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Casey Stephen Greene

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BIOMED Informatics Gen Ops
ORCID ORCID Icon0000-0001-8713-9213 Additional info

    Collapse Research 
    Collapse research activities and funding
    U54OD036472     (CHEN, JAKE YUE)Apr 1, 2024 - Mar 31, 2029
    NIH
    CONNECT: Collaborative Network for Nurturing Ecosystems of Common Fund Team Science
    Role: Co-Principal Investigator
    R01LM013863     (BLEKHMAN, RAN)Sep 15, 2022 - Jul 31, 2026
    NIH
    Human Microbiome Compendium: large-scale curation and processing of human microbiome datasets
    Role: Co-Principal Investigator
    R01CA237170     (GREENE, CASEY S)Apr 1, 2019 - Mar 31, 2025
    NIH
    Characterization of high-grade serous ovarian cancer subtypes via single-cell profiling
    Role: Principal Investigator
    R01HG010067     (GREENE, CASEY S)Jun 12, 2018 - Apr 30, 2024
    NIH
    Network-based algorithms for target identification and drug repositioning from genetic associations
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Davidson NR, Zhang F, Greene CS. BuDDI: BulkDeconvolution withDomainInvariance to predict cell-type-specific perturbations from bulk. bioRxiv. 2024 Apr 04. PMID: 37503097.
      View in: PubMed
    2. 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, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet. 2024 01 04; 111(1):11-23. PMID: 38181729.
      View in: PubMed
    3. 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, Fakhoury K, Liu A, Petit J, Bowles D, Thaker A, Atiyeh K, Goddard J, Hoyer R, Van Bokhoven A, Jordan K, Jimeno A, D'Alessandro A, Raben D, McDermott JD, Karam SD. Publisher Correction: A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nat Cancer. 2024 Jan; 5(1):210. PMID: 38200246.
      View in: PubMed
    4. Davidson NR, Barnard ME, Hippen AA, Campbell A, Johnson CE, 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. 2023 Dec 02. PMID: 37961178.
      View in: PubMed
    5. 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 Biol. 2023 10 20; 24(1):239. PMID: 37864274.
      View in: PubMed
    6. 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. 2023 Oct 11. PMID: 37873416.
      View in: PubMed
    7. 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, Grant SFA, Greene CS. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nat Commun. 2023 09 09; 14(1):5562. PMID: 37689782.
      View in: PubMed
    8. Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Analysis of Pseudomonas aeruginosa transcription in an ex vivo cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus. bioRxiv. 2023 Aug 21. PMID: 37662412.
      View in: PubMed
    9. Zhang S, Heil BJ, Mao W, Chikina M, Greene CS, Heller EA. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. bioRxiv. 2023 Aug 15. PMID: 37577575.
      View in: PubMed
    10. 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 Res. 2023 07 05; 51(W1):W350-W356. PMID: 37070209.
      View in: PubMed
    11. 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, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genom. 2023 Jul 12; 3(7):100340. PMID: 37492101.
      View in: PubMed
    12. Banerjee J, Taroni JN, Allaway RJ, Prasad DV, Guinney J, Greene C. Machine learning in rare disease. Nat Methods. 2023 Jun; 20(6):803-814. PMID: 37248386.
      View in: PubMed
    13. 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, Shapiro JA, Greene CS, Savonen C, Mafra F, Hakonarson H, Curran T, Haldar M. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality. Cell Rep. 2023 Jun 27; 42(6):112600. PMID: 37235472.
      View in: PubMed
    14. Nicholson DN, Alquaddoomi F, Rubinetti V, Greene CS. Changing word meanings in biomedical literature reveal pandemics and new technologies. BioData Min. 2023 May 05; 16(1):16. PMID: 37147665.
      View in: PubMed
    15. Heil BJ, Crawford J, Greene CS. The effect of non-linear signal in classification problems using gene expression. PLoS Comput Biol. 2023 03; 19(3):e1010984. PMID: 36972227.
      View in: PubMed
    16. 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. 2023 04 27; 8(2):e0092722. PMID: 36861991.
