http://www.ncbi.nlm.nih.gov/pubmed/23176822
Am J Hum Genet. 2012 Dec 7;91(6):1033-40. doi:
10.1016/j.ajhg.2012.10.018. Epub 2012 Nov 21.
Differential relationship of DNA replication timing to different forms of human mutation and variation.
Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA.
Archive for the 'SciLit' Category
Differential relationship of DNA replication timing to different forms of human mutation and variation.
December 6, 2013Following the Flavor
December 6, 2013Great tidbits on how olives & wine seem less sour together than individually
Following the Flavor. Great tidbits on retronasal olfaction & how combos #taste different together than individually
http://www.sciencemag.org/content/340/6134/808.summary
Impact of Shale Gas Development on Regional Water Quality
December 6, 2013http://www.sciencemag.org/content/340/6134/1235009.abstract
Impact of Shale #Gas Development on Regional Water Quality: Disposal of #fracking wastewater will be a future issue
http://www.sciencemag.org/content/340/6134/1235009.abstract
1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans
December 1, 2013Cell – Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral Cortex by Control of Radial Glial Fate
November 30, 2013Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral #Cortex: less in mice gives more human-like folds
http://www.cell.com/retrieve/pii/S0092867413003498
And a Glossary of Their Quarry
November 29, 2013Glossary of Their Quarry. #exoplanet types: circumbinary, pulsar, core & rogue. Hot Jupiters, waterworlds, #exomoons
http://www.sciencemag.org/content/340/6132/570.summary
And a Glossary of Their Quarry.
Quoting from the podcast summary…
QT:{{”
So far, scientists have uncovered over 800 exoplanets roaming the cosmos—but as Sara Seager said earlier, we’re still searching for that Earth-like, Goldilocks planet.
…
Most of the planets we’ve discovered up until this point are what’s called Hot
Jupiters, which are gas giants about the size of Jupiter in our solar system with a pretty
big range on either side, so the smallest Hot Jupiters would be about 50 Earth masses.
…
The nastiest place to live would probably be pulsar planets.
…
And I
think another really unpleasant place to be would be a core planet. So core planets, they
sort of resemble something like Mercury, the size of Mercury, maybe even smaller.
…
I think just like in the solar system, actually, some of the best places for potentially
finding life outside of our solar system might be moons. So we call them exomoons or
moons orbiting exoplanets.
…
But we have seen and are seeing more and more of are theses
circumbinary planets,
which means a planet with two suns. So, Tatooine is sort of the iconic example.
…
Yes, waterworlds. So those are pretty diverse, and they are usually super-Earth-size so
they’ll be like 10 times the mass of Earth.
…
And then there are some planets that just go rogue.
“}}
A list of highly influential biomedical researchers, 1996–2011 – Boyack – 2013 – European Journal of Clin ical Investigation – Wiley Online Library
November 27, 2013http://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
Genetic errors identified in 12 major cancer types
November 27, 2013Mutational 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
Epigenomic alterations in localized and advanced prostate cancer – Neoplasia
November 27, 2013Summary 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.
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
November 27, 2013http://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.
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