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Items: 1 to 20 of 75

1.

An optimized protocol for analysis of EST sequences.

Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J.

Nucleic Acids Res. 2000 Sep 15;28(18):3657-65.

2.

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.

Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J.

Nucleic Acids Res. 2001 Jan 1;29(1):159-64.

3.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D71-4.

4.

The TIGR gene indices: reconstruction and representation of expressed gene sequences.

Quackenbush J, Liang F, Holt I, Pertea G, Upton J.

Nucleic Acids Res. 2000 Jan 1;28(1):141-5.

5.

Gene index analysis of the human genome estimates approximately 120,000 genes.

Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J.

Nat Genet. 2000 Jun;25(2):239-40. Erratum in: Nat Genet 2000 Dec;26(4):501.

PMID:
10835646
6.

Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index.

Sonstegard TS, Capuco AV, White J, Van Tassell CP, Connor EE, Cho J, Sultana R, Shade L, Wray JE, Wells KD, Quackenbush J.

Mamm Genome. 2002 Jul;13(7):373-9.

PMID:
12140684
7.

A graph based algorithm for generating EST consensus sequences.

Malde K, Coward E, Jonassen I.

Bioinformatics. 2005 Apr 15;21(8):1371-5. Epub 2004 Nov 30. Erratum in: Bioinformatics. 2005 Jul 1;21(13):3062.

PMID:
15572463
8.

Positional candidate gene selection from livestock EST databases using Gene Ontology.

Harhay GP, Keele JW.

Bioinformatics. 2003 Jan 22;19(2):249-55.

PMID:
12538246
9.

A hitchhiker's guide to expressed sequence tag (EST) analysis.

Nagaraj SH, Gasser RB, Ranganathan S.

Brief Bioinform. 2007 Jan;8(1):6-21. Epub 2006 May 23. Review.

PMID:
16772268
10.
11.

An encyclopedia of mouse genes.

Marra M, Hillier L, Kucaba T, Allen M, Barstead R, Beck C, Blistain A, Bonaldo M, Bowers Y, Bowles L, Cardenas M, Chamberlain A, Chappell J, Clifton S, Favello A, Geisel S, Gibbons M, Harvey N, Hill F, Jackson Y, Kohn S, Lennon G, Mardis E, Martin J, Mila L, McCann R, Morales R, Pape D, Person B, Prange C, Ritter E, Soares M, Schurk R, Shin T, Steptoe M, Swaller T, Theising B, Underwood K, Wylie T, Yount T, Wilson R, Waterston R.

Nat Genet. 1999 Feb;21(2):191-4.

PMID:
9988271
12.

Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.

Poustka AJ, Groth D, Hennig S, Thamm S, Cameron A, Beck A, Reinhardt R, Herwig R, Panopoulou G, Lehrach H.

Genome Res. 2003 Dec;13(12):2736-46.

13.

Global assembly of expressed sequence tags.

Cheung F.

Methods Mol Biol. 2012;883:193-9. doi: 10.1007/978-1-61779-839-9_15.

PMID:
22589135
14.

ECgene: genome annotation for alternative splicing.

Kim P, Kim N, Lee Y, Kim B, Shin Y, Lee S.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D75-9.

15.

Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle.

Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW.

Genome Res. 2001 Apr;11(4):626-30.

16.

Characterization of 954 bovine full-CDS cDNA sequences.

Harhay GP, Sonstegard TS, Keele JW, Heaton MP, Clawson ML, Snelling WM, Wiedmann RT, Van Tassell CP, Smith TP.

BMC Genomics. 2005 Nov 23;6:166.

17.

The alternative oxidase family of Vitis vinifera reveals an attractive model to study the importance of genomic design.

Costa JH, de Melo DF, Gouveia Z, Cardoso HG, Peixe A, Arnholdt-Schmitt B.

Physiol Plant. 2009 Dec;137(4):553-65. doi: 10.1111/j.1399-3054.2009.01267.x. Epub 2009 Jul 6.

PMID:
19682279
18.

An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus.

Ju Z, Wells MC, Martinez A, Hazlewood L, Walter RB.

In Silico Biol. 2005;5(5-6):439-63.

PMID:
16268789
19.

ESTminer: a suite of programs for gene and allele identification.

Nelson RT, Grant D, Shoemaker RC.

Bioinformatics. 2005 Mar 1;21(5):691-3. Epub 2004 Nov 5.

PMID:
15531616
20.

Comparative EST analyses in plant systems.

Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V.

Methods Enzymol. 2005;395:400-18. Review.

PMID:
15984049

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