Recent Preprints

Stein-O'Brien GL, Arora R, Culhane AC, Favorov A, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the matrix: interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics databioRxiv. 10.1101/196915

Way GP, Greene CS. Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders. bioRxiv. 10.1101/174474 [GitHub]

Himmelstein DS, Romero AR, McLaughlin SR, Greshake B, Greene CS. Sci-Hub provides access to nearly all scholarly literature. PeerJ Preprints. [GitHub for Analyses, GitHub for Manuscript, Current build of manuscript]

Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analysesbioRxiv. 10.1101/166207 [GitHub source code]

Beaulieu-Jones BK, Wu ZS, Williams C, Greene CS. Privacy-preserving generative deep neural networks support clinical data sharing. bioRxiv. 10.1101/159756 [GitHub source code]

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferro E, Agapow P, Xie W, Rosen GL, Legenrich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Gitter A+, Greene CS+. Opportunities and Obstacles for Deep Learning in Biology and Medicine. bioRxiv. doi:10.1101/142760 [GitHub]

Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE: Visualizing globally co-occurring pathways in large transcriptomic compendia. bioRxiv. [GitHub to reproduce results, GitHub PathCORE Software, GitHub PathCORE demo server, GitHub crosstalk correction package]

Taroni JN, Greene CS. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. bioRxiv. doi:10.1101/118349. [GitHub]

Zelaya RA, Wong AK, Frase AT, Ritchie MD, Greene CS. Tribe: The collaborative platform for reproducible web-based analysis of gene setsbioRxiv. doi:10.1101/055913 [Bitbucket: Tribe Server; Tribe Client]

Recent Publications

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, Weljie AM, FitzGerald GA. A pilot characterization of the human chronobiomeScientific Reports.

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. [Preprint][GitHub R Package][GitHub Webserver][Running Webserver]

Kacsoh BZ, Greene CS, Bosco G. Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning. G3: Genes | Genomes | Genetics. [Preprint]

Way GP, Youngstrom DW, Hankenson KD, Greene CS*, Grant SFA*. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. European Journal of Human Genetics. [preprintGitHub - Zenodo, Docker - Zenodo]

Byrd JB, Greene CS. Data-Sharing ModelsNEJM. 376:2305-2306.

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. [preprint][Bitbucket]

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. In Press.

Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating ParasitesNature Genetics. 2017;49:483-484.

Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann R, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Medicine. 2017;9:27. [preprint]

Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysisNature Biotechnology. [preprint][Github]

Greene CS. Tell me your neighbors, and I will tell you who you areScience Translational Medicine. 8:370ec203. [Editor's Choice Summary of Khurana et al.]

Way GP, Allaway RA, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics. 2016;18:127. [GitHub, Docker, Preprint]

Greene CS. Cheap-Seq. Science Translational Medicine. 8:370ec203. [Editor's Choice Summary of Tatlow et al.]

Moore JH, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X. No-boundary Thinking in Bioinformatics. Pac Symp Biocomput. 2016;22:646-648.

Greene CS. How to know what we don't. Science Translational Medicine. 8:364ec179. [Editor's Choice Summary of Zhou et al.]

Beaulieu-Jones BK, Greene CS. Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification. Journal of Biomedical Informatics. 2016;64:168-178. [preprint][Github - results built via continuous analysis]

Greene CS. A stromal focus reveals tumor immune signatures. Science Translational Medicine. 2016;8:358ec155. [Editor's Choice Summary]

Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny G, Goode EL, Greene CS*, Doherty JA*. Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypesG3: Genes | Genomes | Genetics. 6(12) 4097-4103. [preprint][source & data][Docker image

Krishnan A, Taroni JN, Greene CS. Integrative networks illuminate biological factors underlying gene-disease associations. Curr Genet Med Rep. 2016. [preprint]

Greene CS. Gut Check. Science Translational Medicine. 8:352ec131. [Editor's Choice Summary]

Greene CS. The future is unsupervisedScience Translational Medicine. 8:346ec108. [Editor's Choice Summary]

