Makedonka Mitreva

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases
    Christina M Taylor
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS Pathog 9:e1003149. 2013
  2. pmc Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data
    John Martin
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    Nucleic Acids Res 40:D720-8. 2012
  3. pmc Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways
    Christina M Taylor
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Pathog 9:e1003505. 2013
  4. pmc HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization
    Sahar Abubucker
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 6:e21832. 2011
  5. pmc Identification and characterization of alternative splicing in parasitic nematode transcriptomes
    Sahar Abubucker
    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St, Louis, MO 63108, USA
    Parasit Vectors 7:151. 2014
  6. pmc TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets
    Cinzia Cantacessi
    Center for Biodiscovery and Molecular Development of Therapeutics, Queensland Tropical Health Alliance, James Cook University, Cairns, Queensland, Australia
    Parasit Vectors 6:156. 2013
  7. pmc The draft genome of the parasitic nematode Trichinella spiralis
    Makedonka Mitreva
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Genet 43:228-35. 2011
  8. ncbi request reprint Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages
    Makedonka Mitreva
    Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, Box 8501, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
    Mol Biochem Parasitol 137:277-91. 2004
  9. pmc Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3
    Ben Wen Li
    Department of Internal Medicine, Washington University School of Medicine, St, Louis, MO 63110, USA
    BMC Genomics 10:267. 2009
  10. pmc Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues
    Zhengyuan Wang
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    Mol Genet Genomics 288:243-60. 2013

