Casey S. Greene - Publications

Pharmacology University of Pennsylvania Perelman School of Medicine 

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. Plos Computational Biology. 15: e1007128. PMID 31233491 DOI: 10.1371/journal.pcbi.1007128  0.92
2018 Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nature Methods. 15: 1009-1010. PMID 30504887 DOI: 10.1038/s41592-018-0230-9  1
2018 Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. Biodata Mining. 11: 14. PMID 29988723 DOI: 10.1186/s13040-018-0175-7  1
2018 Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, ... ... Greene CS, et al. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 173: 321-337.e10. PMID 29625050 DOI: 10.1016/j.cell.2018.03.035  1
2018 Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, ... ... Greene CS, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/rsif.2017.0387  1
2018 Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, et al. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Reports. 23: 239-254.e6. PMID 29617664 DOI: 10.1016/j.celrep.2018.03.076  1
2018 Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports. 23: 172-180.e3. PMID 29617658 DOI: 10.1016/j.celrep.2018.03.046  1
2018 Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Greshake Tzovaras B, Greene CS. Research: Sci-Hub provides access to nearly all scholarly literature. Elife. 7. PMID 29424689 DOI: 10.7554/eLife.32822  0.92
2018 Dahlstrom KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA. A Multimodal Strategy Used By A Large c-di-GMP Network. Journal of Bacteriology. PMID 29311282 DOI: 10.1128/JB.00703-17  0.68
2018 Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 157-167. PMID 29218878  1
2018 Way GP, Greene CS. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 80-91. PMID 29218871  1
2017 Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Current Epidemiology Reports. 4: 211-220. PMID 29226065 DOI: 10.1007/s40471-017-0115-y  1
2017 Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, et al. A Pilot Characterization of the Human Chronobiome. Scientific Reports. 7: 17141. PMID 29215023 DOI: 10.1038/s41598-017-17362-6  0.72
2017 Tan J, Huyck M, Hu D, Zelaya RA, Hogan DA, Greene CS. ADAGE signature analysis: differential expression analysis with data-defined gene sets. Bmc Bioinformatics. 18: 512. PMID 29166858 DOI: 10.1186/s12859-017-1905-4  0.68
2017 Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. European Journal of Human Genetics : Ejhg. PMID 28792001 DOI: 10.1038/ejhg.2017.108  1
2017 Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS. Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. Cell Systems. PMID 28711280 DOI: 10.1016/j.cels.2017.06.003  0.68
2017 Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L. Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics (Oxford, England). PMID 28575147 DOI: 10.1093/bioinformatics/btx344  0.72
2017 Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nature Biotechnology. PMID 28288103 DOI: 10.1038/nbt.3780  1
2017 Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. Bmc Genomics. 18: 127. PMID 28166733 DOI: 10.1186/s12864-017-3519-7  1
2016 Moore JH, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X. NO-BOUNDARY THINKING IN BIOINFORMATICS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 646-648. PMID 27897015  0.72
2016 Tan J, Hammond JH, Hogan DA, Greene CS. ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. Msystems. 1. PMID 27822512 DOI: 10.1128/mSystems.00025-15  0.68
2016 Beaulieu-Jones BK, Greene CS. Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification. Journal of Biomedical Informatics. PMID 27744022 DOI: 10.1016/j.jbi.2016.10.007  1
2016 Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda, Md.). PMID 27729437 DOI: 10.1534/g3.116.033514  1
2016 Greene CS, Himmelstein DS. Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits. Circulation. Cardiovascular Genetics. 9: 179-84. PMID 27094199 DOI: 10.1161/CIRCGENETICS.115.001181  0.92
2016 Himmelstein DS, Greene CS, Moore JH. Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. Biodata Mining. 9: 9. PMID 26848312 DOI: 10.1186/s13040-016-0085-5  0.92
2016 Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. Peerj. 4: e1621. PMID 26844019 DOI: 10.7717/peerj.1621  0.68
2016 Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AJ, Shen L, Greene CS. Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. Biodata Mining. 9: 3. PMID 26788126 DOI: 10.1186/s13040-016-0082-8  0.92
2016 Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 21: 557-67. PMID 26776218  0.68
2015 Rudd J, Zelaya RA, Demidenko E, Goode EL, Greene CS, Doherty JA. Leveraging global gene expression patterns to predict expression of unmeasured genes. Bmc Genomics. 16: 1065. PMID 26666289 DOI: 10.1186/s12864-015-2250-5  0.92
2015 Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, et al. 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. PMID 26483192 DOI: 10.1093/hmg/ddv440  0.92
