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When using data and/or results from the The McDonnell Genome Institute's Nematode.net 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. Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. 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:

Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Rapid TEST determination of nematode cell and organ susceptibility to toxic treatments. International Journal for Parasitology: Drugs and Drug Resistance 2020 Dec pg.167-182. doi: 10.1016/j.ijpddr.2020.10.007. Epub 2020 Oct 20.

Tort JF, Mitreva M, Brehm KR, Rinaldi G. Editorial: Novel Frontiers in Helminth Genomics. Front Genet. 2020 Aug 14;11:791. doi: 10.3389/fgene.2020.00791. PMID: 32922432; PMCID: PMC7456986.

Bernot JP, Rudy G, Erickson PT, Ratnappan R, Haile M, Rosa BA, Mitreva M, O'Halloran DM, Hawdon JM. Transcriptomic analysis of hookworm Ancylostoma ceylanicum life cycle stages reveals changes in G-protein coupled receptor diversity associated with the onset of parasitism. Int J Parasitol. 2020 Jul;50(8):603-610. doi: 10.1016/j.ijpara.2020.05.003. Epub 2020 Jun 25. PMID: 32592811; PMCID: PMC7454011.

Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter ML. Author Correction: A transcriptomic analysis of the phylum Nematoda. Nat Genet. 2020 Jul;52(7):750. doi: 10.1038/s41588-020-0658-6. Erratum for: Nat Genet. 2004 Dec;36(12):1259-67. PMID: 32541926.

Gunderson EL, Vogel I, Chappell L, Bulman CA, Lim KC, Luo M, Whitman JD, Franklin C, Choi YJ, Lefoulon E, Clark T, Beerntsen B, Slatko B, Mitreva M, Sullivan W, Sakanari JA. The endosymbiont Wolbachia rebounds following antibiotic treatment. PLoS Pathog. 2020 Jul 8;16(7):e1008623. doi: 10.1371/journal.ppat.1008623. PMID: 32639986; PMCID: PMC7371230.

Rosa BA, Choi YJ, McNulty SN, Jung H, Martin J, Agatsuma T, Sugiyama H, Le TH, Doanh PN, Maleewong W, Blair D, Brindley PJ, Fischer PU, Mitreva M. Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. Gigascience. 2020 Jul 1;9(7):giaa073. doi: 10.1093/gigascience/giaa073. PMID: 32687148; PMCID: PMC7370270.

Logan J, Pearson MS, Manda SS, Choi YJ, Field M, Eichenberger RM, Mulvenna J, Nagaraj SH, Fujiwara RT, Gazzinelli-Guimaraes P, Bueno L, Mati V, Bethony JM, Mitreva M, Sotillo J, Loukas A. Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms. PLoS Negl Trop Dis. 2020 May 26;14(5):e0008237. doi: 10.1371/journal.pntd.0008237. PMID: 32453752; PMCID: PMC7274458.

Jasmer DP, Rosa BA, Tyagi R, Bulman CA, Beerntsen B, Urban JF Jr, Sakanari J, Mitreva M. De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PLoS Negl Trop Dis. 2020 May 26;14(5):e0007942. doi: 10.1371/journal.pntd.0007942. PMID: 32453724; PMCID: PMC7274465.

Choreño-Parra JA, Bobba S, Rangel-Moreno J, Ahmed M, Mehra S, Rosa B, Martin J, Mitreva M, Kaushal D, Zúñiga J, Khader SA. Mycobacterium tuberculosis HN878 Infection Induces Human-Like B-Cell Follicles in Mice. J Infect Dis. 2020 Apr 27;221(10):1636-1646. doi: 10.1093/infdis/jiz663. PMID: 31832640; PMCID: PMC7184917.

Rosa BA, Mihindukulasuriya K, Hallsworth-Pepin K, Wollam A, Martin J, Snowden C, Dunne WM Jr, Weinstock GM, Burnham CA, Mitreva M. Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics. mSystems. 2020 Feb 25;5(1):e00096-20. doi: 10.1128/mSystems.00096-20. PMID: 32098835; PMCID: PMC7043343.