Collaborators

Detail Information

Publications48

  1. pmc Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases
    Christina M Taylor
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS Pathog 9:e1003149. 2013
    ..elegans, and six compounds also showed efficacy in at least one of the parasitic species. Hypotheses regarding the pathway the compounds may target and their molecular mechanism for activity are discussed...
  2. pmc Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data
    John Martin
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    Nucleic Acids Res 40:D720-8. 2012
    ..With this update, Nematode.net will continue to realize its original goal to disseminate diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner...
  3. pmc Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways
    Christina M Taylor
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Pathog 9:e1003505. 2013
    ..Our lists of prioritized drug targets and drug-like compounds have potential to expedite the discovery of new anthelmintic drugs with broad-spectrum efficacy. ..
  4. pmc HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization
    Sahar Abubucker
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 6:e21832. 2011
    ..HelmCoP is publicly available at: http://www.nematode.net/helmcop.html...
  5. pmc Identification and characterization of alternative splicing in parasitic nematode transcriptomes
    Sahar Abubucker
    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St, Louis, MO 63108, USA
    Parasit Vectors 7:151. 2014
    ..Transcriptomic datasets are available from many species, but data must be revisited with splice-aware assembly protocols to facilitate the study of AS in helminthes...
  6. pmc TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets
    Cinzia Cantacessi
    Center for Biodiscovery and Molecular Development of Therapeutics, Queensland Tropical Health Alliance, James Cook University, Cairns, Queensland, Australia
    Parasit Vectors 6:156. 2013
    ..Currently, knowledge of helminth TIMPs is limited to a small number of studies on canine hookworms, whereas no information is available on the occurrence of TIMPs in other parasitic helminths causing neglected diseases...
  7. pmc The draft genome of the parasitic nematode Trichinella spiralis
    Makedonka Mitreva
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Genet 43:228-35. 2011
    ..This genome sequence and the identified pan-phylum characteristics will contribute to genome evolution studies of Nematoda as well as strategies to combat global parasites of humans, food animals and crops...
  8. ncbi request reprint Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages
    Makedonka Mitreva
    Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, Box 8501, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
    Mol Biochem Parasitol 137:277-91. 2004
    ..The genes discovered, when put into context of functional classification, stage of expression, and biology of the parasite, should substantially enhance experimental potential for research on this parasite...
  9. pmc Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3
    Ben Wen Li
    Department of Internal Medicine, Washington University School of Medicine, St, Louis, MO 63110, USA
    BMC Genomics 10:267. 2009
    ..Radiation effects are especially interesting because irradiated L3 induce partial immunity to filarial infections. The underlying molecular mechanisms responsible for the efficacy of such vaccines are unkown...
  10. pmc Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues
    Zhengyuan Wang
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    Mol Genet Genomics 288:243-60. 2013
    ..A notable finding was very high module similarity between adult reproductive tissues and intestine. Our results provide the most comprehensive assessment of gene expression among tissues of a parasitic nematode to date...
  11. pmc Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance
    Zhengyuan Wang
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    BMC Evol Biol 9:23. 2009
    ....
  12. pmc Molecular determinants archetypical to the phylum Nematoda
    Yong Yin
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
    BMC Genomics 10:114. 2009
    ..Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world...
  13. ncbi request reprint Brugia malayi: effects of radiation and culture on gene expression in infective larvae
    Ben Wen Li
    Infectious Diseases Division, Campus Box 8051, Washington University School of Medicine, 660 S Euclid Avenue, St Louis, MO 63110, USA
    Mol Biochem Parasitol 149:201-7. 2006
    ..This study provides an improved description of the adaptations that accompany the transition from L3i to L3c and the special ability of L3ir to induce protective immunity...
  14. pmc Investigating hookworm genomes by comparative analysis of two Ancylostoma species
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    BMC Genomics 6:58. 2005
    ..Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum...
  15. pmc Transcriptomic and proteomic analyses of a Wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer
    Samantha N McNulty
    Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS ONE 7:e45777. 2012
    ..flexuosa lysate and stained specific worm tissues by immunohistology. Future studies will be required to determine the exact functions of Wolbachia-like peptides and proteins in O. flexuosa and to assess their roles in worm biology...
  16. pmc NemaPath: online exploration of KEGG-based metabolic pathways for nematodes
    Todd Wylie
    The Genome Center at Washington University School of Medicine, St, Louis, MO 63108, USA
    BMC Genomics 9:525. 2008
    ..Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins...
  17. ncbi request reprint Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis
    Yong Yin
    Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, Box 8501, St Louis, MO 63108, USA
    Int J Parasitol 36:829-39. 2006
    ..Our survey provided novel insights into the D. immitis transcriptome and laid a foundation for further comparative studies on biology, parasitism and evolution within the phylum Nematoda...
  18. pmc Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans
    Yong Yin
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Negl Trop Dis 2:e269. 2008
    ..However, the lack of detailed knowledge on the molecular and cellular functions of the intestine and the level of its conservation across nematodes has impeded breakthroughs in this application...
  19. pmc The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi
    Sahar Abubucker
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, United States
    Vet Parasitol 162:89-99. 2009
    ..The identified transcripts are a valuable resource for genomic studies of O. ostertagi and can facilitate the design of control strategies and vaccine programs...
  20. pmc The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences
    Sahar Abubucker
    Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Mol Biochem Parasitol 157:187-92. 2008
    ..Functional classifications of many of the 70% of genes with homology to genes in other species are provided based on gene ontology and KEGG associations and secreted and membrane-bound proteins are also identified...
  21. doi request reprint Strategies for undertaking expressed sequence tag (EST) projects
    Sandra W Clifton
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
    Methods Mol Biol 533:13-32. 2009
    ..Possible funding sources for these projects include well-justified grant proposals, private funding, and/or collaborators with available funds...
  22. pmc Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics
    John Martin
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Nucleic Acids Res 37:D571-8. 2009
    ..The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring...
  23. pmc Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation
    Zhengyuan Wang
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    BMC Genomics 11:307. 2010
    ....
  24. pmc Targeting protein-protein interactions for parasite control
    Christina M Taylor
