A Blogger Investigates Syria’s Chemical Weapons: Is #opensource intell as good as spies? nyr.kr/Ijmuam MT @lyra_k @Brown_Moses
http://www.newyorker.com/reporting/2013/11/25/131125fa_fact_keefe
Steve #Jobs Left a Legacy on Personalized Medicine: $100K on his own #cancer genome as a progenitor to Foundation Med
http://www.technologyreview.com/view/519686/steve-jobs-left-a-legacy-on-personalized-medicine
http://onlinelibrary.wiley.com/doi/10.1111/eci.12171/full
~15M authors => ~150K w/ H>=20 => ~500 w/ highest citations &/or H >75 => 407 w/ further filters => 13 in Genomics & 4 from Yale
The Soaring Cost of a Simple Breath: Regulation requiring removal of CFCs from #asthma inhalers bumped out generics
http://www.nytimes.com/2013/10/13/us/the-soaring-cost-of-a-simple-breath.html
Mutational landscape and significance across 12 major #cancer types: Common genes mutated in different cancers
http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
http://www.sciencedaily.com/releases/2013/10/131016132143.htm
Mutational landscape and significance across 12 major cancer types http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
Summary for:
“Epigenomic Alterations in Localized and Advanced Prostate Cancer” Lin PC, Giannopoulou E, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA*, Elemento O*. 2013. Epigenomic alterations in localized and advanced prostate cancer. Neoplasia
http://www.ncbi.nlm.nih.gov/pubmed/23555183
In this paper, the authors take advantage of new advances in reduced representation bisulfite sequencing, a method for measuring DNA methylation patterns genome-wide, with high coverage and
single-nucleotide resolution, to study methylation patterns in prostate cancer. Working with a prostate cancer cohort already studied with DNA-Seq and RNA-Seq analyses, the authors identified
differentially methylated regions (DMRs), comparing the methylation of prostate cancer samples to benign prostate samples. The analysis found an increase in DNA methylation in prostate cancer samples, and that the methylation was more diverse and heterogeneous compared to the patterns of benign samples. Furthermore, it was found that genes near hypermethylated DMRs tended to have decreased expression, while genes near hypomethylated DMRs tended to have increased expression. Additional analyses revealed that breakpoints associated with prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue. Finally, a study of CpG islands at different stages of prostate cancer (benign vs. PCa vs. CRPC (castration-resistant prostate cancer)) revealed that certain islands become increasingly methylated with disease severity. The authors used this data as the basis for two classification models: one to discriminate between benign prostate tissue and PCa tissue, and another to discriminate between PCa tissue and CRPC tissue. Both models demonstrated high sensitivity and specificity, indicating that CpG islands with high discriminatory power could serve as a diagnostic basis for predicting disease aggressiveness. Finally, additional analyses revealed that breakpoints associated with
prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue.
http://nar.oxfordjournals.org/content/40/D1/D930.long
HaploReg explores functional annotations, such as chromatin states in varied cell types, sequence conservation, regulatory motif
alterations and eQTLs, of linked SNPs or indels within LD block of queried SNPs. The output provides a the guide to develop hypotheses of functional impact of non-coding variants, especially GWAS SNPs. HaploReg is currently limited to known variants (e.g. 1000 Genome variants and dbSNPs) and is unable to deal with private variants.
Interesting discussion of a new sleep medication related to orexin, which is a protein that when removed is associated with narcolepsy.
http://stm.sciencemag.org/content/5/179/179ra44
Genome Res. 2001 Apr;11(4):531-9.
Identification and functional analysis of mutations in the hypocretin (orexin) genes of narcoleptic canines.
Hungs M, Fan J, Lin L, Lin X, Maki RA, Mignot E.
http://www.ncbi.nlm.nih.gov/pubmed/11282968
#Orexin Receptor Antagonists Differ from Standard #Sleep Drugs… Interesting discussion of a new insomnia medication
http://stm.sciencemag.org/content/5/179/179ra44
Worth a read for large-scale project:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285
Ten Simple Rules for Reproducible Computational Research
Geir Kjetil Sandve,
Anton Nekrutenko,
James Taylor,
Eivind Hovig
and related :
http://www.slideshare.net/dullhunk/the-seven-deadly-sins-of-bioinformatics
[tag ReproducibleResearch,from,kbase]