Ahmed M, Thirunavukkarasu S, Rosa BA, Thomas KA, Das S, Rangel-Moreno J, Lu L, Mehra S, Mbandi SK, Thackray LB, Diamond MS, Murphy KM, Means T, Martin J, Kaushal D, Scriba TJ, Mitreva M, Khader SA. Immune correlates of tuberculosis disease and risk translate across species. Sci Transl Med. 2020 Jan 29;12(528):eaay0233. doi: 10.1126/scitranslmed.aay0233. PMID: 31996462; PMCID: PMC7354419.

Choi YJ, Fontenla S, Fischer PU, Le TH, Costábile A, Blair D, Brindley PJ, Tort JF, Cabada MM, Mitreva M. Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species. Mol Biol Evol. 2020 Jan 1;37(1):84-99. doi: 10.1093/molbev/msz204. PMID: 31501870; PMCID: PMC7528651.

Fauver JR, Martin J, Weil GJ, Mitreva M, Fischer PU. De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell. Sci Rep. 2019 Dec 20;9(1):19521. doi: 10.1038/s41598-019-55908-y. PMID: 31863009; PMCID: PMC6925183.

Labuda LA, Adegnika AA, Rosa BA, Martin J, Ateba-Ngoa U, Amoah AS, Lima HM, Meurs L, Mbow M, Manurung MD, Zinsou JF, Smits HH, Kremsner PG, Mitreva M, Yazdanbakhsh M. A praziquantel treatment study of immune and transcriptome profiles in Schistosoma haematobium-infected Gabonese schoolchildren. J Infect Dis. 2019 Dec 17:jiz641. doi: 10.1093/infdis/jiz641. Epub ahead of print. PMID: 31844885.

Zambruni M, Ochoa TJ, Somasunderam A, Cabada MM, Morales ML, Mitreva M, Rosa BA, Acosta GJ, Vigo NI, Riveros M, Arango S, Durand D, Berends MN, Melby P, Utay NS. Stunting Is Preceded by Intestinal Mucosal Damage and Microbiome Changes and Is Associated with Systemic Inflammation in a Cohort of Peruvian Infants. Am J Trop Med Hyg. 2019 Nov;101(5):1009-1017. doi: 10.4269/ajtmh.18-0975. PMID: 31482782; PMCID: PMC6838574.

Kuhlmann FM, Martin J, Hazen TH, Vickers TJ, Pashos M, Okhuysen PC, Gómez- Duarte OG, Cebelinski E, Boxrud D, Del Canto F, Vidal R, Qadri F, Mitreva M, Rasko DA, Fleckenstein JM. Conservation and global distribution of non-canonical antigens in Enterotoxigenic Escherichia coli. PLoS Negl Trop Dis. 2019 Nov 22;13(11):e0007825. doi: 10.1371/journal.pntd.0007825. PMID: 31756188; PMCID: PMC6897418.

Martin I, Kaisar MMM, Wiria AE, Hamid F, Djuardi Y, Sartono E, Rosa BA, Mitreva M, Supali T, Houwing-Duistermaat JJ, Yazdanbakhsh M, Wammes LJ. The Effect of Gut Microbiome Composition on Human Immune Responses: An Exploration of Interference by Helminth Infections. Front Genet. 2019 Nov 6;10:1028. doi: 10.3389/fgene.2019.01028. PMID: 31781154; PMCID: PMC6856646.

Schwimmer JB, Johnson JS, Angeles JE, Behling C, Belt PH, Borecki I, Bross C, Durelle J, Goyal NP, Hamilton G, Holtz ML, Lavine JE, Mitreva M, Newton KP, Pan A, Simpson PM, Sirlin CB, Sodergren E, Tyagi R, Yates KP, Weinstock GM, Salzman NH. Microbiome Signatures Associated With Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease. Gastroenterology. 2019 Oct;157(4):1109-1122. doi: 10.1053/j.gastro.2019.06.028. Epub 2019 Jun 27. PMID: 31255652; PMCID: PMC6756995.

