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R Classes and Methods for SNP Array Data

R Classes and Methods for SNP Array Data

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作者： Robert B. Scharpf Ingo Ruczinski

The Bioconductor project is an “open source and open development software project for the analysis and comprehension of genomic data” (1), primarily based on the R programming language. Infrastructure packages, such as Biobase, are maintained by Bioconductor core developers and serve several key roles to the broader community of Bioconductor software developers and users. In particular, Biobase introduces an S4 class, the eSet, for high-dimensional assay data. Encapsulating the assay data as well as meta-data on the samples, features, and experiment in the eSet class definition ensures propagation of the relevant sample and feature meta-data throughout an analysis. Extending the eSet class promotes code reuse through inheritance as well as interoperability with other R packages and is less error-prone. Recently proposed class definitions for high-throughput SNP arrays extend the eSet class. This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays. less

关键词： programming language genotype SNP array copy number S4 classes

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Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis

Genome-Wide Mapping of Protein-DNA Interaction by Chromatin ...

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作者： Ulrike Göbel Julia Reimer Franziska Turck

Genome-wide targets of chromatin-associated factors can be identified by a combination of chromatin-immunoprecipitation and oligonucleotide microarray hybridization. Genome-wide mircoarray data analysis represents a major challenge for the experimental biologist. This chapter introduces ChIPR, a package written in the R statistical programming language that facilitates the analysis of two-color microarrays from Roche-Nimblegen. The workflow of ChIPR is illustrated with sample data from Arabidopsis thaliana. However, ChIPR supports ChIP-chip data preprocessing, target identification, and cross-annotation of any species for which genome annotation data is available in GFF format. This chapter describes how to use ChIPR as a software tool without the requirement for programming skills in the R language. less

关键词： ChIP Assay Nucleic Acid Microarray Microarray Hybridization Genome Annotation Image Analysis Immunoprecipitation Microarray programming language Data analysis Preprocessing Target identification ChIP-chip ChIPR Cross-annotation

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Fast, single-molecule localization that achieves theoretically minimum uncertainty

Fast, single-molecule localization that achieves theoretical...

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作者： Carlas S Smith Nikolai Joseph Bernd Rieger Keith A Lidke

We describe an iterative algorithm that converges to the maximum likelihood estimate of the position and intensity of a single fluorophore. Our technique efficiently computes and achieves the Cramér-Rao lower bound, an essential tool for parameter estimation. An implementation of the algorithm on graphics processing unit hardware achieved more than 105 combined fits and Cramér-Rao lower bound calculations per second, enabling real-time data analysis for super-resolution imaging and other applications. less

关键词： Super-resolution Microscopy Statistical Calculation Data analysis programming language Single-molecule biophysics Single-molecule fluorescence

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Computing Chromosome Conformation

Computing Chromosome Conformation

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作者： James Fraser Mathieu Rousseau Mathieu Blanchette Josée Dostie

The “Chromosome Conformation Capture” (3C) and 3C-related technologies are used to measure physical contacts between DNA segments at high resolution in vivo. 3C studies indicate that genomes are likely organized into dynamic networks of physical contacts between genes and regulatory DNA elements. These interactions are mediated by proteins and are important for the regulation of genes. For these reasons, mapping physical connectivity networks with 3C-related approaches will be essential to fully understand how genes are regulated. The 3C-Carbon Copy (5C) technology can be used to measure chromatin contacts genome-scale within (cis) or between (trans) chromosomes. Although unquestionably powerful, this approach can be challenging to implement without proper understanding and application of publicly available bioinformatics tools. This chapter explains how 5C studies are performed and describes stepwise how to use currently available bioinformatics tools for experimental design, data analysis, and interpretation. less

关键词： DNA Sequencing Microarray Data analysis programming language DNA Ligation gene expression Chromosome Conformation Capture (3C) 3C-Carbon Copy (5C) spatial genome organization three-dimensional modeling

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CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

CellCognition: time-resolved phenotype annotation in high-th...

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作者： Michael Held Michael H A Schmitz Bernd Fischer Thomas Walter Beate Neumann Michael H Olma Matthias Peter Jan Ellenberg Daniel W Gerlich

Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. Incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions and confusion between different functional states with similar morphology. We demonstrate generic applicability in different assays and perturbation conditions, including a candidate-based RNA interference screen for regulators of mitotic exit in human cells. CellCognition is published as open source software, enabling live-cell imaging–based screening with assays that directly score cellular dynamics. less

关键词： Machine Learning Time Lapse Microscopy Image Analysis Live Cell Imaging Cell And Tissue Culture RNA Interference Transfection Western Blot Microscopy Statistical Calculation RNAi Screening SDS-PAGE Confocal Microscopy Image Processing MetaMorph Python programming language Software Anti-human

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FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

FragSeq: transcriptome-wide RNA structure probing using high...

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作者： Jason G Underwood Andrew V Uzilov Sol Katzman Courtney S Onodera Jacob E Mainzer David H Mathews Todd M Lowe Sofie R Salama David Haussler

Classical approaches to determine structures of noncoding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions. To accelerate RNA structure inference, we developed fragmentation sequencing (FragSeq), a high-throughput RNA structure probing method that uses high-throughput RNA sequencing of fragments generated by digestion with nuclease P1, which specifically cleaves single-stranded nucleic acids. In experiments probing the entire mouse nuclear transcriptome, we accurately and simultaneously mapped single-stranded RNA regions in multiple ncRNAs with known structure. We probed in two cell types to verify reproducibility. We also identified and experimentally validated structured regions in ncRNAs with, to our knowledge, no previously reported probing data. less

关键词： Transcriptomics Cell And Tissue Culture High-Throughput Sequencing RNA Extraction Gel Electrophoresis RNA-seq Sonication PAGE Electrophoresis SOLiD Sequencing Emulsion PCR Phosphorimaging Genome Visualization Genome Assembly Statistical Calculation Python programming language Bioinformatics Next-generation sequencing

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An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites

An Overview of the Computational Analyses and Discovery of T...