    Department of Genetics, The Genome Center, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 6:e18381. 2011
    ..malayi (H. sapiens parasite), which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly applicable...
  25. pmc Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi
    Ben Wen Li
    Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St, Louis, MO 63110, USA
    BMC Genomics 13:184. 2012
    ..Although a first draft genome sequence was released in 2007, very little is understood about transcription programs that govern developmental changes required for the parasite's development and survival in its mammalian and insect hosts...
  26. pmc Effects of doxycycline on gene expression in Wolbachia and Brugia malayi adult female worms in vivo
    Ramakrishna U Rao
    Infectious Diseases Division, Department of Internal Medicine, St, Louis, Missouri, USA
    J Biomed Sci 19:21. 2012
    ..Most filarial nematodes contain Wolbachia symbionts. The purpose of this study was to examine the effects of doxycycline on gene expression in Wolbachia and adult female Brugia malayi...
  27. ncbi request reprint Parasitic nematodes - from genomes to control
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
    Vet Parasitol 148:31-42. 2007
    ..Genomics approaches offer a growing and fundamental base of information, which when coupled with downstream functional genomics and proteomics can accelerate progress towards developing more efficient and sustainable control programs...
  28. pmc Comparative and demographic analysis of orang-utan genomes
    Devin P Locke
    The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA
    Nature 469:529-33. 2011
    ..Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts...
  29. ncbi request reprint Expressed sequence tags from life cycle stages of Trichinella spiralis: application to biology and parasite control
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
    Vet Parasitol 132:13-7. 2005
    ..The foundation laid by this data will also contribute toward development of a more substantial genomic database and technical capacity to dissect molecular interactions between vertebrate hosts and Trichinella spp...
  30. pmc Gender-associated genes in filarial nematodes are important for reproduction and potential intervention targets
    Ben Wen Li
    Infectious Diseases Division, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Negl Trop Dis 5:e947. 2011
    ..We have performed the first genome-wide analysis of gender-associated (GA) gene expression in a filarial nematode to improve understanding of key reproductive processes in these parasites...
  31. doi request reprint Large-scale sequencing and analytical processing of ESTs
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
    Methods Mol Biol 533:153-87. 2009
    ..With appropriate bioinformatics tools, each of these platforms either used independently or coupled together provide a powerful combination for comprehensive exploration of an organism's transcriptome...
  32. pmc Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora
    Esley Heizer
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    BMC Genomics 14:118. 2013
    ..New methods of control and alternative drug targets are necessary. In-depth analysis of transcriptomic data can help provide these targets...
  33. pmc Genome of the human hookworm Necator americanus
    Yat T Tang
    1 The Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, Missouri, USA 2
    Nat Genet 46:261-9. 2014
    ..This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases. ..
  34. ncbi request reprint Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis
    Ben Wen Li
    Infectious Diseases Division, Washington University School of Medicine, Campus Box 8051, 660 S Euclid Avenue, St Louis, MO 63110, USA
    Mol Biochem Parasitol 143:49-57. 2005
    ..malayi; this should lead to improved understanding of reproduction in filarial nematodes. More generally, this approach holds great promise as a means of studying stage-specific or tissue-specific gene expression in parasitic nematodes...
  35. pmc Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer
    Samantha N McNulty
    Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
    PLoS ONE 5:e11029. 2010
    ..The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free...
  36. ncbi request reprint Comparative genomics of nematodes
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Trends Genet 21:573-81. 2005
    ..This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals...
  37. pmc Inter and intra-specific diversity of parasites that cause lymphatic filariasis
    Samantha N McNulty
    Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, United States
    Infect Genet Evol 14:137-46. 2013
    ..Improved information on filarial genetic diversity may increase the chances of success for lymphatic filariasis elimination programs...
  38. pmc Exploring metazoan evolution through dynamic and holistic changes in protein families and domains
    Zhengyuan Wang
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    BMC Evol Biol 12:138. 2012
    ..Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species...
  39. pmc A vertebrate case study of the quality of assemblies derived from next-generation sequences
    Liang Ye
    The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Genome Biol 12:R31. 2011
    ..Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references...
  40. ncbi request reprint Trichinella spiralis: genomic application to control a zoonotic nematode
    Makedonka Mitreva
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Infect Disord Drug Targets 10:376-84. 2010
    ..Examples are discussed in which genomic information may advance understanding of T. spiralis biology and new methods for treating infections by this parasite...
  41. doi request reprint Role of horizontal gene transfer in the evolution of plant parasitism among nematodes
    Makedonka Mitreva
    Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
    Methods Mol Biol 532:517-35. 2009
    ..Finally, we performed a computational high-throughput identification of potential HGT candidates (including ones unrelated to CWDEs) in plant parasitic nematodes using a genomics approach...
  42. pmc Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans
    Makedonka Mitreva
    Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genome Res 14:209-20. 2004
    ..We also provide functional classifications of S. stercoralis clusters...
  43. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  44. pmc Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis
    George Turabelidze
    Missouri Department of Health and Senior Services, St Louis, Missouri, USA
    J Clin Microbiol 51:3950-4. 2013
    ..The backbone DNAs of 9 of 9 and 3 of 3 cases who reported or were unsure about exposure, respectively, were isogenic. Backbone ORF SNP set sequencing offers pathogen differentiation capabilities that exceed those of PFGE and MLVA. ..
  45. pmc Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum
    Bruce A Rosa
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Negl Trop Dis 8:e2678. 2014
    ..We obtained fundamental information about the biology of diverse cell types and potential interactions among tissues within this multicellular organism...
  46. pmc Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem
    Michael C Wendl
    The Genome Institute, Washington University, St Louis, MO, 63108, USA
    J Math Biol 67:1141-61. 2013
    ..The other gives an overview of the data requirements for various types of sequencing milestones, including a desired number of contact reads and contig length, for detection of a rare viral species. ..
  47. pmc Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities
    John Martin
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 7:e36427. 2012
    ..The results of this study identified a strategy that was used to map over 3 tera-bases of microbial sequence against a database of more than 5,000 reference genomes in just over a month...
  48. pmc Metabolic reconstruction for metagenomic data and its application to the human microbiome
    Sahar Abubucker
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Comput Biol 8:e1002358. 2012
    ....