M Blaxter

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. pmc Imagining Sisyphus happy: DNA barcoding and the unnamed majority
    Mark Blaxter
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
  2. pmc The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda
    Philipp H Schiffer
    Zoologisches Institut, Universitat zu Koln, Cologne, NRW, Germany
    BMC Genomics 14:923. 2013
  3. pmc afterParty: turning raw transcriptomes into permanent resources
    Martin Jones
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 14:301. 2013
  4. pmc On the extent and origins of genic novelty in the phylum Nematoda
    James Wasmuth
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Negl Trop Dis 2:e258. 2008
  5. pmc Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes
    Francesco Comandatore
    DIVET, Universita degli Studi di Milano, Milano, Italy
    Genome Biol Evol 5:1668-74. 2013
  6. pmc jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units
    Martin Jones
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS ONE 6:e19259. 2011
  7. pmc Badger--an accessible genome exploration environment
    Ben Elsworth
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Bioinformatics 29:2788-9. 2013
  8. pmc 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
    Sujai Kumar
    Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK
    Nucleic Acids Res 40:D1295-300. 2012
  9. doi request reprint Development: the maternal-zygotic transition revisited
    Mark Blaxter
    Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK Electronic address
    Curr Biol 24:R72-5. 2014
  10. pmc The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
    Emanuel Heitlinger
    Department of Ecology and Parasitology, Zoological Institute, Karlsruhe Institute of Technology, Kornblumenstrasse 13, Karlsruhe, Germany
    BMC Genomics 14:87. 2013

Detail Information

Publications82

  1. pmc Imagining Sisyphus happy: DNA barcoding and the unnamed majority
    Mark Blaxter
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
    ..This article is part of the themed issue 'From DNA barcodes to biomes'. ..
  2. pmc The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda
    Philipp H Schiffer
    Zoologisches Institut, Universitat zu Koln, Cologne, NRW, Germany
    BMC Genomics 14:923. 2013
    ..Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored...
  3. pmc afterParty: turning raw transcriptomes into permanent resources
    Martin Jones
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 14:301. 2013
    ..To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser...
  4. pmc On the extent and origins of genic novelty in the phylum Nematoda
    James Wasmuth
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Negl Trop Dis 2:e258. 2008
    ..Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism...
  5. pmc Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes
    Francesco Comandatore
    DIVET, Universita degli Studi di Milano, Milano, Italy
    Genome Biol Evol 5:1668-74. 2013
    ....
  6. pmc jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units
    Martin Jones
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS ONE 6:e19259. 2011
    ..User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies...
  7. pmc Badger--an accessible genome exploration environment
    Ben Elsworth
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Bioinformatics 29:2788-9. 2013
    ..Here we present Badger, a lightweight and easy-to-install genome exploration environment designed for next generation non-model organism genomes...
  8. pmc 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
    Sujai Kumar
    Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK
    Nucleic Acids Res 40:D1295-300. 2012
    ..In just over a year, this wiki has already fostered new international collaborations and attracted newcomers to the enthusiastic community of nematode genomicists. www.nematodegenomes.org...
  9. doi request reprint Development: the maternal-zygotic transition revisited
    Mark Blaxter
    Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK Electronic address
    Curr Biol 24:R72-5. 2014
    ..However, in the nematode Ascaris the zygotic genome is never silent, and the maternal products are rapidly eliminated. ..
  10. pmc The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
    Emanuel Heitlinger
    Department of Ecology and Parasitology, Zoological Institute, Karlsruhe Institute of Technology, Kornblumenstrasse 13, Karlsruhe, Germany
    BMC Genomics 14:87. 2013
    ..anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known...
  11. pmc Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon
    Ross D Houston
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, UK
    BMC Genomics 13:244. 2012
    ..From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools...
  12. pmc The phylogenetics of Anguillicolidae (Nematoda: Anguillicoloidea), swimbladder parasites of eels
    Dominik R Laetsch
    Department of Ecology and Parasitology, Zoological Institute 1, University of Karlsruhe, 76131, Karlsruhe, Germany
    BMC Evol Biol 12:60. 2012
    ..Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites, but placement of the family within Spirurina is based on limited data...
  13. pmc Nematodes: the worm and its relatives
    Mark Blaxter
    Institute of Evolutionary Biology, The University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
    PLoS Biol 9:e1001050. 2011
  14. pmc A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags
    Trevor Tyson
    Department of Biology, National University of Ireland Maynooth, Maynooth, CO, Kildare, Ireland
    BMC Res Notes 5:68. 2012
    ..In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis...
