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Items: 1 to 20 of 72

1.

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
2.

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.

3.

A parasite's perspective on data sharing.

Park Y, Greene CS.

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

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.

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.

6.

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.

7.

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.

8.

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
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.
18.

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.

19.

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.

20.

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