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Items: 1 to 50 of 198

1.

Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing.

Beaulieu-Jones BK, Wu ZS, Williams C, Lee R, Bhavnani SP, Byrd JB, Greene CS.

Circ Cardiovasc Qual Outcomes. 2019 Jul;12(7):e005122. doi: 10.1161/CIRCOUTCOMES.118.005122. Epub 2019 Jul 9.

PMID:
31284738
2.

Open collaborative writing with Manubot.

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A.

PLoS Comput Biol. 2019 Jun 24;15(6):e1007128. doi: 10.1371/journal.pcbi.1007128. eCollection 2019 Jun.

3.

Show me the models.

Greene CS.

Nat Biotechnol. 2019 Jun;37(6):623-625. doi: 10.1038/s41587-019-0143-x. No abstract available.

PMID:
31138912
4.

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease.

Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, Greene CS.

Cell Syst. 2019 May 22;8(5):380-394.e4. doi: 10.1016/j.cels.2019.04.003.

6.

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

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.

Dev Cell. 2019 Apr 8;49(1):10-29. doi: 10.1016/j.devcel.2019.03.001. Epub 2019 Mar 28. Review.

7.

Seeking treatment for temporomandibular disorders: What patients can expect from non-dental health care providers.

Greene CS, Bertagna AE.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2019 May;127(5):399-407. doi: 10.1016/j.oooo.2019.01.007. Epub 2019 Jan 10.

PMID:
30879915
8.

Bayesian deep learning for single-cell analysis.

Way GP, Greene CS.

Nat Methods. 2018 Dec;15(12):1009-1010. doi: 10.1038/s41592-018-0230-9. No abstract available.

PMID:
30504887
9.

New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.

Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G.

G3 (Bethesda). 2019 Jan 9;9(1):251-267. doi: 10.1534/g3.118.200867.

10.

A parasite's perspective on data sharing.

Park Y, Greene CS.

Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy129.

11.

Authors' response.

Rinchuse DJ, Greene CS.

Am J Orthod Dentofacial Orthop. 2018 Nov;154(5):618. doi: 10.1016/j.ajodo.2018.08.011. No abstract available.

PMID:
30384929
12.

"The Ball on the Hill": A new perspective on TMJ functional anatomy.

Greene CS.

Orthod Craniofac Res. 2018 Nov;21(4):170-174. doi: 10.1111/ocr.12245. Epub 2018 Oct 14. No abstract available.

PMID:
30318699
13.

Learning and Imputation for Mass-spec Bias Reduction (LIMBR).

Crowell AM, Greene CS, Loros JJ, Dunlap JC.

Bioinformatics. 2019 May 1;35(9):1518-1526. doi: 10.1093/bioinformatics/bty828.

PMID:
30247517
14.

Evidence-based dentistry or meta-analysis illness? A commentary on current publishing trends in the field of temporomandibular disorders and bruxism.

Manfredini D, Greene CS, Ahlberg J, De Laat A, Lobbezoo F, Klasser GD.

J Oral Rehabil. 2019 Jan;46(1):1-4. doi: 10.1111/joor.12707. Epub 2018 Sep 10.

PMID:
30203622
15.

An evidence-based evaluation of the concept of centric relation in the 21st century.

Kandasamy S, Greene CS, Obrez A.

Quintessence Int. 2018;49(9):755-760. doi: 10.3290/j.qi.a41011. Review.

PMID:
30202837
16.

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

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.

Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Review.

17.

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.

Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS.

BioData Min. 2018 Jul 3;11:14. doi: 10.1186/s13040-018-0175-7. eCollection 2018.

18.

Scoping review of systematic review abstracts about temporomandibular disorders: Comparison of search years 2004 and 2017.

Rinchuse DJ, Greene CS.

Am J Orthod Dentofacial Orthop. 2018 Jul;154(1):35-46.e9. doi: 10.1016/j.ajodo.2017.12.011. Review.

PMID:
29957316
19.

The Use of Oral Appliances in the Management of Temporomandibular Disorders.

Greene CS, Menchel HF.

Oral Maxillofac Surg Clin North Am. 2018 Aug;30(3):265-277. doi: 10.1016/j.coms.2018.04.003. Epub 2018 Jun 1. Review.

PMID:
29866449
20.

Letter to the Editor on Chronic fibrosing osteomyelitis of the jaws: an important cause of recalcitrant facial pain. A clinicopathologic study of 331 cases in 227 patients by Goldblatt LI, Adams WR, Spolnik KJ, Deardorf KA, Parks ET.

Klasser GD, Laskin DM, Greene CS, Burns JC.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2018 Apr 17. pii: S2212-4403(18)30881-2. doi: 10.1016/j.oooo.2018.02.743. [Epub ahead of print] No abstract available.

PMID:
29748037
21.

Metabolic pathways and immunometabolism in rare kidney diseases.

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; Vasculitis Clinical Research Consortium, the European Renal cDNA Bank cohort, and the Nephrotic Syndrome Study Network.

