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..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...
- 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...