| When publishing or
presenting results using EST sequences from the Washington
University Parasitic Nematode EST Sequencing Project,
please use the following citation:
Wylie, T., J.C. Martin, M. Dante, M. D. Mitreva, S. W. Clifton, A. Chinwalla, R. H. Waterston, R. K. Wilson, and J. P. McCarter. 2004. “Nematode.net: a Tool for Navigating Sequences from Parasitic and Free-living Nematodes,” 32:D423-D426 Nucleic Acids Research, 2004.
For reprint requests contact: nematode@watson.wustl.edu
Project Publications
Biology and genome of Trichinella spiralis | M. Mitreva, 2006, Biology and genome of Trichinella spiralis, Wormbook
Publication Link |
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species | Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. 2006 , Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species., Genome Biol. 2006 Aug 14;7(8):R75
Publication Link |
Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis | Ben-Wen Li, AC Rush, SD Crosby, W Warren, SA Williams, M. Mitreva, GJ Weil. 2005. Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Molecular and Biochemical Parasitology, 143: 49-57
Publication Link |
Detection of Proteins Secreted by the Plant-parasitic Nematode Heterodera schachtii Based on Expressed Sequence Tags Analysis | Vanholme, B., M. Mitreva, W. V. Criekinge, M. Logghe, J. P. McCarter, and G. Gheysen. 2005, Detection of Proteins Secreted by the Plant-parasitic Nematode Heterodera schachtii Based on Expressed Sequence Tags Analysis,Parasitology Research, 98(5):414-24
Publication Link |
A symbiont-independent endo-1,4-beta-xylanase from the plant-parasitic nematode Meloidogyne incognita | Mitreva-Dautova M, Roze E, Overmars H, de Graaff L, Schots A, Helder J, Goverse A, Bakker J, Smant G. 2006, A symbiont-independent endo-1,4-beta-xylanase from the plant-parasitic nematode Meloidogyne incognita, Mol Plant Microbe Interact. 2006 May;19(5):521-9
Publication Link |
Brugia malayi: effects of radiation and culture on gene expression in infective larvae | Li BW, Rush AC, Weil GJ, McCarter JP, Mitreva M. 2006, Brugia malayi: effects of radiation and culture on gene expression in infective larvae, Mol Biochem Parasitol. 2006 Oct;149(2):201-7
Publication Link |
Identification and Analysis of Genes Expressed in the Adult Filiarial Nematode Dirofilaria immitis | Yin, Y., J. Martin, J. P. McCarter, S. W. Clifton, R. K. Wilson, and M. Mitreva. 2006. Identification and Analysis of Genes Expressed in the Adult Filiarial Nematode Dirofilaria immitis. International Journal of Parasitology, 36(7):829-39.
Publication Link |
Detection of Proteins Secreted by the Plant-parasitic Nematode Heterodera schachtii | Vanholme, B., M. Mitreva, W. V. Criekinge, M. Logghe, J. P. McCarter, and G. Gheysen. 2006. Detection of Proteins Secreted by the Plant-parasitic Nematode Heterodera schachtii. Parasitology Research, 98(5):414-24.
Publication Link |
From genomics to chemical genomics: new developments in KEGG | Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.
Publication Link |
A White Paper on Nematode Comparative Genomics | Bird, D. M., M. L. Blaxter, J. P. McCarter, M. Mitreva, P. W. Sternberg, W. K. Thomas. 2005. A White Paper on Nematode Comparative Genomics. Journal of Nematology, 37(4):408-416.
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Nematode Gene Sequences: Update for December, 2005 | McCarter, J. P., D. M. Bird, M. Mitreva. 2005. Nematode Gene Sequences: Update for December 2005. Journal of Nematology, 37(4):417-421.
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Comparative genomics of nematodes. | Mitreva M,Blaxter ML,Bird DM,McCarter JP. 2005. Comparative genomics of nematodes. Trends Genet. 2005 Oct.21(10):573-81.
Publication Link |
Expressed Sequence Tags From Life Cycle Stages of Trichinella spiralis: Application to Biology and Parasite Control | Mitreva, M., J. Appleton, J. P. McCarter, and D. P. Jasmer. 2005. Expressed Sequence Tags From Life Cycle Stages of Trichinella spiralis: Application to Biology and Parasite Control. Veterinary Parasitology, 132:13-17.
