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Casey S. Greene - Publications

Affiliations: 
Pharmacology University of Pennsylvania Perelman School of Medicine 
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Year Citation  Score
2024 Crawford J, Chikina M, Greene CS. Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction. Bioinformatics Advances. 4: vbae004. PMID 38282973 DOI: 10.1093/bioadv/vbae004  0.616
2023 Davidson NR, Barnard ME, Hippen AA, Campbell A, Johnson C, Way GP, Dalley BK, Berchuck A, Salas LA, Peres LC, Marks JR, Schildkraut JM, Greene CS, Doherty JA. Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms. Biorxiv : the Preprint Server For Biology. PMID 37961178 DOI: 10.1101/2023.11.01.565179  0.667
2023 Pividori M, Lu S, Li B, Su C, Johnson ME, Wei WQ, Feng Q, Namjou B, Kiryluk K, Kullo IJ, Luo Y, Sullivan BD, Voight BF, Skarke C, Ritchie MD, ... ... Greene CS, et al. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nature Communications. 14: 5562. PMID 37689782 DOI: 10.1038/s41467-023-41057-4  0.491
2023 Zhang S, Heil BJ, Mao W, Chikina M, Greene CS, Heller EA. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. Biorxiv : the Preprint Server For Biology. PMID 37577575 DOI: 10.1101/2023.07.31.551386  0.658
2023 Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Hetnet connectivity search provides rapid insights into how biomedical entities are related. Gigascience. 12. PMID 37503959 DOI: 10.1093/gigascience/giad047  0.701
2023 Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, ... ... Greene CS, et al. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genomics. 3: 100340. PMID 37492101 DOI: 10.1016/j.xgen.2023.100340  0.772
2023 Banerjee J, Taroni JN, Allaway RJ, Prasad DV, Guinney J, Greene C. Machine learning in rare disease. Nature Methods. PMID 37248386 DOI: 10.1038/s41592-023-01886-z  0.737
2023 Dang MT, Gonzalez MV, Gaonkar KS, Rathi KS, Young P, Arif S, Zhai L, Alam Z, Devalaraja S, Jerrick To TK, Folkert IW, Raman P, Rokita JL, Martinez D, Taroni JN, ... ... Greene CS, et al. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality. Cell Reports. 42: 112600. PMID 37235472 DOI: 10.1016/j.celrep.2023.112600  0.677
2023 Foltz SM, Greene CS, Taroni JN. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. Communications Biology. 6: 222. PMID 36841852 DOI: 10.1038/s42003-023-04588-6  0.724
2023 Zietz M, Himmelstein DS, Kloster K, Williams C, Nagle MW, Greene CS. The probability of edge existence due to node degree: a baseline for network-based predictions. Biorxiv : the Preprint Server For Biology. PMID 36711569 DOI: 10.1101/2023.01.05.522939  0.694
2023 Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Hetnet connectivity search provides rapid insights into how two biomedical entities are related. Biorxiv : the Preprint Server For Biology. PMID 36711546 DOI: 10.1101/2023.01.05.522941  0.697
2022 Nicholson DN, Himmelstein DS, Greene CS. Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. Biodata Mining. 15: 26. PMID 36258252 DOI: 10.1186/s13040-022-00311-z  0.696
2022 Crawford J, Christensen BC, Chikina M, Greene CS. Widespread redundancy in -omics profiles of cancer mutation states. Genome Biology. 23: 137. PMID 35761387 DOI: 10.1186/s13059-022-02705-y  0.591
2022 Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nature Communications. 13: 3695. PMID 35760813 DOI: 10.1038/s41467-022-31411-3  0.746
2022 Rando HM, Boca SM, McGowan LD, Himmelstein DS, Robson MP, Rubinetti V, Velazquez R, Greene CS, Gitter A. An Open-Publishing Response to the COVID-19 Infodemic. Ceur Workshop Proceedings. 2976: 29-38. PMID 35558551  0.698
2022 Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, Greene C. Ten simple rules for large-scale data processing. Plos Computational Biology. 18: e1009757. PMID 35143491 DOI: 10.1371/journal.pcbi.1009757  0.691
2022 Bobak CA, Muse M, Giffin KA, Williamson DA, Greene CS, Moore JH, Wall DP. Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 156-162. PMID 34890145  0.511
2021 Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley S, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, et al. A field guide to cultivating computational biology. Plos Biology. 19: e3001419. PMID 34618807 DOI: 10.1371/journal.pbio.3001419  0.731
2021 Le TT, Himmelstein DS, Hippen AA, Gazzara MR, Greene CS. Analysis of scientific society honors reveals disparities. Cell Systems. 12: 900-906.e5. PMID 34555325 DOI: 10.1016/j.cels.2021.07.007  0.68
