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Items: 1 to 50 of 189

1.

A Parasite's Perspective on Data Sharing.

Park Y, Greene CS.

Gigascience. 2018 Nov 5. doi: 10.1093/gigascience/giy129. [Epub ahead of print]

PMID:
30395209
2.

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
3.

"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
4.

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

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

Bioinformatics. 2018 Sep 24. doi: 10.1093/bioinformatics/bty828. [Epub ahead of print]

PMID:
30247517
5.

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. 2018 Sep 10. doi: 10.1111/joor.12707. [Epub ahead of print]

PMID:
30203622
6.

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.

PMID:
30202837
7.

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.

8.

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.

9.

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
10.

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
11.

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
12.

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.

13.

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.

PMID:
29629986
14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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
21.

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.

22.
24.

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.

25.

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.

26.

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
27.
28.

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.

29.

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.

30.

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
31.

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.

PMID:
28575147
32.

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.

33.

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.

34.

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.

35.

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
36.

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.

37.

Cheap-seq.

Greene CS.

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

PMID:
28003542
38.

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.

39.
40.

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.

41.

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.

42.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

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, Törönen 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, Sedeño-Cortés 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, Fernández 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.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

43.

Pathway and network-based strategies to translate genetic discoveries into effective therapies.

Greene CS, Voight BF.

Hum Mol Genet. 2016 Oct 1;25(R2):R94-R98. Epub 2016 Jun 23. Review.

44.

Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits.

Greene CS, Himmelstein DS.

Circ Cardiovasc Genet. 2016 Apr;9(2):179-84. doi: 10.1161/CIRCGENETICS.115.001181. Review. No abstract available.

PMID:
27094199
45.

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.

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.

Oncotarget. 2016 Mar 29;7(13):17087-102. doi: 10.18632/oncotarget.7718.

46.

Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology.

Himmelstein DS, Greene CS, Moore JH.

BioData Min. 2016 Feb 3;9:9. doi: 10.1186/s13040-016-0085-5. eCollection 2016.

47.

Cross-platform normalization of microarray and RNA-seq data for machine learning applications.

Thompson JA, Tan J, Greene CS.

PeerJ. 2016 Jan 21;4:e1621. doi: 10.7717/peerj.1621. eCollection 2016.

48.

Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts.

Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AJ, Shen L, Greene CS; Alzheimer’s Disease Neuroimaging Initiative.

BioData Min. 2016 Jan 19;9:3. doi: 10.1186/s13040-016-0082-8. eCollection 2016.

49.

COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.

Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y.

Pac Symp Biocomput. 2016;21:557-67.

50.

Leveraging global gene expression patterns to predict expression of unmeasured genes.

Rudd J, Zelaya RA, Demidenko E, Goode EL, Greene CS, Doherty JA.

BMC Genomics. 2015 Dec 15;16:1065. doi: 10.1186/s12864-015-2250-5.

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