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

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 Jul 2017 Notes: in press.

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 May 2017 Notes: in press.

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

Taroni Jaclyn N, Greene Casey S, Martyanov Viktor, Wood Tammara A, Christmann Romy B, Farber Harrison W, Lafyatis Robert A, Denton Christopher P, Hinchcliff Monique E, Pioli Patricia A, Mahoney J Matthew, Whitfield Michael L: A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Medicine 9(1): 27, Mar 2017.

Way Gregory P, Allaway Robert J, Bouley Stephanie J, Fadul Camilo E, Sanchez Yolanda, Greene Casey S: A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics 18(1): 127, Feb 2017.

Beaulieu-Jones Brett K, Greene Casey S: Semi-supervised learning of the electronic health record for phenotype stratification. Journal of biomedical informatics 64: 168-178, Dec 2016.

Way Gregory P, Rudd James, Wang Chen, Hamidi Habib, Fridley Brooke L, Konecny Gottfried E, Goode Ellen L, Greene Casey S, Doherty Jennifer A: Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3: Genes | Genomes | Genetics 6(12): 4097-4103, Dec 2016.

Jiang Yuxiang, Oron Tal Ronnen, Clark Wyatt T, Bankapur Asma R, D'Andrea Daniel, Lepore Rosalba, Funk Christopher S, Kahanda Indika, Verspoor Karin M, Ben-Hur Asa, Koo Da Chen Emily, Penfold-Brown Duncan, Shasha Dennis, Youngs Noah, Bonneau Richard, Lin Alexandra, Sahraeian Sayed M E, Martelli Pier Luigi, Profiti Giuseppe, Casadio Rita, Cao Renzhi, Zhong Zhaolong, Cheng Jianlin, Altenhoff Adrian, Skunca Nives, Dessimoz Christophe, Dogan Tunca, Hakala Kai, Kaewphan Suwisa, Mehryary Farrokh, Salakoski Tapio, Ginter Filip, Fang Hai, Smithers Ben, Oates Matt, Gough Julian, Törönen Petri, Koskinen Patrik, Holm Liisa, Chen Ching-Tai, Hsu Wen-Lian, Bryson Kevin, Cozzetto Domenico, Minneci Federico, Jones David T, Chapman Samuel, Bkc Dukka, Khan Ishita K, Kihara Daisuke, Ofer Dan, Rappoport Nadav, Stern Amos, Cibrian-Uhalte Elena, Denny Paul, Foulger Rebecca E, Hieta Reija, Legge Duncan, Lovering Ruth C, Magrane Michele, Melidoni Anna N, Mutowo-Meullenet Prudence, Pichler Klemens, Shypitsyna Aleksandra, Li Biao, Zakeri Pooya, ElShal Sarah, Tranchevent Léon-Charles, Das Sayoni, Dawson Natalie L, Lee David, Lees Jonathan G, Sillitoe Ian, Bhat Prajwal, Nepusz Tamás, Romero Alfonso E, Sasidharan Rajkumar, Yang Haixuan, Paccanaro Alberto, Gillis Jesse, Sedeño-Cortés Adriana E, Pavlidis Paul, Feng Shou, Cejuela Juan M, Goldberg Tatyana, Hamp Tobias, Richter Lothar, Salamov Asaf, Gabaldon Toni, Marcet-Houben Marina, Supek Fran, Gong Qingtian, Ning Wei, Zhou Yuanpeng, Tian Weidong, Falda Marco, Fontana Paolo, Lavezzo Enrico, Toppo Stefano, Ferrari Carlo, Giollo Manuel, Piovesan Damiano, Tosatto Silvio C E, Del Pozo Angela, Fernández José M, Maietta Paolo, Valencia Alfonso, Tress Michael L, Benso Alfredo, Di Carlo Stefano, Politano Gianfranco, Savino Alessandro, Rehman Hafeez Ur, Re Matteo, Mesiti Marco, Valentini Giorgio, Bargsten Joachim W, van Dijk Aalt D J, Gemovic Branislava, Glisic Sanja, Perovic Vladmir, Veljkovic Veljko, Veljkovic Nevena, Almeida-E-Silva Danillo C, Vencio Ricardo Z N, Sharan Malvika, Vogel Jörg, Kansakar Lakesh, Zhang Shanshan, Vucetic Slobodan, Wang Zheng, Sternberg Michael J E, Wass Mark N, Huntley Rachael P, Martin Maria J, O'Donovan Claire, Robinson Peter N, Moreau Yves, Tramontano Anna, Babbitt Patricia C, Brenner Steven E, Linial Michal, Orengo Christine A, Rost Burkhard, Greene Casey S, Mooney Sean D, Friedberg Iddo, Radivojac Predrag: An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology 17(1): 184, Sep 2016.

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 7(13): 17087-102, 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, Jan 2016.

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Last updated: 07/17/2017
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