□ ECCB'12 - the European Conference on Computational Biology 2012 (9-12.Sep)
>> http://www.eccb12.org/ #ECCB12 #uniprot10
ECCB'12 - the European Conference on Computational Biology - is the key European computational biology event in 2012 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. ECCB'12 will take place 9.-12. September 2012 at the Congress Center Basel, Switzerland.
Participation at ECCB'12 will be the prime opportunity to learn about cutting-edge research in computational biology and bioinformatics and to network with other members of our community. ECCB'12 will be organized in association with the 10th [BC]2 Basel Computational Biology conference - the annual scientific symposium of the SIB Swiss Institute of Bioinformatics.
□ ECCB12:
#eccb12 conference proceedings papers released as open access special issue at Oxford University Press Bioinformatics http://bioinformatics.oxfordjournals.org/content/28/18.toc …
□ ECCB12:
Download the #eccb12 conference app for your iPhone / iPad to plan your personal conference program (Android soon too) http://eccb12.org/app
□ Chris Sander: Protein 3D Structure Computed from Evolutionary Sequence Variation:
>> http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028766
The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7?4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.
□ EVfold: http://evfold.org #ECCB12
Evolutionary Constraints:
Calculate correlated amino acid changes in protein families across evolution.
Use evolutionary couplings as distance constraints to predict 3D structure.
□ compbiobryan:
@razoralign Yeah, it's a great method. Be sure to see the sine qua non underlying contact predictor too: "Direct-coupling analysis of residue coevolution captures native contacts across many protein families." http://www.ncbi.nlm.nih.gov/pubmed/22106262
□ GigaScience:
K Neiselt in Bioimaging session presenting on visual eQTL analytics. Some of this from the BioVis challenge: http://www.biomedcentral.com/1471-2105/13/S8/S8/abstract … #ECCB12
□ BioXSD ? the XML schema for basic bioinformatics data:
>> http://t.co/eb6ipnc4
BioXSD has been developed to fill the niche of missing canonical XML schema-based exchange format for basic bioinformatics data: sequences, alignments, features, references to resources, and identifiers. The canonical format can either be consumed and produced by tools directly, or serve as an intermediate format that the other formats can losslessly be serialized to and from.
バイオインフォマティクス・データに不足している正規なXMLスキーマベース(配列・アラインメント・リソース参照・識別子など)を補完
□ NGS-logistics: data infrastructure for efficient analysis of NGS sequence variants
>> http://cdn.f1000.com/posters/docs/250830577
The main goal of NGS-Logis,cs is to deliver processed NGS data to end users. We offer several modules, which each cover one aspect of analysis, either towards research or diagnos,cs. Complexity of algorithms, queries and data structure are covered by a user-friendly web based interface. The structure of NGS-Logis,cs is designed to cover any type of samples. With NGS- Logis,cs you can easily define a data set, assign samples to that data set and make it accessible to authorized researchers.
□ GigaScience:
Edouard Pauwels next on identifying chemogenomic features from drug-target interaction networks (with a focus on interpretability) #eccb12
□ GenomicsIo:
#eccb12 Denis Noble & Christoph Denot "It's the proportions that matter not the absolutes - both in music and biology"
#eccb12 IBM targeting the pub security market with Watson - visions of a future of total surveillance made possible by cognitive computing
□ ISMBECCB:
Are you sad to leave #ECCB12? Us too. However, we have a new look. Time to get excited for ISMB/ECCB 2013 in Berlin! http://bit.ly/RRKfaT
□ F1000Research:
We’ve had 20 poster submissions already from #eccb12 Why not share yours as well? View & submit #Posters here http://ht.ly/dEOCL
□ appliedgenomics:
V. excited about Allen human brain atlas. Not excited another "Rosetta stone" ref. Guardian: http://www.guardian.co.uk/science/2012/sep/19/scientists-create-atlas-of-human-brain …. Abs: http://www.nature.com/nature/journal/v489/n7416/full/nature11405.html …
□ illumina:
Introducing TruSeq Stranded mRNA & Total RNA Sample Prep kits for superior data quality, even from FFPE smpls. http://bit.ly/SXBcrC
□ EurekAlertAAAS:
BGI Tech develops whole exome sequencing analysis of FFPE DNA samples to boost biomedicine : http://eurekalert.org/e/4qws
□ the_Node:
Vincent Pasque's developmental biology images were among the winners of this year's Wellcome Image Awards. http://fb.me/1h2cTyMEH
□ FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids
>> http://nar.oxfordjournals.org/content/early/2012/09/11/nar.gks856.full
a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base?base FRET).
