Casey S. Greene

faculty photo
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 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

Allaway Robert J, Fischer Dawn A, de Abreu Francine B, Gardner Timothy B, Gordon Stuart R, Barth Richard J, Colacchio Thomas A, Wood Matthew, Kacsoh Balint Z, Bouley Stephanie J, Cui Jingxuan, Hamilton Joanna, Choi Jungbin A, Lange Joshua T, Peterson Jason D, Padmanabhan Vijayalakshmi, Tomlinson Craig R, Tsongalis Gregory J, Suriawinata Arief A, Greene Casey S, Sanchez Yolanda, Smith Kerrington D: Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites. Oncotarget Feb 2016.

Thompson Jeffrey A, Tan Jie, Greene Casey S: Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ 4: e1621, 2016.

Song Ailin, Yan Jingwen, Kim Sungeun, Risacher Shannon Leigh, Wong Aaron K, Saykin Andrew J, Shen Li, Greene Casey S: Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData mining 9: 3, 2016.

Qian David C, Byun Jinyoung, Han Younghun, Greene Casey S, Field John K, Hung Rayjean J, Brhane Yonathan, Mclaughlin John R, Fehringer Gordon, Landi Maria Teresa, Rosenberger Albert, Bickeböller Heike, Malhotra Jyoti, Risch Angela, Heinrich Joachim, Hunter David J, Henderson Brian E, Haiman Christopher A, Schumacher Fredrick R, Eeles Rosalind A, Easton Douglas F, Seminara Daniela, Amos Christopher I: Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Human molecular genetics 24(25): 7406-20, Dec 2015.

Greene Casey S, Krishnan Arjun, Wong Aaron K, Ricciotti Emanuela, Zelaya Rene A, Himmelstein Daniel S, Zhang Ran, Hartmann Boris M, Zaslavsky Elena, Sealfon Stuart C, Chasman Daniel I, FitzGerald Garret A, Dolinski Kara, Grosser Tilo, Troyanskaya Olga G: Understanding multicellular function and disease with human tissue-specific networks. Nature genetics 47(6): 569-76, Jun 2015.

Mahoney J Matthew, Taroni Jaclyn, Martyanov Viktor, Wood Tammara A, Greene Casey S, Pioli Patricia A, Hinchcliff Monique E, Whitfield Michael L: Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. PLoS computational biology 11(1): e1004005, Jan 2015.

Q. Zhu, A. K. Wong, A. Krishman, M. R. Aure, A. Taydych, R. Zhang, D. C. Corney, C. S. Greene, L. A. Bongo, V. N. Kristensen, M. Charikar, K. Li, and O. G. Troyanskaya: Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat. Methods 2015 Notes: in press.

Gui Jiang, Greene Casey S, Sullivan Con, Taylor Walter, Moore Jason H, Kim Carol: Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. BioData mining 8: 17, 2015.

Tan Jie, Ung Matthew, Cheng Chao, Greene Casey S: Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symb Biocomput. Page: 132-43, 2015.

Cordell Heather J, Han Younghun, Mells George F, Li Yafang, Hirschfield Gideon M, Greene Casey S, Xie Gang, Juran Brian D, Zhu Dakai, Qian David C, Floyd James A B, Morley Katherine I, Prati Daniele, Lleo Ana, Cusi Daniele, Gershwin M Eric, Anderson Carl A, Lazaridis Konstantinos N, Invernizzi Pietro, Seldin Michael F, Sandford Richard N, Amos Christopher I, Siminovitch Katherine A: International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nature communications 6: 8019, 2015.

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Last updated: 03/07/2016
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