Article_Nov.1

□ OxfordJournals:
Free in the Review of Economic Studies: oxford.ly/vm9A5x "Bayesian Learning in Social Networks" #socialnetworks #socialmedia
Bayesian equilibrium of a sequential learning model over a general social network.

The stochastic process generating the neighbourhoods defines the network topology. We characterize pure strategy equilibria for arbitrary stochastic and deterministic social networks and characterize the conditions under which there will be asymptotic learning?convergence (in probability) to the right action as the social network becomes large.

□ portablegenomic:
Infographic: College or Incubator for Startup Founders? | Xconomy shar.es/b9Y2V

The graphic, which pulled some of its data directly from TechStars and Y Combinator, gives a sense of just how powerful those programs can be in helping startups stay out of the dead pool.

And according to the stats here, TechStars has a better success rate, with about 7 percent of companies going under, vs. roughly 22 percent for Y Combinator alums.

I was personally a little surprised that such a high percentage?nearly half?of startup founders would have postgraduate degrees, according to the data Gist consulted.

□ そういえばとっくに結果が出ているはずのGenoConの最終審査（ホルムアルデヒド耐性試験）はもう終わったんだろうか。。 >> http://genocon.org/ (合理的ゲノムデザインコンテスト）




□ io-port.net 少し使い辛い。クレジットしか参照できない場合、論文へのリンク表記がないものは、doiコードをコピペしてブラウザからspringerlinkに飛んでやっとabstractが読める、という手間。何でもio-port.net Databaseへの直リンはノンノンよ




□ gaou_ak:
見た感じ結構blatantなレベルでPapersのパクリだな。bit.ly/eeonuR RT @chemstation: 文献管理のキラーアプリとなるか？ 「ReadCube」 - 化学者のつぶやき - bit.ly/uy1ANY




□ foresightnano: 人工ナノシステムを制御する為の人工分子時計。
Controlling artificial molecular machines with an artificial molecular clock of RNA and DNA. goo.gl/AHmTW

In the current work, the authors use such a transcriptional oscillator as a molecular clock to time two other molecular processes. One of these is a DNA nanomechanical device, a DNA tweezers that gives different fluorescent signals when open and when closed. Different RNA molecules produced by the transcriptional oscillator act to either open or close the tweezers. The other process is the synthesis by the transcriptional oscillator of an RNA molecule that binds the dye molecule Malachite Green, changing its fluorescence.

□ Genetic algorithm optimization of force field parameters: application to a coarse-grained model of RNA http://www.springerlink.com/content/n84q75820gq3538r/






□ nygenome: あら素敵なショッピングモール。いいえ、遺伝子研究所です。 NYの街角に溶け込んだオシャレな佇まい
We are officially launching today! nygenome.org/media #nygenome

New York Genome Center (“NYGC”) is an independent, non-profit organization ? leveraging the collaborative resources of leading academic medical centers, research universities, and commercial organizations. Our vision is to transform medical research and clinical care in New York through the creation of what will become one of the largest genomics and bioinformatics facilities in North America.

□ GenCounsNews: Leslie Ordal
American College of Medical Genetics adds "Genomics" to its name bit.ly/vt79Yi






□ rnomics: Fabrice Leclerc
A two-dimensional mutate-and-map strategy for non-coding #RNA structure: Wipapat Kladwang,... bit.ly/rpRPnB #chemfeeds @MyEN

Non-coding RNAs fold into precise base-pairing patterns to carry out critical roles in genetic regulation and protein synthesis, but determining RNA structure remains difficult. Here, we show that coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from ribosomal RNA, ribozymes and riboswitches.

□ AppliedBio: Applied Biosystems
Learn the basic principles of Real-time PCR with this free digital handbook. ow.ly/7etuc #new2qPCR






□ NCBI:
New YouTube Videos: An explanation of BLAST E-values (pt.1) bit.ly/w0r4jH & Answers to a few E-value FAQs (pt.2) bit.ly/v4zh44




□ InsideScience:
bit.ly/vQiZGR - Using Satellite Data To Decode Disease Origins




□ PublicHealth: APHA
Another study looks at using Twitter to track disease outbreaks, this time in the UK: goo.gl/1eTlf

Over several months, the researchers were able to gather a database of over 50 million geo-located tweets, which could then be compared to official data from the UK's National Health Service on flu incidence by region.