2015 Gonzalez GH, Tahsin T, Goodale BC, Greene AC, Greene CS. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Briefings in Bioinformatics. PMID 26420781 DOI: 10.1093/bib/bbv087  0.92
2015 Gui J, Greene CS, Sullivan C, Taylor W, Moore JH, Kim C. 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. PMID 26097506 DOI: 10.1186/s13040-015-0050-8  0.72
2015 Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics. 47: 569-76. PMID 25915600 DOI: 10.1038/ng.3259  0.92
2015 Greene AC, Giffin KA, Greene CS, Moore JH. Adapting bioinformatics curricula for big data. Briefings in Bioinformatics. PMID 25829469 DOI: 10.1093/bib/bbv018  0.92
2015 Tan J, Ung M, Cheng C, Greene CS. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 132-43. PMID 25592575  0.68
2015 Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nature Methods. 12: 211-4, 3 p following. PMID 25581801 DOI: 10.1038/nmeth.3249  0.92
2015 Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff ME, Whitfield ML. Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. Plos Computational Biology. 11: e1004005. PMID 25569146 DOI: 10.1371/journal.pcbi.1004005  0.92
2014 Zieselman AL, Fisher JM, Hu T, Andrews PC, Greene CS, Shen L, Saykin AJ, Moore JH. Computational genetics analysis of grey matter density in Alzheimer's disease. Biodata Mining. 7: 17. PMID 25165488 DOI: 10.1186/1756-0381-7-17  0.92
2014 Penrod NM, Greene CS, Moore JH. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. Genome Medicine. 6: 33. PMID 24944582 DOI: 10.1186/gm550  0.72
2014 Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big data bioinformatics. Journal of Cellular Physiology. 229: 1896-900. PMID 24799088 DOI: 10.1002/jcp.24662  0.72
2013 Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee YS, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M. Defining cell-type specificity at the transcriptional level in human disease. Genome Research. 23: 1862-73. PMID 23950145 DOI: 10.1101/gr.155697.113  0.92
2013 Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. Plos Computational Biology. 9: e1002957. PMID 23516347 DOI: 10.1371/journal.pcbi.1002957  0.92
2012 Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. Plos Computational Biology. 8: e1002816. PMID 23300408 DOI: 10.1371/journal.pcbi.1002816  0.92
2012 Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. 40: W484-90. PMID 22684505 DOI: 10.1093/nar/gks458  0.92
2012 Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Annals of the New York Academy of Sciences. 1260: 95-100. PMID 22268703 DOI: 10.1111/j.1749-6632.2011.06383.x  0.92
2011 Himmelstein DS, Greene CS, Moore JH. Evolving hard problems: Generating human genetics datasets with a complex etiology. Biodata Mining. 4: 21. PMID 21736753 DOI: 10.1186/1756-0381-4-21  0.92
2011 Greene CS, Troyanskaya OG. PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Research. 39: W368-74. PMID 21653547 DOI: 10.1093/nar/gkr440  0.92
2010 Greene CS, Troyanskaya OG. Integrative systems biology for data-driven knowledge discovery. Seminars in Nephrology. 30: 443-54. PMID 21044756 DOI: 10.1016/j.semnephrol.2010.07.002  0.92
2010 Greene CS, Sinnott-Armstrong NA, Himmelstein DS, Park PJ, Moore JH, Harris BT. Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinformatics (Oxford, England). 26: 694-5. PMID 20081222 DOI: 10.1093/bioinformatics/btq009  0.92
2010 Greene CS, Himmelstein DS, Nelson HH, Kelsey KT, Williams SM, Andrew AS, Karagas MR, Moore JH. Enabling personal genomics with an explicit test of epistasis. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 327-36. PMID 19908385  0.92
2009 Greene CS, White BC, Moore JH. Sensible Initialization Using Expert Knowledge for Genome-Wide Analysis of Epistasis Using Genetic Programming. Genetic and Evolutionary Computation Conference : [Proceedings] / Sponsored by Acm Sigevo. Genetic and Evolutionary Computation Conference. 2009: 1289-1296. PMID 21197156 DOI: 10.1109/CEC.2009.4983093  0.92
2009 Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions. Biodata Mining. 2: 5. PMID 19772641 DOI: 10.1186/1756-0381-2-5  0.72
2009 Sinnott-Armstrong NA, Greene CS, Cancare F, Moore JH. Accelerating epistasis analysis in human genetics with consumer graphics hardware. Bmc Research Notes. 2: 149. PMID 19630950 DOI: 10.1186/1756-0500-2-149  0.72
2009 Greene CS, Penrod NM, Williams SM, Moore JH. Failure to replicate a genetic association may provide important clues about genetic architecture. Plos One. 4: e5639. PMID 19503614 DOI: 10.1371/journal.pone.0005639  0.72
2008 Beretta L, Cappiello F, Moore JH, Barili M, Greene CS, Scorza R. Ability of epistatic interactions of cytokine single-nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients. Arthritis and Rheumatism. 59: 974-83. PMID 18576303 DOI: 10.1002/art.23836  0.72
2006 Ganko EW, Greene CS, Lewis JA, Bhattacharjee V, McDonald JF. LTR retrotransposon-gene associations in Drosophila melanogaster. Journal of Molecular Evolution. 62: 111-20. PMID 16408244 DOI: 10.1007/s00239-004-0312-4  0.92
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