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Nematode & Neglected Genomics
The Blaxter lab website, databases and services, version 4.0
Please use the navigation bars above to tour this site
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NEMBASE4
NEMBASE is a comprehensive Nematode Transcriptome Database
including 63 nematode species, over 600,000 ESTs and over 250,000 proteins.
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November 2011 |
Nematode transcriptomics review
preprint available |
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We have written a short review and perspective on nematode transcriptomics for International Journal for Parasitology, including, inter alia an analysis of ALT genes from nematodes Open access to full text here.
Genomics and transcriptomics across the diversity of the Nematoda.
Blaxter M, Kumar S, Kaur G, Koutsovoulos G, Elsworth B.
Parasite Immunol. 2011 Nov 2. doi: 10.1111/j.1365-3024.2011.01342.x. [Epub ahead of print] |
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November 2011 |
The 959 nematodes genomes project:
publication of wiki database
preprint available |
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The 959 nematode genomes project is promoting the sequencing of as many genomes from Nematoda as possible to inform studies of genome evolution, gene evolution, the evolution of parasitic habits, and identify targets for intervention in major nematode diseases. Behind the initiative is a semantic media wiki, and this resource is described in a pre-publication NAR Database Issue article by Sujai Kumar, Philipp Schiffer and Mark Blaxter: Open access to full text here.
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
Sujai Kumar; Philipp H. Schiffer; Mark Blaxter
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr826 |
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July 2011 |
Heligmosomoides proteome |
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James Hewitson of Rick Maizels' group has just published an in-depth survey of the proteome of Heligmosomoides polygyrus, a model gut nematode. GenePool bioinformaticians assisted in this work building transcript models from Sanger and 454 data. See the paper at Journal of Proteomics: Proteomic analysis of secretory products from the model gastrointestinal nematode Heligmosomoides polygyrus reveals dominance of Venom Allergen-Like (VAL) proteins. James P. Hewitson, Yvonne Harcus, Janice Murray, Maaike van Agtmaal, Kara J. Filbey, John R. Grainger, Stephen Bridgett, Mark L. Blaxter, Peter D. Ashton, David A. Ashford, Rachel S. Curwen, R. Alan Wilson, Adam A. Dowle, Rick M. Maizels |
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June 2011 |
NEMBASE4 published |
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June 2011 |
RAD sequencing review |
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In collaboration with colleagues in Oregon we have published a review of RAD sequencing and other reduced representation next generation sequencing methods for genetic analyses of model and non model organisms - see Nature Reviews genetics http://www.nature.com/nrg/journal/v12/n7/full/nrg3012.html |
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May 2011 |
PartiGene version 3.0.6 |
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May 2011 |
From genomes to markers |
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In collaboration with Konrad Lohse and Graham Stone, we have worked on developing exon-primed, intron-spanning markers from ESTs and preliminary next-generation genome 'skim' data. The paper "Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data" by Lohse K, Sharanowski B, Blaxter M, Nicholls JA, Stone GN is in Molecular Ecology Resources : Mol Ecol Resour. 2011 May;11(3):521-9. doi: 10.1111/j.1755-0998.2010.02956.x. Epub 2010 Dec 20. |
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May 2011 |
jMOTU and Taxonerator for DNA barcode analyses |
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May 2011 |
Plutella xylostella genetic map using RAD |
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Insecticide resistance in the diamondback moth pest Plutella xylostella is of major importance. In collaboration with Simon Baxter (Cambridge) we have used RAD sequencing to produce a linkage map for this species. This is (one of) the first time(s) RAD has been used in a non-model species to generate such global data. See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019315 |
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April 2011 |
The worms' turn |
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April 2011 |
Velvet Worms |
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Velvet Worms, or Onychophora, are fascinating and delightful members of the Ecdysozoa. In a short review for Current Biology, Paul Sunnucks and Mark Blaxter discuss their biology, relationships, and the available genetic and genomic resources. see http://dx.doi.org/10.1016/j.cub.2011.02.017 |
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March 2011 and earlier |
OLD NEWS |
previous newsflashes from us... |
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The website is continuously "under reconstruction" - please email mark.blaxter-at-ed.ac.uk if you find a significant broken link.
BaNG website, version 4.01, May 1st 2010
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