Log in to search using one of your social media accounts:

 

Systems Medicine: Sketching the Landscape
To understand the meaning of the term Systems Medicine and to distinguish it from seemingly related other expressions currently in use, such as precision, personalized, -omics, or big data medicine, its underlying history and development into present time needs to be highlighted. Having this development in mind, it becomes evident that Systems Medicine is a genuine concept as well as a novel way of tackling the manifold complexity that occurs in nowadays clinical medicine—and not just a rebranding of what has previously been done in the past. So looking back it seems clear to many in the field that Systems Medicine h...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Taking Bioinformatics to Systems Medicine
Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data ...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness
Recent advances in genomics have led to the rapid and relatively inexpensive collection of patient molecular data including multiple types of omics data. The integration of these data with clinical measurements has the potential to impact on our understanding of the molecular basis of disease and on disease management. Systems medicine is an approach to understanding disease through an integration of large patient datasets. It offers the possibility for personalized strategies for healthcare through the development of a new taxonomy of disease. Advanced computing will be an important component in effectively implementing s...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Next-Generation Pathology
The field of pathology is rapidly transforming from a semiquantitative and empirical science toward a big data discipline. Large data sets from across multiple omics fields may now be extracted from a patient’s tissue sample. Tissue is, however, complex, heterogeneous, and prone to artifact. A reductionist view of tissue and disease progression, which does not take this complexity into account, may lead to single biomarkers failing in clinical trials. The integration of standardized multi-omics big data and the retention of valuable information on spatial heterogeneity are imperative to model complex disease mechanis...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Training in Systems Approaches for the Next Generation of Life Scientists and Medical Doctors
We describe the current challenges and scattered best practices of introducing the wider systems medicine topics into the medical education as well as possibilities for systems medicine training at the doctoral and lifelong levels. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Systems Medicine in Pharmaceutical Research and Development
The development of new drug therapies requires substantial and ever increasing investments from the pharmaceutical company. Ten years ago, the average time from early target identification and optimization until initial market authorization of a new drug compound took more than 10 years and involved costs in the order of one billion US dollars. Recent studies indicate even a significant growth of costs in the meanwhile, mainly driven by the increasing complexity of diseases addressed by pharmaceutical research. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Systems Medicine in Oncology: Signaling Network Modeling and New-Generation Decision-Support Systems
Two different perspectives are the main focus of this book chapter: (1) A perspective that looks to the future, with the goal of devising rational associations of targeted inhibitors against distinct altered signaling-network pathways. This goal implies a sufficiently in-depth molecular diagnosis of the personal cancer of a given patient. A sufficiently robust and extended dynamic modeling will suggest rational combinations of the abovementioned oncoprotein inhibitors. The work toward new selective drugs, in the field of medicinal chemistry, is very intensive. Rational associations of selective drug inhibitors will become ...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Neurological Diseases from a Systems Medicine Point of View
The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurologica...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Systems Medicine and Infection
By using a systems-based approach, mathematical and computational techniques can be used to develop models that describe the important mechanisms involved in infectious diseases. An iterative approach to model development allows new discoveries to continually improve the model and ultimately increase the accuracy of predictions. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Systems Medicine for Lung Diseases: Phenotypes and Precision Medicine in Cancer, Infection, and Allergy
Lung diseases cause an enormous socioeconomic burden. Four of them are among the ten most important causes of deaths worldwide: Pneumonia has the highest death toll of all infectious diseases, lung cancer kills the most people of all malignant proliferative disorders, chronic obstructive pulmonary disease (COPD) ranks third in mortality among the chronic noncommunicable diseases, and tuberculosis is still one of the most important chronic infectious diseases. Despite all efforts, for example, by the World Health Organization and clinical and experimental researchers, these diseases are still highly prevalent and harmful. T...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive
The understanding of the immune response is right now at the center of biomedical research. There are growing expectations that immune-based interventions will in the midterm provide new, personalized, and targeted therapeutic options for many severe and highly prevalent diseases, from aggressive cancers to infectious and autoimmune diseases. To this end, immunology should surpass its current descriptive and phenomenological nature, and become quantitative, and thereby predictive. (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

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

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

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

Network-Assisted Disease Classification and Biomarker Discovery
Developing improved approaches for diagnosis, treatment, and prevention of diseases is a major goal of biomedical research. Therefore, the discovery of biomarker signatures from high-throughput “omics” data is an active research topic in the field of bioinformatics and systems medicine. A major issue is the low reproducibility and the limited biological interpretability of candidate biomarker signatures identified from high-throughput data. This impedes the use of discovered biomarker signatures into clinical applications. Currently, much focus is placed on developing strategies to improve reproducibility and i...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine
Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases. Complex diseases arise from the interactions among disease-influencing factors across multiple levels of biological organization from the environment to molecules. To tackle the enormous challenges posed by complex diseases, we need a modeling and simulation framework capable of capturing and integrating information originating...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study
We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non-exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news

