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
Archive for the 'SciLit' Category
Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids
June 1, 2014Geometric and electronic factors in the rational design of transition-metal-centered boron molecular wheels
June 1, 2014CB9 nice decomposition of sigma bonds: 9*2c-2e + 4*3c-2e
Geometric & electronic factors in… design of… B molecular wheels. Minimum E #isomer via Coalescence Kick (CK)
http://scitation.aip.org/content/aip/journal/jcp/138/13/10.1063/1.4798935
Characterization of the human ESC transcriptome by hybrid sequencing
May 27, 2014Characterization of the… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones
http://www.pnas.org/content/110/50/E4821.long
Inferring Cellular Networks Using Probabilistic Graphical Models
May 26, 2014Inferring… #Networks Using Probabilistic Graphical Models. Nice intro to #Bayesian methods, useful for #teaching
http://www.sciencemag.org/content/303/5659/799.abs
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.
May 20, 2014Hypomethylation in the human germline associates w/ structural mutability: Many #SVs in #genomic #methylation deserts
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002692
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002692
Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.
PLoS Genet. 2012;8(5):e1002692. doi: 10.1371/journal.pgen.1002692. Epub 2012 May 17.
PMID: 22615578 [PubMed – indexed for MEDLINE] Free PMC Article
Mutability as a measure of methylation, viz:
QT:{{
The MI model is based on the fact that in mammals DNA methylation predominantly occurs in CpG dinucleotides, increasing the probability of transitions to TpG or CpA dinucleotides. The MI calculation by Sigurdsson et al. [48] implicitly uses mutability of CpGs in the human genome as an indicator of methylation in the germline. We apply this method of by integrating four million non-redundant SNPs from the HapMap project. Methylation index values were calculated for the same set of 100 Kbp windows used for sperm methylome construction to facilitate comparison.
}}
Also :
Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003333
Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.
PLoS Genet. 2013;9(2):e1003333. doi: 10.1371/journal.pgen.1003333. Epub 2013 Feb 28. No abstract available.
PMID: 23468659 [PubMed – indexed for MEDLINE] Free PMC Article
retroelement functional recruitment
May 12, 2014DUX4 binding to #retroelements creates promoters that are active… Highlights #chipseq binding sites in #repeats
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003947 http://www.ncbi.nlm.nih.gov/pubmed/?term=24278031
PLoS Genet. 2013 Nov;9(11):e1003947. doi:
10.1371/journal.pgen.1003947. Epub 2013 Nov 21.
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ.
A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites : Nature Communications : Nature Publishing Group
May 11, 2014http://www.nature.com/ncomms/2014/140205/ncomms4216/full/ncomms4216.html Mentioned as a mechanism for “occasional presence of templated insertions.”
Nature Genetics calls for data analysis papers
May 9, 2014Call for… analysis papers: nice description of hypothesis generation v. validation & 3 types of #network robustness
http://www.nature.com/ng/journal/v46/n3/full/ng.2914.html
Call for data analysis papers
Nature Genetics 46, 213 (2014) doi:10.1038/ng.2914Published online 26 February 2014
Deadline expired but maybe still relevant…
Another VAT!
May 9, 2014Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data
http://www.cell.com/ajhg/abstract/S0002-9297(14)00176-1
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