Article_Apr.1

(Localization of gene fusions on specific chromosomal regions.)

□ RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

>> http://t.co/71SFLXhY

we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions.

LifeScopeを用いたRNA-Seqマッピング：接尾辞配列アルゴリズムによるキメラ転写産物の検出パイプライン：SOLiDシステムでの試用。






□ MaliciaRogue:
GPGPU, le ? supercalculateur ? du pauvre http://shar.es/rdTKI #bioinformatique #supercalculateur
GPGPU: Supercalculator for Bigdata / Bioinformatics
General-Purpose computation on Graphic Processing Units:

Les analyses sont réalisées sur des couples gène//SNP mais chaque analyse reste indépendante. Ceci est donc un problème parfaitement adapté à la parallélisation. Trois semaines de développement supplémentaires ont été nécessaires pour traduire l’implémentation initiale en C et récrire les tests statistiques sous forme de kernel OpenCL.
Les résultats sont maintenant générés en moins de 2h (sur un simple portable doté d’une NVIDIA GeForce GT 330M). La quantité de jeux de données n’est donc plus un problème, le patron est content et je conserve mon emploi

De nombreux problèmes liés à la bioinformatique sont parallélisables mais la technologie GPGPU n’est pas encore très répandue dans le domaine. Les langages de bas niveau utilisés par les kernels en sont sans doute la cause principale.

グラフィック・プロセッサを用いてバイオインフォマティクスの様々な解析対象を並列化処理。遺伝的連鎖解析、SNPテストをマシンパワーでドライブ。
GPGPUのバイオインフォマティクスへの適用は、スポットの並列化にのみ有効。実装が進んでいない理由はカーネルで使用される低水準言語の学習が主要因。しかしGPU BLASTやCUDSAW+などの共通のツールと比べて、より安価で強力な解析メソッドとなるとのこと。






□ Conflicted: The War for Health

>> http://t.co/15lEYGAN

Robin Coupland, medical adviser to the International Committee of the Red Cross (ICRC) will be opening the conference, followed by speakers including Director of MedAct, Marion Birch, Surgeon Lieutenant Henry Dowlen, and another Red Cross expert, Gilles Thal Larsen. The debate is sure to be fantastic, as the four plenaries will grapple with challenging multisectoral issues that I can’t wait to engage with. The conference will consider the causes of conflict, the emergency humanitarian response and how to achieve sustainable development and peace.

□ Global Next Generation Sequencing (NGS) Market Worth $2,343 Million by 2016.

>> http://t.co/iHnhP8Bb

The global NGS market was valued at $842.5 million in the year 2011, growing at a CAGR of 22.7% from 2012 to 2016. North America commanded the largest share of 51.8% of the overall NGS technology market in 2011.

The Next Generation Sequencing Market is dynamic and innovative; it is also paving its ways into the labs which were previously not involved in sequencing. High pace of NGS research is likely to boost the market for personal genome sequencing in the coming years. Manufacturers predominantly have an inclination towards diagnostic applications both as a supplier and manufacturer. Key players in this market include Illumina (U.S.), Life Technologies (U.S.), 454 Roche (Switzerland), Oxford Nanopore Technologies (U.K.), and Pacific Biosciences (U.S.).

遺伝子関連次世代シーケンシング市場のグローバルトレンド予測。2016年までに急激な成長の見込み。主要プレーヤーにOxford Nanoporeも参戦。




□ MyBioTechniques:
If your RNA data's in the public domain, your identity isn't safe, says Eric Schadt et al. in a Nature Genetics paper. http://awe.sm/5jMkK
Bayesian method to predict individual SNP genotypes from gene expression data

we developed a Bayesian approach to predict SNP genotypes that is based only on RNA expression data. We show that predicted genotypes can accurately and uniquely identify individuals in large populations. When inferring genotypes from an expression data set using eQTLs of the same tissue type (but from an independent cohort), we were able to resolve 99% of the identities of individuals in the cohort at Padjusted ? 1 × 10－5.

