E Michael Gertz

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint WindowMasker: window-based masker for sequenced genomes
    Aleksandr Morgulis
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 22:134-41. 2006
  2. pmc PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD
    Edward Michael Gertz
    National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA
    BMC Bioinformatics 15:47. 2014
  3. pmc Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted
    E Michael Gertz
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
    BMC Genomics 10:566. 2009
  4. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
  5. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
  6. pmc The effectiveness of position- and composition-specific gap costs for protein similarity searches
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:i15-23. 2008
  7. pmc Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:5966-73. 2006
  8. pmc PSI-BLAST pseudocounts and the minimum description length principle
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 37:815-24. 2009
  9. ncbi request reprint A fast and symmetric DUST implementation to mask low-complexity DNA sequences
    Aleksandr Morgulis
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894 USA
    J Comput Biol 13:1028-40. 2006
  10. pmc Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20
    E Michael Gertz
    National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, 20894, USA
    Immunogenetics 65:749-62. 2013

Collaborators

Detail Information

Publications14

  1. ncbi request reprint WindowMasker: window-based masker for sequenced genomes
    Aleksandr Morgulis
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 22:134-41. 2006
    ....
  2. pmc PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD
    Edward Michael Gertz
    National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA
    BMC Bioinformatics 15:47. 2014
    ..Thus it maximizes the full likelihood of the data over marker allele frequencies or conditional allele frequencies on disease and recombination fraction...
  3. pmc Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted
    E Michael Gertz
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
    BMC Genomics 10:566. 2009
    ..For example, some of the oligonucleotides align with the transcripts of more than one gene. We decided to check the annotations for all autosomes and the X chromosome systematically using bioinformatics methods...
  4. pmc Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
    E Michael Gertz
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    BMC Biol 4:41. 2006
    ..Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server...
  5. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
    ..In a typical database search, at least one of these criteria is satisfied by over half the related sequence pairs. Compositional substitution matrix adjustment is now available in NCBI's protein-protein version of blast...
  6. pmc The effectiveness of position- and composition-specific gap costs for protein similarity searches
    Aleksandar Stojmirović
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:i15-23. 2008
    ....
  7. pmc Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
    Yi Kuo Yu
    National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:5966-73. 2006
    ..A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set...
  8. pmc PSI-BLAST pseudocounts and the minimum description length principle
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 37:815-24. 2009
    ..A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default...
  9. ncbi request reprint A fast and symmetric DUST implementation to mask low-complexity DNA sequences
    Aleksandr Morgulis
    National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894 USA
    J Comput Biol 13:1028-40. 2006
    ..The new implementation is at least four times faster than the old on the human genome. We show that both the percentage of additional bases masked and the effect on MegaBLAST outputs are very small...
  10. pmc Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20
    E Michael Gertz
    National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, 20894, USA
    Immunogenetics 65:749-62. 2013
    ....
  11. pmc Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis
    Darawalee Wangsa
    Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
    Int J Cancer 138:98-109. 2016
    ..This is consistent with the view that multiple genetic pathways need to become deregulated in order for cancer to progress...
  12. pmc Inferring models of multiscale copy number evolution for single-tumor phylogenetics
    Salim Akhter Chowdhury
    Joint Carnegie Mellon University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, Computational Biology Branch, National Center for Biotechnology Information, U S National Institutes of Health, Bethesda, MD, USA, Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U S National Institutes of Health, Bethesda, MD, USA and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA Joint Carnegie Mellon University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, Computational Biology Branch, National Center for Biotechnology Information, U S National Institutes of Health, Bethesda, MD, USA, Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U S National Institutes of Health, Bethesda, MD, USA and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh
    Bioinformatics 31:i258-67. 2015
    ....
  13. pmc Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation
    Xiangjun Du
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 42:12367-79. 2014
    ....
  14. pmc Linkage analysis of a large African family segregating stuttering suggests polygenic inheritance
    M Hashim Raza
    National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
    Hum Genet 132:385-96. 2013
    ..For this 2p + 15q analysis, we show LOD scores ranging from 4.69 to 6.57, and the scores are sensitive to which marker is chosen for 15q. Our findings provide strong evidence for linkage at several loci...