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作者： Istvan Ladunga

Here we provide a pragmatic, high-level overview of the computational approaches and tools for the discovery of transcription factor binding sites. Unraveling transcription regulatory networks and their malfunctions such as cancer became feasible due to recent stellar progress in experimental techniques and computational analyses. While predictions of isolated sites still pose notorious challenges, cis-regulatory modules (clusters) of binding sites can now be identified with high accuracy. Further support comes from conserved DNA segments, co-regulation, transposable elements, nucleosomes, and three-dimensional chromosomal structures. We introduce computational tools for the analysis and interpretation of chromatin immunoprecipitation, next-generation sequencing, SELEX, and protein-binding microarray results. Because immunoprecipitation produces overly large DNA segments and well over half of the sequencing reads from constitute background noise, methods are presented for background correction, sequence read mapping, peak calling, false discovery rate estimation, and co-localization analyses. To discover short binding site motifs from extensive immunoprecipitation segments, we recommend algorithms and software based on expectation maximization and Gibbs sampling. Data integration using several databases further improves performance. Binding sites can be visualized in genomic and chromatin context using genome browsers. Binding site information, integrated with co-expression in large compendia of gene expression experiments, allows us to reveal complex transcriptional regulatory networks. less

关键词： Peak Calling ChIP Assay ChIP-seq SELEX Microarray Mutagenesis RNA Interference Cross-linking Sonication Base-calling Bowtie Whole-genome Sequencing Statistical Calculation Monte Carlo Simulations Homology Modeling Molecular Dynamics Simulation ChIP-PCR Statistical Inference Genome Visualization Text Mining programming language computational prediction Transcription factor data integration next-generation sequencing transcriptional regulation transcription factor binding site background correction Anti-GST

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Assessing corollary discharge in humans using noninvasive neurophysiological methods

Assessing corollary discharge in humans using noninvasive ne...

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作者： Judith M Ford Brian J Roach Daniel H Mathalon

In this paper, we present a vocal production protocol for studying the neurophysiological action of the corollary discharge, a mechanism that allows animals to ignore sensations resulting from their own actions, and tag them as 'self'. Electroencephalograms are recorded while subjects say 'ah' about 100 times with minimal throat, jaw and tongue movements (Talk condition). This sequence of sounds is recorded and played back during the Listen condition. Event-related potentials are synchronized to the onset of speech sounds during the Talk and Listen conditions. Neural responses from the auditory cortex to the spoken sound as it is being spoken during the Talk condition are compared with neural responses to the same sounds when played back during the Listen condition. The successful action of the corollary discharge is seen when the response of the auditory cortex is suppressed during the Talk compared with the Listen condition. The protocol takes about 5 min to complete. less

关键词： Electroencephalography Statistical Calculation Data analysis programming language Homo sapiens Auditory system Motor control

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A Method to Discover Phased siRNA Loci

A Method to Discover Phased siRNA Loci

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作者： Michael J. Axtell

Short, interfering RNAs (siRNAs) arise from the processing of long double-stranded RNA (dsRNA) by Dicer enzymes. Dicers generate siRNA duplexes by successive hydrolysis of both strands of the dsRNA phosphodiester backbone at positions determined by measuring 21–24 nucleotides from an exposed dsRNA terminus. Therefore, a population of dsRNAs with precisely identical termini will produce siRNA spaced in regular, 21–24-nucleotide intervals. This chapter presents an easily customized and generally applicable strategy for identifying loci which produce the “phased” siRNAs diagnostic of such processing. Given the input of a large set of expressed small RNAs and of the corresponding genome or transcriptome from which the small RNAs are derived, the methodology produces a ranking of user-defined loci with respect to their likely production of phased siRNAs. Top ranked loci are candidates for further computational and biological analyses. less

关键词： Statistical Calculation NCBI BLAST programming language Python Bioinformatics Plants siRNA microRNA Small RNA Trans-acting siRNA Transitivity

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Teaching programming technique with edutainment robot construction

Teaching programming technique with edutainment robot constr...

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2010 2nd International Conference on Education Technology and Computer(第二届IEEE教育技术与计算机国际会议 ICETC 2010)

作者： Hsien-Tang Lin Tzai-Hsing Kuo Department of Computer Science and Information Engineering Tahwa Institute of Technology ＃1 Tahwa Rd Department of Computer Science National Chiao Tung University 1001 Ta Hsueh Road Hsinchu300 Taiwan

ISBN: (纸本)9781424463671

recently,building robot has become the current trend for the teaching and learning the subject of science in elementary and secondary *** objective of this paper is to propose a teaching approach for programming language by the application of weblog on robot *** is hoped that such an approach may make learning more enjoyable as well as effective and may further motivate students in future experiments.A study of teaching computer program in high school with VPL-based tool to construct robots was *** formed in team to build robots and write program to perform the specified *** result shows that students have achieved good results in terms of learning motivation.

关键词： component Robot programming language blog

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