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 f...
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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
We provide a detailed protocol for robot-assisted, genome-wide measurement of fitness in the model yeast Saccharomyces cerevisiae using Quantitative Fitness Analysis (QFA). We first describe how we construct thousands...
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We provide a detailed protocol for robot-assisted, genome-wide measurement of fitness in the model yeast Saccharomyces cerevisiae using Quantitative Fitness Analysis (QFA). We first describe how we construct thousands of double or triple mutant yeast strains in parallel using Synthetic Genetic Array (SGA) procedures. Strains are inoculated onto solid agar surfaces by liquid spotting followed by repeated photography of agar plates. Growth curves are constructed and the fitness of each strain is estimated. Robot-assisted QFA, can be used to identify genetic interactions and chemical sensitivity/resistance in genome-wide experiments, but QFA can also be used in smaller scale, manual workflows. less
Transcriptomics has played an essential role as proof of concept in the development of experimental and bioinformatics approaches for the generation and analysis of Omics data. We are giving an introduction on how lar...
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Transcriptomics has played an essential role as proof of concept in the development of experimental and bioinformatics approaches for the generation and analysis of Omics data. We are giving an introduction on how large-scale technologies for gene expression profiling, especially microarrays, have changed the view from studying single molecular events to a systems level view of global mechanisms in a cell, the biological processes, and their pathological mutations. The main platforms available for gene expression profiling (from microarrays to RNA-seq) are presented and the general concepts that need to be taken into account for proper data analysis in order to extract objective and general conclusions from transcriptomics experiments are introduced. We also describe the available main bioinformatics resources used for this purpose. less
Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infe...
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Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN. less
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 ...
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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
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 sequenci...
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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
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...
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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
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 lang...
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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.
Methods of achieving program portability are discussed, with particular reference to the mobility of compilers. The method of transferring the BCPL compiler is then described including the specification of OCODE which...
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It is assumed that there is a similarity of function between the data names of a programming language and the file names of an operating system. The two functions are discussed in terms of the same basic concepts in o...
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