      View in: PubMed
    17. 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. 2023 04 27; 8(2):e0092822. PMID: 36861992.
      View in: PubMed
    18. Foltz SM, Greene CS, Taroni JN. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. Commun Biol. 2023 02 25; 6(1):222. PMID: 36841852.
      View in: PubMed
    19. 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. ArXiv. 2023 Jan 23. PMID: 36034485.
      View in: PubMed
    20. Pividori M, Greene CS. A publishing infrastructure for AI-assisted academic authoring. bioRxiv. 2023 Jan 23. PMID: 36747665.
      View in: PubMed
    21. 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. 2023 Jan 07. PMID: 36711546.
      View in: PubMed
    22. 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. 2023 Jan 06. PMID: 36711569.
      View in: PubMed
    23. Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. bioRxiv. 2023 Jan 06. PMID: 36711900.
      View in: PubMed
    24. 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, Fakhoury K, Liu A, Petit J, Bowles D, Thaker A, Atiyeh K, Goddard J, Hoyer R, Van Bokhoven A, Jordan K, Jimeno A, D'Alessandro A, Raben D, McDermott JD, Karam SD. Author Correction: A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nat Cancer. 2023 Jan; 4(1):148. PMID: 36577897.
      View in: PubMed
    25. 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. 2022 12 28; 12. PMID: 37503959.
      View in: PubMed
    26. 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. 2023 02 23; 8(1):e0034222. PMID: 36541762.
      View in: PubMed
    27. 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. 2023 02 23; 8(1):e0034122. PMID: 36541761.
      View in: PubMed
    28. 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, Fakhoury K, Liu A, Petit J, Bowles D, Thaker A, Atiyeh K, Goddard J, Hoyer R, Van Bokhoven A, Jordan K, Jimeno A, D'Alessandro A, Raben D, McDermott JD, Karam SD. A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. Nat Cancer. 2022 11; 3(11):1300-1317. PMID: 36434392.
      View in: PubMed
    29. Hippen AA, Crawford J, Gardner JR, Greene CS. wenda_gpu: fast domain adaptation for genomic data. Bioinformatics. 2022 11 15; 38(22):5129-5130. PMID: 36193991.
      View in: PubMed
    30. Nicholson DN, Himmelstein DS, Greene CS. Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min. 2022 Oct 18; 15(1):26. PMID: 36258252.
      View in: PubMed
    31. 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. 2022 10; 20(5):912-927. PMID: 36216026.
      View in: PubMed
    32. Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Comput Struct Biotechnol J. 2022; 20:4315-4324. PMID: 36016717.
      View in: PubMed
    33. Crawford J, Christensen BC, Chikina M, Greene CS. Widespread redundancy in -omics profiles of cancer mutation states. Genome Biol. 2022 06 27; 23(1):137. PMID: 35761387.
      View in: PubMed
    34. 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. Nat Commun. 2022 06 27; 13(1):3695. PMID: 35760813.
      View in: PubMed
    35. Rando HM, Brueffer C, Lordan R, Dattoli AA, Manheim D, Meyer JG, Mundo AI, Perrin D, Mai D, Wellhausen N, Gitter A, Greene CS. Molecular and Serologic Diagnostic Technologies for SARS-CoV-2. ArXiv. 2022 Apr 26. PMID: 35547240.
      View in: PubMed
    36. Hippen AA, Davidson NR, Greene CS. Computational audits combat disparities in recognition. Nat Hum Behav. 2022 04; 6(4):473-474. PMID: 35039653.
      View in: PubMed
    37. 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, Kalinin AA, Signal B, Lengerich BJ, Triche TJ, Boca SM. Ten quick tips for deep learning in biology. PLoS Comput Biol. 2022 03; 18(3):e1009803. PMID: 35324884.
      View in: PubMed
    38. Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, Greene C. Ten simple rules for large-scale data processing. PLoS Comput Biol. 2022 02; 18(2):e1009757. PMID: 35143491.
      View in: PubMed
    39. Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. PLoS Biol. 2022 02; 20(2):e3001470. PMID: 35104289.
