Posts Tagged ‘pseudogenes’

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer : Nature Communications : Nature Publishing Group

July 2, 2016

lncRNA-mediated sponge regulatory network in prostate cancer http://www.nature.com/ncomms/2016/160315/ncomms10982/full/ncomms10982.html Few explicitly noted #pseudogenes besides PTENP1

BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

July 31, 2015

[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113

Comparative genomics reveals insights into avian genome evolution and adaptation

May 16, 2015

Comparative #genomics reveals insights into avian…#evolution http://www.sciencemag.org/content/346/6215/1311 Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
….
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators : Nature : Nature Publishing Group

February 21, 2015

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators http://www.nature.com/nature/journal/v508/n7497/full/nature13206.html Reconstructed #evolution across 8 species

Daniel W. Bellott,
Jennifer F. Hughes,

Richard A. Gibbs,
Richard K. Wilson
& David C. Page

Nature 508, 494–499 (24 April 2014) doi:10.1038/nature13206

Pgenes make proteins

January 24, 2015

Bioinformatics (2015) 31 (1): 33-39. doi: 10.1093/bioinformatics/btu615

Making novel proteins from #pseudogenes
http://bioinformatics.oxfordjournals.org/content/31/1/33.short Outcomes in 16 cases where one gets stable & functional translated products

http://bioinformatics.oxfordjournals.org/content/31/1/33.short

PLOS Biology: Where Do Introns Come From?

August 23, 2014

Where Do #Introns Come From? A suggestion: exons with premature stops; has implications for #pseudogene formation http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060283

QT:{{
We have proposed a novel hypothesis for the origin of spliceosomal
introns, invoking endogenous production within translatable sequences
(at least in the case of protein-coding genes), facilitated by the
activity of cellular surveillance mechanisms. Despite the mutational
hazard associated with intron presence and proliferation [136], we
argue that, at least initially, introns might represent a favorable
life line for an allele that has acquired an ORF-disrupting mutation.
In this sense, in-frame stop codons need not be dead ends, as often
believed, but rather sequences that occasionally facilitate the
evolution of eukaryotic gene structure, possibly favoring not only
intronization, but also processes such as exonization (following a PTC
loss [137]). Further experimental validation of our hypothesis would
not only support the idea that intron birth/death rates depend on both
the population-genetic [136] and the intracellular environment, but
also shed light on a surprising aspect of the evolution of eukaryotic
gene structure, i.e., the ongoing, stochastic process of mutual
conversion between exons and introns within genes.
"}}

NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes

July 19, 2014

Linial: ClanTox (www.clantox.cs.huji.ac.il) to classify short peptides as toxins. #ismb #kn1

TOLIPS relevant to brain, neuropeptides

Linial mentions NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
http://bioinformatics.oxfordjournals.org/content/early/2014/03/05/bioinformatics.btt725.abstract #ismb #kn1

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

June 1, 2014

Massive Genomic Decay in… a Recently Evolved #Symbiont of Aphids. Creation of #pseudogenes in many COG categories
http://gbe.oxfordjournals.org/content/3/195.long

Gaelen R. Burke & Nancy A. Moran

Encode-annotation interesting paper

April 14, 2014

recent publication from the Donnelly group comparing using GENCODE or Refeq annotation when predicting variants effects.
Choice of transcripts and software has a large effect on variant annotation
Genome Medicine 2014, 6:26 doi:10.1186/gm543

Processed pseudogenes acquired somatically during cancer development

April 12, 2014

http://www.nature.com/ncomms/2014/140409/ncomms4644/full/ncomms4644.html