The researchers deployed state-of-the art machine learning algorithms that automatically figured out which keywords in the database of tweets were associated with elevated levels of flu. In this way they were able to create a predictive model that transformed keyword incidence in tweets into an estimate of the severity of flu in that area.

□ Receptive Field Inference with Localized Priors:
ALD事前分布を用いたマルコフ連鎖モンテカルロ法(MCMC)によって、線形受容野の受ける感覚刺激から作成する一次元変数マッピングのデータを圧縮。
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002219




□ n0rr:

23andme 日本版？ GenoMarker: 遺伝子検査ジェノマーカーで生活習慣病を予防 bit.ly/v01Xom

□ portablegenomic:
Steve Jobs: iCloud may even store medical data - shar.es/bIwFv
ジョブスが病床で流体モニタとx線装置の新設計をスケッチした話も凄い。医療現場をデジタルハブに依存させるのはリスキーだけど、アナログとの冗長性システムを確立が課題。
緊急手術を要する患者さんが運び込まれた時、一刻も早くカルテをiCloudと同期させなきゃいけないのに、突然バックアップとか取り出したりアップデートを落とし始めたら嫌だよね。

One of the passages in Walter Isaacson’s recently published biography of Steve Jobs quotes the former CEO as envisioning Apple’s iCloud as a place where people might store their medical data:

□ masayomasayo:

ヨーロッパ遺伝子治療学会。網膜の遺伝子治療がすごい勢いでどんどん進んでいるのでびっくりした。日本では研究も一つだけ。欧米の独壇場だなあ。

□ Puckrob: 芳賀唯@Tyr

グリーンアノールというトカゲのゲノムを読んだという論文がNatureに載った bit.ly/qFyw5K。哺乳類・鳥類以外の有羊膜類では初のゲノム解読だという。各染色体は鳥類と相同性が高いが、鳥類に見られる高いGC塩基含有量は見られなかったそうな

□ New Study Method Reveals Possible Biomarker for Depression | AT&T Genomics Computing Center (GCC), analyzes risk factors for depression. http://psychcentral.com/news/2011/10/29/new-study-method-reveals-possible-biomarker-for-depression/30881.html






□ PLoSCompBiol:
On @Quora: How valid is Giulio Tononi's mathematical formula for consciousness? Answer: qr.ae/7bw9o




□ DailyNewsGW:
Affymetrix, Broad Institute Collaborate for The Cancer Genome Atlas: read more bit.ly/v56Ssl

About 13,500 cancer samples will be processed on the Affymetrix Genome-wide Human SNP 6.0 Array as part of the partnership. Copy number variation and somatic events will also be studied using the array, as will determining the loss of heterozygosity.

Financial terms of the deal were not disclosed.

□ OpenHelix:
:) MT @dullhunk: Why can't people just say what they mean? bit.ly/sIhWkv new blog post @ O'Really? inspired by @OpenHelix @stephenfry




□ Trends_Endo_Met:
ONLINE NOW: "Galectins: guardians of eutherian pregnancy at the maternal?fetal interface" cell.com/trends/endocri… http://www.sciencedirect.com/science/article/pii/S1043276011001494




□ BioStarQuestion:
What free databases are available to store #enantiomers information? goo.gl/fb/RwjLx #database #chemical #structures



□ BioStarQuestion:
Building a splice junction library for aligining mRNA against the #rat #genome: chrX_random.fa problem goo.gl/fb/gYe6M #rnaseq




□ NCBI:
Genome Workbench (v2.4.5) now available with many new features & bug fixes. 1.usa.gov/rpLq2M Release notes: 1.usa.gov/czzNzA




□ bio_insilico: GoogleとDNAnexusがcloud storageを利用した最大規模のDNAデータベースを公開ヘ。SRAのミラーリング他、$10/1GBでのダウンロード利用が可能。
Google to preserve free DNA database - BioNews: Google to preserve free DNA databaseBioNews'D... bit.ly/v6QXJl #biotech #genomics



□ tonets:

Google Genomeが登場するのも時間の問題ですね

□ planetrdf: Planet RDF
CumulusRDF - RDF triple store on top of Apache Cassandra lists.w3.org/Archives/Publi… via Andreas Harth @aharth and Günter Ladwig




□ DailyNewsGW:
Cofactor Genomics Collaborates with Kentucky Network on Sequencing Data: read more bit.ly/t1XwSL

KBRIN's collaboration with Cofactor has resulted in bringing next-gen sequencing design and analysis to Kentucky's research community, KBRIN Project Director Nigel Cooper said, adding that the KBRIN-INBRE program's goal is to build collaborative research and develop a statewide bioinformatics structure.

