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Bioinformatics Workshop for Helminth Genomics (2015) class materials now freely available!

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When using data and/or results from the The McDonnell Genome Institute's website please cite the following paper:

Martin J, Rosa BA, Ozersky P, Hallsworth-Pepin K, Zhang X, Bhonagiri-Palsikar V, Tyagi R, Wang Q, Choi YJ, Gao X, McNulty SN, Brindley PJ, Mitreva M. expansions to and an introduction to Nucleic Acids Res. 2015 Jan;43(Database issue):D698-706. doi: 10.1093/nar/gku1128. Epub 2014 Nov 11. PubMed PMID: 25392426; PubMed Central PMCID: PMC4383941.

Publications list:

(GenBank summary text ordered by publication month & year)

Rosa BA, McNulty SN, Mitreva M, Jasmer DP. Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. Int J Parasitol. 2017 Apr;47(5):271-279. doi: 10.1016/j.ijpara.2016.12.005. Epub 2017 Feb 20. PubMed PMID: 28223178; PubMed Central PMCID: PMC5423655.

Torbati ME, Mitreva M, Gopalakrishnan V. Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations. Data (Basel). 2016 Dec;1(3). pii: 19. doi: 10.3390/data1030019. Epub 2016 Dec 13. PubMed PMID: 28239609; PubMed Central PMCID: PMC5325162.

Giacomin P, Zakrzewski M, Jenkins TP, Su X, Al-Hallaf R, Croese J, de Vries S, Grant A, Mitreva M, Loukas A, Krause L, Cantacessi C. Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease. Sci Rep. 2016 Nov 9;6:36797. doi: 10.1038/srep36797. PubMed PMID: 27827438; PubMed Central PMCID: PMC5101533.

Zarlenga D, Wang Z, Mitreva M. Trichinella spiralis: Adaptation and parasitism. Vet Parasitol. 2016 Nov 15;231:8-21. doi: 10.1016/j.vetpar.2016.07.003. Epub 2016 Jul 2. PubMed PMID: 27425574; PubMed Central PMCID: PMC5127757.

Choi YJ, Tyagi R, McNulty SN, Rosa BA, Ozersky P, Martin J, Hallsworth-Pepin K, Unnasch TR, Norice CT, Nutman TB, Weil GJ, Fischer PU, Mitreva M. Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont. Nat Microbiol. 2016 Nov 21;2:16207. doi: 10.1038/nmicrobiol.2016.207. PubMed PMID: 27869792.

Hang L, Blum AM, Kumar S, Urban JF Jr, Mitreva M, Geary TG, Jardim A, Stevenson MM, Lowell CA, Weinstock JV. Downregulation of the Syk Signaling Pathway in Intestinal Dendritic Cells Is Sufficient To Induce Dendritic Cells That Inhibit Colitis. J Immunol. 2016 Oct 1;197(7):2948-57. doi: 10.4049/jimmunol.1600063. Epub 2016 Aug 24. PubMed PMID: 27559049; PubMed Central PMCID: PMC5026942.

Wei J, Damania A, Gao X, Liu Z, Mejia R, Mitreva M, Strych U, Bottazzi ME, Hotez PJ, Zhan B. The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates. Parasit Vectors. 2016 Sep 27;9(1):518. PubMed PMID: 27677574; PubMed Central PMCID: PMC5039805.

Wang Q, Heizer E, Rosa BA, Wildman SA, Janetka JW, Mitreva M. Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. Infect Genet Evol. 2016 Apr;39:201-11. doi: 10.1016/j.meegid.2016.01.025. Epub 2016 Jan 30. PubMed PMID: 26829384; PubMed Central PMCID: PMC4789095.

Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol. 2016 Mar 22:1-18. doi: 10.1080/15476286.2016.1166333. [Epub ahead of print] PubMed PMID: 27002534.