  15. pmc Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria
    Katarzyna Kinga Modrzynska
    Institute for Immunology and Infection Research, University of Edinburgh, UK
    BMC Genomics 13:106. 2012
    ..chabaudi in which high level resistance to chloroquine has been progressively selected under laboratory conditions...
  16. pmc Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris
    Thomas J Colgan
    Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
    BMC Genomics 12:623. 2011
    ..Here we describe gene expression in individual specimens of the pre-adult stages, sexes and castes of the key pollinator, the buff-tailed bumblebee Bombus terrestris...
  17. pmc The worm in the world and the world in the worm
    Mark Blaxter
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Biol 10:57. 2012
    ..Rather than being simply a 'soil nematode', C. elegans appears to be a 'plant-rot nematode'. These studies signal a growing interest in the integrated genomics and ecology of these tractable animals...
  18. doi request reprint Genomics and transcriptomics across the diversity of the Nematoda
    M Blaxter
    Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK
    Parasite Immunol 34:108-20. 2012
    ..Whole genome sequencing offers more complete catalogues of genes and assists a systems approach to phenotype dissection. These efforts are being coordinated through the 959 Nematode Genomes initiative...
  19. pmc Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes
    D B Guiliano
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    Genome Biol 3:RESEARCH0057. 2002
    ..elegans and the filarial parasite Brugia malayi...
  20. pmc Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans
    Suresh Swain
    King s College London, Department of Biochemistry, Pharmaceutical Sciences Research Division, 150 Stamford Street, London, UK
    BMC Syst Biol 4:32. 2010
    ....
  21. pmc IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype
    P ng Loke
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Immunol 3:7. 2002
    ..Due in part to a lack of markers, these cells have not been well characterized in vivo and their function remains unknown...
  22. pmc Comparing de novo assemblers for 454 transcriptome data
    Sujai Kumar
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    BMC Genomics 11:571. 2010
    ..We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis...
  23. pmc The components of the Daphnia pulex immune system as revealed by complete genome sequencing
    Seanna J McTaggart
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
    BMC Genomics 10:175. 2009
    ..For each candidate, the gene model was refined, and we conducted an analysis of sequence divergence from homologues from other taxa...
  24. pmc Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans
    Alasdair Anthony
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Genomics 8:418. 2007
    ..elegans and has also been found in MAR from a wide range of other eukaryotes. However the effectiveness of the MRS in specifically and sensitively identifying MAR remains unresolved...
  25. pmc Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus
    Jennifer Owen
    Institute of Evolutionary Biology, University of Edinburgh, King s Buildings, Edinburgh, EH9 3JT, UK
    BMC Genomics 9:266. 2008
    ..The clitellate annelid Lumbricus rubellus is a model organism for soil health testing, but genetic data have been lacking...
  26. pmc Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites
    Paul Hunt
    Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    BMC Genomics 11:499. 2010
    ..Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum...
  27. pmc A P2X receptor from the tardigrade species Hypsibius dujardini with fast kinetics and sensitivity to zinc and copper
    Selvan Bavan
    Department of Cell Physiology and Pharmacology, University of Leicester, Leicester, UK
    BMC Evol Biol 9:17. 2009
    ..Here we describe the functional characterisation of a P2X receptor (HdP2X) from the tardigrade Hypsibius dujardini demonstrating that purinergic signalling is preserved in some ecdysozoa...
  28. pmc iPhy: an integrated phylogenetic workbench for supermatrix analyses
    Martin O Jones
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH93JT, UK
    BMC Bioinformatics 12:30. 2011
    ..Current phylogenetic pipelines are dependency-heavy and have significant technical barriers to use...
  29. pmc TaxMan: a taxonomic database manager
    Martin Jones
    Institute of Evolutionary Biology, King s Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 7:536. 2006
    ..We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study...
  30. pmc Making sense of EST sequences by CLOBBing them
    John Parkinson
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 3:31. 2002
    ..To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity...
  31. pmc prot4EST: translating expressed sequence tags from neglected genomes
    James D Wasmuth
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
    BMC Bioinformatics 5:187. 2004
    ..Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects...
  32. pmc annot8r: GO, EC and KEGG annotation of EST datasets
    Ralf Schmid
    Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
    BMC Bioinformatics 9:180. 2008
    ..To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways...
  33. ncbi request reprint Genes expressed in Brugia malayi infective third stage larvae
    M L Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Mol Biochem Parasitol 77:77-93. 1996
    ..Extensive, genome-wide approaches to the analysis of larval gene expression are now possible for B. malayi. We present several examples of this approach...
