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Items: 1 to 20 of 109

1.

XenMine: A genomic interaction tool for the Xenopus community.

Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC.

Dev Biol. 2016 May 3. pii: S0012-1606(15)30264-5. doi: 10.1016/j.ydbio.2016.02.034. [Epub ahead of print]

PMID:
27157655
2.

From one to many: expanding the Saccharomyces cerevisiae reference genome panel.

Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM.

Database (Oxford). 2016 Mar 17;2016. pii: baw020. doi: 10.1093/database/baw020. Print 2016.

3.

Principles of metadata organization at the ENCODE data coordination center.

Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM.

Database (Oxford). 2016 Mar 15;2016. pii: baw001. doi: 10.1093/database/baw001. Print 2016.

4.

The Saccharomyces Genome Database: A Tool for Discovery.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.top083840. doi: 10.1101/pdb.top083840.

PMID:
26631132
5.

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922.

PMID:
26631126
6.

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914.

PMID:
26631125
7.

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906.

PMID:
26631124
8.

The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes.

Cherry JM.

Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898.

PMID:
26631123
9.

The Saccharomyces Genome Database Variant Viewer.

Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D698-702. doi: 10.1093/nar/gkv1250. Epub 2015 Nov 17.

10.

ENCODE data at the ENCODE portal.

Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. doi: 10.1093/nar/gkv1160. Epub 2015 Nov 2.

11.

Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup.

Overby CL, Heale B, Aronson S, Cherry JM, Dwight S, Milosavljevic A, Nelson T, Niehaus A, Weaver MA, Ramos EM, Williams MS.

Clin Pharmacol Ther. 2016 Feb;99(2):157-60. doi: 10.1002/cpt.270. Epub 2015 Nov 9.

PMID:
26418054
12.

Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae.

Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry JM.

PLoS One. 2015 May 27;10(5):e0129184. doi: 10.1371/journal.pone.0129184. eCollection 2015. No abstract available.

13.

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry JM.

PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. Erratum in: PLoS One. 2015;10(5):e0129184. Gallagher, Jennifer [added]; Choe, Kisurb [added]; Snyder, Michael [added].

14.

Ontology application and use at the ENCODE DCC.

Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL.

Database (Oxford). 2015 Mar 16;2015. pii: bav010. doi: 10.1093/database/bav010. Print 2015. Review.

15.

Gene Ontology Consortium: going forward.

Gene Ontology Consortium.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26.

16.

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A.

Cell. 2014 Jul 31;158(3):673-88. doi: 10.1016/j.cell.2014.06.027. Erratum in: Cell. 2015 Nov 19;163(5):1281-6.

17.

The reference genome sequence of Saccharomyces cerevisiae: then and now.

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM.

G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.

18.

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.

Database (Oxford). 2013 Dec 6;2013:bat077. doi: 10.1093/database/bat077. Print 2013. No abstract available.

19.

Saccharomyces genome database provides new regulation data.

Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D717-25. doi: 10.1093/nar/gkt1158. Epub 2013 Nov 21.

20.

A guide to best practices for Gene Ontology (GO) manual annotation.

Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM.

Database (Oxford). 2013 Jul 9;2013:bat054. doi: 10.1093/database/bat054. Print 2013.

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