□ Cofactor Genomics Collaborates with Kentucky Biomedical Research Infrastructure Network to Expand Genomics Research Throughout State >> http://t.co/uZM0l2T7

The KBRIN-INBRE program seeks to expand biomedical research activities across the state by developing Kentucky’s next generation of biomedical researchers. The network funds student training and career development in the primarily undergraduate universities (PUI)’s.

In addition to scientific workforce development, the INBRE award also builds critically important bioinformatics infrastructure to assist researchers in quantifying large volumes of data produced through genomic techniques. Currently, the institutions in the network that benefit from the collaboration include Morehead State University, Northern Kentucky University, Western Kentucky University, Eastern Kentucky University, the University of Louisville, and the University of Kentucky.

□ DailyNewsGW:
Gentronix, BioQuanta Partner on Genotoxicity Services: read more bit.ly/sm0pwy

UK genotoxicity assay firm Gentronix and French personalized medicine company BioQuanta SA recently announced a deal for the commercialization of services based on BioQuanta's Mitoxis functional metabolomics platform.

□ CBRC_info: 生命情報工学研究センター
razoralignがリツイート
CBRCの清水佳奈研究員の研究成果がプレスリリースされました。「秘密計算による化合物データベースの検索技術－ データベースや検索条件の情報を暗号化したまま類似化合物を検索できる －」詳しくはこちらをご覧ください。aist.go.jp/aist_j/press_r…




□ nutrigenomics:
NOW i need the iPhone RT @cwhogg: Massive Health launches "Eatery" to track food consumption bit.ly/s31MQV





Next-Gen 101: Video Tutorial on Conducting Whole-Exome Sequencing Research

□ yag_ays:

書いた / "動画で学ぶNGS Workshop at WolfEyes Bioinformatics" yag-ays.jp/blog/archives/…

□ dritoshi:

Blog書いた。「先取り! Bioconductor 2.9で追加される ChIP-seq 関連の Library」 blog.hackingisbelieving.org/2011/11/biocon…

□ “Pistoia Alliance Announces NGS Data Compression Algorithm Competition - Bio-IT World” http://htn.to/hxsdbL

The winner of the Pistoia Alliance Sequence Squeeze Competition stands to win a $15,000 prize.

The competition aims to encourage a diverse group of scientists -- including bioinformaticians, mathematicians, physicists, and computer scientists -- to address a thorny problem in the management of NGS data. The Alliance notes that with sequencing costs plummeting faster than the data storage and processing rates predicted by Moore's Law, current NGS instruments can generate more data in a day than any one machine could have produced during the whole of 2005.

□ rnomics:
Flowcell Reverse Transcription Sequencing (FRT-seq): PCR is an... bit.ly/rT5Skc #Information #frt_seq #illumina #RNA-seq




□ PLoS:
Bee Colony Collapse - the role of in-hive antibiotics http://bit.ly/tjXcu6

Methodology/Principal Findings

Using whole-animal bioassays, we demonstrate through inhibition by verapamil that the widely used organophosphate and pyrethroid acaricides coumaphos and τ-fluvalinate, and three neonicotinoid insecticides: imidacloprid, acetamiprid and thiacloprid are substrates of one or more MDR transporters.

Among the candidate inhibitors of honey bee MDR transporters is the in-hive antibiotic oxytetracycline. Bees prefed oxytetracycline were significantly sensitized to the acaricides coumaphos and τ-fluvalinate, suggesting that the antibiotic may interfere with the normal excretion or metabolism of these pesticides.

