Processed pseudogenes: A substrate for evolutionary innovation

Complex Analysis of Retroposed Genes’ Contribution to Human Genome, Proteome and Transcriptome

(2020) Magdalena Regina Kubiak et al.   Genes

Biological plasticity rescues target activity in CRISPR knock outs

(2019) Arne H. Smits et al.   NATURE METHODS

Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer

(2019) Balabhadrapatruni VSK Chakravarthi et al.   NEOPLASIA

Overcoming challenges and dogmas to understand the functions of pseudogenes

(2019) Seth W. Cheetham et al.   NATURE REVIEWS GENETICS

Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

(2018) Ikuo K. Suzuki et al.   CELL

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Repurposing of promoters and enhancers during mammalian evolution

(2018) Francesco N. Carelli et al.   Nature Communications

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Landscape and variation of novel retroduplications in 26 human populations

(2017) Yan Zhang et al.   PLoS Computational Biology

The life history of retrocopies illuminates the evolution of new mammalian genes

(2016) Francesco Nicola Carelli et al.   GENOME RESEARCH

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

Evolutionary direction of processed pseudogenes

(2016) Guoqing Liu et al.   Science China-Life Sciences

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

(2016) James C. Wright et al.   Nature Communications

The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo

(2015) Florian A. Karreth et al.   CELL

VEGFR-1 Pseudogene Expression and Regulatory Function in Human Colorectal Cancer Cells

(2015) X. Ye et al.   MOLECULAR CANCER RESEARCH

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Relocation Facilitates the Acquisition of Short Cis-Regulatory Regions that Drive the Expression of Retrogenes during Spermatogenesis in Drosophila

(2014) Mehran Sorourian et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential

(2014) Xingyi Guo et al.   PLoS One

Processed pseudogene insertions in somatic cells

(2014) Haig H Kazazian   Mobile DNA

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

(2013) Wen-Ling Chan et al.   NUCLEIC ACIDS RESEARCH

The OCT4 pseudogene POU5F1B is amplified and promotes an aggressive phenotype in gastric cancer

(2013) H Hayashi et al.   ONCOGENE

The Origin of the RB1 Imprint

(2013) Deniz Kanber et al.   PLoS One

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

(2013) Daniel R. Schrider et al.   PLoS Genetics

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Processed pseudogenes are located preferentially in regions of low recombination rates in the human genome

(2010) G. LIU et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants

(2010) Michał W Szcześniak et al.   MOLECULAR BIOLOGY AND EVOLUTION

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells

(2010) J. Lai et al.   RNA

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

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

(2010) Zhengdong D Zhang et al.   GENOME BIOLOGY

Assessing the genomic evidence for conserved transcribed pseudogenes under selection

(2009) Amit N Khachane et al.   BMC GENOMICS

Evolutionary Origin and Functions of Retrogene Introns

(2009) M. Fablet et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

A Functional Mouse Retroposed Gene Rps23r1 Reduces Alzheimer's β-Amyloid Levels and Tau Phosphorylation

(2009) Yun-wu Zhang et al.   NEURON

Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites

(2008) John L. Goodier et al.   CELL

What is a gene? An updated operational definition

(2008) Graziano Pesole   GENE

Retrotransposition as a Source of New Promoters

(2008) K. Okamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

(2008) G. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Independent genesis of chimeric TRIM5-cyclophilin proteins in two primate species

(2008) C. A. Virgen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein

(2008) Lia Rosso et al.   PLOS BIOLOGY

Mitochondrial Targeting Adaptation of the Hominoid-Specific Glutamate Dehydrogenase Driven by Positive Darwinian Selection

(2008) Lia Rosso et al.   PLoS Genetics