Casey S. Greene

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Associate Professor of Pharmacology
Department: Pharmacology

Contact information
10-131 Smilow Center for Translational Research
Philadelphia, PA 19104
Graduate Group Affiliations
B.S. (Chemistry)
Berry College, 2005.
Ph.D. (Computational Genetics)
Dartmouth College, 2009.
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Description of Itmat Expertise

Dr. Greene's lab develops computational algorithms to accurately integrate large-scale data measuring genome-wide characteristics into computational models of how biological systems function at the cellular and organismal levels.

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

Taroni Jaclyn N, Grayson Peter C, Hu Qiwen, Eddy Sean, Kretzler Matthias, Merkel Peter A, Greene Casey S: MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. Cell systems 8(5): 380-394.e4, May 2019.

Hu Qiwen, Greene Casey S: Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 24: 362-373, 2019.

Kacsoh Balint Z, Barton Stephen, Jiang Yuxiang, Zhou Naihui, Mooney Sean D, Friedberg Iddo, Radivojac Predrag, Greene Casey S, Bosco Giovanni: New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda, Md.) 9(1): 251-267, 01 2019.

Crowell Alexander M, Greene Casey S, Loros Jennifer J, Dunlap Jay C: Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinformatics (Oxford, England) Sep 2018 Notes:

Grayson Peter C, Eddy Sean, Taroni Jaclyn N, Lightfoot YaĆ­ma L, Mariani Laura, Parikh Hemang, Lindenmeyer Maja T, Ju Wenjun, Greene Casey S, Godfrey Brad, Cohen Clemens D, Krischer Jeffrey, Kretzler Matthias, Merkel Peter A: Metabolic pathways and immunometabolism in rare kidney diseases. Annals of the rheumatic diseases 77(8): 1226-1233, Aug 2018.

Chen Kathleen M, Tan Jie, Way Gregory P, Doing Georgia, Hogan Deborah A, Greene Casey S: PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData mining 11: 14, July 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.

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 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.

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Last updated: 06/12/2019
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