McNulty SN, StrĂ¼be C, Rosa BA, Martin JC, Tyagi R, Choi YJ, Wang Q, Hallsworth Pepin K, Zhang X, Ozersky P, Wilson RK, Sternberg PW, Gasser RB, Mitreva M. Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. Sci Rep. 2016 Feb 9;6:20316. doi: 10.1038/srep20316. PubMed PMID: 26856411; PubMed Central PMCID: PMC4746573.

McNulty SN, Rosa BA, Fischer PU, Rumsey JM, Erdmann-Gilmore P, Curtis KC, Specht S, Townsend RR, Weil GJ, Mitreva M. An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. Mol Cell Proteomics. 2015 Dec;14(12):3224-33. doi: 10.1074/mcp.M115.051953. Epub 2015 Oct 15. PubMed PMID: 26472727; PubMed Central PMCID: PMC4762623.

Tyagi R, Joachim A, Ruttkowski B, Rosa BA, Martin JC, Hallsworth-Pepin K, Zhang X, Ozersky P, Wilson RK, Ranganathan S, Sternberg PW, Gasser RB, Mitreva M. Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. Biotechnol Adv. 2015 Nov 1;33(6 Pt 1):980-91. doi: 10.1016/j.biotechadv.2015.05.004. Epub 2015 May 27. Review. PubMed PMID: 26026709; PubMed Central PMCID: PMC4746232.

Wang Q, Rosa BA, Jasmer DP, Mitreva M. Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential. EBioMedicine. 2015 Jul 29;2(9):1079-89. doi: 10.1016/j.ebiom.2015.07.030. eCollection 2015 Sep. PubMed PMID: 26501106; PubMed Central PMCID: PMC4587998.

Giacomin P, Zakrzewski M, Croese J, Su X, Sotillo J, McCann L, Navarro S, Mitreva M, Krause L, Loukas A, Cantacessi C. Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects. Sci Rep. 2015 Sep 18;5:13797. doi: 10.1038/srep13797. PubMed PMID: 26381211; PubMed Central PMCID: PMC4585380.

Wang Q, Rosa BA, Nare B, Powell K, Valente S, Rotili D, Mai A, Marshall GR, Mitreva M. Targeting Lysine Deacetylases (KDACs) in Parasites. PLoS Negl Trop Dis. 2015 Sep 24;9(9):e0004026. doi: 10.1371/journal.pntd.0004026. eCollection 2015. PubMed PMID: 26402733; PubMed Central PMCID: PMC4581690.

Tyagi R, Rosa BA, Lewis WG, Mitreva M. Pan-phylum Comparison of Nematode Metabolic Potential. PLoS Negl Trop Dis. 2015 May 22;9(5):e0003788. doi: 10.1371/journal.pntd.0003788. eCollection 2015 May. PubMed PMID: 26000881; PubMed Central PMCID: PMC4441503.

Rosa BA, Townsend R, Jasmer DP, Mitreva M. Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. Mol Cell Proteomics. 2015 Apr;14(4):812-27. doi: 10.1074/mcp.M114.046227. Epub 2015 Jan 21. PubMed PMID: 25609831; PubMed Central PMCID: PMC4390262.

Jasmer DP, Rosa BA, Mitreva M. Peptidases compartmentalized to the Ascaris suum intestinal lumen and apical intestinal membrane. PLoS Negl Trop Dis. 2015 Jan 8;9(1):e3375. doi: 10.1371/journal.pntd.0003375. eCollection 2015 Jan. PubMed PMID: 25569475; PubMed Central PMCID: PMC4287503.

Martin J, Rosa BA, Ozersky P, Hallsworth-Pepin K, Zhang X, Bhonagiri-Palsikar V, Tyagi R, Wang Q, Choi YJ, Gao X, McNulty SN, Brindley PJ, Mitreva M. expansions to and an introduction to Nucleic Acids Res. 2015 Jan;43(Database issue):D698-706. doi: 10.1093/nar/gku1128. Epub 2014 Nov 11. PubMed PMID: 25392426; PubMed Central PMCID: PMC4383941.