Andersen BJ, Rosa BA, Kupritz J, Meite A, Serge T, Hertz MI, Curtis K, King CL, Mitreva M, Fischer PU, Weil GJ. Systems analysis-based assessment of post- treatment adverse events in lymphatic filariasis. PLoS Negl Trop Dis. 2019 Sep 26;13(9):e0007697. doi: 10.1371/journal.pntd.0007697. PMID: 31557154; PMCID: PMC6762072.

Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Omics Driven Understanding of the Intestines of Parasitic Nematodes. Front Genet. 2019 Jul 25;10:652. doi: 10.3389/fgene.2019.00652. PMID: 31402928; PMCID: PMC6669237.

Tyagi R, Elfawal MA, Wildman SA, Helander J, Bulman CA, Sakanari J, Rosa BA, Brindley PJ, Janetka JW, Aroian RV, Mitreva M. Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. Sci Rep. 2019 Jun 24;9(1):9085. doi: 10.1038/s41598-019-45548-7. PMID: 31235822; PMCID: PMC6591293.

Martin I, Uh HW, Supali T, Mitreva M, Houwing-Duistermaat JJ. The mixed model for the analysis of a repeated-measurement multivariate count data. Stat Med. 2019 May 30;38(12):2248-2268. doi: 10.1002/sim.8101. Epub 2019 Feb 13. PMID: 30761571; PMCID: PMC6594162.

Wu E, Du Y, Gao X, Zhang J, Martin J, Mitreva M, Ratner L. V1 and V2 Domains of HIV Envelope Contribute to CCR5 Antagonist Resistance. J Virol. 2019 Apr 17;93(9):e00050-19. doi: 10.1128/JVI.00050-19. PMID: 30787151; PMCID: PMC6475789.

Zarlenga DS, Mitreva M, Thompson P, Tyagi R, Tuo W, Hoberg EP. A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria. Parasitology. 2019 Apr;146(4):445-452. doi: 10.1017/S0031182018001701. Epub 2018 Oct 10. PMID: 30301483; PMCID: PMC6422719.

McCoy WH 4th, Otchere E, Rosa BA, Martin J, Mann CM, Mitreva M. Skin Ecology during Sebaceous Drought-How Skin Microbes Respond to Isotretinoin. J Invest Dermatol. 2019 Mar;139(3):732-735. doi: 10.1016/j.jid.2018.09.023. Epub 2018 Oct 24. PMID: 30579608; PMCID: PMC6905187.

Dunlap MD, Howard N, Das S, Scott N, Ahmed M, Prince O, Rangel-Moreno J, Rosa BA, Martin J, Kaushal D, Kaplan G, Mitreva M, Kim KW, Randolph GJ, Khader SA. A novel role for C-C motif chemokine receptor 2 during infection with hypervirulent Mycobacterium tuberculosis. Mucosal Immunol. 2018 Nov;11(6):1727-1742. doi: 10.1038/s41385-018-0071-y. Epub 2018 Aug 16. PMID: 30115997; PMCID: PMC6279476.

Howard NC, Marin ND, Ahmed M, Rosa BA, Martin J, Bambouskova M, Sergushichev A, Loginicheva E, Kurepina N, Rangel-Moreno J, Chen L, Kreiswirth BN, Klein RS, Balada-Llasat JM, Torrelles JB, Amarasinghe GK, Mitreva M, Artyomov MN, Hsu FF, Mathema B, Khader SA. Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes. Nat Microbiol. 2018 Oct;3(10):1099-1108. doi: 10.1038/s41564-018-0245-0. Epub 2018 Sep 17. Erratum in: Nat Microbiol. 2018 Nov;3(11):1327. PMID: 30224802; PMCID: PMC6158078.

