Casey Greene, PhD

Professor, Biomedical Informatics

FacultyPhoto

Website

Languages
English
Department
Biomedical Informatics

Publications

  • 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 Sep 17;9(9). PubMed PMID: 32940333
  • 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 Sep;4(9):972-982. PubMed PMID: 32848231
  • 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, García-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, Köbel 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, García 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 Oct 15;26(20):5411-5423. PubMed PMID: 32554541
  • 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 Oct;586(7829):E14-E16. PubMed PMID: 33057217
  • Byrd JB, Greene AC, Prasad DV, Jiang X, Greene CS. Responsible, practical genomic data sharing that accelerates research. Nat Rev Genet. 2020 Oct;21(10):615-629. PubMed PMID: 32694666
  • Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. 2020 Nov 9;38(5):613-615. PubMed PMID: 33096022
  • Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 Nov 3;9(11). PubMed PMID: 33140829
  • Hu Q, Greene CS, Heller EA. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Res. 2020 May 21;48(9):4709-4724. PubMed PMID: 32319526
  • Hippen AA, Davidson NR, Greene CS. Computational audits combat disparities in recognition. Nat Hum Behav. 2022 Jan 17. [Epub ahead of print] PubMed PMID: 35039653
  • 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 Jun 1;9(6). PubMed PMID: 32479592
  • Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Curr Opin Biotechnol. 2020 Jun;63:126-134. PubMed PMID: 31962244
  • 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. PubMed PMID: 34890145
  • 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, Köhler 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. PubMed PMID: 34839263
  • 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. PubMed PMID: 34726496
  • 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 Oct 26;6(5):e0009521. PubMed PMID: 34698547
  • 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 Jan;44(1):52-66. PubMed PMID: 31583758
  • 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 Oct;19(10):e3001419. PubMed PMID: 34618807
  • Le TT, Himmelstein DS, Hippen AA, Gazzara MR, Greene CS. Analysis of scientific society honors reveals disparities. Cell Syst. 2021 Sep 22;12(9):900-906.e5. PubMed PMID: 34555325
  • 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 Sep 22;10(9). PubMed PMID: 34553212
  • 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. 2021 Sep 17. PubMed PMID: 34545336
  • Heil BJ, Hoffman MM, Markowetz F, Lee SI, Greene CS, Hicks SC. Reproducibility standards for machine learning in the life sciences. Nat Methods. 2021 Oct;18(10):1132-1135. PubMed PMID: 34462593
  • 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 Feb 11;117(6):3167-3173. PubMed PMID: 31980538
  • 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, Rätsch 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 Aug;26(8):1309. PubMed PMID: 32591764
  • 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, Rätsch 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 Aug;26(8):1161-1165. PubMed PMID: 32488218
  • 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. PubMed PMID: 34433496
  • Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Comput Struct Biotechnol J. 2020;18:1414-1428. PubMed PMID: 32637040
  • Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput Biol. 2021 Aug;17(8):e1009290. PubMed PMID: 34428202
  • 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 Aug;5:881-896. PubMed PMID: 34428097
  • 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, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, 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 Oct;16(10):945-951. PubMed PMID: 31562479
  • 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, Böhm 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 Nov 5;29(6):1675-1689.e9. PubMed PMID: 31693904
  • 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 Nov 12;3(21):3214-3227. PubMed PMID: 31698452
  • 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 May 22;8(5):380-394.e4. PubMed PMID: 31121115
  • Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, 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 Aug 5;22(1):220. PubMed PMID: 34353350
  • Crowell AM, Greene CS, Loros JJ, Dunlap JC. Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinformatics. 2019 May 1;35(9):1518-1526. PubMed PMID: 30247517
  • Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment. mSystems. 2021 May 4;6(3). PubMed PMID: 33947804
  • 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 Mar 30;34(13):108917. PubMed PMID: 33789113
  • Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Qi Y, Sun Y, Field JM, Guebila MB, Jadavji NM, Lordan R, Skelly AN, Ramsundar B, Brueffer C, Wang J, Goel RR, Park Y, Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. ArXiv. 2021 Mar 3. PubMed PMID: 33688554
  • Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends Cancer. 2021 Apr;7(4):276-278. PubMed PMID: 33229213
  • Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. PLoS Comput Biol. 2019 Jun;15(6):e1007128. PubMed PMID: 31233491
  • 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 Jan 4;22(1):1. PubMed PMID: 33397451
  • Mueller AC, Piper M, Goodspeed A, Bhuvane S, Williams JS, Bhatia S, Phan AV, Van Court B, Zolman KL, Peña B, Oweida AJ, Zakem S, Meguid C, Knitz MW, Darragh L, Bickett TE, Gadwa J, Mestroni L, Taylor MRG, Jordan KR, Dempsey P, Lucia MS, McCarter MD, Chiaro MD, 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 Jun 15;81(12):3255-3269. PubMed PMID: 33526513
  • Lordan R, Rando HM, Greene CS. Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment. ArXiv. 2021 Feb 3. PubMed PMID: 33564696
  • 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. PubMed PMID: 16408244
  • Rando HM, MacLean AL, Lee AJ, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Sun Y, Mai D, Brueffer C, Byrd JB, Wang J, Lordan R, 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 1. PubMed PMID: 33594340
  • 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. PubMed PMID: 18576303
  • 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. 2022 Dec 21;:e0034222. [Epub ahead of print] PubMed PMID: 36541762
  • 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. PubMed PMID: 21197156
  • 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. 2022 Dec 21;:e0034122. [Epub ahead of print] PubMed PMID: 36541761
  • 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 Nov;3(11):1300-1317. PubMed PMID: 36434392
  • Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP, Gitter A, Greene CS, Consortium TC. The Coming of Age of Nucleic Acid Vaccines during COVID-19. ArXiv. 2022 Oct 14. PubMed PMID: 36263086
  • 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. PubMed PMID: 36258252
  • 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 Oct 7. [Epub ahead of print] PubMed PMID: 36216026
  • Hippen AA, Crawford J, Gardner JR, Greene CS. wenda_gpu: fast domain adaptation for genomic data. Bioinformatics. 2022 Nov 15;38(22):5129-5130. PubMed PMID: 36193991
  • Rando HM, Lordan R, Lee AJ, Naik A, Wellhausen N, Sell E, Kolla L, Consortium CR, Gitter A, Greene CS. Application of Traditional Vaccine Development Strategies to SARS-CoV-2. ArXiv. 2022 Aug 16. PubMed PMID: 36034485
  • 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. PubMed PMID: 36016717
  • Crawford J, Christensen BC, Chikina M, Greene CS. Widespread redundancy in -omics profiles of cancer mutation states. Genome Biol. 2022 Jun 27;23(1):137. PubMed PMID: 35761387
  • 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 Jun 27;13(1):3695. PubMed PMID: 35760813
  • Rando HM, Brueffer C, Lordan R, Dattoli AA, Manheim D, Meyer JG, Mundo AI, Perrin D, Mai D, Wellhausen N, Consortium CR, Gitter A, Greene CS. Molecular and Serologic Diagnostic Technologies for SARS-CoV-2. ArXiv. 2022 Apr 26. PubMed PMID: 35547240
  • 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 Jr, Boca SM. Ten quick tips for deep learning in biology. PLoS Comput Biol. 2022 Mar;18(3):e1009803. PubMed PMID: 35324884
  • 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. PubMed PMID: 19908385
  • 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 1;26(5):694-5. PubMed PMID: 20081222
  • Greene CS, Troyanskaya OG. Integrative systems biology for data-driven knowledge discovery. Semin Nephrol. 2010 Sep;30(5):443-54. PubMed PMID: 21044756
  • 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. PubMed PMID: 21653547
  • Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol. 2012;8(12):e1002816. PubMed PMID: 23300408
  • Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci. 2012 Jul;1260:95-100. PubMed PMID: 22268703
  • 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. PubMed PMID: 22684505
  • 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. PubMed PMID: 23424141
  • 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. PubMed PMID: 23516347
  • 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 Feb;18(2):e1009757. PubMed PMID: 35143491
  • 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. PubMed PMID: 23950145
  • Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. PLoS Biol. 2022 Feb;20(2):e3001470. PubMed PMID: 35104289
  • 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. PubMed PMID: 35076276
  • 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. PubMed PMID: 24297566
  • Hippen AA, Davidson NR, Greene CS. Computational audits combat disparities in recognition. Nat Hum Behav. 2022 Apr;6(4):473-474. PubMed PMID: 35039653
  • 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. PubMed PMID: 34890145
  • 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. PubMed PMID: 24944582