Publication Link |
Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis | Li B, Rush AC, Crosby SD, Warren W, Williams SA, Mitreva M, Weil GJ. 2005. Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Molecular and Biochemical Parasitology, 143: 49-57.
Publication Link |
An Expressed Sequence Tag Analysis of the Life-cycle of the Parasitic Nematode Strongyloides ratti | Thompson, F. J., M. D. Mitreva, G. L. A. Barker, J. Martin, R. H. Waterston, J. P. McCarter, and M. E. Viney. 2005. An Expressed Sequence Tag Analysis of the Life-cycle of the Parasitic Nematode Strongyloides ratti. Molecular and Biochemical Parasitology, 142:32-46
Publication Link |
Investigating Hookworm Genomes by Comparative Analysis of Two Ancylostoma Species | Mitreva, M., J. P. McCarter, P. Arasu, J. Hawdon, J. Martin, M. Dante, T. Wylie, J. Xu, J. E. Stajich, V. Kapulkin, S. W. Clifton, R. H. Waterston, and R. Wilson. 2005. Investigating Hookworm Genomes by Comparative Analysis of Two Ancylostoma Species. BMC Genomics, 6:58,1-19.
Publication Link |
RNA Interference-based Discovery and Validation of New Drug Targets in Filarial Nematodes | Behm, C. A., M. M. Bendig, J. P. McCarter, A. E. Sluder. 2005. RNA Interference-based Discovery and Validation of New Drug Targets in Filarial Nematodes. Trends in Parasitology, 21:97-100.
Publication Link |
A transcriptomic analysis of the phylum Nematoda. | Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter ML. 2004. Nat Genet. 2004 Nov 14. [Epub ahead of print]
Publication Link |
mRNA Sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity among mammalian parasitic nematodes | Jasmer, D. P., M. D. Mitreva, J. P. McCarter. 2004. mRNA Sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity among mammalian parasitic nematodes. Molecular and Biochemical Parasitology, 137:297-305.
PDF File |
Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages | Mitreva, M., D. P. Jasmer, J. Appleton, J. Martin, M. Dante, T. Wylie, S. W. Clifton, and R. H. Waterston, and J. P., McCarter. 2004. Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Molecular and Biochemical Parasitology, 137:277-291.
PDF File |
Genomic Filtering, an Approach to Discovering Novel Trends in Parasitology | McCarter, J. P. 2004. Genomic Filtering, an Approach to Discovering Novel Antiparasitics. Trends in Parasitology, 20:462-468.
PDF File |
A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. | Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, Aluru S, Clifton SW, Bird DM, Baum TJ, McCarter JP. A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. Molecular Genetics and Genomics, 272:2, 138-148, 2004.
Publication Link |
Comparative Genomics of Gene Expression in the Parasitic and Free-living Nematodes Strongyloides stercoralis and Caenorhabditis elegans | Mitreva, M. D., J. P., McCarter, J. Martin, M. Dante, T. Wylie, B. Chiapelli, D. Pape, S. W. Clifton, T. B. Nutman, and R. H. Waterston. Comparative Genomics of Gene Expression in the Parasitic and Free-living Nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Research, 2004 Feb.14(2):209-20.
PDF File |
Nematode.net: A Tool for Navigating Sequences from Parasitic and Free-living Nematodes | Wylie, T., Martin J.C., Dante M., Mitreva M.D., Clifton S.W., Chinwalla A., Waterston R.H., Wilson R.K., and McCarter J.P. 2004. Nematode.net: A Tool for Navigating Sequences from Parasitic and Free-living Nematodes. Nucleic Acids Research, 2004 32:D423-D426.
PDF File |
400,000 Nematode ESTs on the Net | Parkinson, J., M. Mitreva, N. Hall, M. Blaxter, and J. P. McCarter. 400,000 Nematode ESTs on the Net. Trends in Parasitology, 19:283-286, 2003.
