Literature DB >> 14681427

dictyBase: a new Dictyostelium discoideum genome database.

Lisa Kreppel1, Petra Fey, Pascale Gaudet, Eric Just, Warren A Kibbe, Rex L Chisholm, Alan R Kimmel.   

Abstract

Dictyostelium discoideum is a powerful and genetically tractable model system used for the study of numerous cellular molecular mechanisms including chemotaxis, phagocytosis and signal transduction. The past 2 years have seen a significant expansion in the scope and accessibility of online resources for Dictyostelium. Recent advances have focused on the development of a new comprehensive online resource called dictyBase (http://dictybase.org). This database not only provides access to genomic data including functional annotation of genes, gene products and chromosomal mapping, but also to extensive biological information such as mutant phenotypes and corresponding reference material. In conjunction with additional sites (http://genome. imb-jena.de/dictyostelium/, http://dictyensembl. bioch.bcm.tmc.edu and http://www.sanger.ac.uk/Projects/D_discoideum/) from the genome sequencing and assembly centers, these improvements have expanded the scope of the Dictyostelium databases making them accessible and useful to any researcher interested in comparative and functional genomics in metazoan organisms.

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Year:  2004        PMID: 14681427      PMCID: PMC308872          DOI: 10.1093/nar/gkh138

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  9 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Saccharomyces Genome Database.

Authors:  Laurie Issel-Tarver; Karen R Christie; Kara Dolinski; Rey Andrada; Rama Balakrishnan; Catherine A Ball; Gail Binkley; Stan Dong; Selina S Dwight; Dianna G Fisk; Midori Harris; Mark Schroeder; Anand Sethuraman; Kane Tse; Shuai Weng; David Botstein; J Michael Cherry
Journal:  Methods Enzymol       Date:  2002       Impact factor: 1.600

3.  The Protein Data Bank and structural genomics.

Authors:  John Westbrook; Zukang Feng; Li Chen; Huanwang Yang; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

5.  Genomic database resources for Dictyostelium discoideum.

Authors:  Lisa Kreppel; Alan R Kimmel
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Authors:  Selina S Dwight; Midori A Harris; Kara Dolinski; Catherine A Ball; Gail Binkley; Karen R Christie; Dianna G Fisk; Laurie Issel-Tarver; Mark Schroeder; Gavin Sherlock; Anand Sethuraman; Shuai Weng; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 7.  Functional genomics of the social amoebae, Dictyostelium discoideum.

Authors:  Hideko Urushihara
Journal:  Mol Cells       Date:  2002-02-28       Impact factor: 5.034

8.  A proposal for a uniform nomenclature in bacterial genetics.

Authors:  M Demerec; E A Adelberg; A J Clark; P E Hartman
Journal:  Genetics       Date:  1966-07       Impact factor: 4.562

9.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum.

Authors:  Gernot Glöckner; Ludwig Eichinger; Karol Szafranski; Justin A Pachebat; Alan T Bankier; Paul H Dear; Rüdiger Lehmann; Cornelia Baumgart; Genís Parra; Josep F Abril; Roderic Guigó; Kai Kumpf; Budi Tunggal; Edward Cox; Michael A Quail; Matthias Platzer; André Rosenthal; Angelika A Noegel
Journal:  Nature       Date:  2002-07-04       Impact factor: 49.962

  9 in total
  35 in total

1.  Sequence and comparative genomic analysis of actin-related proteins.

Authors:  Jean Muller; Yukako Oma; Laurent Vallar; Evelyne Friederich; Olivier Poch; Barbara Winsor
Journal:  Mol Biol Cell       Date:  2005-09-29       Impact factor: 4.138

2.  Myosin heavy-chain kinase A from Dictyostelium possesses a novel actin-binding domain that cross-links actin filaments.

Authors:  Misty Russ; Daniel Croft; Omar Ali; Raquel Martinez; Paul A Steimle
Journal:  Biochem J       Date:  2006-04-15       Impact factor: 3.857

3.  A Rab21/LIM-only/CH-LIM complex regulates phagocytosis via both activating and inhibitory mechanisms.

Authors:  Taruna Khurana; Joseph A Brzostowski; Alan R Kimmel
Journal:  EMBO J       Date:  2005-06-16       Impact factor: 11.598

4.  Reevaluation of the predicted gene structure of Dictyostelium cystatin A3 (cpiC) by nucleotide sequence determination of its cDNA* and its phylogenetic position in the cystatin superfamily.

Authors:  Medhat S El-Halawany; Hideki Shibata; Kiyotaka Hitomi; Masatoshi Maki
Journal:  Mol Biol Rep       Date:  2005-12       Impact factor: 2.316

5.  An ancestral bacterial division system is widespread in eukaryotic mitochondria.

Authors:  Michelle M Leger; Markéta Petrů; Vojtěch Žárský; Laura Eme; Čestmír Vlček; Tommy Harding; B Franz Lang; Marek Eliáš; Pavel Doležal; Andrew J Roger
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-23       Impact factor: 11.205

6.  Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea.

Authors:  Maura Rojas-Pirela; Diego Andrade-Alviárez; Verónica Rojas; Ulrike Kemmerling; Ana J Cáceres; Paul A Michels; Juan Luis Concepción; Wilfredo Quiñones
Journal:  Open Biol       Date:  2020-11-25       Impact factor: 6.411

7.  Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation.

Authors:  Liliana Malinovska; Sandra Palm; Kimberley Gibson; Jean-Marc Verbavatz; Simon Alberti
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-04       Impact factor: 11.205

8.  Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1.

Authors:  Mustafa H Syed; Tatiana V Karpinets; Michael R Leuze; Guruprasad H Kora; Margaret R Romine; Edward C Uberbacher
Journal:  Bioinformation       Date:  2009-10-15

9.  ABC transporters in Dictyostelium discoideum development.

Authors:  Edward Roshan Miranda; Olga Zhuchenko; Marko Toplak; Balaji Santhanam; Blaz Zupan; Adam Kuspa; Gad Shaulsky
Journal:  PLoS One       Date:  2013-08-14       Impact factor: 3.240

10.  Functional characterization of intracellular Dictyostelium discoideum P2X receptors.

Authors:  Melanie J Ludlow; Latha Durai; Steven J Ennion
Journal:  J Biol Chem       Date:  2009-10-15       Impact factor: 5.157

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