  • 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. PubMed PMID: 37873416
  • 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 Oct 20;24(1):239. PubMed PMID: 37864274
  • 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. PubMed PMID: 25165488
  • 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. PubMed PMID: 37662412
  • 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 Sep 9;14(1):5562. PubMed PMID: 37689782
  • Davidson NR, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. bioRxiv. 2023 Oct 5. PubMed PMID: 37503097
  • 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 Dec 28;12. PubMed PMID: 37503959
  • Zhang S, Heil BJ, Mao W, Chikina M, Greene CS, Heller EA. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. bioRxiv. 2023 Aug 15. PubMed PMID: 37577575
  • Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big data bioinformatics. J Cell Physiol. 2014 Dec;229(12):1896-900. PubMed PMID: 24799088
  • 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. PubMed PMID: 37492101
  • Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ. 2016;4:e1621. PubMed PMID: 26844019
  • 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. PubMed PMID: 37235472
  • Nicholson DN, Alquaddoomi F, Rubinetti V, Greene CS. Changing word meanings in biomedical literature reveal pandemics and new technologies. BioData Min. 2023 May 5;16(1):16. PubMed PMID: 37147665
  • 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. PubMed PMID: 26788126
  • Heil BJ, Crawford J, Greene CS. The effect of non-linear signal in classification problems using gene expression. PLoS Comput Biol. 2023 Mar;19(3):e1010984. PubMed PMID: 36972227
  • 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 Apr 27;8(2):e0092822. PubMed PMID: 36861992
  • 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 Apr 27;8(2):e0092722. PubMed PMID: 36861991
  • Foltz SM, Greene CS, Taroni JN. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. Commun Biol. 2023 Feb 25;6(1):222. PubMed PMID: 36841852
  • Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. bioRxiv. 2023 Jan 6. PubMed PMID: 36711900
  • Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pac Symp Biocomput. 2016;21:557-67. PubMed PMID: 26776218
  • Pividori M, Greene CS. A publishing infrastructure for AI-assisted academic authoring. bioRxiv. 2023 Jan 23. PubMed PMID: 36747665
  • 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 Feb 23;8(1):e0034222. PubMed PMID: 36541762
  • 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. PubMed PMID: 25581801
  • 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 Feb 23;8(1):e0034122. PubMed PMID: 36541761
  • 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. PubMed PMID: 36258252
  • 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. PubMed PMID: 25915600
  • 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 Oct;20(5):912-927. PubMed PMID: 36216026
  • 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. PubMed PMID: 25592575
  • Hippen AA, Crawford J, Gardner JR, Greene CS. wenda_gpu: fast domain adaptation for genomic data. Bioinformatics. 2022 Nov 15;38(22):5129-5130. PubMed PMID: 36193991
  • 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. PubMed PMID: 36016717
  • 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. PubMed PMID: 36034485
  • 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 Jan 4;111(1):11-23. PubMed PMID: 38181729
  • 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. PubMed PMID: 26097506
  • 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 2. PubMed PMID: 37961178
  • Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet. 2015 Dec 20;24(25):7406-20. PubMed PMID: 26483192
  • 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. PubMed PMID: 25569146
  • 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. PubMed PMID: 27094199
  • Beaulieu-Jones BK, Greene CS. Semi-supervised learning of the electronic health record for phenotype stratification. J Biomed Inform. 2016 Dec;64:168-178. PubMed PMID: 27744022
  • Greene CS. Cheap-seq. Sci Transl Med. 2016 Dec 21;8(370):370ec203. PubMed PMID: 28003542
  • Greene AC, Giffin KA, Greene CS, Moore JH. Adapting bioinformatics curricula for big data. Brief Bioinform. 2016 Jan;17(1):43-50. PubMed PMID: 25829469
  • 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. PubMed PMID: 26420781
  • 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). PubMed PMID: 27822512
  • 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. PubMed PMID: 26934555
  • Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Hum Mol Genet. 2016 Oct 1;25(R2):R94-R98. PubMed PMID: 27340225
  • 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. PubMed PMID: 27897015
  • Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol. 2017 Apr;35(4):342-346. PubMed PMID: 28288103
