Casey S. Greene, Ph.D.

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Adjunct Associate Professor of Pharmacology
Department: Systems Pharmacology and Translational Therapeutics
Graduate Group Affiliations

Contact information
13001 E 17th Pl
Office Q20-E1339
Aurora, CO 80045
B.S. (Chemistry)
Berry College, 2005.
Ph.D. (Computational Genetics)
Dartmouth College, 2009.
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Description of Research Expertise

Our overarching goal is to transform how we understand complex biological systems by developing and applying computational algorithms that effectively model processes by integrating multiple types of big data from diverse experiments. This allows us to infer the key contextual information required to interpret such data, and facilitates both the computationally driven asking and answering of basic science and translational research questions.

Selected Publications

Heil BJ, Crawford J, Greene CS.: The effect of non-linear signal in classification problems using gene expression. PLoS Comput Biol 19: e1010984, Mar 2023.

Foltz SM, Greene CS, Taroni JN.: Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. Commun Biol 6: 222, Feb 2023.

Doing G, Lee AJ, Neff SL, Reiter T, Holt JD, Stanton BA, Greene CS, Hogan DA.: Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia. mSystems 8: e0034122, Feb 2023.

Lee AJ, Doing G, Neff SL, Reiter T, Hogan DA, Greene CS.: Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14. mSystems 8: e0034222, Feb 2023.

Hippen AA, Crawford J, Gardner JR, Greene CS.: wenda_gpu: fast domain adaptation for genomic data. Bioinformatics 38: 5129-5130, Nov 2022.

Nicholson DN, Himmelstein DS, Greene CS.: Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min 15: 26, Oct 2022.

Crawford J, Christensen BC, Chikina M, Greene CS.: Widespread redundancy in -omics profiles of cancer mutation states. Genome Biol 23: 137, Jun 2022.

Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S.: GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun 13: 3695, Jun 2022.

Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS.: Examining linguistic shifts between preprints and publications. PLoS Biol 20: e3001470, Feb 2022.

Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS.: SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genomics Proteomics Bioinformatics 2022.

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Last updated: 04/17/2023
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