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Results: 1 to 20 of 73

1.

A computational approach for identifying pseudogenes in the ENCODE regions.

Zheng D, Gerstein MB.

Genome Biol. 2006;7 Suppl 1:S13.1-10. Epub 2006 Aug 7.

PMID:
16925835
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

Solovyev V, Kosarev P, Seledsov I, Vorobyev D.

Genome Biol. 2006;7 Suppl 1:S10.1-12. Epub 2006 Aug 7.

PMID:
16925832
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

PMID:
16925838
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Thierry-Mieg D, Thierry-Mieg J.

Genome Biol. 2006;7 Suppl 1:S12.1-14. Epub 2006 Aug 7.

PMID:
16925834
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Arumugam M, Wei C, Brown RH, Brent MR.

Genome Biol. 2006;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

PMID:
16925839
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

Yao A, Charlab R, Li P.

Nucleic Acids Res. 2006;34(16):4477-85. Epub 2006 Aug 31.

PMID:
16945953
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Integrated pseudogene annotation for human chromosome 22: evidence for transcription.

Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M.

J Mol Biol. 2005 May 27;349(1):27-45. Epub 2005 Apr 2.

PMID:
15876366
[PubMed - indexed for MEDLINE]
8.

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC.

Nucleic Acids Res. 2007;35(12):3953-62. Epub 2007 Jun 6.

PMID:
17553834
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A genome-wide survey of human pseudogenes.

Torrents D, Suyama M, Zdobnov E, Bork P.

Genome Res. 2003 Dec;13(12):2559-67.

PMID:
14656963
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PseudoPipe: an automated pseudogene identification pipeline.

Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M.

Bioinformatics. 2006 Jun 15;22(12):1437-9. Epub 2006 Mar 30.

PMID:
16574694
[PubMed - indexed for MEDLINE]
Free Article
11.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

PMID:
22955987
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

PMID:
17123449
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC.

BMC Bioinformatics. 2009 Jan 23;10:30. doi: 10.1186/1471-2105-10-30.

PMID:
19166590
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genome-wide identification of pseudogenes capable of disease-causing gene conversion.

Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA.

Hum Mutat. 2006 Jun;27(6):545-52.

PMID:
16671097
[PubMed - indexed for MEDLINE]
15.

Segmental duplications in the human genome reveal details of pseudogene formation.

Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

Nucleic Acids Res. 2010 Nov;38(20):6997-7007. doi: 10.1093/nar/gkq587. Epub 2010 Jul 8.

PMID:
20615899
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Flicek P, Brent MR.

Genome Biol. 2006;7 Suppl 1:S8.1-9. Epub 2006 Aug 7.

PMID:
16925842
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.

Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W143-7. Epub 2007 Jun 1.

PMID:
17545197
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Hahn P, Böse J, Edler S, Lengeling A.

BMC Genomics. 2008 Jun 18;9:293. doi: 10.1186/1471-2164-9-293.

PMID:
18564434
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

BMC Genomics. 2008 Feb 28;9:106. doi: 10.1186/1471-2164-9-106.

PMID:
18307801
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Locating potential enhancer elements by comparative genomics using the EEL software.

Palin K, Taipale J, Ukkonen E.

Nat Protoc. 2006;1(1):368-74.

PMID:
17406258
[PubMed - indexed for MEDLINE]

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