Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells | Wang J, Mitreva M, Berriman M, Thorne A, Magrini V, Koutsovouls G, Kumar S, Blaxter ML, Davis RE Developmental Cell. 01 November 2012 doi:10.1016/j.devcel.2012.09.020
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Transcriptomic and proteomic analyses of a wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer | McNulty SN, Abubucker S, Simon GM, Mitreva M, McNulty NP, Fischer K, Curtis KC, Brattig NW, Weil GJ, Fischer PU PLoS One. 2012;7(9):e45777
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Exploring metazoan evolution through dynamic and holistic changes in protein families and domains | Wang Z, Zarlenga D, Martin J, Abubucker S, Mitreva M BMC Evol Biol. 2012 Aug 3;12:138
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Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi | Li BW, Wang Z, Rush AC, Mitreva M, Weil GJ BMC Genomics. 2012 May 14;13:184
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Effects of Doxycycline on gene expression in Wolbachia and Brugia malayi adult female worms in vivo. | Rao RU, Huang Y, Abubucker S, Heinz M, Crosby SD, Mitreva M, Weil GJ J Biomed Sci. 2012 Feb 9;19(1):21 [Epub ahead of print]
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The genome of a blood fluke associated with human cancer. | Mitreva M Nat Genet. 2012 Jan 27;44(2):116-8. doi: 10.1038/ng.1082.
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Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data | Martin J, Abubucker S, Heizer E, Taylor CM and Mitreva M Nucleic Acids Research 2011 first published online December 1, 2011 doi:10.1093/nar/gkr1194
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Stage-specific excretory-secretory small heat shock proteins from the parasitic nematode Strongyloides ratti- putative links to hosts intestinal mucosal defense system. | Younis AE, Geisinger F, Ajonina-Ekoti I, Soblik H, Steen H, Mitreva M, Erttmann KD, Perbandt M, Liebau E, Brattig NW 2011 The FEBS Journal Volume 278, Issue 18, pages 3319–3336, September 2011
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HelmCoP: An Online Resource for Helminth Functional Genomics and Drug and Vaccine Targets Prioritization | Abubucker S, Martin J, Taylor CM, Mitreva M 2011 PLoS One 6(7): e21832. doi:10.1371/journal.pone.0021832
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Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles | Wang J, Czech B, Crunk A, Wallace A, Mitreva M, Hannon GJ, Davis RE Genome Research 2011 gr.121426.111
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RNAi Effector Diversity in Nematodes | Dalzell JJ, McVeigh P, Warnock ND, Mitreva M, Bird DM, Abad P, Fleming CC, Day TA, Mousley A, Marks NJ, Maule AG 2011 PLoS Negl Trop Dis 5(6): e1176. doi:10.1371/journal.pntd.0001176
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Targeting Protein-Protein Interactions for Parasite Control | Taylor CM, Fischer K, Abubucker S, Wang Z, Martin J, Jiang D, Magliano M, Rosso M, Li B, Fischer P, Mitreva M 2011 PLoS ONE 6(4): e18381. doi:10.1371/journal.pone.0018381
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Transcriptomes of Plant-Parasitic Nematodes | Jacob J, Mitreva M 2011 Genomics and Molecular Genetics of Plant-Nematode Interactions Part 2, 119-138, DOI: 10.1007/978-94-007-0434-3_7
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The draft genome of the parasitic nematode Trichinella spiralis | Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L, Minx P, Yang S, Warren WC, Fulton RS, Bhonagiri V, Zhang X, Hallsworth-Pepin K, Clifton SW, McCarter JP, Appleton J, Mardis ER, Wilson RK Nature Genetics 2011 43:228-235
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Gender-Associated Genes in Filarial Nematodes Are Important for Reproduction and Potential Intervention Targets | Li B, Rush AC, Jiang D, Mitreva M, Abubucker S, Weil GJ 2011 PLoS Negl Trop Dis 5(1): e947. doi:10.1371/journal.pntd.0000947
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Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention. | Cantacessi C, Gasser RB, Strube C, Schnieder T, Jex AR, Hall RS, Campbell BE, Young ND, Ranganathan S, Sternberg PW, Mitreva M 2011 Biotechnol Adv. 2011 May-Jun;29(3):261-71. Epub 2010 Dec 22
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First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. | Cantacessi C, Mitreva M, Campbell BE, Hall RS, Young ND, Jex AR, Ranganathan S, Gasser RB. Infect Genet Evol. 2010 Dec;10(8):1199-207. Epub 2010 Aug 6. PubMed PMID: 20692378.
