Emily Sw Wong

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc Biology and genome of Trichinella spiralis
    Makedonka Mitreva
    Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    WormBook . 2006
  2. pmc Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
    Makedonka Mitreva
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genome Biol 7:R75. 2006
  3. 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
  4. 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
  5. 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
  6. pmc An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications
    Ranjeeta Menon
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
    BMC Genomics 13:S10. 2012
  7. pmc Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines
    Axel A Elling
    Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
    Genome Biol 8:R211. 2007
  8. pmc Novel venom gene discovery in the platypus
    Camilla M Whittington
    Faculty of Veterinary Science, The University of Sydney, Regimental Crescent, Camperdown, NSW 2006, Australia
    Genome Biol 11:R95. 2010
  9. 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
  10. 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

Detail Information

Publications45

  1. pmc Biology and genome of Trichinella spiralis
    Makedonka Mitreva
    Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    WormBook . 2006
    ..An overview of these parasites regarding biology, significance as zoonotic pathogens and selected research topics is presented here...
  2. pmc Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
    Makedonka Mitreva
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genome Biol 7:R75. 2006
    ..briggsae were also examined. A total of 25,871,325 codons ere analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms...
  3. 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...
  4. 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...
  5. 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...
  6. pmc An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications
    Ranjeeta Menon
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
    BMC Genomics 13:S10. 2012
    ..circumcincta, there is some potential for the development of a vaccine against this parasite. Hence, we infer excretory/secretory molecules for T. circumcincta as possible immunogens and vaccine candidates...
  7. pmc Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines
    Axel A Elling
    Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
    Genome Biol 8:R211. 2007
    ..A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date...
  8. pmc Novel venom gene discovery in the platypus
    Camilla M Whittington
    Faculty of Veterinary Science, The University of Sydney, Regimental Crescent, Camperdown, NSW 2006, Australia
    Genome Biol 11:R95. 2010
    ..We have constructed and sequenced a cDNA library from an active platypus venom gland to identify the remaining components...
  9. 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
    ....
  10. 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...
  11. pmc Sequence mining and transcript profiling to explore cyst nematode parasitism
    Axel A Elling
    Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
    BMC Genomics 10:58. 2009
    ..These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants...
  12. pmc Alpha-gliadin genes from the A, B, and D genomes of wheat contain different sets of celiac disease epitopes
    Teun W J M van Herpen
    Allergy Consortium Wageningen, PO Box 16, NL 6700 AA Wageningen, The Netherlands
    BMC Genomics 7:1. 2006
    ..However, wheat gluten proteins cause celiac disease (CD) in 0.5 to 1% of the general population. Among these proteins, the alpha-gliadins contain several peptides that are associated to the disease...
  13. 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...
  14. 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
    ....
  15. 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...
  16. 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...
  17. pmc Advances in the sequencing of the genome of the adenophorean nematode Trichinella spiralis
    M Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Parasitology 135:869-80. 2008
    ..The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes...
  18. 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...
  19. 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...
  20. 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...
  21. ncbi request reprint A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans
    M Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, St Louis, USA
    Mol Genet Genomics 272:138-48. 2004
    ..Putative nematode-specific and Pratylenchus -specific genes were identified, and their implications for nematode control strategies are discussed...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. doi request reprint Mining the secretome of the root-knot nematode Meloidogyne chitwoodi for candidate parasitism genes
    Erwin Roze
    Laboratory of Nematology, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
    Mol Plant Pathol 9:1-10. 2008
    ....
  39. doi request reprint Exploring the transcriptome of the burrowing nematode Radopholus similis
    Joachim Jacob
    Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
    Mol Genet Genomics 280:1-17. 2008
    ....
  40. ncbi request reprint A transcriptomic analysis of the phylum Nematoda
    John Parkinson
    Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
    Nat Genet 36:1259-67. 2004
    ..Nematode-specific families are particularly interesting as drug and vaccine targets...
  41. pmc The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism
    Christoph Dieterich
    Max Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tubingen, Germany
    Nat Genet 40:1193-8. 2008
    ..Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle...
  42. ncbi request reprint An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti
    Fiona J Thompson
    School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
    Mol Biochem Parasitol 142:32-46. 2005
    ..Many of the parasitic-specific genes are, as yet, uncharacterised: one of these represents 25% of all ESTs obtained from the parasitic stage...
  43. ncbi request reprint Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii
    Bartel Vanholme
    Molecular Biotechnology Department, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
    Parasitol Res 98:414-24. 2006
    ..The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies...
  44. ncbi request reprint 400000 nematode ESTs on the Net
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, EH9 3JT, Edinburgh, UK
    Trends Parasitol 19:283-6. 2003
    ..Over 400000 nematode ESTs are now available and at least another 130000 are planned. Here, an update is provided on the status of the project and describes the database tools being developed to disseminate these data...
  45. pmc Draft genome of the filarial nematode parasite Brugia malayi
    Elodie Ghedin
    Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
    Science 317:1756-60. 2007
    ..malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design...