We discuss the implications of deriving genotypic information from RNA data deposited in the public domain.

ベイズ法においてeQTLsに関連づけられている遺伝子発現データから、固有のSNP遺伝子型の予測が可能。パブリックドメイン下の個人のRNAデータに安全性の問題。




□ Proteomic Search with Hadoop:

>> https://docs.google.com/present/view?id=djhc3g9_6hb7bkqd7

□ shiumachi:

hadoop はログ解析だけじゃないよという事例を紹介。タンデム型質量分析によるタンパク質の構造決定において、既知の遺伝子にある数千万のペプチドとのスペクトル照合をhadoopを使って高速化した事例

□ New 'Genetic Bar Code' Technique Establishes Ability to Derive DNA Information from RNA

>> http://t.co/HdEtsYxI

Researchers from Mount Sinai School of Medicine have developed a method to derive enough DNA information from non-DNA sources -- such as RNA -- to clearly identify individuals whose biological data are stored in massive research repositories. The approach may raise questions regarding the ability to protect individual identity when high-dimensional data are collected for research purposes.

□ EvolAppl:
New paper: On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat http://ow.ly/1izOQ3

Since the domestication of crop species, humans have derived specific varieties for particular uses and shaped the genetic diversity of these varieties. Here, using an interdisciplinary approach combining ethnobotany and population genetics, we document the within-variety genetic structure of a population-variety of bread wheat (Triticum aestivum L.) in relation to farmers’ practices to decipher their contribution to crop species evolution.

Using 19 microsatellites markers, we conducted two complementary graph theory-based methods to analyze population structure and gene flow among 19 sub-populations of a single population-variety [Rouge de Bordeaux (RDB)]. The ethnobotany approach allowed us to determine the RDB history including diffusion and reproduction events. We found that the complex genetic structure among the RDB sub-populations is highly consistent with the structure of the seed diffusion and reproduction network drawn based on the ethnobotanical study.

作物種の遺伝的多様性：種子交換ネットワークにおける集団品種の遺伝構造を多変量解析。






□ BioMedCentral:
Blog: Sage Bionetworks 3rd Commons Congress http://ow.ly/aaXcX #biology

During the congress, Eric Schadt, Editor-in-Chief of Open Network Biology, will be discussing the journal’s early experiences of promoting its novel approach to publishing data and models, including a description of the new article type, a ‘Model’, being piloted by the journal, which describes models of complex phenotypes derived from integrated large scale genetic and clinical data.

“BUILDING BETTER MODELS OF DISEASES TOGETHER”
>> http://sagecongress.org/WP/2012congress/

The Congress program will include deep dives into the Synapse technical platform and Portable Legal Consent systems that together make data about individual patients the key to large-scale disease research. Platform sessions will detail initiatives to open previously closed clinical trial data and bring patients into the research mix.

Larry Lessig, Harvard University
“Ingredients for innovation”



□ Sagebio:
Amazon Takes Genomics Research to the Clouds http://bit.ly/Ierjw5 "This is just the tip of the iceberg."

<fot size=1>An outfit called Eagle Genomics is running Sequence Squeeze, a competition to see how to best compress a particular sequence of DNA, and this sort of work will make it easier to move data to and fro. Meanwhile, companies such as Oxford Nanopore are working to further reduce the cost of actually sequencing the data. The end result is an exponential increase in the speed of genetics research.

