| 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 |
|
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