      View in: PubMed
    40. 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, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure". mSystems. 2022 Feb 22; 7(1):e0144721. PMID: 35076276.
      View in: PubMed
    41. 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. Pac Symp Biocomput. 2022; 27:156-162. PMID: 34890145.
      View in: PubMed
    42. 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, Chute CG, Coleman BD, Davis HE, Gagnier J, Greene CS, Hillegass WB, Kavuluru R, Kimble WD, Koraishy FM, K?hler S, Liang C, Liu F, Liu H, Madhira V, Madlock-Brown CR, Matentzoglu N, Mazzotti DR, McMurry JA, McNair DS, Moffitt RA, Monteith TS, Parker AM, Perry MA, Pfaff E, Reese JT, Saltz J, Schuff RA, Solomonides AE, Solway J, Spratt H, Stein GS, Sule AA, Topaloglu U, Vavougios GD, Wang L, Haendel MA, Robinson PN. Characterizing Long COVID: Deep Phenotype of a Complex Condition. EBioMedicine. 2021 Dec; 74:103722. PMID: 34839263.
      View in: PubMed
    43. 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, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y, Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. mSystems. 2021 Dec 21; 6(6):e0023321. PMID: 34726496.
      View in: PubMed
    44. 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, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems. 2021 10 26; 6(5):e0009521. PMID: 34698547.
      View in: PubMed
    45. Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, L? Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. A field guide to cultivating computational biology. PLoS Biol. 2021 10; 19(10):e3001419. PMID: 34618807.
      View in: PubMed
    46. Heil BJ, Hoffman MM, Markowetz F, Lee SI, Greene CS, Hicks SC. Reproducibility standards for machine learning in the life sciences. Nat Methods. 2021 10; 18(10):1132-1135. PMID: 34462593.
      View in: PubMed
    47. 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. 2021 09 22; 10(9). PMID: 34553212.
      View in: PubMed
    48. 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. ArXiv. 2021 Sep 17. PMID: 34545336.
      View in: PubMed
    49. 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 Proc. 2021 Sep; 2976:29-38. PMID: 35558551.
      View in: PubMed
    50. 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, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol. 2021 Aug 25; 22(1):246. PMID: 34433496.
      View in: PubMed
    51. Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, V?h?rautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput Biol. 2021 08; 17(8):e1009290. PMID: 34428202.
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    52. Le TT, Himmelstein DS, Hippen AA, Gazzara MR, Greene CS. Analysis of scientific society honors reveals disparities. Cell Syst. 2021 09 22; 12(9):900-906.e5. PMID: 34555325.
      View in: PubMed
    53. L? 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, Righelli D, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol. 2021 08 05; 22(1):220. PMID: 34353350.
      View in: PubMed
    54. 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, Aronow BJ, Zhang J, Vaske O, Alonzo TA, Nathan PC, Poynter JN, Armstrong G, Hahn EE, Wernli KJ, Greene C, DiGiovanna J, Resnick AC, Shalley ER, Nadaf S, Kibbe WA. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO Clin Cancer Inform. 2021 08; 5:881-896. PMID: 34428097.
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    55. Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment. mSystems. 2021 05 04; 6(3). PMID: 33947804.
      View in: PubMed
    56. 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, Shapiro JA, Greene CS, Savonen C, Mafra F, Hakonarson H, Curran T, Haldar M. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality. Cell Rep. 2021 03 30; 34(13):108917. PMID: 33789113.
      View in: PubMed
    57. 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, Guebila MB, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y, Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. ArXiv. 2021 Mar 03. PMID: 33688554.
      View in: PubMed
    58. Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment. ArXiv. 2021 Feb 03. PMID: 33564696.
      View in: PubMed
    59. Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Sun Y, Mai D, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. ArXiv. 2021 Feb 01. PMID: 33594340.