2021 Rando HM, Boca SM, McGowan LD, Himmelstein DS, Robson MP, Rubinetti V, Velazquez R, Consortium CR, Greene CS, Gitter A. An Open-Publishing Response to the COVID-19 Infodemic. Arxiv. PMID 34545336  0.698
2021 Dang MT, Gonzalez MV, Gaonkar KS, Rathi KS, Young P, Arif S, Zhai L, Alam Z, Devalaraja S, To TKJ, Folkert IW, Raman P, Rokita JL, Martinez D, Taroni JN, ... ... Greene CS, et al. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality. Cell Reports. 34: 108917. PMID 33789113 DOI: 10.1016/j.celrep.2021.108917  0.707
2021 Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, ... ... Greene CS, et al. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biology. 22: 1. PMID 33397451 DOI: 10.1186/s13059-020-02207-9  0.668
2020 Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 9. PMID 32940333 DOI: 10.1093/Gigascience/Giaa103  0.529
2020 Talhouk A, George J, Wang C, Budden T, Tan TZ, Chiu DS, Kommoss S, Leong HS, Chen S, Intermaggio MP, Gilks B, Nazeran TM, Volchek M, Elatre W, Bentley RC, ... ... Greene CS, et al. Development and validation of the gene-expression Predictor of high-grade-serous Ovarian carcinoma molecular subTYPE (PrOTYPE). Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32554541 DOI: 10.1158/1078-0432.Ccr-20-0103  0.33
2020 Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 9. PMID 32479592 DOI: 10.1093/Gigascience/Giaa056  0.568
2020 Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biology. 21: 109. PMID 32393369 DOI: 10.1186/S13059-020-02021-3  0.786
2020 Hu Q, Greene CS, Heller EA. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Research. PMID 32319526 DOI: 10.1093/Nar/Gkaa248  0.309
2020 Banerjee J, Allaway RJ, Taroni JN, Baker A, Zhang X, Moon CI, Pratilas CA, Blakeley JO, Guinney J, Hirbe A, Greene CS, Gosline SJ. Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1. Genes. 11. PMID 32098059 DOI: 10.3390/Genes11020226  0.73
2020 Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Current Opinion in Biotechnology. 63: 126-134. PMID 31962244 DOI: 10.1016/J.Copbio.2019.12.021  0.351
2020 Liu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y. Back Cover Image Genetic Epidemiology. 44. DOI: 10.1002/Gepi.22220  0.701
2019 Martinez-Lage M, Lynch TM, Bi Y, Cocito C, Way GP, Pal S, Haller J, Yan RE, Ziober A, Nguyen A, Kandpal M, O'Rourke DM, Greenfield JP, Greene CS, Davuluri RV, et al. Immune landscapes associated with different glioblastoma molecular subtypes. Acta Neuropathologica Communications. 7: 203. PMID 31815646 DOI: 10.1186/S40478-019-0803-6  0.673
2019 Lin YT, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP. Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma. Blood Advances. 3: 3214-3227. PMID 31698452 DOI: 10.1182/Bloodadvances.2019000303  0.7
2019 Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, ... ... Greene CS, et al. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Reports. 29: 1675-1689.e9. PMID 31693904 DOI: 10.1016/J.Celrep.2019.09.071  0.705
2019 Liu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y. Embracing study heterogeneity for finding genetic interactions in large-scale research consortia. Genetic Epidemiology. PMID 31583758 DOI: 10.1002/Gepi.22262  0.768
2019 Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, et al. Voices in methods development. Nature Methods. 16: 945-951. PMID 31562479 DOI: 10.1038/S41592-019-0585-6  0.529
2019 Beaulieu-Jones BK, Wu ZS, Williams C, Lee R, Bhavnani SP, Byrd JB, Greene CS. Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing. Circulation. Cardiovascular Quality and Outcomes. 12: e005122. PMID 31284738 DOI: 10.1161/Circoutcomes.118.005122  0.777
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  0.706
2019 Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, Greene CS. MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. Cell Systems. 8: 380-394.e4. PMID 31121115 DOI: 10.1016/J.Cels.2019.04.003  0.753
2019 Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, et al. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. PMID 30930166 DOI: 10.1016/J.Devcel.2019.03.001  0.325
2019 Gonzalez-Hernandez G, Lu Z, Leaman R, Weissenbacher D, Boland MR, Chen Y, Du J, Fluck J, Greene CS, Holmes J, Kashyap A, Nielsen RL, Ouyang Z, Schaaf S, Taroni JN, et al. PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 449-454. PMID 30864346  0.726
