Nicholas Carriero

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites
    Liang Chen
    Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
    BMC Genet 6:S130. 2005
  2. pmc A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies
    Nicholas Carriero
    Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
    J Am Med Inform Assoc 12:90-8. 2005
  3. ncbi request reprint A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    J Mol Biol 333:885-92. 2003
  4. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
  5. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
  6. pmc Pseudofam: the pseudogene families database
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 37:D738-43. 2009
  7. pmc Hinge Atlas: relating protein sequence to sites of structural flexibility
    Samuel C Flores
    Department of Physics, Yale University, New Haven, CT, USA
    BMC Bioinformatics 8:167. 2007
  8. pmc Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
    Yuen Jong Liu
    Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
    BMC Genomics 10:480. 2009
  9. ncbi request reprint PseudoPipe: an automated pseudogene identification pipeline
    Zhaolei Zhang
    Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada
    Bioinformatics 22:1437-9. 2006
  10. pmc Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
    Paul M Harrison
    Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1
    Nucleic Acids Res 33:2374-83. 2005

Detail Information

Publications10

  1. pmc Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites
    Liang Chen
    Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
    BMC Genet 6:S130. 2005
    ..In this case, the results for SNPs and microsatellites are more consistent. Compared to FBAT, more significant markers are detected with BHTA...
  2. pmc A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies
    Nicholas Carriero
    Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
    J Am Med Inform Assoc 12:90-8. 2005
    ....
  3. ncbi request reprint A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    J Mol Biol 333:885-92. 2003
    ..Data on uhORFs are available from http://pseudogene.org/polyo..
  4. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
    ..The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances...
  5. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  6. pmc Pseudofam: the pseudogene families database
    Hugo Y K Lam
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 37:D738-43. 2009
    ..The statistics also show how the number of genes and pseudogenes in families correlates across different species. Overall, they highlight the fact that housekeeping families tend to be enriched with a large number of pseudogenes...
  7. pmc Hinge Atlas: relating protein sequence to sites of structural flexibility
    Samuel C Flores
    Department of Physics, Yale University, New Haven, CT, USA
    BMC Bioinformatics 8:167. 2007
    ..Efforts in this field have been hampered by the lack of a proper dataset for studying characteristics of hinges...
  8. pmc Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
    Yuen Jong Liu
    Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
    BMC Genomics 10:480. 2009
    ..One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins...
  9. ncbi request reprint PseudoPipe: an automated pseudogene identification pipeline
    Zhaolei Zhang
    Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada
    Bioinformatics 22:1437-9. 2006
    ..These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes...
  10. pmc Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
    Paul M Harrison
    Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1
    Nucleic Acids Res 33:2374-83. 2005
    ..This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TPPsigs is available at: http://www.biology.mcgill.ca/faculty/harrison/tppg/bppg.tov (or) http:pseudogene.org...