Ann Rheum Dis. 2018 Aug;77(8):1226-1233. doi: 10.1136/annrheumdis-2017-212935. Epub 2018 May 3.

22.

Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay.

Weissman GE, Hubbard RA, Ungar LH, Harhay MO, Greene CS, Himes BE, Halpern SD.

Crit Care Med. 2018 Jul;46(7):1125-1132. doi: 10.1097/CCM.0000000000003148.

23.

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

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; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035.

24.

Opportunities and obstacles for deep learning in biology and medicine.

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.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

25.

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

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; Cancer Genome Atlas Research Network, Monnat RJ Jr, Xiao Y, Wang C.

Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076.

26.

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS.

Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.

27.

Sci-Hub provides access to nearly all scholarly literature.

Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Greshake Tzovaras B, Greene CS.

Elife. 2018 Mar 1;7. pii: e32822. doi: 10.7554/eLife.32822.

28.

A Multimodal Strategy Used by a Large c-di-GMP Network.

Dahlstrom KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA.

J Bacteriol. 2018 Mar 26;200(8). pii: e00703-17. doi: 10.1128/JB.00703-17. Print 2018 Apr 15.

29.

Canopy of advantage: Who benefits most from city trees?

Greene CS, Robinson PJ, Millward AA.

J Environ Manage. 2018 Feb 15;208:24-35. doi: 10.1016/j.jenvman.2017.12.015. Epub 2017 Dec 13.

PMID:
29247882
30.

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes.

Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM.

Curr Epidemiol Rep. 2017 Sep;4(3):211-220. doi: 10.1007/s40471-017-0115-y. Epub 2017 Jul 10.

31.
33.

A Pilot Characterization of the Human Chronobiome.

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.

Sci Rep. 2017 Dec 7;7(1):17141. doi: 10.1038/s41598-017-17362-6.

34.

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

Tan J, Huyck M, Hu D, Zelaya RA, Hogan DA, Greene CS.

BMC Bioinformatics. 2017 Nov 22;18(1):512. doi: 10.1186/s12859-017-1905-4.

35.

Orthodontics and the temporomandibular joint: What orthodontic providers need to know.

Greene CS, Galang-Boquiren MTS, Bartilotta BY.

Quintessence Int. 2017;48(10):799-808. doi: 10.3290/j.qi.a39095. Review.

PMID:
28990016
36.
37.

Implicating candidate genes at GWAS signals by leveraging topologically associating domains.

Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF.

Eur J Hum Genet. 2017 Nov;25(11):1286-1289. doi: 10.1038/ejhg.2017.108. Epub 2017 Aug 9.

38.

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS.

Cell Syst. 2017 Jul 26;5(1):63-71.e6. doi: 10.1016/j.cels.2017.06.003. Epub 2017 Jul 12.

39.

Data-Sharing Models

Byrd JB, Greene CS.

N Engl J Med. 2017 Jun 8;376(23):2305. doi: 10.1056/NEJMc1705477. No abstract available.

PMID:
28594152
40.

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules.

Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L; Alzheimer’s Disease Neuroimaging Initiative.

Bioinformatics. 2017 Oct 15;33(20):3250-3257. doi: 10.1093/bioinformatics/btx344.

41.

Celebrating parasites.

Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE.

Nat Genet. 2017 Mar 30;49(4):483-484. doi: 10.1038/ng.3830. No abstract available.

42.

A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.

Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML.

Genome Med. 2017 Mar 23;9(1):27. doi: 10.1186/s13073-017-0417-1.

43.

Reproducibility of computational workflows is automated using continuous analysis.

Beaulieu-Jones BK, Greene CS.

Nat Biotechnol. 2017 Apr;35(4):342-346. doi: 10.1038/nbt.3780. Epub 2017 Mar 13.

44.

Tell me your neighbors, and I will tell you what you are.

Greene CS.

Sci Transl Med. 2017 Feb 8;9(376). pii: eaam6058. doi: 10.1126/scitranslmed.aam6058.

PMID:
28179503
45.

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma.

Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS.

BMC Genomics. 2017 Feb 6;18(1):127. doi: 10.1186/s12864-017-3519-7.

46.

Cheap-seq.

Greene CS.

Sci Transl Med. 2016 Dec 21;8(370):370ec203. doi: 10.1126/scitranslmed.aal3701. No abstract available.

PMID:
28003542
47.

NO-BOUNDARY THINKING IN BIOINFORMATICS.

Moore JH, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X.

Pac Symp Biocomput. 2017;22:646-648. doi: 10.1142/9789813207813_0060.

48.
49.

Semi-supervised learning of the electronic health record for phenotype stratification.

Beaulieu-Jones BK, Greene CS; Pooled Resource Open-Access ALS Clinical Trials Consortium.

J Biomed Inform. 2016 Dec;64:168-178. doi: 10.1016/j.jbi.2016.10.007. Epub 2016 Oct 12.

50.

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes.

Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA.

G3 (Bethesda). 2016 Dec 7;6(12):4097-4103. doi: 10.1534/g3.116.033514.

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