2019 Greene C. Data re-use enables ML-based analysis of rare diseases F1000research. 8. DOI: 10.7490/F1000Research.1116793.1  0.307
2019 Way GP, Greene CS. Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning Annual Review of Biomedical Data Science. 2: 1-17. DOI: 10.1146/ANNUREV-BIODATASCI-072018-021348  0.691
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  0.697
2018 Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G. New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda, Md.). PMID 30463884 DOI: 10.1534/G3.118.200867  0.308
2018 Park Y, Greene CS. A Parasite's Perspective on Data Sharing. Gigascience. PMID 30395209 DOI: 10.1093/Gigascience/Giy129  0.316
2018 Crowell AM, Greene CS, Loros JJ, Dunlap JC. Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinformatics (Oxford, England). PMID 30247517 DOI: 10.1093/Bioinformatics/Bty828  0.318
2018 Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends in Genetics : Tig. PMID 30143323 DOI: 10.1016/J.Tig.2018.07.003  0.339
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  0.75
2018 Grayson PC, Eddy S, Taroni JN, Lightfoot YL, Mariani L, Parikh H, Lindenmeyer MT, Ju W, Greene CS, Godfrey B, Cohen CD, Krischer J, Kretzler M, Merkel PA. Metabolic pathways and immunometabolism in rare kidney diseases. Annals of the Rheumatic Diseases. PMID 29724730 DOI: 10.1136/Annrheumdis-2017-212935  0.714
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  0.698
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  0.766
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  0.701
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  0.706
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  0.697
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  0.727
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  0.697
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  0.712
2018 Lin YT, Way GP, Mariano MC, Marcoulis M, Ferguson I, Greene CS, Wiita AP. Integrating Phosphoproteomics and Transcriptional Classifiers Reveals "Hidden Signaling" in Multiple Myeloma Including Differential KRAS and NRAS Mutant Effects Blood. 132: 469-469. DOI: 10.1182/Blood-2018-99-113683  0.34
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  0.687
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  0.573
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  0.562
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  0.728
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  0.54
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  0.598
2017 Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nature Genetics. 49: 483-484. PMID 28358134 DOI: 10.1038/ng.3830  0.313
2017 Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, 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. 9: 27. PMID 28330499 DOI: 10.1186/S13073-017-0417-1  0.722
2017 Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nature Biotechnology. PMID 28288103 DOI: 10.1038/Nbt.3780  0.779
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  0.69
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  0.459
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  0.53
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  0.795
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  0.696
2016 Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Human Molecular Genetics. PMID 27340225 DOI: 10.1093/Hmg/Ddw160  0.344
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  0.743
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  0.756
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  0.541
2016 Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications Peerj. 2016. DOI: 10.7717/peerj.1621  0.437
2016 Beaulieu-Jones B, Greene C. Reproducible Computational Workflows with Continuous Analysis F1000research. 5. DOI: 10.7490/F1000Research.1112695.1  0.761
2016 Rudd J, Shea EK, Way GP, Greene CS, Doherty JA. Abstract 815: Patterns of metagene activation in ovarian cancer subtypes Cancer Research. 76: 815-815. DOI: 10.1158/1538-7445.Am2016-815  0.326
2016 Greene CS. How to know what we dont Science Translational Medicine. 8: 364ec179-364ec179. DOI: 10.1126/Scitranslmed.Aal0067  0.383
2016 Greene CS. The future is unsupervised Science Translational Medicine. 8: 346ec108-346ec108. DOI: 10.1126/Scitranslmed.Aag3101  0.339
2016 Greene CS. CoINcIDE: All together now Science Translational Medicine. 8: 334ec61-334ec61. DOI: 10.1126/Scitranslmed.Aaf6940  0.373