Cantacessi C, Giacomin P, Croese J, Zakrzewski M, Sotillo J, McCann L, Nolan MJ, Mitreva M, Krause L, Loukas A. Impact of experimental hookworm infection on the human gut microbiota. J Infect Dis. 2014 Nov 1;210(9):1431-4. doi: 10.1093/infdis/jiu256. Epub 2014 May 3. PubMed PMID: 24795483; PubMed Central PMCID: PMC4195438.

Sotillo J, Sanchez-Flores A, Cantacessi C, Harcus Y, Pickering D, Bouchery T, Camberis M, Tang SC, Giacomin P, Mulvenna J, Mitreva M, Berriman M, LeGros G, Maizels RM, Loukas A. Secreted proteomes of different developmental stages of the gastrointestinal nematode Nippostrongylus brasiliensis. Mol Cell Proteomics. 2014 Oct;13(10):2736-51. doi: 10.1074/mcp.M114.038950. Epub 2014 Jul 3. PubMed PMID: 24994561; PubMed Central PMCID: PMC4188999.

Ondrovics M, Silbermayr K, Mitreva M, Young ND, Gasser RB, Joachim A. Proteomics elucidates key molecules involved in exsheathment in vitro in Oesophagostomum dentatum. Int J Parasitol. 2014 Oct 1;44(11):759-64. doi: 10.1016/j.ijpara.2014.06.003. Epub 2014 Jul 15. PubMed PMID: 25036992; PubMed Central PMCID: PMC4249666.

Abubucker S, McNulty SN, Rosa BA, Mitreva M. Identification and characterization of alternative splicing in parasitic nematode transcriptomes. Parasit Vectors. 2014 Apr 1;7:151. doi: 10.1186/1756-3305-7-151. PubMed PMID: 24690220; PubMed Central PMCID: PMC3997825.

Mangiola S, Young ND, Sternberg PW, Strube C, Korhonen PK, Mitreva M, Scheerlinck JP, Hofmann A, Jex AR, Gasser RB. Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. Int J Parasitol. 2014 Mar;44(3-4):251-61. doi: 10.1016/j.ijpara.2013.12.003. Epub 2014 Jan 31. PubMed PMID: 24487001; PubMed Central PMCID: PMC4040346.

Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Wang Q, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Mulvenna J, Sotillo J, Ranganathan S, Rabelo EM, Wilson RK, Felgner PL, Bethony J, Hawdon JM, Gasser RB, Loukas A, Mitreva M. Genome of the human hookworm Necator americanus. Nat Genet. 2014 Mar;46(3):261-9. doi: 10.1038/ng.2875. Epub 2014 Jan 19. PubMed PMID: 24441737; PubMed Central PMCID: PMC3978129.

Rosa BA, Jasmer DP, Mitreva M. Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PLoS Negl Trop Dis. 2014 Feb 6;8(2):e2678. doi: 10.1371/journal.pntd.0002678. eCollection 2014 Feb. PubMed PMID: 24516681; PubMed Central PMCID: PMC3916258.

Wendl MC, Kota K, Weinstock GM, Mitreva M. Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J Math Biol. 2013 Nov;67(5):1141-61. doi: 10.1007/s00285-012-0586-x. Epub 2012 Sep 11. PubMed PMID: 22965653; PubMed Central PMCID: PMC3795925.

Taylor CM, Wang Q, Rosa BA, Huang SC, Powell K, Schedl T, Pearce EJ, Abubucker S, Mitreva M. Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PLoS Pathog. 2013;9(8):e1003505. doi: 10.1371/journal.ppat.1003505. Epub 2013 Aug 1. PubMed PMID: 23935495; PubMed Central PMCID: PMC3731235.

Wang Z, Gao X, Martin J, Yin Y, Abubucker S, Rash AC, Li BW, Nash B, Hallsworth-Pepin K, Jasmer DP, Mitreva M. Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. Mol Genet Genomics. 2013 Jun;288(5-6):243-60. doi: 10.1007/s00438-013-0743-y. Epub 2013 Apr 10. PubMed PMID: 23572074; PubMed Central PMCID: PMC3670759.