      View in: PubMed
    60. Mueller AC, Piper M, Goodspeed A, Bhuvane S, Williams JS, Bhatia S, Phan AV, Van Court B, Zolman KL, Pe?a B, Oweida AJ, Zakem S, Meguid C, Knitz MW, Darragh L, Bickett TE, Gadwa J, Mestroni L, Taylor MRG, Jordan KR, Dempsey P, Lucia MS, McCarter MD, Del Chiaro M, Messersmith WA, Schulick RD, Goodman KA, Gough MJ, Greene CS, Costello JC, Neto AG, Lagares D, Hansen KC, Van Bokhoven A, Karam SD. Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer. Cancer Res. 2021 06 15; 81(12):3255-3269. PMID: 33526513.
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    61. 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, Lu S, Leonard ME, Johnson ME, Hakonarson H, Gilsanz V, Shepherd JA, Oberfield SE, Greene CS, Kelly A, Lawlor DA, Voight BF, Wells AD, Zemel BS, Hankenson KD, Grant SFA. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol. 2021 01 04; 22(1):1. PMID: 33397451.
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    62. Cooley M, Greene CS, Issac D, Pividori M, Sullivan BD. Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. Proc 2021 SIAM Conf Appl Comput Discret Algorithms (2021). 2021; 2021:111-122. PMID: 35391741.
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    63. Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends Cancer. 2021 04; 7(4):276-278. PMID: 33229213.
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    64. Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 11 03; 9(11). PMID: 33140829.
      View in: PubMed
    65. Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. 2020 11 09; 38(5):613-615. PMID: 33096022.
      View in: PubMed
    66. 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, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Transparency and reproducibility in artificial intelligence. Nature. 2020 10; 586(7829):E14-E16. PMID: 33057217.
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    67. 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. 2020 09 17; 9(9). PMID: 32940333.
      View in: PubMed
    68. 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, Primke T, Li W, Inkenbrandt J, Huynh T, Chen E, Lee C, Croatto M, Bentley H, Lu W, Murray R, Travassos M, Coull BA, Openshaw J, Greene CS, Shalem O, King G, Probasco R, Cheng DR, Silbermann B, Zhang F, Lin X. Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing. Nat Hum Behav. 2020 09; 4(9):972-982. PMID: 32848231.
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    69. 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, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, R?tsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Building an international consortium for tracking coronavirus health status. Nat Med. 2020 08; 26(8):1161-1165. PMID: 32488218.
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    70. 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, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, R?tsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nat Med. 2020 08; 26(8):1309. PMID: 32591764.
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    71. Byrd JB, Greene AC, Prasad DV, Jiang X, Greene CS. Responsible, practical genomic data sharing that accelerates research. Nat Rev Genet. 2020 10; 21(10):615-629. PMID: 32694666.
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    72. 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, Senz J, Lum A, Chow V, Sudderuddin H, Mackenzie R, Leong SCY, Liu G, Johnson D, Chen B, Group A, Alsop J, Banerjee SN, Behrens S, Bodelon C, Brand AH, Brinton L, Carney ME, Chiew YE, Cushing-Haugen KL, Cybulski C, Ennis D, Fereday S, Fortner RT, Garc?a-Donas J, Gentry-Maharaj A, Glasspool R, Goranova T, Greene CS, Haluska P, Harris HR, Hendley J, Hernandez BY, Herpel E, Jimenez-Linan M, Karpinskyj C, Kaufmann SH, Keeney GL, Kennedy CJ, K?bel M, Koziak JM, Larson MC, Lester J, Lewsley LA, Lissowska J, Lubinski J, Luk H, Macintyre G, Mahner S, McNeish IA, Menkiszak J, Nevins N, Osorio A, Oszurek O, Palacios J, Hinsley S, Pearce CL, Pike MC, Piskorz AM, Ray-Coquard I, Rhenius V, Rodriguez-Antona C, Sharma R, Sherman ME, De Silva D, Singh N, Sinn P, Slamon D, Song H, Steed H, Stronach EA, Thompson PJ, Toloczko A, Trabert B, Traficante N, Tseng CC, Widschwendter M, Wilkens LR, Winham SJ, Winterhoff B, Beeghly-Fadiel A, Benitez J, Berchuck A, Brenton JD, Brown R, Chang-Claude J, Chenevix-Trench G, deFazio A, Fasching PA, Garc?a MJ, Gayther SA, Goodman MT, Gronwald J, Henderson MJ, Karlan BY, Kelemen LE, Menon U, Orsulic S, Pharoah PDP, Wentzensen N, Wu AH, Schildkraut JM, Rossing MA, Konecny GE, Huntsman DG, Huang RY, Goode EL, Ramus SJ, Doherty JA, Bowtell DD, Anglesio MS. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). Clin Cancer Res. 2020 10 15; 26(20):5411-5423. PMID: 32554541.
