| 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
Role of horizontal gene transfer in the evolution of plant parasitism among nematodes. | Mitreva M, Smant G, Helder J, Methods Mol Biol. 2009;532:517-35. PMID: 19271205 [PubMed - in process]
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Integrating genomics and phylogenetics in understanding the history of Trichinella species. | Zarlenga DS, Rosenthal B, Hoberg E, Mitreva M, Vet Parasitol. 2009 Feb 23;159(3-4):210-3. Epub 2008 Oct 22. PMID: 19046815 [PubMed - in process]
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Sequence mining and transcript profiling to explore cyst nematode parasitism. | Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ, BMC Genomics. 2009 Jan 30;10:58. PMID: 19183474 [PubMed - in process]
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Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. | Wang Z, Martin J, Abubucker S, Yin Y, Gasser RB, Mitreva M, BMC Evol Biol. 2009 Jan 28;9:23. PMID: 19175938 [PubMed - indexed for MEDLINE]
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Strategies for Undertaking Expressed Sequence Tag (EST) Projects. | Clifton SW, Mitreva M, Methods Mol Biol. 2009;533:1-20. PMID: 19277564 [PubMed - in process]
Publication Link |
Large-Scale Sequencing and Analytical Processing of ESTs. | Mitreva M, Mardis, Methods Mol Biol. 2009;533:1-35. PMID: 19277558 [PubMed - in process]
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Exploring the transcriptome of the burrowing nematode Radopholus similis. | Jacob J, Mitreva M, Vanholme B, Gheysen G. Exploring the transcriptome of the burrowing nematode Radopholus similis. Mol Genet Genomics. 2008 Jul;280(1):1-17. Epub 2008 Apr 2. PMID: 18386064 [PubMed - in process]
Publication link |
Integrating genomics and phylogenetics in understanding the history of Trichinella species | Zarlenga DS, Rosenthal B., Hoberg E., Mitreva M., Integrating genomics and phylogenetics in understanding the history of Trichinella species. Veterinary Parasitology Oct 2008
Publication Link |
Molecular Approaches Toward Resistance to Plant-Parasitic Nematodes | JP McCarter, Molecular approaches toward resistance to plant-parasitic nematodes. Chapter in Cell Biology of Plant Nematode Parasitism, Berg, R.H. and C.G. Taylor eds., Series: Plant Cell Monographs, Vol. 15 Springer-Verlag Press, Berlin
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Nematode.net update 2008:improvements enabling more efficient data mining and comparative nematode genomics | Martin J, Abubucker S, Wylie T, Yin Y, Wang Z,Mitreva M, Nematode.net update 2008:improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Research, 2009, Vol. 37, Database issue D571-D578
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The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism | Dietrich C, Clifton SW, Schuster LN, Chinwalla A,Delehaunty K, Dinkelacker I, Fulton L, Fulton R,Godfrey J, Minx P, Mitreva M, Roeseler W, Tian H,Witte H, Yang SP, Wilson RK, Sommer RJ, The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008 Oct, Vol 40(10): 1193-8
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NemaPath: online exploration of KEGG-based metabolic pathways for nematodes | Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter, and Makedonka Mitreva, NemaPath: online exploration of KEGG-based metabolic pathways for nematodes.BMC Genomics. 2008; 9: 525
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Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans | Yin Y, Martin J, Abubucker S, Scott AL, McCarter JP, Wilson RK, Jasmer DP, Mitreva M, Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans. PLoS Negl Trop Dis. 2008 Aug 6, Vol 280(1): 1-17 PMID: 18386064 [PubMed - indexed for MEDLINE]
Publication Link |
Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis | Mitreva M, Jasmer DP, Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis. Parasitology. 2008 Jul, Vol 135(8): 869-80 PMID: 18598573 [PubMed - indexed for MEDLINE]
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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
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Biology and genome of Trichinella spiralis | M. Mitreva, 2006, Biology and genome of Trichinella spiralis, Wormbook
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
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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 |
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 |
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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