  • Greene CS. Tell me your neighbors, and I will tell you what you are. Sci Transl Med. 2017 Feb 8;9(376). PubMed PMID: 28179503
  • 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 Jul 26;5(1):63-71.e6. PubMed PMID: 28711280
  • Byrd JB, Greene CS. Data-Sharing Models. N Engl J Med. 2017 Jun 8;376(23):2305. PubMed PMID: 28594152
  • Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 Mar 30;49(4):483-484. PubMed PMID: 28358134
  • 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 Nov;25(11):1286-1289. PubMed PMID: 28792001
  • 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. PubMed PMID: 28575147
  • 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. PubMed PMID: 29226065
  • Way GP, Greene CS. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pac Symp Biocomput. 2018;23:80-91. PubMed PMID: 29218871
  • 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. PubMed PMID: 29218878
  • 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. PubMed PMID: 29218914
  • 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. PubMed PMID: 29988723
  • 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 Apr;15(141). PubMed PMID: 29618526
  • 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 Apr 3;23(1):172-180.e3. PubMed PMID: 29617658
  • 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 Apr 15;200(8). PubMed PMID: 29311282
  • 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 Jr, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6. PubMed PMID: 29617664
  • 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 Apr 5;173(2):321-337.e10. PubMed PMID: 29625050
  • 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 Aug;77(8):1226-1233. PubMed PMID: 29724730
  • Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nat Methods. 2018 Dec;15(12):1009-1010. PubMed PMID: 30504887
  • 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 Jul;46(7):1125-1132. PubMed PMID: 29629986
  • 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 Oct;34(10):790-805. PubMed PMID: 30143323
  • 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. PubMed PMID: 30963075
  • 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, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 Apr 8;49(1):10-29. PubMed PMID: 30930166
  • 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 Jul;12(7):e005122. PubMed PMID: 31284738
  • Greene CS. Show me the models. Nat Biotechnol. 2019 Jun;37(6):623-625. PubMed PMID: 31138912
  • 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 Jan 4;22(1):1. PubMed PMID: 33397451
  • Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends Cancer. 2020 Nov 20. [Epub ahead of print] PubMed PMID: 33229213
  • Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 Nov 3;9(11). PubMed PMID: 33140829
  • Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. 2020 Nov 9;38(5):613-615. PubMed PMID: 33096022
  • 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 Oct;586(7829):E14-E16. PubMed PMID: 33057217
  • 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 Sep 17;9(9). PubMed PMID: 32940333
  • 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 Sep;4(9):972-982. PubMed PMID: 32848231
  • Byrd JB, Greene AC, Prasad DV, Jiang X, Greene CS. Responsible, practical genomic data sharing that accelerates research. Nat Rev Genet. 2020 Oct;21(10):615-629. PubMed PMID: 32694666
  • Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Comput Struct Biotechnol J. 2020;18:1414-1428. PubMed PMID: 32637040
  • 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, Rätsch 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 Aug;26(8):1309. PubMed PMID: 32591764
  • 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. PubMed PMID: 32577674
  • 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, García-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, Köbel 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, García 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 Oct 15;26(20):5411-5423. PubMed PMID: 32554541
  • 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, Rätsch 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 Aug;26(8):1161-1165. PubMed PMID: 32488218
  • 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 Jun 1;9(6). PubMed PMID: 32479592
  • 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 May 11;21(1):109. PubMed PMID: 32393369
  • Hu Q, Greene CS, Heller EA. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Res. 2020 May 21;48(9):4709-4724. PubMed PMID: 32319526
  • 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 Feb 21;11(2). PubMed PMID: 32098059
  • 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 Feb 11;117(6):3167-3173. PubMed PMID: 31980538
  • Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Curr Opin Biotechnol. 2020 Jun;63:126-134. PubMed PMID: 31962244
  • 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 Jan;44(1):52-66. PubMed PMID: 31583758

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