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
Education:
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

Weissman Gary E, Hubbard Rebecca A, Ungar Lyle H, Harhay Michael O, Greene Casey S, Himes Blanca E, Halpern Scott D: Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay. Critical c=Care Medicine 46(7): 1125-1132, Apr 2018.

Sanchez-Vega Francisco, Mina Marco, Armenia Joshua, Chatila Walid K, Luna Augustin, La Konnor C, Dimitriadoy Sofia, Liu David L, Kantheti Havish S, Saghafinia Sadegh, Chakravarty Debyani, Daian Foysal, Gao Qingsong, Bailey Matthew H, Liang Wen-Wei, Foltz Steven M, Shmulevich Ilya, Ding Li, Heins Zachary, Ochoa Angelica, Gross Benjamin, Gao Jianjiong, Zhang Hongxin, Kundra Ritika, Kandoth Cyriac, Bahceci Istemi, Dervishi Leonard, Dogrusoz Ugur, Zhou Wanding, Shen Hui, Laird Peter W, Way Gregory P, Greene Casey S, Liang Han, Xiao Yonghong, Wang Chen, Iavarone Antonio, Berger Alice H, Bivona Trever G, Lazar Alexander J, Hammer Gary D, Giordano Thomas, Kwong Lawrence N, McArthur Grant, Huang Chenfei, Tward Aaron D, Frederick Mitchell J, McCormick Frank, Meyerson Matthew, Van Allen Eliezer M, Cherniack Andrew D, Ciriello Giovanni, Sander Chris, Schultz Nikolaus: Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173(2): 321-337.e10, Apr 2018.

Knijnenburg Theo A, Wang Linghua, Zimmermann Michael T, Chambwe Nyasha, Gao Galen F, Cherniack Andrew D, Fan Huihui, Shen Hui, Way Gregory P, Greene Casey S, Liu Yuexin, Akbani Rehan, Feng Bin, Donehower Lawrence A, Miller Chase, Shen Yang, Karimi Mostafa, Chen Haoran, Kim Pora, Jia Peilin, Shinbrot Eve, Zhang Shaojun, Liu Jianfang, Hu Hai, Bailey Matthew H, Yau Christina, Wolf Denise, Zhao Zhongming, Weinstein John N, Li Lei, Ding Li, Mills Gordon B, Laird Peter W, Wheeler David A, Shmulevich Ilya, Monnat Raymond J, Xiao Yonghong, Wang Chen: Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell reports 23(1): 239-254.e6, Apr 2018.

Way Gregory P, Sanchez-Vega Francisco, La Konnor, Armenia Joshua, Chatila Walid K, Luna Augustin, Sander Chris, Cherniack Andrew D, Mina Marco, Ciriello Giovanni, Schultz Nikolaus, Sanchez Yolanda, Greene Casey S: Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell reports 23(1): 172-180.e3, Apr 2018.

Himmelstein Daniel S, Romero Ariel Rodriguez, Levernier Jacob G, Munro Thomas Anthony, McLaughlin Stephen Reid, Greshake Tzovaras Bastian, Greene Casey S: Sci-Hub provides access to nearly all scholarly literature. eLife 7, Mar 2018.

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 200(8), 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.

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Last updated: 07/25/2018
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