Casey S. Greene, Ph.D.

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Assistant Professor of Pharmacology
Department: Pharmacology

Contact information
10-131 Smilow Center for Translational Research
Philadelphia, PA 19104
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

Dahlstrom Kurt M, Collins Alan J, Doing Georgia, Taroni Jaclyn N, Gauvin Timothy J, Greene Casey S, Hogan Deborah A, O'Toole George A: A Multimodal Strategy Used By A Large c-di-GMP Network. Journal of bacteriology Jan 2018.

Way Gregory P, Greene Casey S: Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pac Symp Biocomput 23: 80-91, Jan 2018.

Harrington Lia X, Way Gregory P, Doherty Jennifer A, Greene Casey S: Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. Pac Symp Biocomput 23: 157-167, Jan 2018.

Skarke Carsten, Lahens Nicholas F, Rhoades Seth D, Campbell Amy, Bittinger Kyle, Bailey Aubrey, Hoffmann Christian, Olson Randal S, Chen Lihong, Yang Guangrui, Price Thomas S, Moore Jason H, Bushman Frederic D, Greene Casey S, Grant Gregory R, Weljie Aalim M, FitzGerald Garret A: A Pilot Characterization of the Human Chronobiome. Scientific reports 7(1): 17141, Dec 2017.

Tan Jie, Huyck Matthew, Hu Dongbo, Zelaya René A, Hogan Deborah A, Greene Casey S: ADAGE signature analysis: differential expression analysis with data-defined gene sets. BMC bioinformatics 18(1): 512, Nov 2017.

Yao Xiaohui, Yan Jingwen, Liu Kefei, Kim Sungeun, Nho Kwangsik, Risacher Shannon L, Greene Casey S, Moore Jason H, Saykin Andrew J, Shen Li: Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics 33(20): 3250-3257, Oct 2017.

Kacsoh Balint Z, Greene Casey S, Bosco Giovanni: Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning. G3: Genes | Genomes | Genetics Page: g3.300172.2017, Sep 2017.

Way Gregory P, Youngstrom Daniel W, Hankenson Kurt D, Greene Casey S, Grant Struan Fa: Implicating candidate genes at GWAS signals by leveraging topologically associating domains. European Journal of Human Genetics : EJHG 25(11): 1286-1289, Aug 2017.

Tan Jie, Doing Georgia, Lewis Kimberley A, Price Courtney E, Chen Kathleen M, Cady Kyle C, Perchuk Barret, Laub Michael T, Hogan Deborah A, Greene Casey S: Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. Cell Systems 5(1): 63-71, Jul 2017.

Beaulieu-Jones Brett K, Greene Casey S: Reproducibility of computational workflows is automated using continuous analysis. Nature Biotechnology 35(4): 342-346, Apr 2017.

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Last updated: 01/22/2018
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