PDF File |
Horizontally Transferred Genes in Plant-parasitic Nematodes: A High-Throughput Genomic Approach | Scholl, E. H., J. L. Thorne, J. P. McCarter, D. McK. Bird. Horizontally Transferred Genes in Plant-parasitic Nematodes: A High-Throughput Genomic Approach, Genome Biology, 4:R39, 1-12, 2003.
Publication Link |
Analysis and Functional Classification of Transcripts from the Nematode Meloidogyne incognita | McCarter, J. P., M. D. Mitreva, J. Martin, M. Dante, T. Wylie, U. Rao, D. Pape, Y. Bowers, B. Theising, C. Murphy, A. P. Kloek, B. Chiapelli, S. W. Clifton, D. McK. Bird, and R. H. Waterston. 2003. Analysis and Functional Classification of Transcripts from the Nematode Meloidogyne incognita. Genome Biology, 4:R26,1-19, 2003.
PDF File |
Nematode Gene Sequences, Update for December, 2003 | McCarter, J. P., M. Mitreva, S. W. Clifton, D. McK. Bird and R. H. Waterston. 2003. Nematode Gene Sequences, Update for December 2003. Journal of Nematology, 2003.
PDF File |
Nematode Gene Sequences, Update for June 2002 | McCarter, J. P., S. W. Clifton, D. McK. Bird and R. H. Waterston. 2002. Nematode Gene Sequences, Update for June 2002. Journal of Nematology, 34(2):71-74.
PDF File |
Nematode Gene Sequences, Update for December 2000 | McCarter, J. P., D. McK. Bird, S. W. Clifton, and R. H. Waterston. 2000. Nematode Gene Sequences, Update for December 2000. Journal of Nematology, 32(4):331-333.
PDF File |
Rapid Gene Discovery in Plant Parasitic Nematodes Via Expressed Sequence Tags | McCarter, J., P. Abad, J. T. Jones, and D. Bird. 2000. Rapid Gene Discovery in Plant Parasitic Nematodes Via Expressed Sequence Tags. Nematology, 2(7):719-731.
Order Publication |
A Bibliography
of Parasitic Nematode Genome References: (last update
2/2002)
Blaxter, M. L., N. Raghavan, I. Ghosh, D. Guiliano, W.
Lu, S. A. Williams, B. Slatko, and A. L. Scott. 1996.
Genes
expressed in Brugia malayi infective third stage larvae.
Molecular and Biochemical Parasitology 77:77-93.
Blaxter, M., M. Aslett, D. Guiliano, J. Daub, and the
Filarial Genome Project. 1999. Parasitic helminth genomics.
Parasitology 118:S39-S51.
Blaxter, M. 2000. Genes and genomes of Necator americanus
and related hookworms. International Journal of
Parasitology 30:347-355.
The C. elegans Sequencing Consortium. 1998. Genome Sequence
of the nematode C. elegans: a platform for
investigating biology. Science 282:2012-2018.
Daub, J., A. Loukas, D. I. Pritchard, M. Blaxter. 2000.
A survey of genes expressed in adults of the human
hookworm, Necator americanus. Parasitology 120:171-184.
Dautova, M., M. N. Rosso, P. Abad, F. J. Gommers, J.
Bakker, G. Smant. 2001. Single pass cDNA sequencing -
a
powerful tool to analyse gene expression in preparasitic
juveniles of the southern root-knot nematode Meloidogyne
incognita.
Nematology 3:129-139.
Fraser, A. G., R. S. Kamath, P. Zipperlen, M. Martinez-Campos,
M. Sohrmann, J. Ahringer. 2000. Functional genomic
analysis of C. elegans chromosome I by systematic RNA
interference. Nature 408:325-330.
Hoekstra, R., A. Visser, M. Otsen, J. Tibben, J. A. Lenstra,
and M. H. Roos. 2000. EST sequencing of the parasitic
nematode Haemonchus contortus suggests a shift in gene
expression during transition to the parasitic stages.
Molecular and
Biochemical Parasitology 110:53-68.
Jones, S. J. M., D. L. Riddle, A. T. Pouzyrev, V. E.
Velculescu, L. Hillier, S. R. Eddy, S. L. Stricklin, D.
L. Baillie, R.
Waterston, and M. A. Marra. 2001. Changes in gene expression
associated with developmental arrest and longevity in
Caenorhabditis elegans. Genome Research 11:1346-1352.