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TrichinellaSpiralis: genomic application to control a zoonotic nematode. | Mitreva M, Jasmer DP. Infect Disord Drug Targets. 2010 Oct 1;10(5):376-84. PubMed PMID: 20701572.
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A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. | Cantacessi C, Jex AR, Hall RS, Young ND, Campbell BE, Joachim A, Nolan MJ, Abubucker S, Sternberg PW, Ranganathan S, Mitreva M, Gasser RB. Nucleic Acids Res. 2010 Sep 1;38(17):e171. Epub 2010 Aug 3. PubMed PMID: 20682560; PubMed Central PMCID: PMC2943614.
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Identification of hookworm DAF-16/FOXO response elements and direct gene targets. | Gao X, Wang Z, Martin J, Abubucker S, Zhang X, Mitreva M, Hawdon JM. PLoS One. 2010 Aug 19;5(8):e12289. PubMed PMID: 20808816; PubMed Central PMCID:PMC2924398.
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Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans. | Severance S, Rajagopal A, Rao AU, Cerqueira GC, Mitreva M, El-Sayed NM, Krause M, Hamza I. PLoS Genet. 2010 Jul 29;6(7):e1001044. PubMed PMID: 20686661; PubMed Central PMCID: PMC2912396.
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Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. | McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. PLoS One. 2010 Jun 9;5(6):e11029. PubMed PMID: 20543958; PubMed Central PMCID: PMC2882956.
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Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. | Wang Z, Abubucker S, Martin J, Wilson RK, Hawdon J, Mitreva M. BMC Genomics. 2010 May 14;11:307. PubMed PMID: 20470405; PubMed Central PMCID: PMC2882930.
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Massively parallel sequencing and analysis of the Necator americanus transcriptome. | Cantacessi C, Mitreva M, Jex AR, Young ND, Campbell BE, Hall RS, Doyle MA, Ralph SA, Rabelo EM, Ranganathan S, Sternberg PW, Loukas A, Gasser RB. PLoS Negl Trop Dis. 2010 May 11;4(5):e684. PubMed PMID: 20485481; PubMed Central PMCID: PMC2867931.
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Helminth genomics: The implications for human health. | Brindley PJ, Mitreva M, Ghedin E, Lustigman S. PLoS Negl Trop Dis. 2009 Oct 26;3(10):e538. PubMed PMID: 19855829; PubMed Central PMCID: PMC2757907.
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Transcripts analysis of the entomopathogenic nematode Steinernema carpocapsae induced in vitro with insect haemolymph. | Hao YJ, Montiel R, Abubucker S, Mitreva M, Simões N. Mol Biochem Parasitol. 2009 Oct 26. [Epub ahead of print] PubMed PMID: 19836423.
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Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. | Li BW, Rush AC, Mitreva M, Yin Y, Spiro D, Ghedin E, Weil GJ. BMC Genomics. 2009 Jun 15;10:267. PubMed PMID: 19527522; PubMed Central PMCID: PMC2708187.
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Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: the first transcriptome analysis of an Anguinid nematode. | Haegeman A, Jacob J, Vanholme B, Kyndt T, Mitreva M, Gheysen G. Mol Biochem Parasitol. 2009 Sep;167(1):32-40. Epub 2009 Apr 19. PubMed PMID: 19383517; PubMed Central PMCID:PMC2694848.
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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]
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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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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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The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. | Abubucker S, Zarlenga DS, Martin J, Yin Y, Wang Z, McCarter JP, Gasbarree L, Wilson RK, Mitreva M. Vet Parasitol. 2009 May 26;162(1-2):89-99. Epub 2009 Feb 27. PubMed PMID: 19346077; PubMed Central PMCID: PMC2677129.
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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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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]
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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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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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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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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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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
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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]
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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
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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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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
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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
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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]
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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.
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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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