Citing dictyBase

Please cite us in your publication if dictyBase helped you achieve your results. Thank you!

• Fey, P., Dodson, R., Basu, S., Chisholm, R. L. (2013). 'One Stop Shop for Everything Dictyostelium: dictyBase and the Dicty Stock Center'. Dictyostelium discoideum Protocols. Methods Mol. Biol. 983:59-92, edited by Ludwig Eichinger and Francisco Rivero.
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• Basu, S., Fey, P., Pandit, Y., Dodson, R. J., Kibbe, W. A., Chisholm, R. L. (2013). DictyBase 2013: integrating multiple Dictyostelid species. Nucleic Acids Res. 41 (Database issue): D676-83.
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• Gaudet, P., Fey, P., Basu, S., Bushmanova, Y. A., Dodson, R., Sheppard K. A., Just, E. M., Kibbe, W. A., Chisholm, R. L. (2011). dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. Nucleic Acids Res. (Database issue): D620-D24.
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• Fey, P., Gaudet, P., Curk, T., Zupan, B., Just, E. M., Basu, S., Merchant, S. N., Bushmanova, Y. A., Shaulsky, G., Kibbe, W. A., Chisholm, R. L. (2009). dictyBase - a Dictyostelium bioinformatics resource update. Nucleic Acids Res. 37, (Database issue): D515-19.
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• Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA. (2006). dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res. 34 (Database issue): D423-7.
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• Fey P, Gaudet P, Pilcher KE, Franke J and Chisholm RL. 2006. dictyBase and the Dicty Stock Center. In Dictyostelium discoideum Protocols. L. Eichinger and F. Rivero, editors. Humana Press, 346: 51-74.
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• Chisholm RL. 2005. dictyBase: Using the Genome to Organize Dictyostelium Biology. In Dictyostelium Genomics. W. Loomis and A. Kuspa, editors. Horizon Press. Pp. 23-39.
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• Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR. (2004) dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res. 32 (Database issue): D332-3.
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Citing the Dictyostelium Genome

• Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435(7038): 43-57.

• See also the Guidelines on use of data in publications from Sanger Center and the Institute of Molecular Biotechnology in Jena.

• Ribosomal DNA sequence:
  Sucgang R, Chen G, Liu W, Lindsay R, Lu J, Muzny D, Shaulsky G, Loomis WF, Gibbs R and Kuspa A. (2003) Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucl. Acids Res. 31(9):2361-2368.
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• Chromosome 2 sequence:
  Gloeckner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF, Guigo R, Kumpf K, Tunggal B, the Dictyostelium Genome Sequencing Consortium, Cox E, Quail MA, Platzer M, Rosenthal A & Noegel AA. Dictyostelium Genome Sequencing Consortium. (2002) Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418(6893):79-85.
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• Mitochondrial genome:
  Ogawa S, Yoshino R, Angata K, Iwamoto M, Pi M, Kuroe K, Matsuo K, Morio T, Urushihara H, Yanagisawa K, Tanaka Y. (2000) The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol. Gen. Genet. 263(3):514-9
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Citing the cDNA project

The Dictyostelium cDNA project has been initiated in 1996 at the University of Tsukaba in Japan.

• Morio T, Urushihara H, Saito T, Ugawa Y, Mizuno H, Yoshida M, Yoshino R, Mitra BN, Pi M, Sato T, Takemoto K, Yasukawa H, Williams J, Maeda M, Takeuchi I, Ochiai H, Tanaka Y. (1998) The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development. DNA Res. 5(6):335-40.
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• Description of EST assemblies:
  Urushihara H, Morio T, Saito T, Kohara Y, Koriki E, Ochiai H, Maeda M, Williams JG, Takeuchi I, Tanaka Y. (2004) Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum. Nucleic Acids Res. 32(5):1647-53.

HAPPY Mapping

HAPPY mapping of the Dictyostelium genome is done at the MRC Laboratory of Molecular Biology, Cambridge.

• Konfortov BA, Cohen HM, Bankier AT, Dear PH. (2000) A High-Resolution HAPPY Map of Dictyostelium discoideum Chromosome 6. Genome Res. 10(11):1737-42.
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• A high resolution HAPPY map of the Dictyostelium discoideum genome. Pachebat JA, Bankier AT, Konfortov BA, Dear PH, Gloeckner G, Szafranski K, Sucgang R, Rajandream M.-A, Davies R, Bloomfield G, Noegel A. (2003) The Dictyostelium Genome Sequencing Consortium. Abstract from the International Dictyostelium conference.

GenBank Sequences

• If GenBank sequence entries are to be cited, the citation should include the sequence name and GenBank accession number. For example: The GenBank accession number for the sequence reported in this paper is U12980.
  The GenBank accession number for the full genome sequence is AAFI00000000.