□ CGShark:
The Eye of a pufferfish Anilao by Sol Alcazar pic.twitter.com/RpTY6Qg6ir
□ BICEPTWO:
How long did we know we had a signal? "The signals gradually emerged from the fog over time." -Clem Pryke #BICEP2
□ QQ equality: Context effects produced by question orders reveal quantum nature of human judgments: 量子意思決定理論:
>> http://www.pnas.org/content/111/26/9431.full …
the theory implies an a priori and precise prediction called the quantum question (QQ) equality. ベイズ確率に依らない人間の意思決定の量子モデル
□ FastCoExist:
Visualizing which countries people are trying to get away from, and where they're going. http://f-st.co/7hrlvFt
<iframe src="http://wl.figshare.com/articles/988822/embed?show_title=1" width="350" height="338" frameborder="0"></iframe>
□ Using fitness landscapes to visualize evolution in action by Østman, Bjørn; Olson, Randy (2014):
>> http://figshare.com/articles/Using_fitness_landscapes_to_visualize_evolution_in_action/988822 …
□ Robust detection of dynamic community structure networks: modularity-optimization null model
>> http://scitation.aip.org/content/aip/journal/chaos/23/1/10.1063/1.4790830 …
a method to construct representative partitions that uses a null model to correct for statistical noise in sets of partitions. To illustrate our results, we employ ensembles of time-dependent networks extracted from both nonlinear oscillators and empirical neuroscience data.
□ Oxford Nanoporeが第四世代DNAシーケンシング・デバイス"PromethION"を公表へ。
PromethION: 2,000 channels producing data at the rate of 1G/min.
>> http://nextgenseek.com/2014/06/oxford-nanopore-hints-at-a-new-product-promethion/ …
□ Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA for large-scale phenotypic change
>> http://biorxiv.org/content/early/2014/07/02/006775 …
□ 2017 Next Generation Sequencing Industry most lucrative segment in the genomics space w/ an estimated growth of 16.3%
>> http://www.rnrmarketresearch.com/next-generation-sequencing-ngs-market-platforms-illumina-hiseq-miseq-life-technologies-ion-protonpgm-454-roche-bioinformatics-rna-seq-chip-seq-pyrosequencing-sbs-smrt-diagnostics-market-report.html?src=whatech …
□ SURPI: Ultrarapid cloud-compatible clinical sample NGS bioinformatics pipeline for pathogen identification:
>> http://m.genome.cshlp.org/content/early/2014/05/16/gr.171934.113 …
SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7?500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h.
□ DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation with RSEM-EVAL and REF-EVAL. http://biorxiv.org/content/biorxiv/early/2014/06/13/006338.full.pdf …
varying the parameters of Trinity is relatively small effect on the accuracy of resulting assemblies, as compared to Oases, SOAPdenovo-Trans
"REF-EVALおよびRSEM-EVALが示唆するアセンブリの相対精度において、TrinityはコンティグとヌクレオチドレベルのF1とKC Scoreに関して最も正確なアセンブリを生成する。"
□ A Node.js JavaScript library for client & server side bioinformatics: reimplement biopython, biohaskell, etc methods
>> https://github.com/bionode/bionode
to manipulate biological data and not to visually represent it, unlike BioJS which is "Reusable components for presenting Biological data".
□ Appistry CloudDx: Appistry Launches Cloud-based Service for Clinically actionable Genomic Test
>> http://www.appistry.com/genomically-enhanced-medicine/ …
>> http://www.pharmiweb.com/pressreleases/pressrel.asp?ROW_ID=92053#.U4kmKl5R5K8 …
Appistry社が臨床ゲノミクスの為のクラウドツールを開発。LDTsへの一元的アクセスを提供。診断と治療の意思決定に対し、正確なデータ収集による実効性の定量付けを行えるのが最大のメリット。データとサンプルの管理プロセスはHIPAA及びCLIAガイドラインに準拠するとのこと。
□ vsbuffalo:
Sambamba: SAM/BAM file processing tool written in D ? 4x faster than samtools.
>> http://lomereiter.github.io/sambamba/
□ Omega: an Overlap-graph de novo Assembler for Metagenomics: comparison of SOAPdenovo, IDBA-UD, and MetaVelvet.
>> http://bioinformatics.oxfordjournals.org/content/early/2014/06/19/bioinformatics.btu395.abstract …
□ Evaluation of de novo and hybrid genome assembly techs http://ht.ly/yltcZ best = Illumina + PacBio + ALLPATHS-LG via @oxfordjournals
□ SVAMP: Sequence Variation Analysis, Maps / Phylogeny: a stand-alone visualise genomic variants > geographical metadata
>> http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu176.full.pdf …
□ Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships
>> http://www.humgenomics.com/content/pdf/1479-7364-8-9.pdf
As NGDBs will include inter- and intra-tissue genetic heterogeneity, one factor that needs to be considered is the importance of quantifying variants that result in genetic heterogeneity, particularly if they are present within individual genes, rather than simply recording their presence.
□ SeqComplete:
Promoters and enhancers in the human genome | MassGenomics
>> http://massgenomics.org/2014/05/promoters-enhancers-human-genome.html …,
FANTOM5 generated all of the data on a single molecule sequencing platform (Helicos), there’s no PCR or cloning bias to worry about. Every read represents the 5′ end of a unique RNA molecule. Thus, the FANTOM5 dataset nicely complements the open chromatin, CHiP-Seq, and RNA-seq data generated by the ENCODE project.
□ SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision:
>> http://bioinformatics.oxfordjournals.org/content/early/2014/05/19/bioinformatics.btu343.abstract …
The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next generation sequencing data.
def getTestStatistics(x: Seq[Int], y: Seq[Int]): Double
Method for computing test statistics of two-sample Kolmogorov-Smirnov test
□ RepARK: Repetitive motif detection by Assembly of Repetitive Kmers: de novo creation of repeat libraries fm NGS reads
>> http://nar.oxfordjournals.org/content/early/2014/03/14/nar.gku210.full …
RepARK Velvet or CLC Assembly Cell (RepARK CLC) was orders of magnitude (14×?465×) faster than when using de novo state-of-the-art methods. The vast majority >99% of consensuses frm RepARK had an average nucleotide coverage >10× & most repetitive consensuses align fewer than 100x
□ Oxford Nanopore MinION Gets Ready for Shipping:
>> http://nextgenseek.com/2014/03/oxford-nanopore-minion-gets-ready-for-shipping/ …
□ Comparative primate genomics: emerging patterns of genome content and dynamics
>> http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3707.html …
□ VAT: Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data:
>> http://www.cell.com/ajhg/abstract/S0002-9297(14)00176-1 …
Variant-, genotype-, and sample-level QC can flag or remove variant sites, calls, or samples according to various QC metrics that are provided with the sequence data.
Ti/Tv can be calculated & assessed by empirical rules, e.g., ~2 for whole-genome variants, ~2.7 for novel exome variants, and ~3.4 for known
□ An experimental approach to identify dynamical models of transcriptional regulation in living cells
>> http://scitation.aip.org/content/aip/journal/chaos/23/2/10.1063/1.4808247 …
□ RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA
>> http://nar.oxfordjournals.org/content/early/2014/05/26/nar.gku473.full …
RAMICS uses models of codon substitution to give synonymous codon substitutions higher transition probabilities as well as favoring more likely non-synonymous substitutions.
□ LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs:
>> http://www.biomedcentral.com/content/pdf/1471-2105-15-152.pdf …
□ MEIGO: an Open-source software based on metaheuristics for global optimization in systems biology & bioinformatics
>> http://www.biomedcentral.com/1471-2105/15/136/abstract …
The toolbox includes the eSS for cNLP / MINLP / VNS for Integer Programming (IP) problems and BayesFit for parameter estimation.
□ Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models:
>> http://bioinformatics.oxfordjournals.org/content/30/8/1154.short …
We suggest applying Bayesian mixture models of different types of distributions to further study the distribution of the correlation measure. The implicit classification of the mixture models is used to detect genes with differences between two conditions in both gene transcription and histone modification. The method is applied to different datasets, and its superiority to a naive separate analysis of both data types is demonstrated.
□ BEAST 2: A Software Platform for Bayesian Evolutionary Analysis:
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003537 …
new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning.
□ Uniprotのインターフェイスが綺麗になった。BLAST周りも改善 MT @marc_rr: the new @uniprot is Informative and beautiful: http://beta.uniprot.org/ http://insideuniprot.blogspot.ch/2014/05/have-you-tried-new-uniprot-beta-site.html …
□ XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons:
>> http://www.biomedcentral.com/1471-2164/15/343/abstract …
exonFCin = mean (log2FCin); exonFCout = mean (log2FCout). difference between exons included and excluded: In-Out = |exonFCin| - |exonFCout|. the paired Wilcoxon signed-rank test |exonFCin|
□ ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
>> http://www.biomedcentral.com/content/pdf/1471-2105-15-116.pdf …
□ rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids:
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003571 …
□ Machine Learning Helps Identify CHRONO as a Circadian Clock Component:
>> http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001840 …
"Gm129 physically interacts with core clock genes and regulates the molecular oscillator." Gm129 oscillates in multiple tissues, functionally represses the activity of CLOCK/BMAL1 transcriptional complex & renamed the gene Chrono.
□ Pre! site for the new human assembly GRCh38: Distinct UniGene BLAST hits 348,921, Distinct UniProt BLAST hits 451,431
>> http://www.ensembl.info/blog/2014/04/07/pre-site-for-the-new-human-assembly-grch38-is-live/ …
GENCODE 19 models mapped from e!75: 61,349
CCDS models mapped from e!75: 28,781
RefSeq annotation release 106 models: 26,670
□ Choice of transcripts and software has a large effect on variant annotation: ANNOVAR & VEP using ENSEMBL transcripts
>> http://genomemedicine.com/content/pdf/gm543.pdf …
□ genomeresearch:
FANTOM5 comparison of CAGE and RNA-seq transcriptome profiling http://ow.ly/v2ZSR
□ Bayesian Neural Networks for Genetic Association Studies of Complex Disease:
>> http://arxiv.org/pdf/1404.3989.pdf …
BNN was the only method for a variety of genetic models & more adept at detecting purely epistatic signals across the MAFs and effect sizes.
□ CaSPIAN: A Causal Compressive Sensing Algorithm for Discovering Directed Interactions in Gene Networks:
>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090781 …
CaSPIAN is a reverse engineering algorithm based on list-SP: a low-complexity, scans the expression profiles for low-dimensional subspaces.
□ HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data:
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003502 …
HapTree chooses how alleles of the newly added SNP may be assigned to chromosomes incl only those assignments that are sufficiently likely.
□ MegaSeq: Supercomputing for the parallelization of whole genome analysis:
>> http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu071.abstract …
Cray XE6