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Results: 1 to 20 of 30

1.

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.

Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr, Surek B, Thomsen CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK.

PLoS One. 2012;7(11):e50226. doi: 10.1371/journal.pone.0050226. Epub 2012 Nov 21.

PMID:
23185583
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Light-regulated and cell-specific methylation of the maize PEPC promoter.

Tolley BJ, Woodfield H, Wanchana S, Bruskiewich R, Hibberd JM.

J Exp Bot. 2012 Feb;63(3):1381-90. doi: 10.1093/jxb/err367. Epub 2011 Dec 5.

PMID:
22143916
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Characterization of statistical features for plant microRNA prediction.

Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu XG.

BMC Genomics. 2011 Feb 16;12:108. doi: 10.1186/1471-2164-12-108.

PMID:
21324149
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Physiological and proteomic responses of rice peduncles to drought stress.

Muthurajan R, Shobbar ZS, Jagadish SV, Bruskiewich R, Ismail A, Leung H, Bennett J.

Mol Biotechnol. 2011 Jun;48(2):173-82. doi: 10.1007/s12033-010-9358-2.

PMID:
21132544
[PubMed - indexed for MEDLINE]
5.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

PMID:
20727200
[PubMed]
Free PMC Article
6.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.

Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, de Los Reyes BG.

BMC Plant Biol. 2010 Jan 25;10:16. doi: 10.1186/1471-2229-10-16.

PMID:
20100339
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.

Shrestha R, Arnaud E, Mauleon R, Senger M, Davenport GF, Hancock D, Morrison N, Bruskiewich R, McLaren G.

AoB Plants. 2010;2010:plq008. doi: 10.1093/aobpla/plq008. Epub 2010 May 27.

PMID:
22476066
[PubMed]
Free PMC Article
8.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. doi: 10.1073/pnas.0900992106. Epub 2009 Jul 13.

PMID:
19597147
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

Thongjuea S, Ruanjaichon V, Bruskiewich R, Vanavichit A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D996-1000. doi: 10.1093/nar/gkn638. Epub 2008 Sep 27.

PMID:
18820292
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Meeting review: plant bioinformatics at the NSF and NPGI (PAMGX satellite) meetings.

Bruskiewich R.

Comp Funct Genomics. 2002;3(2):176. doi: 10.1002/cfg.158.

PMID:
18628836
[PubMed]
Free PMC Article
11.

The generation challenge programme platform: semantic standards and workbench for crop science.

Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M, Simon R, Balaji J, Akintunde A, Mauleon R, Wanchana S, Shah T, Anacleto M, Portugal A, Ulat VJ, Thongjuea S, Braak K, Ritter S, Dereeper A, Skofic M, Rojas E, Martins N, Pappas G, Alamban R, Almodiel R, Barboza LH, Detras J, Manansala K, Mendoza MJ, Morales J, Peralta B, Valerio R, Zhang Y, Gregorio S, Hermocilla J, Echavez M, Yap JM, Farmer A, Schiltz G, Lee J, Casstevens T, Jaiswal P, Meintjes A, Wilkinson M, Good B, Wagner J, Morris J, Marshall D, Collins A, Kikuchi S, Metz T, McLaren G, van Hintum T.

Int J Plant Genomics. 2008;2008:369601. doi: 10.1155/2008/369601.

PMID:
18483570
[PubMed]
Free PMC Article
12.

Development of a novel data mining tool to find cis-elements in rice gene promoter regions.

Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S.

BMC Plant Biol. 2008 Feb 27;8:20. doi: 10.1186/1471-2229-8-20.

PMID:
18302796
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

International crop information system for germplasm data management.

Portugal A, Balachandra R, Metz T, Bruskiewich R, McLaren G.

Methods Mol Biol. 2007;406:459-71.

PMID:
18287707
[PubMed - indexed for MEDLINE]
14.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
18089549
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The Generation Challenge Programme comparative plant stress-responsive gene catalogue.

Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte M, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K, van Hintum T, Bruskiewich RM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D943-6. Epub 2007 Oct 11.

PMID:
17933772
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
17210932
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Generation Challenge Programme (GCP): standards for crop data.

Bruskiewich R, Davenport G, Hazekamp T, Metz T, Ruiz M, Simon R, Takeya M, Lee J, Senger M, McLaren G, Van Hintum T.

OMICS. 2006 Summer;10(2):215-9. Review.

PMID:
16901229
[PubMed - indexed for MEDLINE]
19.

Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes.

McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H.

Plant Physiol. 2006 May;141(1):26-31. No abstract available.

PMID:
16684934
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering.

Ji XM, Raveendran M, Oane R, Ismail A, Lafitte R, Bruskiewich R, Cheng SH, Bennett J.

Plant Mol Biol. 2005 Dec;59(6):945-64.

PMID:
16307368
[PubMed - indexed for MEDLINE]

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