Evgeny M Zdobnov

Summary

Affiliation: University of Geneva
Country: Switzerland

Publications

  1. ncbi Quantification of insect genome divergence
    Evgeny M Zdobnov
    University of Geneva Medical School, Department of Genetic Medicine and Development, Geneva 1211, Switzerland
    Trends Genet 23:16-20. 2007
  2. pmc Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes
    Robert M Waterhouse
    Division of Cell and Molecular Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Science 316:1738-43. 2007
  3. pmc Computational and transcriptional evidence for microRNAs in the honey bee genome
    Daniel B Weaver
    Bee Power, LP, Lynn Grove Road, 16481 CR 319, Navasota, TX 77868, USA
    Genome Biol 8:R97. 2007
  4. pmc The bovine lactation genome: insights into the evolution of mammalian milk
    Danielle G Lemay
    Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 10:R43. 2009
  5. pmc New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features
    Caroline Tapparel
    Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
    BMC Genomics 8:224. 2007
  6. pmc Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates
    Toshiaki Matsui
    Department of Applied Biological Sciences, School of Agricultural Sciences, Nagoya University, Chikusa, Nagoya 464 8601, Japan
    BMC Genomics 10:17. 2009
  7. pmc Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice
    Marilena D Papaioannou
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Mol Cell Proteomics 10:M900587MCP200. 2011
  8. pmc OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
    Robert M Waterhouse
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
    Nucleic Acids Res 41:D358-65. 2013
  9. pmc Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi
    Robert M Waterhouse
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Genome Biol Evol 3:75-86. 2011
  10. pmc miROrtho: computational survey of microRNA genes
    Daniel Gerlach
    Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211 Geneva, Switzerland
    Nucleic Acids Res 37:D111-7. 2009

