Archive for the 'SciLit' Category

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Orexin Receptor Antagonists Differ from Standard Sleep Drugs by Promoting Sleep at Doses That Do Not Disrupt Cognition

November 27, 2013

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

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All Ten Simple Rules for Reproducible Computational Research: from PLOS Computational Biology

November 26, 2013

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]

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The Protein-Folding Problem, 50 Years On

November 23, 2013

Interesting discussion by Ken Dill reviewing the field of protein folding over the past 50 years. Dr Dill links it to a number of diseases such as Alzheimer’s, Parkinson’s and type II diabetes, which are transmitted by aberrantly folding proteins. There is also a bit of discussion about folding landscapes in the funnel.

http://www.sciencemag.org/content/338/6110/1042

The #Protein-Folding Problem, 50 Years On: Broad review, ranging from funnels to misfolded proteins & Alzheimer’s
http://www.sciencemag.org/content/338/6110/1042

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How to Build a Smarter Rock

November 21, 2013

Interesting discussion about the creation of smart rocks and smart pebbles, which allow the tracking of current. These contain a data logger embedded in either aluminum or plastic. The tricky bit is how one finds them after they have been dropped off. Some ways might be radio transmitters, metal detectors and so forth but all of these have downsides.

How to Build a Smarter #Rock? Put a data #logger into aluminum or plastic; then track via radio or metal detector
http://www.sciencemag.org/content/338/6113/1412.summary

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Half a Million DVDs in Your DNA | Science/AAAS | News

November 19, 2013

Half a Million DVDs in Your #DNA: Nice writeup of Goldman et al paper, highlighting 3X density incr. to >2 PB / g DNA
http://news.sciencemag.org/biology/2013/01/half-million-dvds-your-dna

Very interesting discussion outside of science about the potential of storing large quantities of archival data on DNA. The statistic is that you can store a little more than 2 petabytes in a gram of DNA. This is actually cost effective relative to magnetic tape if one wants to do storage for >500 years. However one imagines that as the price of DNA sequencing and synthesis goes down this will become more favorable, perhaps being reasonable for archival storage in the ~50 year regimen. One of the issues with DNA storage, of course, is the lack of random access and the inability to rewrite over already stored media. But for long-term archival storage DNA is considerably more stable than the magnetic storage on tape or disk.

http://news.sciencemag.org/biology/2013/01/half-million-dvds-your-dna http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html

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haploseq

November 19, 2013

http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2728.html

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

HaploSeq: #haplotype reconstruction using proximity-ligation. Nice adaptation of functional genomics tech to assembly
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2728.html

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A list of highly influential biomedical researchers, 1996–2011 – Boyack – 2013 – European Journal of Clin ical Investigation – Wiley Online Library

November 13, 2013

~400 top authors by h-score & citations from 15K in biomed.
http://onlinelibrary.wiley.com/doi/10.1111/eci.12171/abstract

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Emergent Sensing of Complex Environments by Mobile Animal Groups

November 13, 2013

#Emergent Sensing of Complex Environments by Mobile Animal Groups: Fish swarm into dark patches from speed adjustment
http://www.sciencemag.org/content/339/6119/574.abstract

An interesting discussion of how fish swarms reflect collective behavior. The basic idea is that fish like to swim in dark patches of water as opposed to light patches and one question is how a swarm finds this quickly. It turns out that it is not related to individual fish swimming away from light and dark but rather that the fish in light water swimming more quickly than those in dark water and the fish also trying to stay together as a swarm. The latter acts essentially as almost an axle between two wheels that are moving at different speeds forcing the fish to naturally turn into dark areas. A very intuitive discussion of this topic and a nice comparison to how this type of collective behavior is what one sees in the nervous system as well – One would not want to be making mental decisions on the basis of an individual neuron.

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The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future : Genetics in Medicine : Nature Publishing Group

November 11, 2013

http://www.nature.com/gim/journal/v15/n10/full/gim201372a.html

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RGASP papers online

November 11, 2013

The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!

Some notes from a senior author:

* Due to space constraints unfortunately most of the results are in the supplemental data.

* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.

* The papers are not open access, unfortunately.

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