□ rnomics:
Top story: TopHat :: Center for Bioinformatics and Computational Biology http://goo.gl/8egIp
TopHat 2.0.0 release 4/09/2012

Version 2.0.0 is a major release adding Bowtie 2 support, better parallelization and the ability to align RNA-Seq reads across potential fusion points.
TopHat now uses Bowtie2 by default (if found in the system) although it can also fall back on Bowtie 1 (which is still required for SOLiD reads).
Bowtie 2 integration features:…

□ dnanexus:
Blog: On the Scene at AMIA: Clinical Promise and Informatics Opportunities for Whole-Genome Sequencing https://dnanexus.com/blog/2012-04-04-amia




□ geneXplain:
NHGRI Plans to Fund More Clinical Sequencing Projects - GenomeWeb Daily http://bit.ly/HxJpdt | http://1.usa.gov/HxJsFY

The CSER program was designed to support multi-disciplinary studies involving clinicians, bioinformaticians, and ethicists to explore through specific projects the challenges, opportunities, and ethical questions related to using genome sequence data in clinical care. The research should address critical questions about how to apply genomic sequencing to clinical care in individual cases, "from generation of genomic sequence data, to interpretation and translation of the data for the physician," NHGRI said in a notice about its plans to fund more CSER awards.

□ Research that Pays Off: Experts Make the Case for Federal R&D Spending in Capitol Hill Briefings

>> http://t.co/XZAy3Rhn

The Human Genome Project, funded by the federal government at a cost of $5.6 billion (in 2010 dollars) over 13 years, has had a fundamental impact on areas as diverse as human health, agriculture, forensics, and veterinary medicine, with an economic payoff in 2010 alone of $67 billion, according to a study by the Battelle Memorial Institute.

The cumulative impact of the human genome sequencing effort from 1988 to 2010 was estimated at $796.3 billion, with $243.9 billion in personal income for U.S. workers and federal tax revenues of $48.9 billion, far more than the $5.6 billion federal investment in the project.

□ jeff_hayes:
Allscripts launches native iPad EHR app, Wand http://bit.ly/ItgULN

Allscripts announced the much-anticipated release of Allscripts Wand™, which provides users of Allscripts Electronic Health Records a unique, native iPad application that extends the most commonly used functions of Allscripts Professional™ and Enterprise™ solutions.

□ jeff_hayes:
AlignTech: More Than One-Third of IT Budgets Now Spent on Cloud: Survey - Forbes http://bit.ly/IIXUfM




□ BiologyOpen:
For all you iPhone and Android users out there, the new BiO mobile web site has launched at... http://fb.me/1lepBzpqM




□ sociallifeofdna:
Genomic sovereignty & the African promise: mining the African #genome for the benefit of #Africa http://bit.ly/HsCXC7 cc: @ruha9 #bioethics




□ KauffmanFDN:
[Growthology] Peer Reviewed vs. Entrepreneur Reviewed: Noam Wasserman’s new book The Founder’s Dilemmas came out... http://kff.mn/HZMkbJ




□ markgf:
Here's why @wellcometrust is launching new #openaccess journal eLife. http://ow.ly/1Khjud




□ glynmoody:
WorldBank Announces Open Access Policy for Research & Knowledge, Launches Open Knowledge Repository - http://bit.ly/HuClRp (v @petersuber)

>> https://openknowledge.worldbank.org/

While much of the Bank’s research outputs and knowledge products have been available for free on the institution’s web site, and on other channels, the new Open Access policy marks a significant shift in how Bank content is disseminated and shared. For the first time, the Bank will have an aggregated portal to research and knowledge products, where the metadata is curated, the content is discoverable and easily downloaded, and third parties are free to use, reuse, and build on it.

The Open Knowledge Repository is interoperable with other repositories and will support optimal discoverability and re-usability of the content by complying with Dublin Core metadata standards and the Open Archives Initiatives protocol for metadata harvesting.

