Science. 2008 Nov 28;322(5906):1377-80. doi: 10.1126/science.1164266.
Mullighan CG1, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing JR.
Interesting older paper
Genomic analysis of the clonal origins of relapsed ALL
http://www.sciencemag.org/content/322/5906/1377.abs Older paper, describing relapse as arising from minor subclone
Neuroscience
Scientific American 310, 70 – 77 (2014)
Published online: 18 March 2014 | doi:10.1038/scientificamerican0414-70
The Genetic Geography of the Brain
Ed Lein & Mike Hawrylycz
http://www.scientificamerican.com/article/genetic-maps-of-the-brain-lead-to-surprises
#DataScience & Prediction: Nice overview of the field, emphasizing testable models, even when causation isn’t implied
http://cacm.acm.org/magazines/2013/12/169933-data-science-and-prediction/fulltext
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
CB9 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… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones
http://www.pnas.org/content/110/50/E4821.long
Inferring… #Networks Using Probabilistic Graphical Models. Nice intro to #Bayesian methods, useful for #teaching
http://www.sciencemag.org/content/303/5659/799.abs
#Viruses Reconsidered: Some huge, megabase-scale #genomes but no ribosomes. Usually filtered out in metagenomics
http://www.the-scientist.com/?articles.view/articleNo/39244/title/Viruses-Reconsidered
Phylogenetic…Studies of Informational Genes… Highlight Existence of a 4th Domain of Life Including Giant #Viruses
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015530
M. Boyer et al., “Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4th domain of life including giant viruses,” PLOS ONE, 5:e15530, 2010.
Clustering polymerase reveals TRUC – new Domains to life
Hypomethylation 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
DUX4 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.