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    73. 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, Primke T, Li C, Inkenbrandt J, Huynh T, Chen E, Lee C, Croatto M, Bentley H, Lu W, Murray R, Travassos M, Openshaw J, Coull B, Greene C, Shalem O, King G, Probasco R, Cheng D, Silbermann B, Zhang F, Lin X. Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States. medRxiv. 2020 Jun 11. PMID: 32577674.
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    74. Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Comput Struct Biotechnol J. 2020; 18:1414-1428. PMID: 32637040.
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    75. Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 2020 06 01; 9(6). PMID: 32479592.
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    76. Hu Q, Greene CS, Heller EA. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Res. 2020 05 21; 48(9):4709-4724. PMID: 32319526.
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    77. Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biol. 2020 05 11; 21(1):109. PMID: 32393369.
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    78. 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 (Basel). 2020 02 21; 11(2). PMID: 32098059.
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    79. Clay ME, Hammond JH, Zhong F, Chen X, Kowalski CH, Lee AJ, Porter MS, Hampton TH, Greene CS, Pletneva EV, Hogan DA. Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. Proc Natl Acad Sci U S A. 2020 02 11; 117(6):3167-3173. PMID: 31980538.
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    80. Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Curr Opin Biotechnol. 2020 06; 63:126-134. PMID: 31962244.
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    81. 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, Dahmane N. Immune landscapes associated with different glioblastoma molecular subtypes. Acta Neuropathol Commun. 2019 11 29; 7(1):203. PMID: 31815646.
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    82. 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, Dalkiran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fern?ndez JM, Gemovic B, Perovic VR, Davidovic RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, T?r?nen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijevic V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Bj?rne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, ?muc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 11 19; 20(1):244. PMID: 31744546.
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    83. 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 Adv. 2019 11 12; 3(21):3214-3227. PMID: 31698452.
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    84. 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, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, B?hm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OM, Haussler D, Gastier-Foster JM, Kolb EA, Gorlick R, Li XN, Reynolds CP, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 11 05; 29(6):1675-1689.e9. PMID: 31693904.
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    85. 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. Genet Epidemiol. 2020 01; 44(1):52-66. PMID: 31583758.
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    86. Anikeeva P, Boyden E, Brangwynne C, Ciss? II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X. Voices in methods development. Nat Methods. 2019 10; 16(10):945-951. PMID: 31562479.
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    87. 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. Circ Cardiovasc Qual Outcomes. 2019 07; 12(7):e005122. PMID: 31284738.
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    88. Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. PLoS Comput Biol. 2019 06; 15(6):e1007128. PMID: 31233491.
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    89. Greene CS. Show me the models. Nat Biotechnol. 2019 Jun; 37(6):623-625. PMID: 31138912.
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    90. 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 Syst. 2019 05 22; 8(5):380-394.e4. PMID: 31121115.
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    91. Crowell AM, Greene CS, Loros JJ, Dunlap JC. Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinformatics. 2019 05 01; 35(9):1518-1526. PMID: 30247517.
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    92. 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, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, B?nnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 04 08; 49(1):10-29. PMID: 30930166.
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    93. Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G. New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda). 2019 01 09; 9(1):251-267. PMID: 30463884.
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    94. Hu Q, Greene CS. Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. Pac Symp Biocomput. 2019; 24:362-373. PMID: 30963075.
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    95. Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nat Methods. 2018 12; 15(12):1009-1010. PMID: 30504887.