McNulty SN, Mitreva M, Weil GJ, Fischer PU. Inter and intra-specific diversity of parasites that cause lymphatic filariasis. Infect Genet Evol. 2013 Mar;14:137-46. doi: 10.1016/j.meegid.2012.11.002. Epub 2012 Nov 29. Review. PubMed PMID: 23201850; PubMed Central PMCID: PMC3801268.

Taylor CM, Martin J, Rao RU, Powell K, Abubucker S, Mitreva M. Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases. PLoS Pathog. 2013 Feb;9(2):e1003149. doi: 10.1371/journal.ppat.1003149. Epub 2013 Feb 14. PubMed PMID: 23459584; PubMed Central PMCID: PMC3573124.

Heizer E, Zarlenga DS, Rosa B, Gao X, Gasser RB, De Graef J, Geldhof P, Mitreva M. Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. BMC Genomics. 2013 Feb 22;14:118. doi: 10.1186/1471-2164-14-118. PubMed PMID: 23432754; PubMed Central PMCID: PMC3599158.

McNulty SN, Abubucker S, Simon GM, Mitreva M, McNulty NP, Fischer K, Curtis KC, Brattig NW, Weil GJ, Fischer PU. Transcriptomic and proteomic analyses of a Wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer. PLoS One. 2012;7(9):e45777. doi: 10.1371/journal.pone.0045777. Epub 2012 Sep 26. PubMed PMID: 23049857; PubMed Central PMCID: PMC3458923.

Wang Z, Zarlenga D, Martin J, Abubucker S, Mitreva M. Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evol Biol. 2012 Aug 3;12:138. doi: 10.1186/1471-2148-12-138. PubMed PMID: 22862991; PubMed Central PMCID: PMC3483195.

Li BW, Wang Z, Rush AC, Mitreva M, Weil GJ. Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi. BMC Genomics. 2012 May 14;13:184. doi: 10.1186/1471-2164-13-184. PubMed PMID: 22583769; PubMed Central PMCID: PMC3414817.

Martin J, Abubucker S, Heizer E, Taylor CM, Mitreva M. update addition of data sets and tools featuring next-generation sequencing data. Nucleic Acids Res. 2012 Jan;40(Database issue):D720-8. doi: 10.1093/nar/gkr1194. Epub 2011 Dec 1. PubMed PMID: 22139919; PubMed Central PMCID: PMC3245159.

Abubucker S, Martin J, Taylor CM, Mitreva M. HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PLoS One. 2011;6(7):e21832. doi: 10.1371/journal.pone.0021832. Epub 2011 Jul 8. PubMed PMID: 21760913; PubMed Central PMCID: PMC3132748.

Taylor CM, Fischer K, Abubucker S, Wang Z, Martin J, Jiang D, Magliano M, Rosso MN, Li BW, Fischer PU, Mitreva M. Targeting protein-protein interactions for parasite control. PLoS One. 2011 Apr 27;6(4):e18381. doi: 10.1371/journal.pone.0018381. PubMed PMID: 21556146; PubMed Central PMCID: PMC3083401.

Ye L, Hillier LW, Minx P, Thane N, Locke DP, Martin JC, Chen L, Mitreva M, Miller JR, Haub KV, Dooling DJ, Mardis ER, Wilson RK, Weinstock GM, Warren WC. A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 2011;12(3):R31. doi: 10.1186/gb-2011-12-3-r31. Epub 2011 Mar 31. PubMed PMID: 21453517; PubMed Central PMCID: PMC3129681.

Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L, Minx P, Yang SP, Warren WC, Fulton RS, Bhonagiri V, Zhang X, Hallsworth-Pepin K, Clifton SW, McCarter JP, Appleton J, Mardis ER, Wilson RK. The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet. 2011 Mar;43(3):228-35. doi: 10.1038/ng.769. Epub 2011 Feb 20. PubMed PMID: 21336279; PubMed Central PMCID: PMC3057868.