  34. pmc Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005
    Mark Blaxter
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, King s Buildings, Edinburgh EH9 3JT, UK
    Genome Biol 6:329. 2005
  35. ncbi request reprint Nematode spliced leaders--ubiquity, evolution and utility
    M Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, U K
    Int J Parasitol 26:1025-33. 1996
    ....
  36. pmc DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades
    Mark Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, King s Buildings, Edinburgh EH9 3JT, UK
    Proc Biol Sci 271:S189-92. 2004
    ..Some morphological taxa contained well-separated MOTU, perhaps indicating the existence of cryptic taxa. DNA sequence-based MOTU proved to be a revealing method for meiofaunal diversity studies...
  37. ncbi request reprint A molecular evolutionary framework for the phylum Nematoda
    M L Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Nature 392:71-5. 1998
    ..We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species...
  38. pmc The promise of a DNA taxonomy
    Mark L Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, King s Buildings, Edinburgh EH9 3JT, UK
    Philos Trans R Soc Lond B Biol Sci 359:669-79. 2004
    ..Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible...
  39. ncbi request reprint Genes and genomes of Necator americanus and related hookworms
    M Blaxter
    ICAPB, University of Edinburgh, Edinburgh, UK
    Int J Parasitol 30:347-55. 2000
    ..The inception of an expressed sequence tag program on the human hookworm, N. americanus, promises to yield many new genes with novel functions in the biology of these important parasites...
  40. ncbi request reprint Symbiont genes in host genomes: fragments with a future?
    Mark Blaxter
    Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, King s Buildings, University of Edinburgh, West Mains Road, Edinburgh, Scotland EH9 3JT, UK
    Cell Host Microbe 2:211-3. 2007
    ..In a recent issue of Science, Dunning Hotopp et al. identified instances of transfer of Wolbachia DNA to host genomes. It is unknown whether these transfers represent innovation in animal evolution...
  41. ncbi request reprint Opinion piece. Genome sequencing: time to widen our horizons
    Mark Blaxter
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, University of Edinburgh, EH9 3JT, UK
    Brief Funct Genomic Proteomic 1:7-9. 2002
  42. ncbi request reprint The Brugia malayi genome project: expressed sequence tags and gene discovery
    Mark Blaxter
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK
    Trans R Soc Trop Med Hyg 96:7-17. 2002
    ..Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species...
  43. pmc NEMBASE: a resource for parasitic nematode ESTs
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK
    Nucleic Acids Res 32:D427-30. 2004
    ..Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families...
  44. doi request reprint Obtaining accurate translations from expressed sequence tags
    James Wasmuth
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
    Methods Mol Biol 533:221-39. 2009
    ..We describe how this integrated approach goes a long way to overcoming the deficit in training data...
  45. pmc Phylogenetic relationships of the Wolbachia of nematodes and arthropods
    Katelyn Fenn
    Institutes of Evolutionary Biology and Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Pathog 2:e94. 2006
    ..volvulus from its cattle-parasitic sister species, O. ochengi. The long association between filarial nematodes and Wolbachia symbionts may permit more frequent genetic exchange between their genomes...
  46. ncbi request reprint A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics
    Claire Whitton
    Ashworth Laboratories, Institution of Cell, Animal and Polulation Biology, School of Biological Sciences, University of Edinburgh, King s Buildings, Edinburgh EH9 3JT, UK
    Mol Biochem Parasitol 137:215-27. 2004
    ..B. malayi is estimated to have over 18,500 protein-coding genes...
  47. ncbi request reprint PartiGene--constructing partial genomes
    John Parkinson
    School of Biological Sciences, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
    Bioinformatics 20:1398-404. 2004
    ..nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations...
  48. ncbi request reprint 400000 nematode ESTs on the Net
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, EH9 3JT, Edinburgh, UK
    Trends Parasitol 19:283-6. 2003
    ..Over 400000 nematode ESTs are now available and at least another 130000 are planned. Here, an update is provided on the status of the project and describes the database tools being developed to disseminate these data...
  49. ncbi request reprint SimiTri--visualizing similarity relationships for groups of sequences
    John Parkinson
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    Bioinformatics 19:390-5. 2003
    ..SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors...
  50. ncbi request reprint Molecular barcodes for soil nematode identification
    Robin Floyd
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    Mol Ecol 11:839-50. 2002
    ..Correlation with a database of sequences from known species offers a route to application of the technique in ecological surveys addressing biological as well as genetic diversity...
  51. pmc Defining operational taxonomic units using DNA barcode data
    Mark Blaxter
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King s Buildings, Edinburgh EH9 3JT, UK
    Philos Trans R Soc Lond B Biol Sci 360:1935-43. 2005
    ..Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data...
