Overcoming challenges and dogmas to understand the functions of pseudogenes

SW Cheetham, GJ Faulkner, ME Dinger - Nature Reviews Genetics, 2020 - nature.com
Pseudogenes are defined as regions of the genome that contain defective copies of genes.
They exist across almost all forms of life, and in mammalian genomes are annotated in …

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

D Zheng, MB Gerstein - Trends in Genetics, 2007 - cell.com
Pseudogenes have long been considered to be 'dead', nonfunctional by-products of
genome evolution. However, several lines of evidence now show that some pseudogenes …

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

D Zheng, A Frankish, R Baertsch, P Kapranov… - Genome …, 2007 - genome.cshlp.org
Arising from either retrotransposition or genomic duplication of functional genes,
pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of …

A genome-wide survey of human pseudogenes

D Torrents, M Suyama, E Zdobnov, P Bork - Genome research, 2003 - genome.cshlp.org
We screened all intergenic regions in the human genome to identify pseudogenes with a
combination of homology searches and a functionality test using the ratio of silent to …

Large-scale analysis of pseudogenes in the human genome

ZL Zhang, M Gerstein - Current opinion in genetics & development, 2004 - Elsevier
Pseudogenes are considered as genomic fossils: disabled copies of functional genes that
were once active in the ancient genome. Recently, whole-genome computational …

Pseudogene. org: a comprehensive database and comparison platform for pseudogene annotation

JE Karro, Y Yan, D Zheng, Z Zhang… - Nucleic acids …, 2007 - academic.oup.com
The Pseudogene. org knowledgebase serves as a comprehensive repository for
pseudogene annotation. The definition of a pseudogene varies within the literature, resulting …

The GENCODE pseudogene resource

B Pei, C Sisu, A Frankish, C Howald, L Habegger… - Genome biology, 2012 - Springer
Background Pseudogenes have long been considered as nonfunctional genomic
sequences. However, recent evidence suggests that many of them might have some form of …

PseudoPipe: an automated pseudogene identification pipeline

Z Zhang, N Carriero, D Zheng, J Karro… - …, 2006 - academic.oup.com
Motivation: Mammalian genomes contain many 'genomic fossils' ie pseudogenes. These are
disabled copies of functional genes that have been retained in the genome by gene …

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

ZD Zhang, A Frankish, T Hunt, J Harrow, M Gerstein - Genome biology, 2010 - Springer
Background Unitary pseudogenes are a class of unprocessed pseudogenes without
functioning counterparts in the genome. They constitute only a small fraction of annotated …

[HTML][HTML] Re-recognition of pseudogenes: From molecular to clinical applications

X Chen, L Wan, W Wang, WJ Xi, AG Yang, T Wang - Theranostics, 2020 - ncbi.nlm.nih.gov
Pseudogenes were initially regarded as “nonfunctional” genomic elements that did not have
protein-coding abilities due to several endogenous inactivating mutations. Although …