2016 Krishnan A, Taroni JN, Greene CS. Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations Current Genetic Medicine Reports. 4: 155-162. DOI: 10.1007/S40142-016-0102-5  0.701
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  0.335
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  0.319
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  0.356
2015 Cordell HJ, Han Y, Mells GF, Li Y, Hirschfield GM, Greene CS, Xie G, Juran BD, Zhu D, Qian DC, Floyd JA, Morley KI, Prati D, Lleo A, Cusi D, et al. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nature Communications. 6: 8019. PMID 26394269 DOI: 10.1038/Ncomms9019  0.306
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  0.604
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  0.789
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  0.591
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  0.489
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  0.755
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  0.756
2015 Rudd J, Zelaya RA, Demidenko E, Greene CS, Doherty JA. Abstract 2171: Leveraging global gene expression patterns to identify gene sets that predict expression of large numbers of unmeasured genes Cancer Research. 75: 2171-2171. DOI: 10.1158/1538-7445.Am2015-2171  0.309
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  0.614
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  0.765
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  0.675
2014 Cheng C, Moore J, Greene C. Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 412-6. PMID 24297566  0.467
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  0.6
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  0.686
2013 Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer (FKT) improves prediction accuracy for a wide range of state-of-the-art classification algorithms. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1002957.G004  0.636
2013 Bogenberger JM, Rudd J, Chow D, Kassner M, Fauble V, Mesa RA, Yin H, Greene C, Tibes R. Pharmacological Validation Of Potentiating Targets From SAHA RNA-Interference Modifier Screens In Acute Myeloid Leukemia Blood. 122: 3832-3832. DOI: 10.1182/Blood.V122.21.3832.3832  0.321
2013 Bogenberger JM, Rudd JE, Chow D, Kassner M, Yin H, Greene CS, Tibes R. Abstract A28: Identification of HDAC inhibitor potentiating targets in acute myeloid leukemia cells by large-scale RNA-interference Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-A28  0.327
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  0.612
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  0.678
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  0.601
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  0.771
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  0.625
2011 Himmelstein DS, Greene CS, Moore JH. Evolving hard problems: Generating human genetics datasets with a complex etiology Biodata Mining. 4. DOI: 10.1186/1756-0381-4-21  0.72
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  0.574
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  0.784
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  0.771
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  0.567
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  0.782
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  0.612
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  0.764
2009 Tyler AL, White BC, Greene CS, Andrews PC, Cowper-Sal lari R, Moore JH. Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture 2009 Ieee Congress On Evolutionary Computation, Cec 2009. 2907-2912. DOI: 10.1109/CEC.2009.4983308  0.644
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  0.598
2008 Greene CS, Moore JH. Solving complex problems in human genetics using GP Acm Sigevolution. 3: 2-8. DOI: 10.1145/1527063.1527064  0.627
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  0.307
Low-probability matches (unlikely to be authored by this person)
2017 Kacsoh BZ, Greene CS, Bosco G. Machine Learning Analysis Identifies DrosophilaGrunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning. G3 (Bethesda, Md.). PMID 28889104 DOI: 10.1534/G3.117.300172  0.299
2020 Byrd JB, Greene AC, Prasad DV, Jiang X, Greene CS. Responsible, practical genomic data sharing that accelerates research. Nature Reviews. Genetics. PMID 32694666 DOI: 10.1038/S41576-020-0257-5  0.294
