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Items 1 - 20 of 148
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1:

Full-length messenger RNA sequences greatly improve genome annotation.

Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL.

Genome Biol. 2002;3(6):RESEARCH0029. Epub 2002 May 30.

PMID: 12093376 [PubMed - indexed for MEDLINE]

2:

Features of Arabidopsis genes and genome discovered using full-length cDNAs.

Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA.

Plant Mol Biol. 2006 Jan;60(1):69-85.

PMID: 16463100 [PubMed - indexed for MEDLINE]

3:

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O.

Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.

PMID: 14500829 [PubMed - indexed for MEDLINE]

4:

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.

Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB.

BMC Bioinformatics. 2006 Jan 23;7:33.

PMID: 16426464 [PubMed - indexed for MEDLINE]

5:

Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.

Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB.

Plant Physiol. 2007 May;144(1):32-42. Epub 2007 Mar 9.

PMID: 17351049 [PubMed - indexed for MEDLINE]

6:

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.

PMID: 16305752 [PubMed - indexed for MEDLINE]

7:

Empirical analysis of transcriptional activity in the Arabidopsis genome.

Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR.

Science. 2003 Oct 31;302(5646):842-6.

PMID: 14593172 [PubMed - indexed for MEDLINE]

8:

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.

PMID: 15705189 [PubMed - indexed for MEDLINE]

9:

Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.

Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y, Gaasterland T; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1290-300.

PMID: 12819126 [PubMed - indexed for MEDLINE]

10:

Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.

Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P.

Bioinformatics. 1999 Nov;15(11):887-99.

PMID: 10743555 [PubMed - indexed for MEDLINE]

11:

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.

Rensing SA, Fritzowsky D, Lang D, Reski R.

BMC Genomics. 2005 Mar 22;6(1):43.

PMID: 15784153 [PubMed - indexed for MEDLINE]

12:

Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.

Castelli V, Aury JM, Jaillon O, Wincker P, Clepet C, Menard M, Cruaud C, Quétier F, Scarpelli C, Schächter V, Temple G, Caboche M, Weissenbach J, Salanoubat M.

Genome Res. 2004 Mar;14(3):406-13.

PMID: 14993207 [PubMed - indexed for MEDLINE]

13:

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.

Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J.

BMC Genomics. 2005 Oct 19;6:144.

PMID: 16236172 [PubMed - indexed for MEDLINE]

14:

Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis.

Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD.

Genome Res. 2005 Apr;15(4):487-95.

PMID: 15805490 [PubMed - indexed for MEDLINE]

15:

Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring.

Usuka J, Brendel V.

J Mol Biol. 2000 Apr 14;297(5):1075-85.

PMID: 10764574 [PubMed - indexed for MEDLINE]

16:

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays.

Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC, Hegeman A, Nelson C, Rancour D, Bednarek S, Ulrich EL, Zhao Q, Wrobel RL, Newman CS, Fox BG, Phillips GN Jr, Markley JL, Sussman MR.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4453-8. Epub 2005 Mar 8.

PMID: 15755812 [PubMed - indexed for MEDLINE]

17:

The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing.

Wang BB, Brendel V.

Genome Biol. 2004;5(12):R102. Epub 2004 Nov 29.

PMID: 15575968 [PubMed - indexed for MEDLINE]

18:

The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence.

Fizames C, Muños S, Cazettes C, Nacry P, Boucherez J, Gaymard F, Piquemal D, Delorme V, Commes T, Doumas P, Cooke R, Marti J, Sentenac H, Gojon A.

Plant Physiol. 2004 Jan;134(1):67-80.

PMID: 14730065 [PubMed - indexed for MEDLINE]

19:

Computational evidence for hundreds of non-conserved plant microRNAs.

Lindow M, Krogh A.

BMC Genomics. 2005 Sep 13;6:119.

PMID: 16159385 [PubMed - indexed for MEDLINE]

20:

Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.

Wang XJ, Gaasterland T, Chua NH.

Genome Biol. 2005;6(4):R30. Epub 2005 Mar 15.

PMID: 15833117 [PubMed - indexed for MEDLINE]

Items 1 - 20 of 148
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