Archive for the 'SciLit' Category

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Cancer N/S ratio

October 20, 2012

From XJM:

A few references about nonsynonymous/synonymous ratio in Cancer: Here is a Nature paper finding nonsynonymous/synonymous ratio to be 3:1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712719/

Here is an article reporting the ratio to be about 4:1
http://www.nature.com/ng/journal/v43/n11/full/ng.950.html

Another one:
http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2012.00976.x/full

An online powerpoint reporting 2:1 ratio:
http://www.genome.gov/Pages/Research/DIR/DIRNewsFeatures/Next-Gen101/Samuels_WholeExomeSequencing.pdf

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Predicting Publishing Futures | The Scientist Magazine(R)

October 19, 2012

http://www.the-scientist.com/?articles.view/articleNo/32603/title/Predicting%20Publishing%20Futures http://www.nature.com/nature/journal/v489/n7415/full/489201a.html http://klab.smpp.northwestern.edu/h-index.html

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Spectrum of somatic mitochondrial mutations in five cancers

October 19, 2012

http://www.pnas.org/content/109/35/14087.abstract
Allusion to whole genome data, but focus is on coding regions & mitochondrial mutations

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Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns

October 12, 2012

http://www.sciencemag.org/content/early/2012/10/10/science.1227833.abs

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Observation of dually decoded regions of the human genome using ribosome profiling data Genome Res. 2012

October 8, 2012

http://www.ncbi.nlm.nih.gov/pubmed/22593554

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A transcriptomic hourglass in plant embryogenesis

October 6, 2012

http://www.nature.com/nature/journal/v490/n7418/full/nature11394.html

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PPI networks refined by 3D structure

October 6, 2012

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature11503.html
Doesn’t seem to refer to SIN, Dynasin or that much earlier work on structural interaction network

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Exome sequencing and the genetic basis of complex traits

September 30, 2012

Figure 1 in a recent Nature Genetics paper useful for LOF — saturation of LoF, essentially something that describes how many LoF variants we see as we keep adding more samples :

http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html

QT:”
Basically, LoF variants are so enriched for ultra-rare variants that they show no sign of saturation, and the catalogue will continue to grow as more and more exomes are sequenced.
“

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Dissecting the genomic complexity underlying medulloblastoma : Nature : Nature Publishing Group

September 26, 2012

http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs

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Fast gapped-read alignment with Bowtie 2

September 25, 2012

http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html
perhaps useful for SVs?

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