□ GenesDev:
"Erasing the signs of aging in cells is now a reality" - bit.ly/vKq4Lv




□ IHUB_1M:
$MRNA : Marina Biotech demonstrates that its novel UsiRNA Oligonucleotide Abrogates Cytotoxicity resulting from microR investorshub.advfn.com/boards/read_ms…




□ AIP_Publishing:
Video: World's First Electric Fish Orchestra ow.ly/7gygn #AIP_DBIS




□ InsideScience:
Chemical elements once known as 110, 111 and 112 will be called darmstadtium (Ds), roentgenium (Rg) and copernicium (Cn), IUPAP announces.


□ AJEnglish:
Kenya issues attack warning over Twitter aje.me/ufUVnI






□ CSHL Genome Informatics 2011.

>> http://meetings.cshl.edu/meetings/info11.shtml

The focus for this conference is large-scale genome informatics. Biology is an experimental science that is experiencing an explosion of new data. This requires biologists to increase the scale and sophistication in the information technology used for their research.

The conference scope encompasses the management and the analysis of these data, such as whole genome comparisons within and among species and strains, the analysis of results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify regulatory sequence motifs.

□ genetics_blog:
Flux simulator for simulating RNA-seq data bit.ly/thFQDa #gi2011






□ genetics_blog:
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) plosbiology.org/article/info:d… #gi2011 #bioinformatics #PLoS #OA



□ genetics_blog:
It's a competition of genome assembly competitions at #gi2011. Next up, S. Salzburg on @gagecompetition gage.cbcb.umd.edu #bioinformatics






□ Cain: CloVR - cloud virtual resource automated pipeline for sequence analysis from the desktop http://clovr.org/




□ byuhobbes:
Fiume: less than 2% of genetics software has GUI; not a problem for geeks, but definitely a problem in the delivery of medical care #gi2011




□ chalkless:
RGASP: RNAseq Genome Annotation Assessment Project - gencodegenes.org/rgasp/ #cshlgi #gi2011

The project is run as part of the "Sequence Mapping and Assembly Assessment Project (SMAAP)", a collaborative effort to compare and evaluate methods and strategies for de novo genome assembly (dnGASP)and RNASeq read alignment(RGASP3) using data from second generation sequencing platforms.

□ genetics_blog:
Now speaking at #gi2011: Mark Gerstein on genomic variation in ENCODE TFBSs and transcribed RNAs. Slides here: lectures.gersteinlab.org




□ genomeresearch:
bit.ly/scgRJb MT @genetics_blog: C. Sahinalp - VariationHunter compbio.cs.sfu.ca/strvar.htm #gi2011

In this paper we provide a complete and novel formulation to discover both loci and classes of transposons inserted into genomes sequenced with high-throughput sequencing technologies.

In addition, we also present “conflict resolution” improvements to our earlier combinatorial SV detection algorithm (VariationHunter) by taking the diploid nature of the human genome into consideration.

We test our algorithms with simulated data from the Venter genome (HuRef) and are able to discover > 85% of transposon insertion events with precision of > 90%. We also demonstrate that our conflict resolution algorithm (denoted as VariationHunter-CR) outperforms current state of the art (such as original VariationHunter, BreakDancer and MoDIL) algorithms when tested on the genome of the Yoruba African individual (NA18507).

□ rubbish_talk. - オートメーションのための分化。

所定のフォーマットをユーザ側が用意するよりも、アップロードした段階で調整のためのインターフェースが立ち上がる方が進歩あるよね。それってリテラシーやスキルの対価（退化）と言えるのかな。

例えばデータ食わせるだけで論文が書き上がるシステムなんかは、研究者を煩わしい業務から解放するだけでなく、より必要な時に向けて構成力を磨く時間を提供出来るかもしれない。経験や場数が大事っていうのも分かるけれど。


フォーマットの要求って、それは「一様なユーザ」についてスキルや対価を求める代わりに、 それを必要としない層については隘路の障害の方が大きくて、それって入力側がナローパスに陥っていて、大きなロスでしかないんじゃないか

どこまでも突き詰めると、「誰かに要求されるスキル」って、いつの時代も「現時点で踏まざるを得ない過程」だからってことでしかない。一般化されたスキルを磨くっていうのは、その面で進歩に遡行する意味もある。逸脱せよ常にだ。