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 papers that discuss data commons or meshes that leverage Gen3 or discuss analyses that were performed on or made possible by a Gen3 system. If you see we are missing your paper please let us know by submitting this form.
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.
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.
Chapman, Katie, et al. "Scholarly Data Share 2.0: Granular Access to Research Data." Practice and Experience in Advanced Research Computing. 2023. 177-180.
Chen, Weijie, et al. "Machine learning with multimodal data for COVID-19." Heliyon (2023).
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).
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.
Duncan, Jamie. "Data protection beyond data rights: Governing data production through collective intermediaries." Internet Policy Review 12.3 (2023): 1-22.
Gamage, Thiranja P. Babarenda, et al. "Vision for the 12 LABOURS Digital Twin Platform."
García-Closas, Montserrat, et al. "Moving Toward Findable, Accessible, Interoperable, Reusable Practices in Epidemiologic Research." American Journal of Epidemiology 192.6 (2023): 995-1005.
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.
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.
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.
Le Duc, Huy. On-premise containerized, light-weight software solutions for Biomedicine. Diss. 2023.
Liu, Suxing, et al. "Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping." The Plant Phenome Journal 6.1 (2023): e20068.
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.
Makar, Jana, et al. "NeSI 2022 Annual Review." (2023).
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.
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.
Pomp, André, et al. "Check for updates 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.
Stephens, Keri. "MIDRC Lends Medical Imaging Expertise to New Biomedical Data Program." AXIS Imaging News (2023).
Te Aika, Ben, et al. "Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data." Molecular Ecology Resources (2023).
Walsh, Brian, Jordan Lee, and Kyle Ellrott. "pfb_fhir: A utility to extract clinical data systems into a portable format." medRxiv (2023): 2023-06.
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).
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.
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.
Borges, Vânia, et al. "Implementation Solutions for FAIR Clinical Research Data Management." International Conference on Enterprise Information Systems. Cham: Springer Nature Switzerland, 2022.
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.
Garcia-Closas, Montserrat, et al. "Moving towards FAIR practices in epidemiological research." arXiv preprint arXiv:2206.06159 (2022).
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.
Hung, Ling-Hong, et al. "Accessible, interactive and cloud-enabled genomic workflows integrated with the NCI Genomic Data Commons." bioRxiv (2022): 2022-08.
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.
O'Hara, Thomas, et al. "Economical Utilization of Health Information with Learning Healthcare System Data Commons." Perspectives in Health Information Management 19.Spring (2022).
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.
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)
Sheffield, Nathan C., et al. "From biomedical cloud platforms to microservices: next steps in FAIR data and analysis." Scientific Data 9.1 (2022): 553.
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.
Su, Jing, et al. "The Alcoholic Hepatitis Network Research Data Commons (ARDaC): Design and Development." AMIA. 2022.
Trunnell, Matthew, et al. "The Pandemic Response Commons." medRxiv (2022): 2022-06.
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.
Bhattacharya, Sanchita, Zicheng Hu, and Atul J. Butte. "Opportunities and challenges in democratizing immunology datasets." Frontiers in immunology 12 (2021): 846.
Conway, Mike, and Deep Patel. "Issues in Data Sharing for Environmental Health Sciences."
Giger, Maryellen. "Medical imaging of COVID-19." Journal of Medical Imaging 8.Suppl 1 (2021).
Grossman, Robert L., et al. "BloodPAC Data Commons for liquid biopsy data." JCO Clinical Cancer Informatics 5 (2021): 479-486.
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.
Plana, Alejandro, et al. "Pediatric cancer data commons: Federating and democratizing data for childhood cancer research." JCO Clinical Cancer Informatics 5 (2021): 1034-1043.
Tsai, Emily B., et al. "The RSNA international COVID-19 open radiology database (RICORD)." Radiology 299.1 (2021): E204-E213.
Rehm, Heidi L., et al. "GA4GH: International policies and standards for data sharing across genomic research and healthcare." Cell genomics 1.2 (2021).
Richter, Heiko. "The law and policy of government access to private sector data (‘B2G data sharing’)." Data Access, Consumer Interests and Public Welfare. Nomos Verlagsgesellschaft mbH & Co. KG, 2021.
Voisin, Craig, et al. "GA4GH Passport standard for digital identity and access permissions." Cell Genomics 1.2 (2021).
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.
Elbers, Danne C., et al. "The Veterans Affairs Precision Oncology Data Repository, a clinical, genomic, and imaging research database." Patterns 1.6 (2020).
Jain, Anshu K., et al. "Provider engagement in radiation oncology data science: workshop report." JCO Clinical Cancer Informatics 4 (2020).
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.
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.
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.
Basney, Jim. "CILogon." (2019). https://www.nitrd.gov/nitrdgroups/images/2022/MAGIC-Jim-Basney-04062022.pdf
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.
Hughes, LaRon, et al. "Harmonization of clinical data across Gen3 data commons." (2019): e18094-e18094.
Madduri, Ravi, et al. "Reproducible big data science: A case study in continuous FAIRness." PloS one 14.4 (2019): e0213013.
Grossman, Robert L. "Progress towards cancer data ecosystems." Cancer journal (Sudbury, Mass.) 24.3 (2018): 122.