management 19.Spring (2022). View Article
Papa, Yvan, et al. "Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of potential fine-scale adaptation and a temperature-associated cline amid panmixia." Frontiers in Ecology and Evolution 10 (2022): 862930. View Article
Pieneman-Elbers, Danne Charlotte Emily. Building a Learning Healthcare System: a path to optimizing big health data to inform clinical care decisions. The University of Vermont and State Agricultural College, 2022. View Article
Schatz, Michael C., et al. "Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space." Cell Genomics 2.1 (2022). View Article
Sheffield, Nathan C., et al. "From biomedical cloud platforms to microservices: next steps in FAIR data and analysis." Scientific Data 9.1 (2022): 553. View Article
Sandoval-Castillo, Jonathan, Luciano B. Beheregaray, and Maren Wellenreuther. "Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)." G3 12.3 (2022): jkac015. View Article
Sowalsky, Adam G., et al. "Assessment of Androgen Receptor splice variant-7 as a biomarker of clinical response in castration-sensitive prostate cancer." Clinical Cancer Research 28.16 (2022): 3509-3525. View Article
Su, Jing, et al. "The Alcoholic Hepatitis Network Research Data Commons (ARDaC): Design and Development." AMIA. 2022. View Article
Trunnell, Matthew, et al. "The Pandemic Response Commons." medRxiv (2022): 2022-06. View Article
Waller, Stephanie J., et al. "Cloacal virome of an ancient host lineage–The tuatara (Sphenodon punctatus)–Reveals abundant and diverse diet-related viruses." Virology 575 (2022): 43-53. View Article
Berman, Ari E. "Building Data Ecosystems for Modern Biomedical Research: To derive value from fast-growing data collections, research organizations are using high-performance platforms, exploring standards, and prioritizing FAIRness." Genetic Engineering & Biotechnology News 41.10 (2021): 60-62. View Article
Bhattacharya, Sanchita, Zicheng Hu, and Atul J. Butte. "Opportunities and challenges in democratizing immunology datasets." Frontiers in immunology 12 (2021): 846. View Article
Catanach, Andrew, et al. "The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus." BMC genomics 22 (2021): 1-16. View Article
Conway, Mike, and Deep Patel. "Issues in Data Sharing for Environmental Health Sciences." View Article
Giger, Maryellen. "Medical imaging of COVID-19." Journal of Medical Imaging 8.Suppl 1 (2021). View Article
Grossman, Robert L., et al. "BloodPAC Data Commons for liquid biopsy data." JCO Clinical Cancer Informatics 5 (2021): 479-486. View Article
Kerlavage, Anthony R., et al. "Cancer informatics for cancer centers: Scientific drivers for informatics, data science, and care in pediatric, adolescent, and young adult cancer." JCO clinical cancer informatics 5 (2021): 881-896. View Article
Koot, Emily, et al. "Genome‐wide analysis reveals the genetic stock structure of hoki (Macruronus novaezelandiae)." Evolutionary Applications 14.12 (2021): 2848-2863. View Article
Martini, Denise, et al. "Evolution of the “world’s only alpine parrot”: Genomic adaptation or phenotypic plasticity, behaviour and ecology?." Molecular Ecology 30.23 (2021): 6370-6386.View Article
Miller, Allison K., et al. "Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae." Virus Evolution 7.2 (2021): veab050. View Article
Plana, Alejandro, et al. "Pediatric cancer data commons: Federating and democratizing data for childhood cancer research." JCO Clinical Cancer Informatics 5 (2021): 1034-1043. View Article
Tsai, Emily B., et al. "The RSNA international COVID-19 open radiology database (RICORD)." Radiology 299.1 (2021): E204-E213. View Article
Rehm, Heidi L., et al. "GA4GH: International policies and standards for data sharing across genomic research and healthcare." Cell genomics 1.2 (2021). View Article
Voisin, Craig, et al. "GA4GH Passport standard for digital identity and access permissions." Cell Genomics 1.2 (2021). View Article
Cimino, James J., et al. "Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE)." 2020 IEEE 21st International Conference on Information Reuse and Integration for Data Science (IRI). IEEE, 2020. View Article
Elbers, Danne C., et al. "The Veterans Affairs Precision Oncology Data Repository, a clinical, genomic, and imaging research database." Patterns 1.6 (2020). View Article
Jain, Anshu K., et al. "Provider engagement in radiation oncology data science: workshop report." JCO Clinical Cancer Informatics 4 (2020). View Article
Khomtchouk, Bohdan B., et al. "HeartBioPortal2. 0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations." Database 2020 (2020): baaa115. View Article
Major, Ajay, Suzanne M. Cox, and Samuel L. Volchenboum. "Using big data in pediatric oncology: Current applications and future directions." Seminars in Oncology. Vol. 47. No. 1. WB Saunders, 2020. View Article
Tee, H. S., et al. "Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium." The ISME Journal 14.8 (2020): 2164-2178. View Article
Almeida, Jonas S., et al. "Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time." PeerJ 7 (2019): e6230. View Article
Basney, Jim. "CILogon." (2019). View Article
Do, Nhan, et al. "The Veterans Precision Oncology Data Commons: transforming VA data into a national resource for research in precision oncology." Seminars in Oncology. Vol. 46. No. 4-5. WB Saunders, 2019. View Article
Dussex, Nicolas, et al. "Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction." Biology Letters 15.9 (2019): 20190491. View Article
Hughes, LaRon, et al. "Harmonization of clinical data across Gen3 data commons." (2019): e18094-e18094. View Article
Madduri, Ravi, et al. "Reproducible big data science: A case study in continuous FAIRness." PloS one 14.4 (2019): e0213013. View Article
Thrimawithana, Amali H., et al. "A whole genome assembly of Leptospermum scoparium (Myrtaceae) for mānuka research." New Zealand Journal of Crop and Horticultural Science 47.4 (2019): 233-260.View Article
Wellenreuther, Maren, et al. "Domestication and temperature modulate gene expression signatures and growth in the Australasian snapper Chrysophrys auratus." G3: Genes, Genomes, Genetics 9.1 (2019): 105-116. View Article
Grossman, Robert L. "Progress towards cancer data ecosystems." Cancer journal (Sudbury, Mass.) 24.3 (2018): 122. View Article
Alley, Maurice R., et al. "Diphtheritic stomatitis in Yellow-eyed penguins (Megadyptes antipodes) in New Zealand." Journal of Wildlife Diseases 53.1 (2017): 102-110. View Article
Fraser, Ceridwen I., et al. "Genetic and morphological analyses of the southern bull kelp durvillaea antarctica (phaeophyceae: durvillaeales) in new zealand reveal cryptic species 1." Journal of Phycology 45.2 (2009): 436-443. View Article