Howard NC, Marin ND, Ahmed M, Rosa BA, Martin J, Bambouskova M, Sergushichev A, Loginicheva E, Kurepina N, Rangel-Moreno J, Chen L, Kreiswirth BN, Klein RS, Balada-Llasat JM, Torrelles JB, Amarasinghe GK, Mitreva M, Artyomov MN, Hsu FF, Mathema B, Khader SA. Publisher Correction: Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes. Nat Microbiol. 2018 Nov;3(11):1327. doi: 10.1038/s41564-018-0281-9. Erratum for: Nat Microbiol. 2018 Oct;3(10):1099-1108. PMID: 30327492.

Leroux LP, Nasr M, Valanparambil R, Tam M, Rosa BA, Siciliani E, Hill DE, Zarlenga DS, Jaramillo M, Weinstock JV, Geary TG, Stevenson MM, Urban JF Jr, Mitreva M, Jardim A. Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. Sci Rep. 2018 Oct 29;8(1):15921. doi: 10.1038/s41598-018-34174-4. PMID: 30374177; PMCID: PMC6206011.

Martin I, Djuardi Y, Sartono E, Rosa BA, Supali T, Mitreva M, Houwing- Duistermaat JJ, Yazdanbakhsh M. Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia. PLoS Negl Trop Dis. 2018 Aug 9;12(8):e0006620. doi: 10.1371/journal.pntd.0006620. PMID: 30091979; PMCID: PMC6084808.

Tyagi R, Maddirala AR, Elfawal M, Fischer C, Bulman CA, Rosa BA, Gao X, Chugani R, Zhou M, Helander J, Brindley PJ, Tseng CC, Greig IR, Sakanari J, Wildman SA, Aroian R, Janetka JW, Mitreva M. Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics. ACS Infect Dis. 2018 Jul 13;4(7):1130-1145. doi: 10.1021/acsinfecdis.8b00090. Epub 2018 May 14. PMID: 29718656; PMCID: PMC6283408.

International Molecular Helminthology Annotation Network (IMHAN); IMHAN consortium authors include, Palevich N, Britton C, Kamenetzky L, Mitreva M, de Moraes Mourão M, Bennuru S, Quack T, Scholte LLS, Tyagi R, Slatko BE. Tackling Hypotheticals in Helminth Genomes. Trends Parasitol. 2018 Mar;34(3):179-183. doi: 10.1016/j.pt.2017.11.007. Epub 2017 Dec 14. PMID: 29249363.

Magrini V, Gao X, Rosa BA, McGrath S, Zhang X, Hallsworth-Pepin K, Martin J, Hawdon J, Wilson RK, Mitreva M. Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC Genomics. 2018 Mar 1;19(1):172. doi: 10.1186/s12864-018-4555-7. PMID: 29495964; PMCID: PMC5833154.

Rosa BA, Supali T, Gankpala L, Djuardi Y, Sartono E, Zhou Y, Fischer K, Martin J, Tyagi R, Bolay FK, Fischer PU, Yazdanbakhsh M, Mitreva M. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. Microbiome. 2018 Feb 28;6(1):33. doi: 10.1186/s40168-018-0416-5. PMID: 29486796; PMCID: PMC6389212.

Martin J, Tyagi R, Rosa BA, Mitreva M. A Multi-Omics Database for Parasitic Nematodes and Trematodes. Methods Mol Biol. 2018;1757:371-397. doi: 10.1007/978-1-4939-7737-6_13. PMID: 29761465; PMCID: PMC6314195.

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. 2017 Oct 3;14(10):1335-1352. doi: 10.1080/15476286.2016.1166333. Epub 2016 Mar 22. PMID: 27002534; PMCID: PMC5711464.

Norice-Tra CT, Ribeiro J, Bennuru S, Fay MP, Tyagi R, Mitreva M, Nutman TB. Insights Into Onchocerca volvulus Population Biology Through Multilocus Immunophenotyping. J Infect Dis. 2017 Sep 15;216(6):736-743. doi: 10.1093/infdis/jix394. PMID: 28934436; PMCID: PMC5853885.

