David R Nelson

Summary

Affiliation: University of Tennessee
Country: USA

Publications

  1. ncbi Introductory remarks on human CYPs
    David R Nelson
    Department of Biochemistry, Tennessee Health Science Center, University of Tennessee, Memphis 38163, USA
    Drug Metab Rev 34:1-5. 2002
  2. pmc Gene nomenclature by default, or BLASTing to Babel
    David R Nelson
    The University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
    Hum Genomics 2:196-201. 2005
  3. ncbi Cytochrome P450 nomenclature, 2004
    David R Nelson
    Department of Biochemistry, University of Tennessee, Memphis, USA
    Methods Mol Biol 320:1-10. 2006
  4. pmc The cytochrome P450 (CYP) gene superfamily in Daphnia pulex
    William S Baldwin
    Clemson University, Biological Sciences, Institute of Environmental Toxicology, Pendleton, SC, USA
    BMC Genomics 10:169. 2009
  5. pmc 'A variant of uncertain significance' and the proliferation of human disease gene databases
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
    Hum Genomics 2:70-4. 2005
  6. pmc 'Frankenstein genes', or the Mad Magazine version of the human pseudogenome
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
    Hum Genomics 1:310-6. 2004
  7. pmc Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot
    David R Nelson
    Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA
    Plant Physiol 135:756-72. 2004
  8. ncbi Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, Memphis, TN 38163, USA
    Pharmacogenetics 14:1-18. 2004
  9. ncbi Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, 858 Madison Avenue, Memphis 38163, USA
    Arch Biochem Biophys 409:18-24. 2003
  10. pmc The truth about mouse, human, worms and yeast
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA
    Hum Genomics 1:146-9. 2004