These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.
核酸内のフェルスター共鳴エネルギー転移ナノダイナミクスの解析および設計ソフト
□ Transcriptome Sequencing ? U.S. Army RFQ:
>> https://www.fbo.gov/?s=opportunity&mode=form&id=719a4dd675ae7d5e8dc6351544b24674&tab=core&_cview=0
This is a Request for Quote (RFQ). This procurement is conducted unrestricted with full and open competition, open to both large and small businesses. The associated North American Industry Classification System (NAICS) code for the procurement is 541380 and the Small Business size standard is $12.0 Million.
The US Army Corps of Engineers, Engineer Research and Development Center Contracting Office, has a requirement for contractor support to assess the chemical stress effects of munitions constituents (MCs) and intensive munitions (IMs) on global gene expression networks in highly sensitive Leopard Frog tadpoles of the species Rana pipien.
アメリカ陸軍工兵隊による軍需的トランスクリプトーム見積依頼。 ある種のオタマジャクシのグローバル遺伝子発現ネットワークと、軍需品の化学的ストレス影響評価
□ Complete Genomics to be bought by Chinese firm for $117.6 million:
>> http://mobile.reuters.com/article/idUSBRE88G0LP20120917?irpc=932
□ bioitworld:
BGI acquires Complete Genomics ($GNOM) for $3.15/share (last close $2.67). Deal worth $117M. Move into clinical genomics space continues.
□ DailyNewsGW:
Complete Genomics, BGI Agree to $117.6M Merger http://bit.ly/Uf45gU
Complete GenomicsとBGIの合併については、個人的に思う所アリアリなのだけど、初夏の人員削減からハプロタイピングにおける『LFR技術』論文(株価を50%改善）、高精度の解析。アジア太平洋地域で締結したばかりの代理店供給が、BGIに統括されて水準を保てるかどうか
□ siRNA as a tool to delineate pathway channelization in H2O2 induced apoptosis of primary Leydig cells in vitro:
>> http://www.springerlink.com/content/h3n42w780245618m/
□ ENCODE_NIH:
Annotation of functional variants: RegulomeDB http://genome.cshlp.org/content/22/9/1790 … #ENCODE
□ caseybergman:
Many parallels btwn. computational biologists & "data scientists" (http://bit.ly/Pr05qI ) >> #bioinformatics is good training for "sexy" jobs
□ Chem_Central:
New software in #JCheminf 'OMG: open molecule generator' http://goo.gl/vf9t4 #cheminformatics
□ PaulLikeMe:
Medicine 2.0 takes Harvard Medical School by Storm http://soc.li/Cjn6WXc
□ BiologyOpen:
BiO has passed the scientific and technical evaluation stages for inclusion in PMC and PubMed. Contracts to sign... http://fb.me/29y8AjCL0
□ Efficient experimental design and analysis strategies: DESeq algorithm performs more conservatively than edgeR & NBPSeq
>> http://www.biomedcentral.com/1471-2164/13/484/abstract
□ moorejh:
Big #science, #bigdata, and a big role for biomedical #informatics JAMIA special issue http://jamia.bmj.com/content/19/e1/e1.full … #bioinformatics #datascience
□ PBL awarded two US patents on RNAi: US Patent No. 8,258,285. / No. 8,263,569:
>> http://www.bionity.com/en/news/139697/pbl-awarded-two-us-patents-on-rnai.html?WT.mc_id=ca0067
□ TrendsCognSci:
Do you think that probabilistic, Bayesian, and optimal computation are synonyms? If yes, you must read this TiCS review http://bit.ly/RQjZO8
Probability has played a central role in models of perception for more than a century, but a look at probabilistic concepts in the literature raises many questions. Is being Bayesian the same as being optimal? Are recent Bayesian models fundamentally different from classic signal detection theory models? Do findings of near-optimal inference provide evidence that neurons compute with probability distributions? This review aims to disentangle these concepts and to classify empirical evidence accordingly.
□ A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
>> http://nar.oxfordjournals.org/content/early/2012/09/08/nar.gks804.full
Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation ?0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation ?0.91) are reported.
□ c_z:
My latest upload : Systems Bioinformatics Workshop 2012 on @slideshare http://www.slideshare.net/keiono/systems-bioinformatics-workshop-2012 …
□ RNA-Seq analsys: FIMM - Institute for Molecular Medicine Finland (CSC - June, 2010) http://www.slideserve.com/oni/rna-seq-analysis …
□ ReLiance: a machine learning and literature-based prioritization of receptor?ligand pairings
>> http://homes.esat.k