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  0.293
2017 Greene CS. Tell me your neighbors, and I will tell you what you are. Science Translational Medicine. 9. PMID 28179503 DOI: 10.1126/Scitranslmed.Aam6058  0.289
2016 Greene CS. Nothing but a hound dog Science Translational Medicine. 8: 340ec83-340ec83. DOI: 10.1126/Scitranslmed.Aaf9196  0.288
2020 Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Computational and Structural Biotechnology Journal. 18: 1414-1428. PMID 32637040 DOI: 10.1016/J.Csbj.2020.05.017  0.287
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Greene CS, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.285
2016 Doherty JA, Greene CS, Rudd JE, Tafe LJ, Alberg AJ, Bandera EV, Barnholtz-Sloan J, Bondy M, Cote ML, Funkhouser E, Moorman PG, Peters ES, Schwartz AG, Terry P, Bentley R, et al. Abstract 3407: Gene expression subtypes of high grade serous ovarian cancer in African American women Cancer Research. 76: 3407-3407. DOI: 10.1158/1538-7445.Am2016-3407  0.282
2016 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, ... ... Greene CS, et al. 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. PMID 26934555 DOI: 10.18632/Oncotarget.7718  0.272
2020 Millstein J, Budden T, Goode EL, Anglesio MS, Talhouk A, Intermaggio MP, Leong HS, Chen S, Elatre W, Gilks B, Nazeran T, Volchek M, Bentley RC, Wang C, Chiu DS, ... ... Greene CS, et al. Prognostic gene expression signature for high-grade serous ovarian cancer. Annals of Oncology : Official Journal of the European Society For Medical Oncology. PMID 32473302 DOI: 10.1016/J.Annonc.2020.05.019  0.272
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Greene CS, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.269
2019 Greene CS. Show me the models. Nature Biotechnology. PMID 31138912 DOI: 10.1038/S41587-019-0143-X  0.269
2022 Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genomics, Proteomics & Bioinformatics. PMID 36216026 DOI: 10.1016/j.gpb.2022.09.011  0.266
2016 Greene CS. A stromal focus reveals tumor immune signatures Science Translational Medicine. 8: 358ec155-358ec155. DOI: 10.1126/Scitranslmed.Aai8224  0.262
2019 Hu Q, Greene CS. Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 362-373. PMID 30963075  0.253
2019 Hu Q, Greene CS. Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 362-373. PMID 30864337  0.253
2020 Clay ME, Hammond JH, Zhong F, Chen X, Kowalski CH, Lee AJ, Porter MS, Hampton TH, Greene CS, Pletneva EV, Hogan DA. mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. Proceedings of the National Academy of Sciences of the United States of America. PMID 31980538 DOI: 10.1073/Pnas.1917576117  0.251
2020 Allen WE, Altae-Tran H, Briggs J, Jin X, McGee G, Shi A, Raghavan R, Kamariza M, Nova N, Pereta A, Danford C, Kamel A, Gothe P, Milam E, Aurambault J, ... ... Greene CS, et al. Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing. Nature Human Behaviour. PMID 32848231 DOI: 10.1038/S41562-020-00944-2  0.247
2020 Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, ... ... Greene CS, et al. Building an international consortium for tracking coronavirus health status. Nature Medicine. PMID 32488218 DOI: 10.1038/S41591-020-0929-X  0.238
2008 Greene CS, White BC, Moore JH. Ant colony optimization for genome-wide genetic analysis Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5217: 37-47. DOI: 10.1007/978-3-540-87527-7_4  0.235
2013 Gonzalez G, Cohen KB, Greene CS, Hahn U, Kann MG, Leaman R, Shah N, Ye J. Text and data mining for biomedical discovery. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 368-72. PMID 23424141 DOI: 10.1142/9789814583220_0030  0.235
2018 Weissman GE, Hubbard RA, Ungar LH, Harhay MO, Greene CS, Himes BE, Halpern SD. Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay. Critical Care Medicine. PMID 29629986 DOI: 10.1097/Ccm.0000000000003148  0.233
2015 Way GP, Rudd J, Greene CS, Doherty JA. Abstract 1928: High-grade serous ovarian cancer subtypes are similar across diverse populations Cancer Research. 75: 1928-1928. DOI: 10.1158/1538-7445.Am2015-1928  0.232
2018 Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Tzovaras BG, Greene CS. Author response: Sci-Hub provides access to nearly all scholarly literature Elife. DOI: 10.7554/Elife.32822.022  0.23
2022 Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Computational and Structural Biotechnology Journal. 20: 4315-4324. PMID 36016717 DOI: 10.1016/j.csbj.2022.08.012  0.222
