This website maintains all the data and tools associated with previous pseudogene publications from Gerstein lab. Publications are organized by species. Please click to see the reference, or to see the supporting data or tools.

A complete list of pseudogene publications is also available here.


Human Pseudogene
  • Sisu et al. Comparative analysis of pseudogenes across three phyla, PNAS 111(37):13361-6, 2014.   
  • Pei et al., The GENCODE pseudogene resource, Genome Biol 13:R51, 2012.   
  • Khurana et al., Segmental duplications in the human genome reveal details of pseudogene formation, Nucleic Acids Res. 38(20): 6997–7007, 2010.   
  • Liu et al., 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, BMC Genomics 10:480, 2009.  
  • Balasubramanian et al., Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes, Genome Biol. 10:R2, 2009.  
  • Lam et al., Pseudofam: the pseudogene families database, Nucleic Acids Res 37:D738-43.  
  • Zheng et al., Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories, Mol. Biol. Evol. 25:131-43, 2008.  
  • Zheng et al., Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution, Genome Res. 17:839-51, 2007.  
  • Zheng et al., A computational Approach for Identifying Pseudogenes in the ENCODE Regions, Genome Bio. 7 Suppl 1:S13.1-10., 2006.  
  • Zheng et al., Integrated pseudogene annotation for human chromosome 22: evidence for transcription, J Mol Biol 349:27-45, 2005.  
  • Harrison et al., Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability, Nucleic Acids Res 33:2374-83, 2005.  
  • Zhang et al., Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome, Genome Res. 13:2541-58, 2003.  
  • Zhang et al., Patterns of nucleotide substitution, insertion and deletion in the human genome, Nucleic Acids Res 31:5338-48, 2003.  
  • Zhang et al., The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse, Gene 312:61-72, 2003.  
  • Zhang et al., Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome, Genomics 81:468-80, 2003.  
  • Harrison et al., Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22, Genome Res 12:272-80, 2002.  
  • Zhang et al., Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes, J Mol Biol 323:811-22, 2002.  
  • Zhang et al., Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome, Genome Res. 12:1466-82, 2002.  
  • Balasubramanian et al., SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes, Pharmacogenomics 3:393-402, 2002.  
  • Echols et al., Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes, Nucleic Acids Res 30:2515-23, 2002.   (This is a deprecated web link. Some functions may not work as they are supposed to.)
Mouse Pseudogene
  • Zhang et al., Comparative analysis of processed pseudogenes in the mouse and human genomes, Trends Genet 20:62-7, 2004.  
Worm Pseudogene
  • Sisu et al. Comparative analysis of pseudogenes across three phyla, PNAS 111(37):13361-6, 2014.   
  • Harrison et al., Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome, Nucleic Acids Res. 29:818-30, 2001.  
Fly Pseudogene
  • Sisu et al. Comparative analysis of pseudogenes across three phyla, PNAS 111(37):13361-6, 2014.   
  • Harrison et al., Identification of pseudogenes in the Drosophila melanogaster genome, Nucleic Acids Res. 31:1033-7, 2003.  
Rice Pseudogene
  • Guo et al., Small RNAs originated from pseudogenes: cis- or trans-acting?, PLoS Comput Biol 5:e1000449, 2009.  
Other Eukaryotes Pseudogene
  • Zhang et al., PseudoPipe: an automated pseudogene identification pipeline, Bioinformatics 22:1437-9, 2006.  
Prokaryotes Pseudogene
  • Li et al., Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes, Genome Biol 5:R64, 2004.  
  • Harrison et al., A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORF, J Mol Biol 333:885-92, 2003.  
Quick Links to other Publications
  • Abyzov et al., Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division, Genome Res 23:2042-52, 2013. 
  • Balasubramanian et al., Gene inactivation and its implications for annotation in the era of personal genomics, Genes Dev 25:1-10, 2011. 
  • Zhang et al., Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates, Genome Biol 11:R26, 2010. 
  • Holford et al., Using semantic web rules to reason on an ontology of pseudogenes, Bioinformatics 26:i71-8, 2010. 
  • Sasidharan et al., Genomics: protein fossils live on as RNA, Nature 453:729-31, 2008. 
  • Zheng et al., The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they, Trends Genet 23:219-24, 2007. 
  • Gerstein et al., The real life of pseudogenes, Sci Am 295:48-55, 2006. 
  • Zhang et al., Large-scale analysis of pseudogenes in the human genome, Curr Opin Genet Dev 14:328-35, 2004. 
  • Harrison et al., A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution, J Mol Biol 316:409-19, 2002. 
  • Harrison et al., Studying genomes through the aeons: protein families, pseudogenes and proteome evolution, J Mol Biol 318:1155-74, 2002. 
  • Kumar et al., An integrated approach for finding overlooked genes in yeast, Nat Biotechnol 20:58-63, 2001. 
Quick Links to other Tools
  • Human Fragment Browser
  • Mouse Fragment Browser
  • Worm Fragment Browser