Greene, Casey S.

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

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Opportunities and obstacles for deep learning in biology and medicine

Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface

Machine Learning in HealthcareArtificial Intelligence in Healthcare and Education

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Understanding multicellular function and disease with human tissue-specific networks

Greene, C. S., Krishnan, A., Wong, A. K., Ricciotti, E., Zelaya, R. A., Himmelstein, D. S., Zhang, R., Hartmann, B. M., Zaslavsky, E., Sealfon, S. C., et al. (2015) · Nature Genetics

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

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Transparency and reproducibility in artificial intelligence

Haibe-Kains, B., Adam, G. A., Hosny, A., Khodakarami, F., Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha, T., Kusko, R., Sansone, S.-A., Tong, W., Wolfinger, R. D., et al. (2020) · Nature

Explainable Artificial Intelligence (XAI)Ethics and Social Impacts of AI

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

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International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

Cordell, H. J., Han, Y., Mells, G. F., Li, Y., Hirschfield, G. M., Greene, C. S., Xie, G., Juran, B. D., Zhu, D., Qian, D. C., et al. (2015) · Nature Communications

Liver Diseases and ImmunityGenetic Associations and Epidemiology

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Characterizing long COVID: deep phenotype of a complex condition

Deer, R. R., Rock, M. A., Vasilevsky, N., Carmody, L., Rando, H., Anzalone, A. J., Basson, M. D., Bennett, T. D., Bergquist, T., Boudreau, E. A., et al. (2021) · EBioMedicine

Long-Term Effects of COVID-19Biomedical Text Mining and Ontologies

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Reproducible Computational Workflows with Continuous Analysis

Beaulieu-Jones, B. K., & Greene, C. S. (2016) · Nature Biotechnology

Scientific Computing and Data ManagementResearch Data Management Practices

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A publishing infrastructure for AI-assisted academic authoring

Pividori, M., & Greene, C. S. (2023) · Journal of the American Medical Informatics Association

Academic Writing and PublishingPublishing and Scholarly Communication

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Incorporating biological structure into machine learning models in biomedicine

Crawford, J., & Greene, C. S. (2020) · Current Opinion in Biotechnology

Bioinformatics and Genomic NetworksMachine Learning in Bioinformatics

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Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

Weber, L. M., Hippen, A. A., Hickey, P. F., Berrett, K. C., Gertz, J., Doherty, J. A., Greene, C. S., & Hicks, S. C. (2021) · GigaScience

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

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Alzheimer’s disease genetics converges on microglial and neuronal dysregulation

Uffelmann, E., Wightman, D. P., Bahrami, S., Shadrin, A. A., Fominykh, V., Ojima, T., Jiang, C., Benner, C., Moreno, E., Campos, A. I., et al. (2026) · Nature

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

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