2020 Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, ... ... Greene CS, et al. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nature Medicine. PMID 32591764 DOI: 10.1038/S41591-020-0983-4  0.217
2020 Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends in Cancer. PMID 33229213 DOI: 10.1016/j.trecan.2020.10.011  0.216
2024 Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, ... ... Greene CS, et al. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. American Journal of Human Genetics. 111: 11-23. PMID 38181729 DOI: 10.1016/j.ajhg.2023.12.001  0.206
2022 Doing G, Lee AJ, Neff SL, Reiter T, Holt JD, Stanton BA, Greene CS, Hogan DA. Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia. Msystems. e0034122. PMID 36541761 DOI: 10.1128/msystems.00341-22  0.204
2023 Avila R, Rubinetti V, Zhou X, Hu D, Qian Z, Cano MA, Rodolpho E, Tsueng G, Greene C, Wu C. MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. Nucleic Acids Research. PMID 37070209 DOI: 10.1093/nar/gkad289  0.203
2013 Tan J, Grant GD, Whitfield ML, Greene CS. Time-point specific weighting improves coexpression networks from time-course experiments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7833: 11-22. DOI: 10.1007/978-3-642-37189-9_2  0.199
2021 Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Plos Computational Biology. 17: e1009290. PMID 34428202 DOI: 10.1371/journal.pcbi.1009290  0.186
2021 Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Ben Guebila M, Jadavji NM, ... ... Greene CS, et al. Identification and Development of Therapeutics for COVID-19. Msystems. e0023321. PMID 34726496 DOI: 10.1128/mSystems.00233-21  0.18
2019 Greene CS. Decision letter: Tracking the popularity and outcomes of all bioRxiv preprints Elife. DOI: 10.7554/Elife.45133.053  0.18
2023 Abdill RJ, Graham SP, Rubinetti V, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. Biorxiv : the Preprint Server For Biology. PMID 37873416 DOI: 10.1101/2023.10.11.560955  0.18
2021 Weber LM, Hippen AA, Hickey PF, Berrett KC, Gertz J, Doherty JA, Greene CS, Hicks SC. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. Gigascience. 10. PMID 34553212 DOI: 10.1093/gigascience/giab062  0.18
2020 Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 9. PMID 33140829 DOI: 10.1093/gigascience/giaa117  0.177
2022 Cooley M, Greene CS, Issac D, Pividori M, Sullivan BD. Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. Proceedings of the 2021 Siam Conference On Applied and Computational Discrete Algorithms. Siam Conference On Applied and Computational Discrete Algorithms (2021 : Online). 2021: 111-122. PMID 35391741 DOI: 10.1137/1.9781611976830.11  0.176
2023 Heil BJ, Crawford J, Greene CS. The effect of non-linear signal in classification problems using gene expression. Plos Computational Biology. 19: e1010984. PMID 36972227 DOI: 10.1371/journal.pcbi.1010984  0.174
2023 Davidson NR, Greene CS. BuDDI: to predict cell-type-specific perturbations from bulk. Biorxiv : the Preprint Server For Biology. PMID 37503097 DOI: 10.1101/2023.07.20.549951  0.17
2024 Zietz M, Himmelstein DS, Kloster K, Williams C, Nagle MW, Greene CS. The probability of edge existence due to node degree: a baseline for network-based predictions. Gigascience. 13. PMID 38323677 DOI: 10.1093/gigascience/giae001  0.169
2023 Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Analysis of transcription in an cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus. Biorxiv : the Preprint Server For Biology. PMID 37662412 DOI: 10.1101/2023.08.21.554169  0.162
2022 Hippen AA, Crawford J, Gardner JR, Greene CS. wenda_gpu: fast domain adaptation for genomic data. Bioinformatics (Oxford, England). PMID 36193991 DOI: 10.1093/bioinformatics/btac663  0.162
2024 Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. transcriptome analysis of metal restriction in cystic fibrosis sputum. Microbiology Spectrum. e0315723. PMID 38385740 DOI: 10.1128/spectrum.03157-23  0.158
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  0.155
2020 Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. PMID 33096022 DOI: 10.1016/j.ccell.2020.10.014  0.15
2023 Hippen AA, Omran DK, Weber LM, Jung E, Drapkin R, Doherty JA, Hicks SC, Greene CS. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors. Genome Biology. 24: 239. PMID 37864274 DOI: 10.1186/s13059-023-03077-7  0.145
