Huala E, Dickerman A, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang J, Huang W, Mueller L, Bhattacharyya D, Bhaya D, Sobral B, Beavis B, Somerville C, Rhee SY: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001, 29 (1): 102-5. 10.1093/nar/29.1.102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Auken KV, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD: WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 2005, 33: D383-D389.
Article
PubMed Central
CAS
PubMed
Google Scholar
Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, Mouse Genome Database Group: The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 2011, 39 (Suppl 1): D842-D848.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D: SGD: Saccharomyces Genome Database. Nucleic Acids Res. 1998, 26 (1): 73-80. 10.1093/nar/26.1.73.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium: FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 2009, 37: D555-D559. 10.1093/nar/gkn788.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kurata N, Yamazaki Y: Oryzabase. An integrated biological and genome information database for rice. Plant Physiol. 2006, 140: 12-17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR: Gramene, a tool for grass genomics. Plant Physiol. 2002, 130: 1606-1613. 10.1104/pp.015248.
Article
PubMed Central
CAS
PubMed
Google Scholar
Phytozome. [http://www.phytozome.net/soybean]
Grant D, Nelson RT, Cannon SB, Shoemaker RC: SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010, 38: D843-D846. 10.1093/nar/gkp798.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shultz JL, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA: The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res. 2006, 34 (Database issue): D758-D765.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alkharouf NW, Matthews BF: SGMD: the Soybean Genomics and Microarray Database. Nucleic Acids Res. 2004, 32 (Suppl 1): D398-D400.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA: Genome sequence of the palaeopolyploid soybean. Nature. 2010, 463: 178-83. 10.1038/nature08670.
Article
CAS
PubMed
Google Scholar
Apache. [http://httpd.apache.org]
PHP. [http://www.php.net]
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006.
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30 (1): 207-210. 10.1093/nar/30.1.207.
Article
PubMed Central
CAS
PubMed
Google Scholar
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A: ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2011, 39 (Database issue): D1002-D1004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Joshi T, Yao Q, Franklin LD, Brechenmacher L, Valliyodan B, Stacey G, Nguyen H, Xu D: SoyMetDB: The Soybean Metabolome Database. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010). 2010, Hong Kong, 203-208.
Chapter
Google Scholar
Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier JD, Farmer A, May G, Meyers BC, Stacey G: Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 2010, 11 (Suppl 1): S14-10.1186/1471-2105-11-S1-S14.
Article
PubMed Central
PubMed
Google Scholar
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT: SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010, 11: 469-10.1186/1471-2164-11-469.
Article
PubMed Central
PubMed
Google Scholar
Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27.
Article
PubMed Central
CAS
PubMed
Google Scholar
Goffard N, Weiller G: GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics. 2007, 8: 87-10.1186/1471-2105-8-87.
Article
PubMed Central
PubMed
Google Scholar
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M: MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37 (6): 914-39. 10.1111/j.1365-313X.2004.02016.x.
Article
CAS
PubMed
Google Scholar
Wang Z, Eickholt J, Cheng J: MULTICOM: a multi-level combination approach to protein structure prediction and its assessment in CASP8. Bioinformatics. 2010, 26 (7): 882-888. 10.1093/bioinformatics/btq058.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jmol. [http://jmol.sourceforge.net]
Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen H, Xu D, Stacey G, Cheng J: SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 2010, 10: 14-10.1186/1471-2229-10-14.
Article
PubMed Central
PubMed
Google Scholar
Guttikonda SK, Joshi T, Bisht NC, Chen H, An YQ, Pandey S, Xu D, Yu O: Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. BMC Plant Biol. 2010, 10: 243-10.1186/1471-2229-10-243.
Article
PubMed Central
PubMed
Google Scholar
Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, Rombauts S, Rouzé P, De Moor B, Marchal K: INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. Bioinformatics. 2002, 18 (2): 331-332. 10.1093/bioinformatics/18.2.331.
Article
CAS
PubMed
Google Scholar
Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouzé P, Moreau Y: A higher order background model improves the detection of regulatory elements by Gibbs sampling. Bioinformatics. 2001, 17 (12): 1113-1122. 10.1093/bioinformatics/17.12.1113.
Article
CAS
PubMed
Google Scholar
Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res. 2004, 14: 1188-1190. 10.1101/gr.849004.
Article
PubMed Central
CAS
PubMed
Google Scholar