Affiliation: Yale University
- Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellitesLiang 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...
- A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studiesNicholas Carriero
Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
J Am Med Inform Assoc 12:90-8. 2005....
- A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFsPaul 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..
- Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomesSuganthi 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...
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controlsJoel 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...
- Pseudofam: the pseudogene families databaseHugo 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...
- Hinge Atlas: relating protein sequence to sites of structural flexibilitySamuel 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...
- Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activityYuen 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...
- PseudoPipe: an automated pseudogene identification pipelineZhaolei 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..Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts...
- Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding abilityPaul 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...