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Items: 26

1.

Survey of genes involved in rice secondary cell wall formation through a co-expression network.

Hirano K, Aya K, Morinaka Y, Nagamatsu S, Sato Y, Antonio BA, Namiki N, Nagamura Y, Matsuoka M.

Plant Cell Physiol. 2013 Nov;54(11):1803-21. doi: 10.1093/pcp/pct121. Epub 2013 Oct 1.

PMID:
24089433
2.

Identification of transcription factors involved in rice secondary cell wall formation.

Hirano K, Kondo M, Aya K, Miyao A, Sato Y, Antonio BA, Namiki N, Nagamura Y, Matsuoka M.

Plant Cell Physiol. 2013 Nov;54(11):1791-802. doi: 10.1093/pcp/pct122. Epub 2013 Oct 1.

PMID:
24089432
3.

Global transcriptome profile of rice root in response to essential macronutrient deficiency.

Takehisa H, Sato Y, Antonio BA, Nagamura Y.

Plant Signal Behav. 2013 Jun;8(6):e24409. doi: 10.4161/psb.24409. Epub 2013 Apr 19.

4.

Deciphering and prediction of transcriptome dynamics under fluctuating field conditions.

Nagano AJ, Sato Y, Mihara M, Antonio BA, Motoyama R, Itoh H, Nagamura Y, Izawa T.

Cell. 2012 Dec 7;151(6):1358-69. doi: 10.1016/j.cell.2012.10.048.

5.

RiceFREND: a platform for retrieving coexpressed gene networks in rice.

Sato Y, Namiki N, Takehisa H, Kamatsuki K, Minami H, Ikawa H, Ohyanagi H, Sugimoto K, Itoh J, Antonio BA, Nagamura Y.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1214-21. doi: 10.1093/nar/gks1122. Epub 2012 Nov 24.

6.

RiceXPro version 3.0: expanding the informatics resource for rice transcriptome.

Sato Y, Takehisa H, Kamatsuki K, Minami H, Namiki N, Ikawa H, Ohyanagi H, Sugimoto K, Antonio BA, Nagamura Y.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1206-13. doi: 10.1093/nar/gks1125. Epub 2012 Nov 23.

7.

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions.

Takehisa H, Sato Y, Igarashi M, Abiko T, Antonio BA, Kamatsuki K, Minami H, Namiki N, Inukai Y, Nakazono M, Nagamura Y.

Plant J. 2012 Jan;69(1):126-40. doi: 10.1111/j.1365-313X.2011.04777.x. Epub 2011 Oct 25.

8.

Rice TOGO Browser: A platform to retrieve integrated information on rice functional and applied genomics.

Nagamura Y, Antonio BA, Sato Y, Miyao A, Namiki N, Yonemaru J, Minami H, Kamatsuki K, Shimura K, Shimizu Y, Hirochika H.

Plant Cell Physiol. 2011 Feb;52(2):230-7. doi: 10.1093/pcp/pcq197. Epub 2011 Jan 6.

9.

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions.

Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1141-8. doi: 10.1093/nar/gkq1085. Epub 2010 Nov 2.

10.

Plant genomics: Sorghum in sequence.

Sasaki T, Antonio BA.

Nature. 2009 Jan 29;457(7229):547-8. doi: 10.1038/457547a. No abstract available.

PMID:
19177121
11.

Development in rice genome research based on accurate genome sequence.

Matsumoto T, Wu J, Antonio BA, Sasaki T.

Int J Plant Genomics. 2008;2008:348621. doi: 10.1155/2008/348621.

12.

The Rice Annotation Project Database (RAP-DB): 2008 update.

Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D1028-33. Epub 2007 Dec 17.

13.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.

Genome Res. 2007 Feb;17(2):175-83. Epub 2007 Jan 8.

14.

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information.

Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D741-4.

15.

From mapping to sequencing, post-sequencing and beyond.

Sasaki T, Matsumoto T, Antonio BA, Nagamura Y.

Plant Cell Physiol. 2005 Jan;46(1):3-13. Epub 2005 Jan 19. Review.

PMID:
15659433
16.

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

Ito Y, Arikawa K, Antonio BA, Ohta I, Naito S, Mukai Y, Shimano A, Masukawa M, Shibata M, Yamamoto M, Ito Y, Yokoyama J, Sakai Y, Sakata K, Nagamura Y, Namiki N, Matsumoto T, Higo K, Sasaki T.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D651-5.

17.

The genome sequence and structure of rice chromosome 1.

Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T.

Nature. 2002 Nov 21;420(6913):312-6.

PMID:
12447438
18.

RiceGAAS: an automated annotation system and database for rice genome sequence.

Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K.

Nucleic Acids Res. 2002 Jan 1;30(1):98-102.

19.

Rice at the forefront of plant genome informatics.

Antonio BA, Sakata K, Sasaki T.

Genome Inform Ser Workshop Genome Inform. 2000;11:3-11.

PMID:
11700582
20.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes.

Saji S, Umehara Y, Antonio BA, Yamane H, Tanoue H, Baba T, Aoki H, Ishige N, Wu J, Koike K, Matsumoto T, Sasaki T.

Genome. 2001 Feb;44(1):32-7.

PMID:
11269353
21.

INE: a rice genome database with an integrated map view.

Sakata K, Antonio BA, Mukai Y, Nagasaki H, Sakai Y, Makino K, Sasaki T.

Nucleic Acids Res. 2000 Jan 1;28(1):97-101.

22.

A high-density rice genetic linkage map with 2275 markers using a single F2 population.

Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T.

Genetics. 1998 Jan;148(1):479-94.

23.

Rice molecular genetic map using RFLPs and its applications.

Nagamura Y, Antonio BA, Sasaki T.

Plant Mol Biol. 1997 Sep;35(1-2):79-87. Review.

PMID:
9291962
24.

Physical mapping of rice chromosomes 8 and 9 with YAC clones.

Antonio BA, Emoto M, Wu J, Ashikawa I, Umehara Y, Kurata N, Sasaki T.

DNA Res. 1996 Dec 31;3(6):393-400.

PMID:
9097041
25.

Comparison off genetic distance and order off DNA markers in five populations of rice.

Antonio BA, Inoue T, Kajiya H, Nagamura Y, Kurata N, Minobe Y, Yano M, Nakagahra M, Sasaki T.

Genome. 1996 Oct;39(5):946-56.

PMID:
18469946
26.

A 300 kilobase interval genetic map of rice including 883 expressed sequences.

Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, et al.

Nat Genet. 1994 Dec;8(4):365-72.

PMID:
7894488

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