News/GMOD Paper Cuts, Nov 22nd, 2013

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GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Genome Database for Rosaceae (GDR): year 10 update [1]

The Genome Database for Rosaceae (GDR), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality.

Lots of GMOD goodness in the Genome Database for Rosaceae, which is built using Tripal, includes Pathway Tools data, and has integrated GBrowse and GBrowse syn instances for sequence and synteny viewing respectively.


FlyBase 102—advanced approaches to interrogating FlyBase [2]

FlyBase is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.

A followup to the FlyBase 101 paper [3] with updates on new features and functionality at FlyBase. FlyBase use the Chado database schema and users can query the database directly.


PATRIC, the bacterial bioinformatics database and analysis resource [4]

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC). [...] PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata.

PATRIC provides an immense data bank on bacteria: over 10,000 bacterial genomes as of Sept. 2013, projections of 15,000 by 2014. This paper details the resources provided, including their JBrowse-based genome browser, and Disease View, which integrates data on pathogens, genes, diseases, and geolocation of disease reports. Very cool!


Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells [5]

The discovery of gene body methylation, which refers to DNA methylation within gene coding region, suggests an as yet unknown role of DNA methylation at actively transcribed genes. In invertebrates, gene bodies are the primary targets of DNA methylation, and only a subset of expressed genes is modified.

Some interesting results from studies of gene body methylation in the sea squirt Ciona intestinalis during development.


Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources [6]

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. [...] The [RIKEN Brachypodium FL cDNA] database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.

TriFLDB, or the Triticeae full-length CDS database, is a new resource of Brachypodium full length cDNA clones and other resources; it includes GBrowse for exploring the B. distachyon genome and its annotations further.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1012
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1092
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkr1030
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1099
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1756-8935-6-38
  6. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0075265
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/22
Facts about "News/GMOD Paper Cuts, Nov 22nd, 2013"RDF feed
Date published2013 + and 2012 +
Has DOI10.1093/nar/gkt1012 +, 10.1093/nar/gkt1092 +, 10.1093/nar/gkr1030 +, 10.1093/nar/gkt1099 +, 10.1186/1756-8935-6-38 + and 10.1371/journal.pone.0075265 +
Has authorJung S +, Ficklin SP +, Lee T +, Cheng CH +, Blenda A +, Zheng P +, Yu J +, Bombarely A +, Cho I +, Ru S +, Evans K +, Peace C +, Abbott AG +, Mueller LA +, Olmstead MA +, Main D +, St. Pierre SE +, Ponting L +, Stefancsik R +, McQuilton P +, Thurmond J +, Wattam AR +, Abraham D +, Dalay O +, Disz TL +, Driscoll T +, Gabbard JL +, Gillespie JJ +, Gough R +, Hix D +, Kenyon R +, Machi D +, Mao C +, Nordberg EK +, Olson R +, Overbeek R +, Pusch GD +, Shukla M +, Schulman J +, Stevens RL +, Sullivan DE +, Vonstein V +, Warren A +, Will R +, Wilson MJC +, Yoo HS +, Zhang C +, Zhang Y +, Sobral BW +, Suzuki MM +, Yoshinari A +, Obara M +, Takuno S +, Shigenobu S +, Sasakura Y +, Kerr AR +, Webb S +, Bird A +, Nakayama A +, Mochida K +, Uehara-Yamaguchi Y +, Takahashi F +, Yoshida T +, Sakurai T + and Shinozaki K +
Has publication detailsNucleic Acids Research : +, Nucleic Acids Research 40:D1 D706-D714 +, Epigenetics & Chromatin 6:1 38 + and PLoS ONE 8:10 e75265 +
Has titleThe Genome Database for Rosaceae (GDR): year 10 update +, FlyBase 102--advanced approaches to interrogating FlyBase +, FlyBase 101 - the basics of navigating FlyBase +, PATRIC, the bacterial bioinformatics database and analysis resource +, Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells + and Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources +
Published inNucleic Acids Research +, Epigenetics & Chromatin + and PLoS ONE +