Jiang Y, Oron TR, Clark WT, Bankapur A, ... [>100 authors]. An expanded evaluation of protein function prediction methods shows an improvement in accuracyGenome Biology. 2016. 17:184. [preprint]

Greene CS. Nothing but a hound dogScience Translational Medicine. 8:340ec83. [Editor's Choice Summary]

Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Human Molecular Genetics. doi:10.1093/hmg/ddw160. [preprint]

Greene CS. CoINcIDE: All together now. Science Translational Medicine. 8:334ec61. [Editor's Choice Summary]

Greene CS, Himmelstein DS. Genetic Association Guided Analysis of Gene Networks for the Study of Complex Traits. Circulation: Cardiovascular Genetics. 2016 9:179-184. [source & data][free full text]

Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AD, 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. 2016 9:3. doi:10.1186/s13040-016-0082-8. [source & data]

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 interactionsmSystems. 2016 1(1):e00025-15. doi: 10.1128/mSystems.00025-15. [preprint][source & data]

Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ. 2016 4:e1621. [preprint][R package][source & data]

Allaway RJ*, Fischer DA*, de Abreu FB, Gardner TB, Gordon SR, Barth RJ, Colacchio TA, Wood M, Kacsoh BZ, Bouley SJ, Cui J, Hamilton J, Choi JA, Lange JT, Peterson JD, Padmanabhan V, Tomlinson CR, Tsongalis GJ, Suriawinata A, Greene CS*, Sanchez Y*, Smith KD. 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 25. doi: 10.18632/oncotarget.7718. [Epub ahead of print]. [source & data]

Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. Computational approaches to study microbes and microbiomesPac Sym Biocomput. 2016 21:557-67. [pdf]

Rudd J, Zelaya RA, Demidenko E, Goode EL, Greene CS, Doherty JA. Leveraging global gene expression patterns to predict expression of unmeasured genesBMC Genomics. 2015 16:1065. doi:10.1186/s12864-015-2250-5. [source & data]

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, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. 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. Hum Mol Genet. 2015 Dec 20;24(25):7406-20. doi: 10.1093/hmg/ddv440.

Gonzalez GH, Tahsin T, Goodale BC, Greene AC, Greene CS. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform. 2015 Sep 29. pii: bbv087. [Epub ahead of print]

Cordell HJ, Han Y, Mells GF, Li Y, Hirschfield GM, Greene CS et al. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat Commun. 2015; PMID:26394269

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 Min. 2015; PMID:26097506

Greene CS, Krishnan A, Wong AK,  Riccioti 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. Nat Genetics. 2015; PMID:25915600 [processed networks][raw networks][webserver]

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. Nat Methods. 2015; PMID:25581801 [webserver]

Greene AC, Giffin KA, Greene CS, Moore JH. Adapting bioinformatics curricula for big data. Brief Bioinform. 2015; PMID:25829469

Tan J, Ung M, Cheng C, and Greene, CS. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput. 2015; 20:132-43. PMID:25592575 [data & results]

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 Comput Biol. 2015; 11(1):e1004005. PMID:25569146

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 Min. 2014; 7:17. PMID: 25165488

Penrod NM, Greene CS, Moore JH. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. Genome Med 2014; 6(4):33. PMID: 24944582

Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big Data Bioinformatics. J Cell Physiol 2014 May 6. PMID: 24799088

Tan J, Grant GD, Whitfield ML, Greene, CS. Time-Point specific weighting improves coexpression networks from time-course experiments. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO) 2013. 11-22.

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 Res 2013 Nov; 23(11):1862-73. PMID: 23950145 [Highlighted by Nature Reviews Genetics]

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 Comput Biol 2013; 9(3):e1002957. PMID: 23516347

Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol 2012; 8(12):e1002816. PMID: 23300408

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 Res 2012 Jul; 40(Web Server issue):W484-90. PMID: 22684505

Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci 2012 Jul; 1260:95-100. PMID: 22268703

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