Li BW, Rush AC, Jiang DJ, Mitreva M, Abubucker S, Weil GJ. Gender-associated genes in filarial nematodes are important for reproduction and potential intervention targets. PLoS Negl Trop Dis. 2011 Jan 25;5(1):e947. doi: 10.1371/journal.pntd.0000947. PubMed PMID: 21283610; PubMed Central PMCID: PMC3026763.

Mitreva M, Jasmer DP. Trichinella spiralis: genomic application to control a zoonotic nematode. Infect Disord Drug Targets. 2010 Oct;10(5):376-84. Review. PubMed PMID: 20701572.

Gao X, Wang Z, Martin J, Abubucker S, Zhang X, Mitreva M, Hawdon JM. Identification of hookworm DAF-16/FOXO response elements and direct gene targets. PLoS One. 2010 Aug 19;5(8):e12289. doi: 10.1371/journal.pone.0012289. PubMed PMID: 20808816; PubMed Central PMCID: PMC2924398.

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. Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One. 2010 Jun 9;5(6):e11029. doi: 10.1371/journal.pone.0011029. PubMed PMID: 20543958; PubMed Central PMCID: PMC2882956.

Wang Z, Abubucker S, Martin J, Wilson RK, Hawdon J, Mitreva M. Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics. 2010 May 14;11:307. doi: 10.1186/1471-2164-11-307. PubMed PMID: 20470405; PubMed Central PMCID: PMC2882930.

Brindley PJ, Mitreva M, Ghedin E, Lustigman S. Helminth genomics: The implications for human health. PLoS Negl Trop Dis. 2009 Oct 26;3(10):e538. doi: 10.1371/journal.pntd.0000538. Review. PubMed PMID: 19855829; PubMed Central PMCID: PMC2757907.

Li BW, Rush AC, Mitreva M, Yin Y, Spiro D, Ghedin E, Weil GJ. Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. BMC Genomics. 2009 Jun 15;10:267. doi: 10.1186/1471-2164-10-267. PubMed PMID: 19527522; PubMed Central PMCID: PMC2708187.

Abubucker S, Zarlenga DS, Martin J, Yin Y, Wang Z, McCarter JP, Gasbarree L, Wilson RK, Mitreva M. The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. Vet Parasitol. 2009 May 26;162(1-2):89-99. doi: 10.1016/j.vetpar.2009.02.023. Epub 2009 Feb 27. PubMed PMID: 19346077; PubMed Central PMCID: PMC2677129.

Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter JP, Wilson RK, Mitreva M. Molecular determinants archetypical to the phylum Nematoda. BMC Genomics. 2009 Mar 18;10:114. doi: 10.1186/1471-2164-10-114. PubMed PMID: 19296854; PubMed Central PMCID: PMC2666764.

Wang Z, Martin J, Abubucker S, Yin Y, Gasser RB, Mitreva M. Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol. 2009 Jan 28;9:23. doi: 10.1186/1471-2148-9-23. PubMed PMID: 19175938; PubMed Central PMCID: PMC2644674.

Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M. update improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D571-8. doi: 10.1093/nar/gkn744. Epub 2008 Oct 21. PubMed PMID: 18940860; PubMed Central PMCID: PMC2686480.

Wylie T, Martin J, Abubucker S, Yin Y, Messina D, Wang Z, McCarter JP, Mitreva M. NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics. 2008 Nov 4;9:525. doi: 10.1186/1471-2164-9-525. PubMed PMID: 18983679; PubMed Central PMCID: PMC2588608.

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;2(8):e269. doi: 10.1371/journal.pntd.0000269. PubMed PMID: 18682827; PubMed Central PMCID: PMC2483350.

Mitreva M, Jasmer DP. Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis. Parasitology. 2008 Jul;135(8):869-80. doi: 10.1017/S0031182008004472. Review. PubMed PMID: 18598573; PubMed Central PMCID: PMC3718030.

Abubucker S, Martin J, Yin Y, Fulton L, Yang SP, Hallsworth-Pepin K, Johnston JS, Hawdon J, McCarter JP, Wilson RK, Mitreva M. The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. Mol Biochem Parasitol. 2008 Feb;157(2):187-92. Epub 2007 Nov 9. PubMed PMID: 18082904; PubMed Central PMCID: PMC2265417.

