Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 204

1.

Immune landscapes associated with different glioblastoma molecular subtypes.

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.

Acta Neuropathol Commun. 2019 Nov 29;7(1):203. doi: 10.1186/s40478-019-0803-6.

2.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

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, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović 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, Törönen 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, Gligorijević 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, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc 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.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

3.

Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma.

Lin YT, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP.

Blood Adv. 2019 Nov 12;3(21):3214-3227. doi: 10.1182/bloodadvances.2019000303.

4.

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

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.

Cell Rep. 2019 Nov 5;29(6):1675-1689.e9. doi: 10.1016/j.celrep.2019.09.071.

5.

Embracing study heterogeneity for finding genetic interactions in large-scale research consortia.

Liu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y.

Genet Epidemiol. 2019 Oct 4. doi: 10.1002/gepi.22262. [Epub ahead of print]

PMID:
31583758
6.

Voices in methods development.

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.

Nat Methods. 2019 Oct;16(10):945-951. doi: 10.1038/s41592-019-0585-6. No abstract available.

PMID:
31562479
7.

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
8.

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.

9.

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
10.

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.

12.

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.

13.

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
14.

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
15.

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.

16.

A parasite's perspective on data sharing.

Park Y, Greene CS.

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

17.

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
18.

"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
19.

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
20.

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
21.

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
22.

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.

23.

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.

24.

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
25.

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
26.

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
27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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
36.

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.

37.
39.

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.

40.

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.

41.

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
42.
43.

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.

44.

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.

45.

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
46.

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.

47.

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.

48.

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.

49.

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.

50.

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

Supplemental Content

Loading ...
Support Center