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

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 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.

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, Jan 2016.

Rudd James, Zelaya René A, Demidenko Eugene, Goode Ellen L, Greene Casey S, Doherty Jennifer A: Leveraging global gene expression patterns to predict expression of unmeasured genes. BMC genomics 16(1): 1065, Dec 2015.

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.

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: 09/28/2016
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