A complete list of pseudogene publications is also available here.

• 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.)

• Zhang et al., Comparative analysis of processed pseudogenes in the mouse and human genomes, Trends Genet 20:62-7, 2004.  

• 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.  

• 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.  

• Guo et al., Small RNAs originated from pseudogenes: cis- or trans-acting?, PLoS Comput Biol 5:e1000449, 2009.  

• Zhang et al., PseudoPipe: an automated pseudogene identification pipeline, Bioinformatics 22:1437-9, 2006.  

• 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.  

• 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. 

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