  52. ncbi request reprint Quantification of Wolbachia bacteria in Brugia malayi through the nematode lifecycle
    Katelyn Fenn
    Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, King s Buildings, Edinburgh EH93JT, UK
    Mol Biochem Parasitol 137:361-4. 2004
  53. ncbi request reprint The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions
    Martin Jones
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Mol Phylogenet Evol 43:583-95. 2007
    ..Mitochondrial sequence data are subject to systematic bias that is positively misleading for evolutionary inference and thus extreme methodological care must be taken when using them to infer phylogenies...
  54. ncbi request reprint Expressed sequence tags: analysis and annotation
    John Parkinson
    Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh, UK
    Methods Mol Biol 270:93-126. 2004
    ..The systems are written to use the public-domain LINUX environment and other openly available analytical tools...
  55. ncbi request reprint Wolbachia genomes: revealing the biology of parasitism and mutualism
    Katelyn Fenn
    Institute of Evolutionary Biology and Institute of Immunology and Infection Research, School of Biological Sciences, Universityof Edinburgh, Ashworth Laboratories, King s Buildings, Edinburgh EH9 3JT, UK
    Trends Parasitol 22:60-5. 2006
    ..The Wolbachia surface protein might carry out this function...
  56. ncbi request reprint Ancient origin of glycosyl hydrolase family 9 cellulase genes
    Angus Davison
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 22:1273-84. 2005
    ..Several paralogous subfamilies of GHF9 can be identified in plants, and genes from primitive species tend to arise basally to angiosperm representatives. In contrast, GHF9 subgroup E2 genes are relatively rare in bacteria...
  57. pmc Both free-living and parasitic nematodes induce a characteristic Th2 response that is dependent on the presence of intact glycans
    Salah Tawill
    Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, United Kingdom
    Infect Immun 72:398-407. 2004
    ..These data thus have important implications for how the mammalian host responds to widely divergent metazoan invaders and suggest that the powerful C. elegans model system can be used to address these questions...
  58. ncbi request reprint Expressed sequence tags: medium-throughput protocols
    Claire Whitton
    Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh, UK
    Methods Mol Biol 270:75-92. 2004
    ..In a nonnormalized library, these 2000 ESTs should identify between 1000 and 1500 different genes, and thus possibly between 10 and 20% of the genes of any target parasite...
  59. ncbi request reprint Hox gene evolution in nematodes: novelty conserved
    Aziz Aboobaker
    Institute of Cell, Animal and Population Biology, University of Edingburgh, Edingburgh, UK
    Curr Opin Genet Dev 13:593-8. 2003
    ..Hox patterning also differs greatly between C. elegans and a second 'model' nematode, Pristionchus pacificus. The pattern of Hox gene evolution may be indicative of the move to deterministic developmental modes in nematodes...
  60. ncbi request reprint Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5' promoter sequences functional in Caenorhabditis elegans
    Natalia Gomez-Escobar
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Mol Biochem Parasitol 125:59-71. 2002
    ..We conclude that the high level of alt transcription in filarial L3s is not due to expression from a multi-copy gene family but to a set of strong promoter elements shared between the two alt genes...
  61. pmc Operon conservation and the evolution of trans-splicing in the phylum Nematoda
    David B Guiliano
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 2:e198. 2006
    ..Mapping these phenotypes onto the robust molecular phylogeny for the Nematoda suggests that operons evolved before SL2-like spliced leaders, which are an evolutionary invention of the rhabditine lineage...
  62. ncbi request reprint A transcriptomic analysis of the phylum Nematoda
    John Parkinson
    Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
    Nat Genet 36:1259-67. 2004
    ..Nematode-specific families are particularly interesting as drug and vaccine targets...
  63. ncbi request reprint Genomic tools and cDNA derived markers for butterflies
    Alexie Papanicolaou
    Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, Kings Buildings, West Mains Road, University of Edinburgh, EH9 3JT, Edinburgh, UK
    Mol Ecol 14:2883-97. 2005
    ..erato and H. melpomene. These markers will be used for comparative linkage mapping in Heliconius and will have applications in other phylogenetic and genomic studies in the Lepidoptera...
  64. ncbi request reprint The evolution of biased codon and amino acid usage in nematode genomes
    Asher D Cutter
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
    Mol Biol Evol 23:2303-15. 2006
    ....
