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Literature DB >> 23494302

One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.

Petra Fey¹, Robert J Dodson, Siddhartha Basu, Rex L Chisholm.

Abstract

dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Protozoan Proteins

Year: 2013 PMID： 23494302 PMCID： PMC3762881 DOI： 10.1007/978-1-62703-302-2_4

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

32 in total

1. The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development.

Authors: T Morio; H Urushihara; T Saito; Y Ugawa; H Mizuno; M Yoshida; R Yoshino; B N Mitra; M Pi; T Sato; K Takemoto; H Yasukawa; J Williams; M Maeda; I Takeuchi; H Ochiai; Y Tanaka
Journal: DNA Res Date: 1998-12-31 Impact factor: 4.458

2. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization.

Authors: S Ogawa; R Yoshino; K Angata; M Iwamoto; M Pi; K Kuroe; K Matsuo; T Morio; H Urushihara; K Yanagisawa; Y Tanaka
Journal: Mol Gen Genet Date: 2000-04

3. Textpresso: an ontology-based information retrieval and extraction system for biological literature.

Authors: Hans-Michael Müller; Eimear E Kenny; Paul W Sternberg
Journal: PLoS Biol Date: 2004-09-21 Impact factor: 8.029

4. Conserved developmental transcriptomes in evolutionarily divergent species.

Authors: Anup Parikh; Edward Roshan Miranda; Mariko Katoh-Kurasawa; Danny Fuller; Gregor Rot; Lan Zagar; Tomaz Curk; Richard Sucgang; Rui Chen; Blaz Zupan; William F Loomis; Adam Kuspa; Gad Shaulsky
Journal: Genome Biol Date: 2010-03-17 Impact factor: 13.583

5. Ensembl Genomes: extending Ensembl across the taxonomic space.

Authors: P J Kersey; D Lawson; E Birney; P S Derwent; M Haimel; J Herrero; S Keenan; A Kerhornou; G Koscielny; A Kähäri; R J Kinsella; E Kulesha; U Maheswari; K Megy; M Nuhn; G Proctor; D Staines; F Valentin; A J Vilella; A Yates
Journal: Nucleic Acids Res Date: 2009-11-01 Impact factor: 16.971

6. Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum.

Authors: Hideko Urushihara; Takahiro Morio; Tamao Saito; Yuji Kohara; Eiko Koriki; Hiroshi Ochiai; Mineko Maeda; Jeffrey G Williams; Ikuo Takeuchi; Yoshimasa Tanaka
Journal: Nucleic Acids Res Date: 2004-03-09 Impact factor: 16.971

7. UniProt Knowledgebase: a hub of integrated protein data.

Authors: Michele Magrane
Journal: Database (Oxford) Date: 2011-03-29 Impact factor: 3.451

8. The Pfam protein families database.

Authors: Marco Punta; Penny C Coggill; Ruth Y Eberhardt; Jaina Mistry; John Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman; Robert D Finn
Journal: Nucleic Acids Res Date: 2011-11-29 Impact factor: 16.971

9. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Authors: Gabriel Ostlund; Thomas Schmitt; Kristoffer Forslund; Tina Köstler; David N Messina; Sanjit Roopra; Oliver Frings; Erik L L Sonnhammer
Journal: Nucleic Acids Res Date: 2009-11-05 Impact factor: 16.971

10. High-throughput analysis of spatio-temporal dynamics in Dictyostelium.

Authors: Satoshi Sawai; Xiao-Juan Guan; Adam Kuspa; Edward C Cox
Journal: Genome Biol Date: 2007 Impact factor: 13.583

69 in total

1. Polyphosphate is an extracellular signal that can facilitate bacterial survival in eukaryotic cells.

Authors: Ramesh Rijal; Louis A Cadena; Morgan R Smith; Joseph F Carr; Richard H Gomer
Journal: Proc Natl Acad Sci U S A Date: 2020-12-02 Impact factor: 11.205

2. The autophagic machinery ensures nonlytic transmission of mycobacteria.

Authors: Lilli Gerstenmaier; Rachel Pilla; Lydia Herrmann; Hendrik Herrmann; Monica Prado; Geno J Villafano; Margot Kolonko; Rudolph Reimer; Thierry Soldati; Jason S King; Monica Hagedorn
Journal: Proc Natl Acad Sci U S A Date: 2015-02-02 Impact factor: 11.205

One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.

1. The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development.

2. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization.

3. Textpresso: an ontology-based information retrieval and extraction system for biological literature.

4. Conserved developmental transcriptomes in evolutionarily divergent species.

5. Ensembl Genomes: extending Ensembl across the taxonomic space.

6. Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum.

7. UniProt Knowledgebase: a hub of integrated protein data.

8. The Pfam protein families database.

9. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

10. High-throughput analysis of spatio-temporal dynamics in Dictyostelium.

1. Polyphosphate is an extracellular signal that can facilitate bacterial survival in eukaryotic cells.

2. The autophagic machinery ensures nonlytic transmission of mycobacteria.

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

4. A Diaphanous-related formin links Ras signaling directly to actin assembly in macropinocytosis and phagocytosis.

5. WASH drives early recycling from macropinosomes and phagosomes to maintain surface phagocytic receptors.

6. Collective regulation of cell motility using an accurate density-sensing system.

7. The physiological regulation of macropinocytosis during Dictyostelium growth and development.

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

9. A novel human receptor involved in bitter tastant detection identified using Dictyostelium discoideum.

10. Dissection of Francisella-Host Cell Interactions in Dictyostelium discoideum.