Dobbs KR, Embury P, Vulule J, Odada PS, Rosa BA, Mitreva M, Kazura JW, Dent AE. Monocyte dysregulation and systemic inflammation during pediatric falciparum malaria. JCI Insight. 2017 Sep 21;2(18):e95352. doi: 10.1172/jci.insight.95352. PMID: 28931756; PMCID: PMC5621919.

Tomassini Barbarossa I, Ozdener MH, Melania, Love-Gregory L, Mitreva M, Abumrad NA, Pepino MY. Variant in a common odorant-binding protein gene is associated with bitter sensitivity in people. Behav Brain Res. 2017 Jun 30;329:200-204. doi: 10.1016/j.bbr.2017.05.015. Epub 2017 May 6. PMID: 28487220; PMCID: PMC5534261.

Choi YJ, Bisset SA, Doyle SR, Hallsworth-Pepin K, Martin J, Grant WN, Mitreva M. Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PLoS Genet. 2017 Jun 23;13(6):e1006857. doi: 10.1371/journal.pgen.1006857. PMID: 28644839; PMCID: PMC5507320.

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. PMID: 28223178; PMCID: PMC5423655.

McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, Fontenla S, Choi YJ, Tyagi R, Hallsworth-Pepin K, Mann VH, Kammili L, Latham PS, Dell'Oca N, Dominguez F, Carmona C, Fischer PU, Brindley PJ, Mitreva M. Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers. PLoS Genet. 2017 Jan 6;13(1):e1006537. doi: 10.1371/journal.pgen.1006537. PMID: 28060841; PMCID: PMC5257007.

Rosa BA, Hallsworth-Pepin K, Martin J, Wollam A, Mitreva M. Genome Sequence of Christensenella minuta DSM 22607T. Genome Announc. 2017 Jan 12;5(2):e01451-16. doi: 10.1128/genomeA.01451-16. PMID: 28082495; PMCID: PMC5256218.

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):19. doi: 10.3390/data1030019. Epub 2016 Dec 13. PMID: 28239609; PMCID: PMC5325162.

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. PMID: 27869792; PMCID: PMC5512550.

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. PMID: 27827438; 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. PMID: 27425574; PMCID: PMC5127757.

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. PMID: 27559049; PMCID: PMC5026942.

Lewis AL, Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson LS, Hallsworth- Pepin K, Wollam A, Mitreva M, Lewis WG. Genome Sequences of 11 Human Vaginal Actinobacteria Strains. Genome Announc. 2016 Sep 29;4(5):e00887-16. doi: 10.1128/genomeA.00887-16. PMID: 27688328; PMCID: PMC5043546.

Weimer CM, Deitzler GE, Robinson LS, Park S, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL. Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. Genome Announc. 2016 Sep 29;4(5):e00882-16. doi: 10.1128/genomeA.00882-16. PMID: 27688327; PMCID: PMC5043545.

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. doi: 10.1186/s13071-016-1795-8. PMID: 27677574; PMCID: PMC5039805.

Deitzler GE, Ruiz MJ, Lu W, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL. Genome Sequences of Nine Gram- Negative Vaginal Bacterial Isolates. Genome Announc. 2016 Sep 29;4(5):e00889-16. doi: 10.1128/genomeA.00889-16. PMID: 27688330; PMCID: PMC5043548.

Li BW, McNulty SN, Rosa BA, Tyagi R, Zeng QR, Gu KZ, Weil GJ, Mitreva M. Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini. Parasit Vectors. 2016 Sep 13;9(1):497. doi: 10.1186/s13071-016-1785-x. PMID: 27619014; PMCID: PMC5020434.

Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson L, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis AL, Lewis WG. Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. Genome Announc. 2016 Sep 29;4(5):e00888-16. doi: 10.1128/genomeA.00888-16. PMID: 27688329; PMCID: PMC5043547.

Zhang J, Gao X, Martin J, Rosa B, Chen Z, Mitreva M, Henrich T, Kuritzkes D, Ratner L. Evolution of coreceptor utilization to escape CCR5 antagonist therapy. Virology. 2016 Jul;494:198-214. doi: 10.1016/j.virol.2016.04.010. Epub 2016 Apr 26. PMID: 27128349; PMCID: PMC4913893.