  65. ncbi request reprint Hox Gene Loss during Dynamic Evolution of the Nematode Cluster
    A Aziz Aboobaker
    Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT, Scotland, Edinburgh, United Kingdom
    Curr Biol 13:37-40. 2003
    ..The Hox clusters of nematodes are the product of a dynamic mix of gene loss and rapid sequence evolution, with the most derived state observed in the model C. elegans...
  66. ncbi request reprint Comparative genomics of nematodes
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Trends Genet 21:573-81. 2005
    ..This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals...
  67. ncbi request reprint A gene family of cathepsin L-like proteases of filarial nematodes are associated with larval molting and cuticle and eggshell remodeling
    David B Guiliano
    Department of Biological Sciences, Imperial College of Science and Technology, London SW7 2AY, UK
    Mol Biochem Parasitol 136:227-42. 2004
    ....
  68. pmc Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
    Yvonne M Harcus
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
    Genome Biol 5:R39. 2004
    ..Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity...
  69. ncbi request reprint Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont
    Jeremy M Foster
    New England Biolabs, 32 Tozer Rd, Beverly, MA 01915, USA
    Int J Parasitol 34:733-46. 2004
    ..malayi forms the basis of a genomic sequencing effort for this bacterium, circumventing the difficult challenge of purifying sufficient endosymbiont DNA from a tropical parasite for a whole genome shotgun sequencing strategy...
  70. ncbi request reprint Functional genomics for parasitic nematodes and platyhelminths
    A Aziz Aboobaker
    Department of Integrative Biology, 3060 VLSB No 3140, University of California Berkeley, Berkeley, CA 94720 3140, USA
    Trends Parasitol 20:178-84. 2004
  71. pmc ButterflyBase: a platform for lepidopteran genomics
    Alexie Papanicolaou
    Institute for Evolutionary Biology, University of Edinburgh, King s Buildings, EH9 3JT, UK
    Nucleic Acids Res 36:D582-7. 2008
    ..ButterflyBase is expanding to include additional genomic sequence, ecological and mapping data for key species...
  72. ncbi request reprint Nematoda: genes, genomes and the evolution of parasitism
    Mark L Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, King s Buildings, Edinburgh, EH9 3JT, UK
    Adv Parasitol 54:101-95. 2003
    ..With the advent of functional genomics techniques in parasites, and in particular the possibility of gene knockout using RNA interference, the roles of many putative parasitism genes call now be tested...
  73. ncbi request reprint Most of the response elicited against Wolbachia surface protein in filarial nematode infection is due to the infective larval stage
    Tracey J Lamb
    Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, United Kingdom
    J Infect Dis 189:120-7. 2004
    ..Significant exposure to the endosymbiotic bacteria may occur earlier in nematode infection than previously thought, and the level of exposure to infective insect bites may be a key determinant of disease progression...
  74. ncbi request reprint Characterization of a novel filarial serine protease inhibitor, Ov-SPI-1, from Onchocerca volvulus, with potential multifunctional roles during development of the parasite
    Louise Ford
    Laboratory of Molecular Parasitology, Lindsley F Kimball Research Institute, New York Blood Center, New York, New York 10021, USA
    J Biol Chem 280:40845-56. 2005
    ..The localization data in adults also indicate that these inhibitors may be involved in other processes such as embryogenesis and spermatogenesis...
  75. ncbi request reprint Caenorhabditis elegans has a circadian clock
    Fred Kippert
    Curr Biol 12:R47-9. 2002
  76. ncbi request reprint An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa
    Birgit H M Meldal
    School of Ocean and Earth Science, Southampton Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
    Mol Phylogenet Evol 42:622-36. 2007
    ..Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling...
  77. ncbi request reprint Molecular phylogenetic analysis of the genus Strongyloides and related nematodes
    Mark Dorris
    Centre for Marine Biodiversity and Biotechnology, Heriot Watt University, Riccarton, EH14 4AS, Edinburgh, UK
    Int J Parasitol 32:1507-17. 2002
    ..The highly pathogenic human parasite Strongyloides fuelleborni kelleyi is not supported as a subspecies of the primate parasite S. fuelleborni fuelleborni, but is most likely derived from a local zoonotic source...
  78. ncbi request reprint Use of RNA interference to investigate gene function in the human filarial nematode parasite Brugia malayi
    A Aziz Aboobaker
    Institute of Cell, Animal and Population Biology, Kings Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK
    Mol Biochem Parasitol 129:41-51. 2003
    ..From these data we conclude that RNAi may be a useful method for assessment of drug target potential of genes identified in filarial gene discovery projects...
  79. pmc Draft genome of the filarial nematode parasite Brugia malayi
    Elodie Ghedin
    Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
    Science 317:1756-60. 2007
    ..malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design...