2022 Lee AJ, Doing G, Neff SL, Reiter T, Hogan DA, Greene CS. Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14. Msystems. e0034222. PMID 36541762 DOI: 10.1128/msystems.00342-22  0.143
2022 Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. Plos Biology. 20: e3001470. PMID 35104289 DOI: 10.1371/journal.pbio.3001470  0.142
2009 Greene CS, Hill DP, Moore JH. Environmental noise improves epistasis models of genetic data discovered using a computational evolution system Proceedings of the 11th Annual Genetic and Evolutionary Computation Conference, Gecco-2009. 1785-1786. DOI: 10.1145/1569901.1570160  0.138
2023 Nicholson DN, Alquaddoomi F, Rubinetti V, Greene CS. Changing word meanings in biomedical literature reveal pandemics and new technologies. Biodata Mining. 16: 16. PMID 37147665 DOI: 10.1186/s13040-023-00332-2  0.135
2021 Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, ... ... Greene CS, et al. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. Msystems. 6: e0009521. PMID 34698547 DOI: 10.1128/mSystems.00095-21  0.132
2021 Rando HM, MacLean AL, Lee AJ, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, ... ... Greene CS, et al. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure. Arxiv. PMID 33594340  0.13
2011 Gilmore JM, Greene CS, Andrews PC, Kiralis J, Moore JH. An analysis of new expert knowledge scaling methods for biologically inspired computing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5778: 286-293. DOI: 10.1007/978-3-642-21314-4_36  0.129
2011 Greene CS, Hill DP, Moore JH. An open-ended computational evolution strategy for evolving parsimonious solutions to human genetics problems Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5777: 313-320. DOI: 10.1007/978-3-642-21283-3_39  0.128
2021 Mueller AC, Piper M, Goodspeed A, Bhuvane S, Williams JS, Bhatia S, Phan AV, Van Court B, Zolman KL, Peña B, Oweida AJ, Zakem S, Meguid C, Knitz MW, Darragh L, ... ... Greene CS, et al. Induction of ADAM10 by RT drives fibrosis, resistance, and EMT in pancreatic cancer. Cancer Research. PMID 33526513 DOI: 10.1158/0008-5472.CAN-20-3892  0.128
2023 Pividori M, Greene CS. A publishing infrastructure for AI-assisted academic authoring. Biorxiv : the Preprint Server For Biology. PMID 36747665 DOI: 10.1101/2023.01.21.525030  0.127
2021 Deer RR, Rock MA, Vasilevsky N, Carmody L, Rando H, Anzalone AJ, Basson MD, Bennett TD, Bergquist T, Boudreau EA, Bramante CT, Byrd JB, Callahan TJ, Chan LE, Chu H, ... ... Greene CS, et al. Characterizing Long COVID: Deep Phenotype of a Complex Condition. Ebiomedicine. 74: 103722. PMID 34839263 DOI: 10.1016/j.ebiom.2021.103722  0.124
2021 Kerlavage AR, Kirchhoff AC, Guidry Auvil JM, Sharpless NE, Davis KL, Reilly K, Reaman G, Penberthy L, Deapen D, Hwang A, Durbin EB, Gallotto SL, Aplenc R, Volchenboum SL, Heath AP, ... ... Greene C, et al. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. Jco Clinical Cancer Informatics. 5: 881-896. PMID 34428097 DOI: 10.1200/CCI.21.00040  0.122
2024 Rando HM, Graim K, Hampikian G, Greene CS. Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs. Journal of the American Veterinary Medical Association. 1-8. PMID 38417257 DOI: 10.2460/javma.23.07.0372  0.12
2022 Lee BD, Gitter A, Greene CS, Raschka S, Maguire F, Titus AJ, Kessler MD, Lee AJ, Chevrette MG, Stewart PA, Britto-Borges T, Cofer EM, Yu KH, Carmona JJ, Fertig EJ, et al. Ten quick tips for deep learning in biology. Plos Computational Biology. 18: e1009803. PMID 35324884 DOI: 10.1371/journal.pcbi.1009803  0.119
2017 Byrd BJ, Greene CS. Data-Sharing Models The New England Journal of Medicine. 376: 2305. PMID 28594152  0.115
2023 Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. Biorxiv : the Preprint Server For Biology. PMID 36711900 DOI: 10.1101/2023.01.05.522943  0.113
2016 Greene CS. Cheap-seq. Science Translational Medicine. 8: 370ec203. PMID 28003542 DOI: 10.1126/scitranslmed.aal3701  0.111
2021 Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Qi Y, Sun Y, Field JM, Guebila MB, Jadavji NM, Lordan R, Skelly AN, ... ... Greene CS, et al. Identification and Development of Therapeutics for COVID-19. Arxiv. PMID 33688554  0.107
2021 Heil BJ, Hoffman MM, Markowetz F, Lee SI, Greene CS, Hicks SC. Reproducibility standards for machine learning in the life sciences. Nature Methods. PMID 34462593 DOI: 10.1038/s41592-021-01256-7  0.104