Detail Information

Publications31

  1. ncbi Quantification of insect genome divergence
    Evgeny M Zdobnov
    University of Geneva Medical School, Department of Genetic Medicine and Development, Geneva 1211, Switzerland
    Trends Genet 23:16-20. 2007
    ..Our results show that there is only limited selection for conservation of gene order and reveal a few hundred genes, proximity among which seems to be vital...
  2. pmc Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes
    Robert M Waterhouse
    Division of Cell and Molecular Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Science 316:1738-43. 2007
    ..These dynamics reflect in part continuous readjustment between accommodation and rejection of pathogens and suggest how innate immunity may have evolved...
  3. pmc Computational and transcriptional evidence for microRNAs in the honey bee genome
    Daniel B Weaver
    Bee Power, LP, Lynn Grove Road, 16481 CR 319, Navasota, TX 77868, USA
    Genome Biol 8:R97. 2007
    ..The recently sequenced honey bee genome provides an opportunity to detect novel miRNAs in both this species and others, and to begin to infer the roles of miRNAs in honey bee development...
  4. pmc The bovine lactation genome: insights into the evolution of mammalian milk
    Danielle G Lemay
    Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 10:R43. 2009
    ..The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes...
  5. pmc New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features
    Caroline Tapparel
    Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
    BMC Genomics 8:224. 2007
    ..The lack of HRV full-length genome sequences and the absence of analysis comparing picornaviruses at the whole genome level limit our knowledge of the genomic features supporting these differences...
  6. pmc Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates
    Toshiaki Matsui
    Department of Applied Biological Sciences, School of Agricultural Sciences, Nagoya University, Chikusa, Nagoya 464 8601, Japan
    BMC Genomics 10:17. 2009
    ....
  7. pmc Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice
    Marilena D Papaioannou
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Mol Cell Proteomics 10:M900587MCP200. 2011
    ..Altogether, our study, which is one of the few in vivo analyses of miRNA effects on protein output, suggests that, at least in our system, miRNAs play a significant role in translation control...
  8. pmc OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
    Robert M Waterhouse
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
    Nucleic Acids Res 41:D358-65. 2013
    ..With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups...
  9. pmc Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi
    Robert M Waterhouse
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Genome Biol Evol 3:75-86. 2011
    ....
  10. pmc miROrtho: computational survey of microRNA genes
    Daniel Gerlach
    Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211 Geneva, Switzerland
    Nucleic Acids Res 37:D111-7. 2009
    ....
  11. pmc miRmap web: Comprehensive microRNA target prediction online
    Charles E Vejnar
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Nucleic Acids Res 41:W165-8. 2013
    ..MiRmap web integrates sorting, filtering and exporting of results from multiple queries, as well as providing programmatic access, and is available at http://mirmap.ezlab.org. ..
  12. pmc A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits
    Jia Li
    Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel Servet 1, 1211 Geneva, Switzerland
    BMC Evol Biol 11:337. 2011
    ..Here, we exploited available arthropod genomic resources to trace the origin of TipE-like genes by mapping their evolutionary histories and examining their genomic architectures...
  13. pmc Quantification of ortholog losses in insects and vertebrates
    Stefan Wyder
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
    Genome Biol 8:R242. 2007
    ....
  14. pmc OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
    Robert M Waterhouse
    Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, Rue Michel Servet 1, 1211 Geneva, Switzerland
    Nucleic Acids Res 39:D283-8. 2011
    ..OrthoDB is freely accessible from http://cegg.unige.ch/orthodb...
  15. pmc Integration of microRNA miR-122 in hepatic circadian gene expression
    David Gatfield
    Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
    Genes Dev 23:1313-26. 2009
    ....
  16. pmc MiRmap: comprehensive prediction of microRNA target repression strength
    Charles E Vejnar
    Department of Genetic Medicine and Development, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 40:11673-83. 2012
    ..We combined all the features into an integrated model that almost doubles the predictive power of TargetScan. miRmap is freely available from http://cegg.unige.ch/mirmap...
  17. pmc The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
    Thomas Junier
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel Servet, 1211 Geneva, Switzerland
    Bioinformatics 26:1669-70. 2010
    ..As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes...
  18. pmc OrthoDB: the hierarchical catalog of eukaryotic orthologs
    Evgenia V Kriventseva
    Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel Servet, Geneva, Switzerland
    Nucleic Acids Res 36:D271-5. 2008
    ..The database is freely available at http://cegg.unige.ch/orthodb...
  19. pmc Mapping of small RNAs in the human ENCODE regions
    Christelle Borel
    Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva 1211, Switzerland
    Am J Hum Genet 82:971-81. 2008
    ..Notably, most of the remaining candidates showed a larger hybridizing band ( approximately 100 nt) that could be a microRNA precursor. The small RNA transcriptome is emerging as an important and abundant component of the genome function...
  20. pmc Sertoli cell Dicer is essential for spermatogenesis in mice
    Marilena D Papaioannou
    Department of Genetic Medicine and Development, University of Geneva Medical School, 1, rue Michel Servet, 1211 Geneva 4, Switzerland
    Dev Biol 326:250-9. 2009
    ..Overall, our results reveal novel essential roles played by the Dicer-dependent pathway in mammalian reproductive function, and thus pave the way for new insights into human infertility...
  21. ncbi Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  22. ncbi Consistency of genome-based methods in measuring Metazoan evolution
    Evgeny M Zdobnov
    EMBL Heidelberg, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    FEBS Lett 579:3355-61. 2005
    ..The deviations from the clock-like scenario in some lineages are observed consistently by several measures, implicitly confirming their reliability...
  23. pmc Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 15:98-110. 2005
    ....
  24. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  25. pmc Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
    Evgeny M Zdobnov
    EMBL Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:946-54. 2005
    ..To automatically annotate RETRA genes in other vertebrate genomes, we provide as a tool a set of marker protein domains and a manually refined list of domesticated or ancestral RETRA genes for rescuing genes with vertebrate functions...
  26. pmc AnoEST: toward A. gambiae functional genomics
    Evgenia V Kriventseva
    European Molecular Biology Laboratory, D69117 Heidelberg, Germany
    Genome Res 15:893-9. 2005
    ..Consequently, we expect that many as yet unconfirmed clusters are likely to be actual A. gambiae genes. [AnoEST is publicly available at http://komar.embl.de, and is also accessible as a Distributed Annotation Service (DAS).]...
  27. pmc VectorBase: a home for invertebrate vectors of human pathogens
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 35:D503-5. 2007
    ....
  28. doi The genome of the model beetle and pest Tribolium castaneum
    Stephen Richards
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:949-55. 2008
    ..Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control...
  29. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  30. ncbi The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...