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;39:201-211. doi: 10.1016/j.meegid.2016.01.025. Epub 2016 Jan 30. PMID: 26829384; PMCID: PMC4789095.

McNulty SN, Strübe 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. PMID: 26856411; PMCID: PMC4746573.

Blair D, Nawa Y, Mitreva M, Doanh PN. Gene diversity and genetic variation in lung flukes (genus Paragonimus). Trans R Soc Trop Med Hyg. 2016 Jan;110(1):6-12. doi: 10.1093/trstmh/trv101. PMID: 26740357.

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. PMID: 26472727; 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. PMID: 26026709; PMCID: PMC4746232.

Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA. The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia. PLoS Genet. 2015 Oct 6;11(10):e1005493. doi: 10.1371/journal.pgen.1005493. PMID: 26439490; PMCID: PMC4595289.

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. PMID: 26381211; 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. PMID: 26402733; PMCID: PMC4581690.

Ordiz MI, May TD, Mihindukulasuriya K, Martin J, Crowley J, Tarr PI, Ryan K, Mortimer E, Gopalsamy G, Maleta K, Mitreva M, Young G, Manary MJ. The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children. Microbiome. 2015 Sep 3;3:37. doi: 10.1186/s40168-015-0102-9. PMID: 26334878; PMCID: PMC4558878.

Davis C, Kota K, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wylie KM, Khetani R, Hudson ME, Weinstock GM, Mitreva M. mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. J Data Mining Genomics Proteomics. 2015 Aug;4(3):135. doi: 10.4172/2153-0602.1000135. Epub 2013 Jul 31. PMID: 26500804; PMCID: PMC4612494.

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. PMID: 26501106; PMCID: PMC4587998.

Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun. 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486. PMID: 26123276; PMCID: PMC4491183.

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. PMID: 26000881; 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. PMID: 25609831; PMCID: PMC4390262.

Shi B, Chang M, Martin J, Mitreva M, Lux R, Klokkevold P, Sodergren E, Weinstock GM, Haake SK, Li H. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. mBio. 2015 Feb 17;6(1):e01926-14. doi: 10.1128/mBio.01926-14. PMID: 25691586; PMCID: PMC4337560.

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. Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res. 2015 Jan;43(Database issue):D698-706. doi: 10.1093/nar/gku1128. Epub 2014 Nov 11. PMID: 25392426; PMCID: PMC4383941.

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. PMID: 25569475; PMCID: PMC4287503.

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. PMID: 24795483; PMCID: PMC4195438.

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. PMID: 25036992; PMCID: PMC4249666.

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. PMID: 24994561; PMCID: PMC4188999.

McNulty SN, Fischer PU, Townsend RR, Curtis KC, Weil GJ, Mitreva M. Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens. PLoS Negl Trop Dis. 2014 Oct 16;8(10):e3242. doi: 10.1371/journal.pntd.0003242. PMID: 25329661; PMCID: PMC4199545.

Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, Fischbach MA. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014 Sep 11;158(6):1402-1414. doi: 10.1016/j.cell.2014.08.032. PMID: 25215495; PMCID: PMC4164201.

Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M. The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS One. 2014 May 14;9(5):e97279. doi: 10.1371/journal.pone.0097279. PMID: 24827833; PMCID: PMC4020798.

Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR, Johnston BD, Burnham CA, Weinstock ES, Weinstock GM, Wylie TN, Mitreva M, Abubucker S, Zhou Y, Stevens HJ, Hall-Moore C, Julian S, Shaikh N, Warner BB, Tarr PI. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis. 2014 May;58(9):1211-8. doi: 10.1093/cid/ciu084. Epub 2014 Mar 18. PMID: 24647013; PMCID: PMC3982840.

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. PMID: 24690220; PMCID: PMC3997825.

