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]
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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]
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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]
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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]
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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]
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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]
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