Kent, W. J., A. M. Zahler. 2000. Conservation, regulation,
synteny, and introns in a large-scale C. briggsae - C.
elegans genomic alignment. Genome Research 10:1115-1125.
Kim, S. K., J. Lund, M. Kiraly, K. Duke, M. Jiang, J.
M. Stuart, A. Eizinger, B. N. Wylie, G. S. Davidson. 2001.
A gene
expression map for Caenorhabditis elegans. Science 293:2087-2092.
Lizotte-Waniewski, M., W. Tawe, D. B. Guiliano, W. Lu,
J. Liu, S. A. Williams, and S. Lustigman. 2000.
Identification of potential vaccine and drug target candidates
by expressed sequence tag analysis and immunoscreening
of
Onchocerca volvulus cDNA libraries. Infection and Immunity
68:3491-3501.
Maizels, R. M. K. K. A. Tetteh, A. Loukas. 2000. Toxocara
canis: genes expressed by the arrested infective larval
stage of a parasitic nematode. International Journal of
Parasitology 30:495-508.
Marra, M. A., L. Hillier, and R. H. Waterston. 1998.
Expressed sequence tags - ESTabilishing bridges between
genomes. Trends in Genetics 14:4-7.
McCarter, J. Abad, J. T. Jones, and D. Bird. 2000a. Rapid
gene discovery in plant parasitic nematodes via expressed
sequence tags. Nematology 2:719-731.
McCarter, J. P., D. McK. Bird, S. W. Clifton, R. H. Waterston.
2000b. Nematode gene sequences, December 2000
Update. Journal of Nematology 32:331-333.
McCombie, W. R., M. D. Adams, J. M. Kelley, M. G. Fitzgerald,
T. R. Utterback, M. Khan, M. Dubnick, A. R.
Kerlavage, J. C. Venter, and C. Fields. 1992. Caenorhabditis
elegans expressed sequence tags identify gene families
and
potential disease gene homologues. Nature Genetics 1:124-131.
Moore, T. A., S. Ramachandran, A. A. Gam, F. A. Neva,
W. Lu, L. Saunders, S. A. Williams, and T. B. Nutman.
1996. Identification of novel sequences and codon usage
in Strongyloides stercoralis. Molecular and Biochemical
Parasitology 79:243-248.
Parkinson J, C. Whitton, D. Guiliano, J. Daub, M. Blaxter.
2001. 200,000 nematode expressed sequence tags on the
Net. Trends in Parasitology 17:394-396.
Popeijus, H., V. C. Blok, L. Cardle, J. Bakker, M. S.
Phillips, J. Helder, G. Smant, J. T. Jones. 2000. Analysis
of genes
expressed in second stage juveniles of the potato cyst
nematodes Globodera rostochiensis and G. pallida using
the expressed
sequence tag approach. Nematology, 2:567-574.
Stein, L., P. Sternberg, R. Durbin, J. Thierry-Mieg,
J. Spieth. 2001. Wormbase: network access to the genome
and
biology of Caenorhabditis elegans. Nucleic Acids Research
29:82-86.
Tetteh, K. K. A., A. Loukas, C. Tripp, and R. M. Maizels.
1999. Identification of abundantly expressed novel and
conserved genes from the infective larval stage of Toxocara
canis by an expressed sequence tag strategy. Infection
and
Immunity 67:4771-4779.
Unnasch, T. R., S. A. Williams. 2000. The genomes of
Onchocerca volvulus. International Journal of Parasitology
30:543-452.
Waterston, R., C. Martin, M. Craxton, C. Huynh, A. Coulson,
L. Hillier, R. Durbin, P. Green, R. Shownkeen, N.
Metzstein, T. Hawkins, R. Wilson, M. Berks, Z. Du, K.
Thomas, J. Thierry-Mieg, and J. Sulston. 1992. A survey
of
expressed genes in Caenorhabditis elegans. Nature Genetics
1:114-123.
Williams, S. A., S. J. Laney, M. Lizotte-Waniewski, L.
A. Bierwert. 2002. The Riverblindness Genome Project.
Trends in Parasitology 18:86-90. |