世界銀行が“オープンナレッジ・リポジトリ”を立ち上げ。CC BYを適用しサードパーティの学術誌までを参照可能に。ダブリン・コアなどのメタデータ標準にも準拠

昨夜のロンドンとの会議でも話題に上がっていたけれど、もともと機関利用向けの研究成果・統計情報を誰でも入手出来るという破壊力もさることながら、2013年までに関連データセットや、各国語への翻訳まで着手するという徹底ぶり。



□ Sagebio:
Excellent! - British Government backs Wellcome Trust public access proposal http://bit.ly/IuW5ED #OA #OpenScience
Government backs calls for research data to be made freely available
因みに英国政府はオープンアクセスを推進するウェルカムトラスト財団に再び支持を表明




□ timoreilly:
US CIO @StevenVDC says that machine readable #opendata must be the new default in government http://oreil.ly/HHUS9K #gov20 Hear, hear!




□ finchtalk:
#ISBsymp JCV synthetic genomics: to date, we've cataloged ~100 million genes; these are the future design components




□ ScottGottliebMD:
Report: Public wants genetic research results because of perceived personal and clinical utility (10 focus group data) http://dnapolicy.org/resources/GIMPaperFocusGroupsonReturnofResults.pdf




□ SPARC_NA:
World Bank President Zoellick supports Open Access; Bank announces new OA Policy - http://tinyurl.com/cr3s3b6




□ alicebell:

@iansample Open access does not equal open science. We're a long, long, long way from that (just ask Prof Durant...)

□ MaliciaRogue:
Présentation du #Master #Bioinformatique de Bordeaux par @nallias #formation #universitaire

>> http://bioinfo-fr.net/presentation-du-master-bioinformatique-de-bordeaux

Foyer du fondateur de #bioinfo-fr (ainsi que quelques habitués), le Master de BioInformatique de l’Université Bordeaux 1 existe depuis 2003. Les cours sont dispensés à la fois sur le campus Pessac/Talence (université de Bordeaux 1) et le campus Carreire (université de Bordeaux Segalen). Ces deux campus se partagent respectivement les cours du domaine informatique et biologique, en partenariat avec le LaBRI (Laboratoire Bordelais de Recherche en Informatique).

□ Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data

>> http://www.biomedcentral.com/1471-2164/13/S2/S6/

SNVQ : >> http://t.co/rKgwPRO3
A new bayesian method for SNV discovery and genotyping based on quality scores.

Presented here is a strategy to more reliably map transcriptome reads by taking advantage of the availability of both the genome reference sequence and transcript databases such as CCDS. The authors also present a novel Bayesian model for SNV discovery and genotyping based on quality scores.

□ GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

>> http://code.google.com/p/tud-scaffolding/

The resulting optimization problem is solved using an Expectation-Maximization (EM) procedure and an unconstrained binary quadratic programming approximation of the original problem.

・Scaffold optimizer (solves the MIQP optimization problem formulation to produce scaffold nucleotide sequences)
・Data linker (uses available information sources to derive scaffolding constraints; currently supports paired ends and mate pairs, and reference genomes)




□ Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
　Linear additive and ANOVA models transcriptome and genotype integration.

>> http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/




□ DailyNewsGW:
ISS Recommends Illumina Shareholders Vote Against Roche's Nominees for Board: read more http://bit.ly/IzGHkN




□ portablegenomic:
Roche to Illumina: You Are Not Apple http://on.wsj.com/HxfIbe PG to Illumina: You are closer to Apple than Roche will ever be




□ Visual Evaluation and Statistics to Promote Annotation (VESPA): integration of peptide-centric proteomics data... http://www.biopilot.org/docs/Software/Vespa.php




□ MapAl is a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks http://www.bioinf.boku.ac.at/pub/MapAl/




□ OMICSGroup:
RNA Interference (RNAi) - An antiviral Strategy for Enteroviruses http://wso.li/1Vth




□ geneXplain:
Open biohacking - DIY genetic engineering, synbio, join the fight against disease and death http://bit.ly/IxISJI via @tomozo




□ sciencemagazine:
Compbio collection: computational approaches to understanding embryo development http://scim.ag/IhhGuj






