Dan Graur

Summary

Affiliation: University of Houston
Country: USA

Publications

  1. pmc Estimates of positive darwinian selection are inflated by errors in sequencing, annotation, and alignment
    Adrian Schneider
    , , Switzerland
    Genome Biol Evol 2009:114-8. 2009
  2. pmc On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE
    Dan Graur
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Genome Biol Evol 5:578-90. 2013
  3. pmc 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve
    Eran Elhaik
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biol Direct 5:10. 2010
  4. pmc Neutral evolution of robustness in Drosophila microRNA precursors
    Nicholas Price
    Department of Biology and Biochemistry, University of Houston, USA
    Mol Biol Evol 28:2115-23. 2011
  5. pmc A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Virol J 6:144. 2009
  6. doi request reprint Comparative testing of DNA segmentation algorithms using benchmark simulations
    Eran Elhaik
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Mol Biol Evol 27:1015-24. 2010
  7. pmc Same-strand overlapping genes in bacteria: compositional determinants of phase bias
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Biol Direct 3:36. 2008
  8. pmc A method for the simultaneous estimation of selection intensities in overlapping genes
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS ONE 3:e3996. 2008
  9. pmc Detection of functional overlapping genes: simulation and case studies
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    J Mol Evol 71:308-16. 2010
  10. pmc The multiple personalities of Watson and Crick strands
    Reed A Cartwright
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 5001, USA
    Biol Direct 6:7. 2011

Research Grants

Detail Information

Publications13

  1. pmc Estimates of positive darwinian selection are inflated by errors in sequencing, annotation, and alignment
    Adrian Schneider
    , , Switzerland
    Genome Biol Evol 2009:114-8. 2009
    ..We conclude that some estimates on the prevalence of positive Darwinian selection in the literature may be inflated and should be treated with caution...
  2. pmc On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE
    Dan Graur
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Genome Biol Evol 5:578-90. 2013
    ..The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten...
  3. pmc 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve
    Eran Elhaik
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biol Direct 5:10. 2010
    ..They claimed that an inscribed sphere of radius r = 1/ square root 3 contains almost all points corresponding to various genomes, implying that S <r2. The distribution of the points P obtained by S was studied using the Z-curve...
  4. pmc Neutral evolution of robustness in Drosophila microRNA precursors
    Nicholas Price
    Department of Biology and Biochemistry, University of Houston, USA
    Mol Biol Evol 28:2115-23. 2011
    ..Instead, the high robustness of Drosophila pre-miRNAs appears to be mostly intrinsic and likely a consequence of selection for functional structures...
  5. pmc A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Virol J 6:144. 2009
    ....
  6. doi request reprint Comparative testing of DNA segmentation algorithms using benchmark simulations
    Eran Elhaik
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Mol Biol Evol 27:1015-24. 2010
    ..However, even these algorithms perform poorly in certain instances because of the arbitrary choice of a segmentation-stopping criterion...
  7. pmc Same-strand overlapping genes in bacteria: compositional determinants of phase bias
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Biol Direct 3:36. 2008
    ..We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes...
  8. pmc A method for the simultaneous estimation of selection intensities in overlapping genes
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS ONE 3:e3996. 2008
    ..Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases...
  9. pmc Detection of functional overlapping genes: simulation and case studies
    Niv Sabath
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    J Mol Evol 71:308-16. 2010
    ..Finally, we examined three cases of overlap in the human genome. We find varying signatures of purifying selection acting on these overlaps, raising the possibility that two of the overlapping genes may not be functional...
  10. pmc The multiple personalities of Watson and Crick strands
    Reed A Cartwright
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 5001, USA
    Biol Direct 6:7. 2011
    ..Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent...
  11. doi request reprint Characterization of pairwise and multiple sequence alignment errors
    Giddy Landan
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204 5001, USA
    Gene 441:141-7. 2009
    ..Progressive MSA utilizes a guide-tree in the reconstruction of MSAs. The quality of the guide-tree was found to affect MSA error levels only marginally...
  12. doi request reprint Can GC content at third-codon positions be used as a proxy for isochore composition?
    Eran Elhaik
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Mol Biol Evol 26:1829-33. 2009
    ..We conclude that the GC content of third-codon position cannot be used as stand-in for isochoric composition...
  13. pmc Detecting negative selection on recurrent mutations using gene genealogy
    Kiyoshi Ezawa
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204 5001, USA
    BMC Genet 14:37. 2013
    ..Such "recurrent mutations" might be revealed as deleterious by exploiting the signal of negative selection in the gene genealogy enhanced by their recurrence...

Research Grants2

  1. Error Correction in Multiple Sequence Alignments
    Dan Graur; Fiscal Year: 2009
    ..We estimate that our work will substantially increase the reliability of alignments and downstream procedures that use alignment as input. ..
  2. Error Correction in Multiple Sequence Alignments
    Dan Graur; Fiscal Year: 2010
    ..We estimate that our work will substantially increase the reliability of alignments and downstream procedures that use alignment as input. ..