检索结果-内蒙古大学图书馆

作者： Jason M. Ko Reza Mousavi Daniel Lobo

Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis. less

关键词： Machine Learning Mathematical Modeling MATLAB Python Recombinant Protein Expression Cell And Tissue Culture STRING programming language Morphogenesis Systems Biology Computational Biology

来源：评论

学校读者我要写书评

暂无评论

Array-Based Multiplex and High-Throughput Serology Assays

Array-Based Multiplex and High-Throughput Serology Assays

引用

作者： Jennie Olofsson Ceke Hellström Eni Andersson Jamil Yousef Lovisa Skoglund Ronald Sjöberg Anna Månberg Peter Nilsson Elisa Pin

The detection of antibody responses using serological tests provides means to diagnose infections, follow disease transmission, and monitor vaccination responses. The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, highlighted the need for rapid development of robust and reliable serological tests to follow disease spreading. Moreover, the rise of SARS-CoV-2 variants emphasized the need to monitor their transmission and prevalence in the population. For this reason, multiplex and flexible serological assays are needed to allow for rapid inclusion of antigens representing new variants as soon as they appear. In this chapter, we describe the generation and application of a multiplex serological test, based on bead array technology, to detect anti-SARS-CoV-2 antibodies in a high-throughput manner, using only a few microliters of sample. This method is currently expanding to include a multi-disease antigen panel that will allow parallel detection of antibodies towards several infectious agents. less

关键词： Protein Array Data analysis Vaccination Cross-linking PCR programming language SARS-CoV-2 Serology Serum Antibody Multiplex Plasma High-throughput Anti-COVID Anti-human

来源：评论

学校读者我要写书评

暂无评论

Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs

Using Deep Sequencing Data for Identification of Editing Sit...

引用

作者： Shahar Alon Eli Eisenberg

Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less

关键词： Deep Sequencing Genomics Statistical Calculation Bowtie Illumina Sequencing programming language Mus musculus Bioinformatics miRNA A-to-I editing

来源：评论

学校读者我要写书评

暂无评论

Constructing Computational Pipelines

Constructing Computational Pipelines

引用

作者： Mark Halling-Brown Adrian J. Shepherd

Many bioinformatics tasks involve creating a computational pipeline from existing software components and algorithms. The traditional approach is to glue components together using scripts written in a programming language such as Perl. However, a new, more powerful approach is emerging that promises to revolutionise the way bioinformaticians create applications from existing components, an approach based on the concept of the scientific workflow. Scientific workflows are created in graphical environments known as workflow management systems. They have many benefits over traditional program scripts, including speed of development, portability, and their suitability for developing complex, distributed applications. This chapter explains how to design and implement bioinformatics workflows using free, Open Source software tools, such as the Tav-erna workflow management system. We also demonstrate how new and existing tools can be deployed as Web services so that they can be easily integrated into novel computational pipelines using the scientific workflow paradigm. less

关键词： programming language Web service Computational pipeline scientific workflow workflow management system applications server

来源：评论

学校读者我要写书评

暂无评论

Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions

Gene Regulatory Networks from Single Cell Data for Exploring...

引用

作者： Thalia E. Chan Michael P. Stumpf Ann C. Babtie

Single cell experimental techniques now allow us to quantify gene expression in up to thousands of individual cells. These data reveal the changes in transcriptional state that occur as cells progress through development and adopt specialized cell fates. In this chapter we describe in detail how to use our network inference algorithm (PIDC)—and the associated software package ***—to infer functional interactions between genes from the observed gene expression patterns. We exploit the large sample sizes and inherent variability of single cell data to detect statistical dependencies between genes that indicate putative (co-)regulatory relationships, using multivariate information measures that can capture complex statistical relationships. We provide guidelines on how best to combine this analysis with other complementary methods designed to explore single cell data, and how to interpret the resulting gene regulatory network models to gain insight into the processes regulating cell differentiation. less

关键词： Real-time PCR RNA-seq MATLAB Neuronal Differentiation Statistical Calculation programming language Python Gene regulation Network inference Single cell Information theory Cell development

来源：评论

学校读者我要写书评

暂无评论

RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System

RNA Sequencing and Quantitation Using the Helicos Genetic An...

引用

作者： Tal Raz Marie Causey Daniel R. Jones Alix Kieu Stan Letovsky Doron Lipson Edward Thayer John F. Thompson Patrice M. Milos

The recent transition in gene expression analysis technology to ultra high-throughput cDNA sequencing provides a means for higher quantitation sensitivity across a wider dynamic range than previously possible. Sensitivity of detection is mostly a function of the sheer number of sequence reads generated. Typically, RNA is converted to cDNA using random hexamers and the cDNA is subsequently sequenced (RNA-Seq). With this approach, higher read numbers are generated for long transcripts as compared to short ones. This length bias necessitates the generation of very high read numbers to achieve sensitive quantitation of short, low-expressed genes. To eliminate this length bias, we have developed an ultra high-throughput sequencing approach where only a single read is generated for each transcript molecule (single-molecule sequencing Digital Gene Expression (smsDGE)). So, for example, equivalent quantitation accuracy of the yeast transcriptome can be achieved by smsDGE using only 25% of the reads that would be required using RNA-Seq. For sample preparation, RNA is first reverse-transcribed into single-stranded cDNA using oligo-dT as a primer. A poly-A tail is then added to the 3′ ends of cDNA to facilitate the hybridization of the sample to the Helicos® single-molecule sequencing Flow-Cell to which a poly dT oligo serves as the substrate for subsequent sequencing by synthesis. No PCR, sample-size selection, or ligation steps are required, thus avoiding possible biases that may be introduced by such manipulations. Each tailed cDNA sample is injected into one of 50 flow-cell channels and sequenced on the Helicos® Genetic Analysis System. Thus, 50 samples are sequenced simultaneously generating 10–20 million sequence reads on average for each sample channel. The sequence reads can then be aligned to the reference of choice such as the transcriptome, for quantitation of known transcripts, or the genome for novel transcript discovery. This chapter provides a summary of the met