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    96. Park Y, Greene CS. A parasite's perspective on data sharing. Gigascience. 2018 11 01; 7(11). PMID: 30395209.
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    97. 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 Genet. 2018 10; 34(10):790-805. PMID: 30143323.
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    98. 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 Min. 2018; 11:14. PMID: 29988723.
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    99. 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. Crit Care Med. 2018 07; 46(7):1125-1132. PMID: 29629986.
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    100. 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. Ann Rheum Dis. 2018 08; 77(8):1226-1233. PMID: 29724730.
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    101. 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, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10. PMID: 29625050.
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    102. 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, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 04 03; 23(1):239-254.e6. PMID: 29617664.
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    103. 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 Rep. 2018 04 03; 23(1):172-180.e3. PMID: 29617658.
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    104. 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, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018 04; 15(141). PMID: 29618526.
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    105. 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. J Bacteriol. 2018 04 15; 200(8). PMID: 29311282.
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    106. Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Greshake Tzovaras B, Greene CS. Sci-Hub provides access to nearly all scholarly literature. Elife. 2018 03 01; 7. PMID: 29424689.
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    107. Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. Pac Symp Biocomput. 2018; 23:157-167. PMID: 29218878.
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    108. Way GP, Greene CS. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pac Symp Biocomput. 2018; 23:80-91. PMID: 29218871.
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    109. Gonzalez-Hernandez G, Sarker A, O'Connor K, Greene C, Liu H. Advances in Text Mining and Visualization for Precision Medicine. Pac Symp Biocomput. 2018; 23:559-565. PMID: 29218914.
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    110. 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 Chronobiome. Sci Rep. 2017 12 07; 7(1):17141. PMID: 29215023.
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    111. 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. 2017 Nov 22; 18(1):512. PMID: 29166858.
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    112. 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 (Bethesda). 2017 11 06; 7(11):3705-3718. PMID: 28889104.
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    113. 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. 2017 Oct 15; 33(20):3250-3257. PMID: 28575147.
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    114. Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. Eur J Hum Genet. 2017 11; 25(11):1286-1289. PMID: 28792001.
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    115. 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 Syst. 2017 07 26; 5(1):63-71.e6. PMID: 28711280.
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    116. Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Curr Epidemiol Rep. 2017 Sep; 4(3):211-220. PMID: 29226065.
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    117. Byrd JB, Greene CS. Data-Sharing Models N Engl J Med. 2017 06 08; 376(23):2305. PMID: 28594152.
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    118. Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 03 30; 49(4):483-484. PMID: 28358134.
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    119. 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 Med. 2017 03 23; 9(1):27. PMID: 28330499.
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    120. Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol. 2017 04; 35(4):342-346. PMID: 28288103.
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    121. Greene CS. Tell me your neighbors, and I will tell you what you are. Sci Transl Med. 2017 02 08; 9(376). PMID: 28179503.
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    122. 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. 2017 02 06; 18(1):127. PMID: 28166733.
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    123. 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. 2017; 22:646-648. PMID: 27897015.
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    124. Greene CS. Cheap-seq. Sci Transl Med. 2016 12 21; 8(370):370ec203. PMID: 28003542.
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    125. 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). 2016 12 07; 6(12):4097-4103. PMID: 27729437.
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    126. Beaulieu-Jones BK, Greene CS. Semi-supervised learning of the electronic health record for phenotype stratification. J Biomed Inform. 2016 12; 64:168-178. PMID: 27744022.
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    127. 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, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, T?r?nen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sede?o-Cort?s AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fern?ndez JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 09 07; 17(1):184. PMID: 27604469.
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    128. Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Hum Mol Genet. 2016 Oct 01; 25(R2):R94-R98. PMID: 27340225.
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    129. Greene CS, Himmelstein DS. Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits. Circ Cardiovasc Genet. 2016 Apr; 9(2):179-84. PMID: 27094199.
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    130. 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 AA, 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. 2016 Mar 29; 7(13):17087-102. PMID: 26934555.
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    131. Himmelstein DS, Greene CS, Moore JH. Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. BioData Min. 2016; 9:9. PMID: 26848312.
