A transcriptomic analysis of the phylum Nematoda (original) (raw)

• De Ley, P. & Blaxter, M.L. Systematic position and phylogeny. in The Biology of Nematodes (ed. Lee, D.) 1–30 (Taylor & Francis, London, 2002).
  Google Scholar
• Platt, H.M. Foreword. in The Phylogenetic Systematics of Free-living Nematodes (Lorenzen, S.) (The Ray Society, London, 1994).
  Google Scholar
• Lambshead, P.J.D. Recent developments in marine benthic biodiversity research. Oceanis 19, 5–24 (1993).
  Google Scholar
• Blaxter, M.L. et al. A molecular evolutionary framework for the phylum Nematoda. Nature 392, 71–75 (1998).
  Article CAS PubMed Google Scholar
• Chan, M.-S. The global burden of intestinal nematode infections - fifty years on. Parasitol. Today 13, 438–443 (1997).
  Article CAS PubMed Google Scholar
• Barker, K.R., Hussey, R.S. & Krusberg, L.R. Plant and Soil Nematodes: Societal Impact and Focus on the Future (Committee on National Needs and Priorities in Nematology, Society of Nematologists, Marceline, Missouri, USA, 1994).
  Google Scholar
• The C. elegans Genome Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).
• Wood, W.B. (ed.) The Nematode Caenorhabditis elegans 667 (Cold Spring Harbor Laboratory Press, New York, 1988).
  Google Scholar
• Riddle, D. Blumenthal, T., Meyer, B. & Priess, J. (eds.) C. elegans II 1222 (Cold Spring Harbor Laboratory Press, New York, 1997).
  Google Scholar
• Stein, L.D. et al. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol. 1, E45 (2003).
  Article PubMed PubMed Central CAS Google Scholar
• Parkinson, J., Mitreva, M., Hall, N., Blaxter, M. & McCarter, J.P. 400000 nematode ESTs on the Net. Trends Parasitol. 19, 283–286 (2003).
  Article CAS PubMed Google Scholar
• Boguski, M.S., Lowe, T.M. & Tolstoshev, C.M. dbEST - database for “expressed sequence tags”. Nat. Genet. 4, 332–333 (1993).
  Article CAS PubMed Google Scholar
• Lizotte-Waniewski, M. et al. Identification of potential vaccine and drug target candidates by expressed sequence tag analysis and immunoscreening of Onchocerca volvulus larval cDNA libraries. Infect. Immun. 68, 3491–3501 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Tetteh, K.K., Loukas, A., Tripp, C. & Maizels, R.M. Identification of abundantly expressed novel and conserved genes from the infective larval stage of Toxocara canis by an expressed sequence tag strategy. Infect. Immun. 67, 4771–4779 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Daub, J., Loukas, A., Pritchard, D.I. & Blaxter, M. A survey of genes expressed in adults of the human hookworm, Necator americanus. Parasitology 120, 171–184 (2000).
  Article CAS PubMed Google Scholar
• Blaxter, M.L. et al. Genes expressed in Brugia malayi infective third stage larvae. Mol. Biochem. Parasitol. 77, 77–96 (1996).
  Article CAS PubMed Google Scholar
• McCarter, J.P. et al. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 4, R26 (2003).
  Article PubMed PubMed Central Google Scholar
• Mitreva, M. et al. Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res. 14, 209–220 (2004).
  Article PubMed PubMed Central Google Scholar
• Mitreva, M. et al. Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol. Biochem. Parasitol. 137, 277–291 (2004).
  Article PubMed Google Scholar
• Harcus, Y.M. et al. Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites. Genome Biol. 5, R39 (2004).
  Article PubMed PubMed Central Google Scholar
• Whitton, C. et al. A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics. Mol. Biochem. Parasitol. 137, 215–227 (2004).
  Article PubMed Google Scholar
• Parkinson, J., Whitton, C., Schmid, R., Thomson, M. & Blaxter, M. NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Res. 32, D427–D430 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Wylie, T. et al. Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 32, D423–D426 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Tatusov, R.L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Blaxter, M.L. Caenorhabditis elegans is a nematode. Science 282, 2041–2046 (1998).
  Article CAS PubMed Google Scholar
• Wang, D.Y., Kumar, S. & Hedges, S.B. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond. B Biol. Sci. 266, 163–171 (1999).
  Article CAS Google Scholar
• Reboul, J. et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34, 35–41 (2003).
  Article PubMed Google Scholar
• Kamath, R.S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237 (2003).
  Article CAS PubMed Google Scholar
• Barnes, T.M., Kohara, Y., Coulson, A. & Hekimi, S. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141, 159–179 (1995).
  CAS PubMed PubMed Central Google Scholar
• Simmer, F. et al. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 1, E12 (2003).
  Article PubMed PubMed Central Google Scholar
• Gregory, W.F. & Parkinson, J. Caenorhabditis elegans – applications to nematode genomics. Comp. Funct. Genomics 4, 194–202 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Parkinson, J. & Blaxter, M.L. SimiTri - visualising similarity relationships for large groups of sequences. Bioinformatics 19, 390–395 (2002).
  Article CAS Google Scholar
• Aboobaker, A.A. & Blaxter, M.L. Hox gene loss during dynamic evolution of the nematode cluster. Curr. Biol. 13, 37–40 (2003).
  Article CAS PubMed Google Scholar
• Roy, P.J., Stuart, J.M., Lund, J. & Kim, S.K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975–979 (2002).
  Article CAS PubMed Google Scholar
• Enright, A.J., Van Dongen, S. & Ouzounis, C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575–1584 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Zdobnov, E.M. & Apweiler, R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001).
  Article CAS PubMed Google Scholar
• Hutter, H. et al. Conservation and novelty in the evolution of cell adhesion and extracellular matrix genes. Science 287, 989–994 (2000).
  Article CAS PubMed Google Scholar
• Johnstone, I.L. & Barry, J.D. Temporal reiteration of a precise gene expression pattern during nematode development. EMBO J. 15, 3633–3639 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Hawdon, J.M., Jones, B.F., Hoffman, D.R. & Hotez, P.J. Cloning and characterization of _Ancylostoma_-secreted protein. A novel protein associated with the transition to parasitism by infective hookworm larvae. J. Biol. Chem. 271, 6672–6678 (1996).
  Article CAS PubMed Google Scholar
• The Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res 11, 1425–1433 (2001).
• Blaxter, M. Nematoda: Genes, genomes and the evolution of parasitism. Adv. Parasitol. 54, 102–195 (2003).
  Google Scholar
• Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Ghedin, E., Wang, S., Foster, J.M. & Slatko, B.E. First sequenced genome of a parasitic nematode. Trends Parasitol. 20, 151–153 (2004).
  Article CAS PubMed Google Scholar
• Williams, S.A. et al. The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi. Int. J. Parasitol. 30, 411–419 (2000).
  Article CAS PubMed Google Scholar
• Hillier, L.D. et al. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807–828 (1996).
  Article CAS PubMed Google Scholar
• Whitton, C., Daub, J., Thompson, M. & Blaxter, M. Expressed sequence tags: medium throughput protocols. in Parasite Genomics (ed. Melville, S.E.) (Humana, New York, in the press).
• Parkinson, J. et al. PartiGene - constructing partial genomes. Bioinformatics 20, 1398–1404 (2004).
  Article CAS PubMed Google Scholar
• Parkinson, J., Guiliano, D. & Blaxter, M. Making sense of EST sequences by CLOBBing them. BMC Bioinf. 3, 31 (2002).
  Article Google Scholar
• Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
  Article CAS PubMed PubMed Central Google Scholar