Collaborators

Detail Information

Publications28

  1. ncbi Introductory remarks on human CYPs
    David R Nelson
    Department of Biochemistry, Tennessee Health Science Center, University of Tennessee, Memphis 38163, USA
    Drug Metab Rev 34:1-5. 2002
  2. pmc Gene nomenclature by default, or BLASTing to Babel
    David R Nelson
    The University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
    Hum Genomics 2:196-201. 2005
    ..The example of rat cytochrome P450 (Cyp) genes is presented here, but other gene families are also likely to be affected...
  3. ncbi Cytochrome P450 nomenclature, 2004
    David R Nelson
    Department of Biochemistry, University of Tennessee, Memphis, USA
    Methods Mol Biol 320:1-10. 2006
    ..CYP clans are defined as clusters of CYP families. The clan names are useful in describing higher-order evolution of the gene superfamily. The nomenclature of orthologs and pseudogenes is also discussed...
  4. pmc The cytochrome P450 (CYP) gene superfamily in Daphnia pulex
    William S Baldwin
    Clemson University, Biological Sciences, Institute of Environmental Toxicology, Pendleton, SC, USA
    BMC Genomics 10:169. 2009
    ..The latter form a critical component of detoxification systems...
  5. pmc 'A variant of uncertain significance' and the proliferation of human disease gene databases
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
    Hum Genomics 2:70-4. 2005
    ..The percentage of all possible point mutations for a protein (the mutation space) is calculated for each gene and the question 'How much mutation data is enough?' is raised...
  6. pmc 'Frankenstein genes', or the Mad Magazine version of the human pseudogenome
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
    Hum Genomics 1:310-6. 2004
    ..Failure to do so will flood the databases with thousands of false-positive predictions. Indeed, they are already there...
  7. pmc Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot
    David R Nelson
    Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA
    Plant Physiol 135:756-72. 2004
    ....
  8. ncbi Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, Memphis, TN 38163, USA
    Pharmacogenetics 14:1-18. 2004
    ..It is therefore of interest to catalog the genetic similarities and differences, and to clarify the limits of extrapolation from mouse to human...
  9. ncbi Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, 858 Madison Avenue, Memphis 38163, USA
    Arch Biochem Biophys 409:18-24. 2003
    ..In the CYP2 family, only CYP2R1 and CYP2U1 are conserved as recognizable subfamilies across species. Intron-exon boundaries are largely preserved across 420 million years of evolution...
  10. pmc The truth about mouse, human, worms and yeast
    David R Nelson
    Department of Molecular Sciences and The UT Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163, USA
    Hum Genomics 1:146-9. 2004
    ..Current large disparities between human Unigene predictions (127,835 genes) and gene-scanning methods (45,000 genes) still need to be resolved. This will be the challenge during the next few years...
  11. ncbi Mining databases for cytochrome P450 genes
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee 38163, USA
    Methods Enzymol 357:3-15. 2002
  12. pmc A world of cytochrome P450s
    David R Nelson
    Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA
    Philos Trans R Soc Lond B Biol Sci 368:20120430. 2013
    ..The contributions to this issue range from evolution on the billion year scale to the colour of roses, from Darwin to Rachel Carson; all as seen through the lens of cytochrome P450...
  13. pmc The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s
    David R Nelson
    Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA
    Philos Trans R Soc Lond B Biol Sci 368:20120474. 2013
    ....
  14. doi Progress in tracing the evolutionary paths of cytochrome P450
    David R Nelson
    Dept of Molecular Sciences, University of Tennessee Health Science Center, 858 Madison Ave, Suite G01, Memphis, TN 38163, USA
    Biochim Biophys Acta 1814:14-8. 2011
    ..The special niche of filamentous fungal P450s acting in secondary metabolite gene clusters is discussed. From one quarter to one third of P450s in these fungi may be dedicated to these roles...
  15. pmc The cytochrome p450 homepage
    David R Nelson
    Department of Molecular Sciences, University of Tennessee, 858 Madison Avenue, Memphis, TN 38163, USA
    Hum Genomics 4:59-65. 2009
    ..The organisation and content of the Homepage are described...
  16. pmc gln3 mutations dissociate responses to nitrogen limitation (nitrogen catabolite repression) and rapamycin inhibition of TorC1
    Rajendra Rai
    Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
    J Biol Chem 288:2789-804. 2013
    ..We also found that Gln3 possesses at least one Tor1-interacting site in addition to the one previously reported...
  17. pmc Cyclophilin nomenclature problems, or, 'a visit from the sequence police'
    Daniel W Nebert
    Department of Environmental Health and Center for Environmental Genetics CEG, University of Cincinnati Medical Center, Cincinnati, OH 45267 0056, USA dan nerbert uc edu
    Hum Genomics 1:381-8. 2004
    ....
  18. pmc The Chlamydomonas genome reveals the evolution of key animal and plant functions
    Sabeeha S Merchant
    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
    Science 318:245-50. 2007
    ....
  19. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  20. ncbi Dynamics of molecular motors with finite processivity on heterogeneous tracks
    Yariv Kafri
    Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 71:041906. 2005
    ..A similar spectral analysis also provides a very efficient method for studying the dynamics of motors with infinite processivity...
  21. ncbi Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2)
    David C Lamb
    Institute of Biological Sciences, University of Wales Aberystwyth, Aberystwyth, UK
    Biochem Biophys Res Commun 307:610-9. 2003
    ..Amongst this range of CYPs are forms associated with avermectin, filipin, geosmin, and pentalenolactone biosynthesis as well as unknown pathways of secondary metabolism...
  22. pmc Dynamics of molecular motors and polymer translocation with sequence heterogeneity
    Yariv Kafri
    Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
    Biophys J 86:3373-91. 2004
    ..Similar sequence heterogeneity effects may arise in the packing of viral DNA...
  23. pmc Genome landscapes and bacteriophage codon usage
    Julius B Lucks
    FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
    PLoS Comput Biol 4:e1000001. 2008
    ..Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages...
  24. pmc Identification and characterization of a repeat-in-toxin gene cluster in Vibrio anguillarum
    Ling Li
    Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
    Infect Immun 76:2620-32. 2008
    ..Finally, wild-type and mutant strains were tested for virulence in juvenile Atlantic salmon. Only strains containing an rtxA mutation had reduced virulence, suggesting that RtxA is a major virulence factor for V. anguillarum...
  25. ncbi Genomic analysis of detoxification genes in the mosquito Aedes aegypti
    Clare Strode
    Vector Group, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
    Insect Biochem Mol Biol 38:113-23. 2008
    ..This 'Ae. aegypti Detox Chip' will facilitate the implementation of insecticide resistance management strategies for arboviral control programmes...
  26. ncbi International integrated database for the evaluation of severe sepsis and drotrecogin alfa (activated) therapy: 28-day survival and safety
    Pierre Francois Laterre
    Department of Critical Care Medicine, Hôpital St Luc, Universite Catholique de Louvain, B 1200 Brussels, Belgium
    J Crit Care 22:142-52. 2007
    ..Initial analyses evaluated the 28-day survival in the placebo group and further assessed the treatment effect of drotrecogin alfa (activated) (DrotAA)...
  27. ncbi A quasispecies on a moving oasis
    Michael M Desai
    Department of Physics, Jefferson Laboratories, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA
    Theor Popul Biol 67:33-45. 2005
    ..This switching velocity is analogous to the quasispecies mutational error threshold. Above this velocity, the population cannot maintain adaptations to the properties of the oasis...
  28. pmc Identification and characterization of a hemolysin gene cluster in Vibrio anguillarum
    Jessica L Rock
    Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
    Infect Immun 74:2777-86. 2006
    ..anguillarum. At least three genes (plp, llpA, and vah1) are responsible for one hemolytic activity. The data also suggest that plp acts as a negative regulator of vah1 and llpA...