关键词： RNA-seq Genetic Analysis Gene Expression Analysis High-Throughput Sequencing PCR Spectroscopy Gel Electrophoresis Titration Data analysis cDNA sequencing DNA Ligation Python programming language Expression analysis Single-molecule sequencing smsDGE

来源：评论

学校读者我要写书评

暂无评论

Prediction of miRNA–mRNA Interactions Using miRGate

Prediction of miRNA–mRNA Interactions Using miRGate

引用

作者： Eduardo Andrés-León Gonzalo Gómez-López David G. Pisano

miRGate (http://*** /) is a freely available database that contains predicted and experimentally validated microRNA–messenger RNA (miRNA–mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3′-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus. The approach intends to circumvent one of the main drawbacks in this area, as diverse sequences and gene database versions cause poor overlap among different target prediction methods even with experimentally confirmed targets. As a result, miRGate predictions have been successfully validated using functional assays in several laboratories. This chapter describes how a user can access target information via miRGate’s web interface. It also shows how automatically access the database through the programmatic interface based on representational state transfer services (REST), using the application programming interface (API) available at http://***/API . less

关键词： Database Management System programming language Ensembl MicroRNA Prediction 3′-UTR Validated API Target site

来源：评论

学校读者我要写书评

暂无评论

Confocal-FRAP Analysis of ECM Molecular Interactions

Confocal-FRAP Analysis of ECM Molecular Interactions

引用

作者： Timothy Hardingham Philip Gribbon

Extracellular matrices (ECM) contain a mixture of fibrillar and nonfibrillar macromolecular components, which together form a composite structure (1–3). It is the ECM that defines the architecture, the form, and the biomechanical properties of different tissues (4,5). Among the nonfibrillar macromolecules, the highly charged proteoglycans and hyaluronan are major components that occur at high concentration and greatly influence the movement of solutes and water between the tissue and the circulation, and control the access to cells of nutrients, metabolites, growth factors, and chemokines (6–7). This local environmental regulation may have important consequences on cellular functions, especially in tissues with large dense ECMs, such as articular cartilage. less

关键词： Fluorescence Labeling Dialysis Ultrafiltration FRAP Image Processing Data analysis programming language

来源：评论

学校读者我要写书评

暂无评论

Genotyping for Species Identification and Diversity Assessment Using Double-Digest Restriction Site-Associated DNA Sequencing (ddRAD-Seq)

Genotyping for Species Identification and Diversity Assessme...

引用

作者： Anita A. Severn-Ellis Armin Scheben Ting Xiang Neik Nur Shuhadah Saad Aneeta Pradhan Jacqueline Batley

Genotyping-by-sequencing (GBS) is a powerful approach for studying the genetic diversity of legume species. By using restriction enzymes or other methods to generate a reduced representation of the genome for sequencing, GBS can provide genome-wide single nucleotide polymorphisms (SNP) for diversity analysis at high throughput and low cost. Here we describe a novel double-digest restriction site-associated DNA sequencing (ddRAD-seq) approach. We also describe the downstream bioinformatic analysis of the sequencing data, including alignment to a reference genome, de novo assembly, SNP calling, phylogenetic analysis, and structure analysis. less

关键词： Restriction Enzyme Digestion DNA Sequencing Whole-genome Sequencing Genotyping PCR SNP Calling Structure Analysis Freeze-thaw Method Principal Component Analysis Statistical Calculation DNA Ligation programming language Trimmomatic SAMtools Genotyping-by-sequencing GBS ddRAD-seq

来源：评论

学校读者我要写书评

暂无评论

Considerations regarding the source code of digital poetry

引用

REVISTA DE LETRAS 2010年第2期50卷 447-467页

作者： Tavares, Otavio Guimaraes Univ Fed Santa Catarina Ctr Comunicacio & Expressao BR-88040970 Florianopolis SC Brazil

This article has aims on mapping and analyzing aspects of computer science, on how they affect creation, aesthetic reception and operating mode of digital poetry. Specifically, it means to look at the programming language as part of the creation and constitution of the digital literary work, as that which stands behind what is shown to the reader, as a restriction and potentiality of creation, and as a signifier in a construction that has its own materiality as a giver of meaning. And finally, it intends on comprehending up to what point the knowledge of these modes and mediums are necessary for both the creation and reception of the digital literary works.

关键词： Digital literature Technology Computer science programming language Creation Aesthetic reception

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：