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 RW, 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):261-269. doi: 10.1038/ng.2875. Epub 2014 Jan 19. PMID: 24441737; PMCID: PMC3978129.

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. PMID: 24487001; PMCID: PMC4040346.

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. PMID: 24516681; 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. PMID: 22965653; 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. PMID: 23935495; 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. PMID: 23572074; 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. PMID: 23201850; 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. PMID: 23459584; 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. PMID: 23432754; 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. PMID: 23049857; 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. PMID: 22862991; PMCID: PMC3483195.

Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One. 2012;7(6):e36427. doi: 10.1371/journal.pone.0036427. Epub 2012 Jun 13. PMID: 22719831; PMCID: PMC3374613.

Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez- Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8(6):e1002358. doi: 10.1371/journal.pcbi.1002358. Epub 2012 Jun 13. PMID: 22719234; PMCID: PMC3374609.

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. PMID: 22583769; PMCID: PMC3414817.

Martin J, Abubucker S, Heizer E, Taylor CM, Mitreva M. Nematode.net 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. PMID: 22139919; 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. PMID: 21760913; 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. PMID: 21556146; 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. PMID: 21453517; 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. PMID: 21336279; PMCID: PMC3057868.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687. PMID: 21270892; PMCID: PMC3060778.

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. PMID: 21283610; 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. doi: 10.2174/187152610793180830. 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. PMID: 20808816; 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. PMID: 20543958; 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. PMID: 20470405; 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. PMID: 19855829; 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. PMID: 19527522; 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. PMID: 19346077; 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. PMID: 19296854; PMCID: PMC2666764.

Zarlenga DS, Rosenthal B, Hoberg E, Mitreva M. Integrating genomics and phylogenetics in understanding the history of Trichinella species. Vet Parasitol. 2009 Feb 23;159(3-4):210-3. doi: 10.1016/j.vetpar.2008.10.061. Epub 2008 Oct 22. PMID: 19046815.

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. PMID: 19175938; PMCID: PMC2644674.

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 Res. 2009 Jan;37(Database issue):D571-8. doi: 10.1093/nar/gkn744. Epub 2008 Oct 21. PMID: 18940860; 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. PMID: 18983679; PMCID: PMC2588608.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added]. PMID: 18464734; PMCID: PMC2803040.

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. PMID: 18682827; 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. PMID: 18598573; 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. doi: 10.1016/j.molbiopara.2007.11.001. Epub 2007 Nov 9. PMID: 18082904; 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. doi: 10.1016/j.vetpar.2007.05.008. Epub 2007 Jun 7. PMID: 17560034.

Mitreva M, Jasmer DP. Biology and genome of Trichinella spiralis. WormBook. 2006 Nov 23:1-21. doi: 10.1895/wormbook.1.124.1. PMID: 18050431; 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. doi: 10.1016/j.molbiopara.2006.05.013. Epub 2006 Jun 22. 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. doi: 10.1016/j.ijpara.2006.03.002. Epub 2006 Mar 31. PMID: 16697384.

Mitreva M, Blaxter ML, Bird DM, McCarter JP. Comparative genomics of nematodes. Trends Genet. 2005 Oct;21(10):573-81. doi: 10.1016/j.tig.2005.08.003. PMID: 16099532.

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. doi: 10.1016/j.molbiopara.2005.05.005. PMID: 15992941.

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. doi: 10.1016/j.vetpar.2005.05.023. PMID: 15993542.

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. doi: 10.1186/1471-2164-6-58. PMID: 15854223; 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. doi: 10.1016/j.molbiopara.2004.05.015. 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. doi: 10.1007/s00438-004-1054-0. Epub 2004 Aug 28. 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. doi: 10.1101/gr.1524804. PMID: 14762059; PMCID: PMC327096.

Wylie T, Martin JC, Dante M, Mitreva MD, Clifton SW, Chinwalla A, Waterston RH, Wilson RK, McCarter JP. Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D423-6. doi: 10.1093/nar/gkh010. PMID: 14681448; PMCID: PMC308745.

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. PMID: 19277564.

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