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    132. Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ. 2016; 4:e1621. PMID: 26844019.
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    133. 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 Min. 2016; 9:3. PMID: 26788126.
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    134. 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. 2016 Jan-Feb; 1(1). PMID: 27822512.
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    135. Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pac Symp Biocomput. 2016; 21:557-67. PMID: 26776218.
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    136. 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. 2015 Dec 15; 16:1065. PMID: 26666289.
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    137. Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeb?ller 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. PMID: 26483192.
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    138. 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. 2016 Jan; 17(1):33-42. PMID: 26420781.
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    139. 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, Gershwin ME, Anderson CA, Lazaridis KN, Invernizzi P, Seldin MF, Sandford RN, Amos CI, Siminovitch KA. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat Commun. 2015 Sep 22; 6:8019. PMID: 26394269.
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    140. 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; 8:17. PMID: 26097506.
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    141. 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. Nat Genet. 2015 Jun; 47(6):569-76. PMID: 25915600.
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    142. Greene AC, Giffin KA, Greene CS, Moore JH. Adapting bioinformatics curricula for big data. Brief Bioinform. 2016 Jan; 17(1):43-50. PMID: 25829469.
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    143. 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 Mar; 12(3):211-4, 3 p following 214. PMID: 25581801.
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    144. 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 Jan; 11(1):e1004005. PMID: 25569146.
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    145. Tan J, Ung M, Cheng C, Greene CS. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput. 2015; 132-43. PMID: 25592575.
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    146. Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big data bioinformatics. J Cell Physiol. 2014 Dec; 229(12):1896-900. PMID: 24799088.
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    147. 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.
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    148. 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.
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    149. Cheng C, Moore J, Greene C. Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing. Pac Symp Biocomput. 2014; 412-6. PMID: 24297566.
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    150. 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.
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    151. 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.
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    152. Gonzalez G, Cohen KB, Greene CS, Hahn U, Kann MG, Leaman R, Shah N, Ye J. Text and data mining for biomedical discovery. Pac Symp Biocomput. 2013; 2013:368-72. PMID: 23424141.
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    153. Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol. 2012; 8(12):e1002816. PMID: 23300408.
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    154. 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.
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    155. 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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    156. Himmelstein DS, Greene CS, Moore JH. Evolving hard problems: Generating human genetics datasets with a complex etiology. BioData Min. 2011 Jul 07; 4(1):21. PMID: 21736753.
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    157. Greene CS, Troyanskaya OG. PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W368-74. PMID: 21653547.
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    158. Greene CS, Troyanskaya OG. Integrative systems biology for data-driven knowledge discovery. Semin Nephrol. 2010 Sep; 30(5):443-54. PMID: 21044756.
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    159. 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. 2010 Mar 01; 26(5):694-5. PMID: 20081222.
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    160. 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. Pac Symp Biocomput. 2010; 327-36. PMID: 19908385.
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    161. Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min. 2009 Sep 22; 2(1):5. PMID: 19772641.
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    162. Sinnott-Armstrong NA, Greene CS, Cancare F, Moore JH. Accelerating epistasis analysis in human genetics with consumer graphics hardware. BMC Res Notes. 2009 Jul 24; 2:149. PMID: 19630950.
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    163. Greene CS, Penrod NM, Williams SM, Moore JH. Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One. 2009 Jun 02; 4(6):e5639. PMID: 19503614.
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    164. Greene CS, White BC, Moore JH. Sensible Initialization Using Expert Knowledge for Genome-Wide Analysis of Epistasis Using Genetic Programming. Genet Evol Comput Conf. 2009 May 18; 2009:1289-1296. PMID: 21197156.
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    165. 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 Rheum. 2008 Jul 15; 59(7):974-83. PMID: 18576303.
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    166. Ganko EW, Greene CS, Lewis JA, Bhattacharjee V, McDonald JF. LTR retrotransposon-gene associations in Drosophila melanogaster. J Mol Evol. 2006 Jan; 62(1):111-20. PMID: 16408244.
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