Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine
Regenerative medicine, ranging from stem cell therapy to organ regeneration, is promising to revolutionize treatments of diseases and aging. These approaches require a perfect understanding of cell reprogramming and differentiation. Predictive modeling of cellular systems has the potential to provide insights about the dynamics of cellular processes, and guide their control. Moreover in many cases, it provides alternative to experimental tests, difficult to perform for practical or ethical reasons. The variety and accuracy of biological processes represented in mathematical models grew in-line with the discovery of underly...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
RNA Systems Biology for Cancer: From Diagnosis to Therapy
It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to th...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD
In conclusion, in our hands the scope and efforts of systems medicine need to concurrently consider these aspects of clinical implementation, which inherently drives the selection of the most relevant and urgent issues and methods that need further development in a systems analysis of disease. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine
Modern high-throughput techniques offer immense opportunities to investigate whole-systems behavior, such as those underlying human diseases. However, the complexity of the data presents challenges in interpretation, and new avenues are needed to address the complexity of both diseases and data. Constraint-based modeling is one formalism applied in systems biology. It relies on a genome-scale reconstruction that captures extensive biochemical knowledge regarding an organism. The human genome-scale metabolic reconstruction is increasingly used to understand normal cellular and disease states because metabolism is an importa...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design
Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction b...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs
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 usi...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Prediction of miRNA Targets
Computational methods for miRNA target prediction are currently undergoing extensive review and evaluation. There is still a great need for improvement of these tools and bioinformatics approaches are looking towards high-throughput experiments in order to validate predictions. The combination of large-scale techniques with computational tools will not only provide greater credence to computational predictions but also lead to the better understanding of specific biological questions. Current miRNA target prediction tools utilize probabilistic learning algorithms, machine learning methods and even empirical biologically de...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Detection of Post-Transcriptional RNA Editing Events
The advent of deep sequencing technologies has greatly improved the study of complex eukaryotic genomes and transcriptomes, providing the unique opportunity to investigate posttranscriptional molecular mechanisms as alternative splicing and RNA editing at single base-pair resolution. RNA editing by adenosine deamination (A-to-I) is widespread in humans and can lead to a variety of biological effects depending on the RNA type or the RNA region involved in the editing modification. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Transcriptome Assembly and Alternative Splicing Analysis
Alternative Splicing (AS) is the molecular phenomenon whereby multiple transcripts are produced from the same gene locus. As a consequence, it is responsible for the expansion of eukaryotic transcriptomes. Aberrant AS is involved in the onset and progression of several human diseases. Therefore, the characterization of exon–intron structure of a gene and the detection of corresponding transcript isoforms is an extremely relevant biological task. Nonetheless, the computational prediction of AS events and the repertoire of alternative transcripts is yet a challenging issue. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Quantifying Entire Transcriptomes by Aligned RNA-Seq Data
Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and noncoding RNAs. Although RNA quality and library preparation protocols are the main source of variability, the bioinformatics pipelines for RNA-seq data analysis are very complex and the choice of different tools at each stage of the analysis can significantly affect the overall results. In this chapter we describe the pipelines we use to detect miRNA and mRNA differential expression. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Fast Prediction of RNA–RNA Interaction Using Heuristic Algorithm
We describe the algorithm’s concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Modeling and Predicting RNA Three-Dimensional Structures
Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis–Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structur...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Drawing and Editing the Secondary Structure(s) of RNA
We describe the file formats and structural descriptions accepted by popular RNA visualization tools. We also provide command lines and Python scripts to ease the user’s access to advanced features. Finally, we discuss and illustrate alternative approaches to visualize the secondary structure in the presence of probing data, pseudoknots, RNA–RNA interactions, and comparative data. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
De Novo Secondary Structure Motif Discovery Using RNAProfile
We describe here how conserved secondary structure motifs shared by functionally related RNA sequences can be detected through the software tool RNAProfile. RNAProfile takes as input a set of unaligned RNA sequences expected to share a common motif, and outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
RNA Secondary Structure Prediction from Multi-Aligned Sequences
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary s...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