□ Systems Biology & the Microbiome | ISB Symposium

>> https://www.systemsbiology.org/symposium/index.html


□ b0yle:
Panel at #isbsymp focuses on microbiome apps for fuel and pharma: http://bit.ly/Y7DWf & http://bit.ly/HJEggn & http://bit.ly/bykFX6




□ digitalbio:
Christophe Schilling: started with computational biochemistry models for producing chemical with large existing market #ISBsymp




□ GenesDev:
"Salk scientists discover how plants grow to escape shade" - http://bit.ly/HHMZzm




□ NASAAmes:
We're seeking an experienced research scientist to develop new interdisciplinary Space Synthetic Biology effort. http://1.usa.gov/HEEpXi




□ Getting Started with JAGS, rjags, and Bayesian Modelling

>> http://t.co/9WjAVFkF

JAGS stands for Just Another Gibbs Sampler. To quote the program author, Martyn Plummer, "It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation..." It uses a dialect of the BUGS language, similar but a little different to OpenBUGS and WinBUGS.

□ Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore

>> http://jcp.aip.org/resource/1/jcpsa6/v135/i5/p055103_s1

We conducted a numerical study on the translocation of a biopolymer from the cis side to the trans side of a membrane through a synthetic nano-pore driven by an external electric field in the presence of hydrodynamic interactions (HIs). The motion of the polymer is simulated by 3D Langevin dynamics technique using a worm-like chain model of N identical beads, while HI between the polymer and fluid are incorporated by the lattice Boltzmann equation.

□ Sequilabs:
Physicists Create First Long-Distance Quantum Link: Weird atom-to-atom connection could serve as basis for truly... http://bit.ly/ISishZ

Quantum connection. Researchers have built the first true quantum link using two widely separate atoms. Many such links combined may one day form a complete quantum network, suitable for exchanging information that is in theory impossible to spy on.

□ AIP_Publishing:
Perspective: Time scales & clocks | Statistical modeling of atomic clocks & design of time scales http://ow.ly/a9Dlm #AIP_RSI




□ NatureJapan:
Nature Cover Story: 真菌という脅威：自然生態系と食糧確保を脅かす新興病原体 http://nature.asia/IThvpI





(Network gerenated from the entire Mozart's sonata.)

□ reaktorplayer:
Complex Network Application in Music: Uncovering Universal Properties in Human Perception of Music http://cktse.eie.polyu.edu.hk/MUSIC/article.html

a data-driven transformation to represent a musical score as a complex network. We find that musical scores which are widely perceived to be "good" generate complex networks with certain invariant properties: scale-free networks with strong clustering of nodes within the network. We describe a method to generate random musical compositions from these networks and find that scores generated in this manner are also perceived to be "good" and are qualitatively similar to the specific score from which the generating network was produced.

□ EurekAlertAAAS:
Geographic information systems demonstrate links between #health and location : http://eurekalert.org/e/4hjx

Each of the six studies uses the latest concepts and methods in geographic information systems (GIS)-based research to determine how the geographic location affects physical health. A study titled "Spatial Classification of Youth Physical Activity Patterns" shows, for example, that while rural youth get the largest proportion of their physical activity while at school, urban and suburban youth are most active when commuting. Not only does this finding suggest that the walk to school might be just as important to some children's health as is the physical education they receive as part of the school curriculum, it is also important given that adolescent health behaviors are predictive of behaviors in adults.

□ guardiantech:
Selling arms and snooping technology is no way to help democracy, Cameron | Eric King http://bit.ly/ItNv7L




□ Brian_Whit:
Yemen: the Saleh regime fights back. Ousting the old guard is a long and difficult task http://bit.ly/HCO8aW (http://al-bab.com)




□ 大学時代の情報工学の教授が、現在バイオインフォマティクスに関わっていることを思わぬ繋がりで知って驚いた。あの頃すでに先端科学技術インキュベーションセンターのコンサルだったのか。学生の頃にお話したかった…