Mitreva M, Zarlenga DS, McCarter JP, Jasmer DP. Parasitic nematodes - from genomes to control. Vet Parasitol. 2007 Aug 19;148(1):31-42. Epub 2007 Jun 7. Review. PubMed PMID: 17560034.

Mitreva M, Jasmer DP. Biology and genome of Trichinella spiralis. WormBook. 2006 Nov 23:1-21. Review. PubMed PMID: 18050431; PubMed Central PMCID: PMC4781409.

Li BW, Rush AC, Weil GJ, McCarter JP, Mitreva M. Brugia malayi: effects of radiation and culture on gene expression in infective larvae. Mol Biochem Parasitol. 2006 Oct;149(2):201-7. Epub 2006 Jun 22. PubMed PMID: 16824625.

Yin Y, Martin J, McCarter JP, Clifton SW, Wilson RK, Mitreva M. Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis. Int J Parasitol. 2006 Jun;36(7):829-39. Epub 2006 Mar 31. PubMed PMID: 16697384.

Mitreva M, Blaxter ML, Bird DM, McCarter JP. Comparative genomics of nematodes. Trends Genet. 2005 Oct;21(10):573-81. PubMed PMID: 16099532.

Mitreva M, Appleton J, McCarter JP, Jasmer DP. Expressed sequence tags from life cycle stages of Trichinella spiralis: application to biology and parasite control. Vet Parasitol. 2005 Sep 5;132(1-2):13-7. Review. PubMed PMID: 15993542.

Li BW, Rush AC, Crosby SD, Warren WC, Williams SA, Mitreva M, Weil GJ. Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Mol Biochem Parasitol. 2005 Sep;143(1):49-57. PubMed PMID: 15992941.

Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin W, Clifton SW, Waterston RH, Wilson RK. Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. 2005 Apr 26;6:58. PubMed PMID: 15854223; PubMed Central PMCID: PMC1112591.

Mitreva M, Jasmer DP, Appleton J, Martin J, Dante M, Wylie T, Clifton SW, Waterston RH, McCarter JP. Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol Biochem Parasitol. 2004 Oct;137(2):277-91. PubMed PMID: 15383298.

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. Mol Genet Genomics. 2004 Sep;272(2):138-48. Epub 2004 Aug 28. PubMed PMID: 15338281.

Mitreva M, McCarter JP, Martin J, Dante M, Wylie T, Chiapelli B, Pape D, Clifton SW, Nutman TB, Waterston RH. Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res. 2004 Feb;14(2):209-20. PubMed PMID: 14762059; PubMed Central PMCID: PMC327096.

Wylie T, Martin JC, Dante M, Mitreva MD, Clifton SW, Chinwalla A, Waterston RH, Wilson RK, McCarter JP. a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D423-6. PubMed PMID: 14681448; PubMed Central PMCID: PMC308745.

McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. Epub 2003 Mar 31. PubMed PMID: 12702207; PubMed Central PMCID: PMC154577.

Clifton SW, Mitreva M. Strategies for undertaking expressed sequence tag (EST) projects. Methods Mol Biol. 2009;533:13-32. doi: 10.1007/978-1-60327-136-3_2. Review. PubMed PMID: 19277564.

Mitreva M, Mardis ER. Large-scale sequencing and analytical processing of ESTs. Methods Mol Biol. 2009;533:153-87. doi: 10.1007/978-1-60327-136-3_8. PubMed PMID: 19277558.

Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biol. 2006;7(8):R75. PubMed PMID: 26271136; PubMed Central PMCID: PMC1779591.

Mitreva M, Smant G, Helder J. Role of horizontal gene transfer in the evolution of plant parasitism among nematodes. Methods Mol Biol. 2009;532:517-35. doi: 10.1007/978-1-60327-853-9_30. Review. PubMed PMID: 19271205. v4.0(AWS)    Copyright Statement
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