2022 Rando HM, Brueffer C, Lordan R, Dattoli AA, Manheim D, Meyer JG, Mundo AI, Perrin D, Mai D, Wellhausen N, Consortium CR, Gitter A, Greene CS. Molecular and Serologic Diagnostic Technologies for SARS-CoV-2. Arxiv. PMID 35547240  0.104
2020 Allen WE, Altae-Tran H, Briggs J, Jin X, McGee G, Raghavan R, Shi A, Kamariza M, Nova N, Pereta A, Danford C, Kamel A, Gothe P, Milam E, Aurambault J, ... ... Greene C, et al. Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States. Medrxiv : the Preprint Server For Health Sciences. PMID 32577674 DOI: 10.1101/2020.06.09.20126813  0.099
2021 Cao KL, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, ... ... Greene CS, et al. Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology. 22: 246. PMID 34433496 DOI: 10.1186/s13059-021-02468-y  0.097
2009 Greene CS, Gilmore JM, Kiralis J, Andrews PC, Moore JH. Optimal use of expert knowledge in ant colony optimization for the analysis of epistasis in human disease Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5483: 92-103. DOI: 10.1007/978-3-642-01184-9_9  0.096
2021 Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Singh A, ... ... Greene CS, et al. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology. 22: 220. PMID 34353350 DOI: 10.1186/s13059-021-02433-9  0.094
2020 Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, et al. Transparency and reproducibility in artificial intelligence. Nature. 586: E14-E16. PMID 33057217 DOI: 10.1038/s41586-020-2766-y  0.092
2003 Granitz N, Greene CS. Applying E-Marketing Strategies to Online Distance Learning Journal of Marketing Education. 25: 16-30. DOI: 10.1177/0273475302250569  0.082
2022 Darragh LB, Knitz MM, Hu J, Clambey ET, Backus J, Dumit A, Samedi V, Bubak A, Greene C, Waxweiler T, Mehrotra S, Bhatia S, Gadwa J, Bickett T, Piper M, et al. A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nature Cancer. 3: 1300-1317. PMID 36434392 DOI: 10.1038/s43018-022-00450-6  0.08
2022 Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, ... ... Greene CS, et al. Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure". Msystems. 7: e0144721. PMID 35076276 DOI: 10.1128/msystems.01447-21  0.078
2022 Hippen AA, Davidson NR, Greene CS. Computational audits combat disparities in recognition. Nature Human Behaviour. PMID 35039653 DOI: 10.1038/s41562-021-01279-2  0.078
2021 Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment. Msystems. 6. PMID 33947804 DOI: 10.1128/mSystems.00122-21  0.074
2018 Gonzalez-Hernandez G, Sarker A, O'Connor K, Greene C, Liu H. Advances in Text Mining and Visualization for Precision Medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 559-565. PMID 29218914  0.064
2023 Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP, Gitter A, Greene CS. The Coming of Age of Nucleic Acid Vaccines during COVID-19. Msystems. e0092822. PMID 36861992 DOI: 10.1128/msystems.00928-22  0.064
2021 Lordan R, Rando HM, Consortium CR, Greene CS. Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment. Arxiv. PMID 33564696  0.059
2024 Darragh LB, Knitz MM, Hu J, Clambey ET, Backus J, Dumit A, Samedi V, Bubak A, Greene C, Waxweiler T, Mehrotra S, Bhatia S, Gadwa J, Bickett T, Piper M, et al. Publisher Correction: A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nature Cancer. PMID 38200246 DOI: 10.1038/s43018-024-00724-1  0.057
2022 Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP, Gitter A, Greene CS, Consortium TC. The Coming of Age of Nucleic Acid Vaccines during COVID-19. Arxiv. PMID 36263086  0.056
2022 Darragh LB, Knitz MM, Hu J, Clambey ET, Backus J, Dumit A, Samedi V, Bubak A, Greene C, Waxweiler T, Mehrotra S, Bhatia S, Gadwa J, Bickett T, Piper M, et al. Author Correction: A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nature Cancer. PMID 36577897 DOI: 10.1038/s43018-022-00507-6  0.056
2023 Rando HM, Lordan R, Lee AJ, Naik A, Wellhausen N, Sell E, Kolla L, Gitter A, Greene CS. Application of Traditional Vaccine Development Strategies to SARS-CoV-2. Msystems. e0092722. PMID 36861991 DOI: 10.1128/msystems.00927-22  0.05
2022 Rando HM, Lordan R, Lee AJ, Naik A, Wellhausen N, Sell E, Kolla L, Consortium CR, Gitter A, Greene CS. Application of Traditional Vaccine Development Strategies to SARS-CoV-2. Arxiv. PMID 36034485  0.048
2016 Greene CS. Gut check Science Translational Medicine. 8: 352ec131-352ec131. DOI: 10.1126/scitranslmed.aah5494  0.023
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