Modeling and Simulation Tools: From Systems Biology to Systems Medicine
Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of “Software as a Medical Device” and what this may imply for the migration of research-oriented, simulation software into the domain of human health. (Source: Sprin...
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

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

A Simple Protocol for the Inference of RNA Global Pairwise Alignments
In conclusion, the proposed workflow for pairwise RNA alignment depends on the input RNA primary sequence identity and the availability of reliable secondary structures. (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

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

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

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

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

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

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

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

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

NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data
RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling
In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Deciphering Metatranscriptomic Data
Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms w...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

RIP-Seq Data Analysis to Determine RNA–Protein Associations
Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we prov...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Quality Control of RNA-Seq Experiments
Direct sequencing of the complementary DNA (cDNA) using high-throughput sequencing technologies (RNA-seq) is widely used and allows for more comprehensive understanding of the transcriptome than microarray. In theory, RNA-seq should be able to precisely identify and quantify all RNA species, small or large, at low or high abundance. However, RNA-seq is a complicated, multistep process involving reverse transcription, amplification, fragmentation, purification, adaptor ligation, and sequencing. Improper operations at any of these steps could make biased or even unusable data. Additionally, RNA-seq intrinsic biases (such as ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Accurate Mapping of RNA-Seq Data
The mapping of RNA-Seq data on genome is not the same as DNA-Seq data, because the junction reads span two exons and have no identical matches at reference genome. In this chapter, we describe a junction read aligner SpliceMap that is based on an algorithm of “half-read seeding” and “seeding extension.” Four analysis steps are integrated in SpliceMap (half-read mapping, seeding selection, seeding extension and junction search, and paired-end filtering), and all toning parameters of these steps can be editable in a single configuration file. Thus, SpliceMap can be executed by a single command. While ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

The ViennaRNA Web Services
The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detect...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit
Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human diseases. Exploiting the RNA editing potential in complete RNA-Seq datasets, however, is a challenging task. Indeed, no dedicated software is available, and sometimes deep computational skills and appropriate hardware resources are required. To explore the impact of known RNA editing events in massive transcriptome sequencing experiments, we developed the ExpEdit web service application. In the present work, we provide ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection
Gene expression regulatory elements are scattered in gene promoters and pre-mRNAs. In particular, RNA elements lying in untranslated regions (5′ and 3′UTRs) are poorly studied because of their peculiar features (i.e., a combination of primary and secondary structure elements) which also pose remarkable computational challenges. Several years ago, we began collecting experimentally characterized UTR regulatory elements, developing the specialized database UTRsite. This paper describes the detailed guidelines to annotate cis-regulatory elements in 5′ and 3′ UnTranslated Regions (UTRs) by computational...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Rfam: Annotating Families of Non-Coding RNA Sequences
The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into “families” and related families are further grouped into “clans.” We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

ASPicDB: A Database Web Tool for Alternative Splicing Analysis
Alternative splicing (AS) is a basic molecular phenomenon that increases the functional complexity of higher eukaryotic transcriptomes. Indeed, through AS individual gene loci can generate multiple RNAs from the same pre-mRNA. AS has been investigated in a variety of clinical and pathological studies, such as the transcriptome regulation in cancer. In human, recent works based on massive RNA sequencing indicate that>95 % of pre-mRNAs are processed to yield multiple transcripts. Given the biological relevance of AS, several computational efforts have been done leading to the implementation of novel algorithms and specifi...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista
Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process is highly regulated and makes up a large part of the differences between species, cell types, and states. The key to compare AS across different genes or organisms is to tokenize the AS phenomenon into atomary units, so-called AS events. These events then usually are grouped by common patterns to investigate the underlying molecular mechanisms that drive their regulation. However, attempts to decompose loci with AS ob...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Computational Design of Artificial RNA Molecules for Gene Regulation
RNA interference (RNAi) is a powerful tool for the regulation of gene expression. Small exogenous noncoding RNAs (ncRNAs) such as siRNA and shRNA are the active silencing agents, intended to target and cleave complementary mRNAs in a specific way. They are widely and successfully employed in functional studies, and several ongoing and already completed siRNA-based clinical trials suggest encouraging results in the regulation of overexpressed genes in disease. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news

Mining the Electronic Health Record for Disease Knowledge
The growing amount and availability of electronic health record (EHR) data present enhanced opportunities for discovering new knowledge about diseases. In the past decade, there has been an increasing number of data and text mining studies focused on the identification of disease associations (e.g., disease–disease, disease–drug, and disease–gene) in structured and unstructured EHR data. This chapter presents a knowledge discovery framework for mining the EHR for disease knowledge and describes each step for data selection, preprocessing, transformation, data mining, and interpretation/validation. Topics ...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news

Systematic Drug Repurposing Through Text Mining
Drug development remains a time-consuming and highly expensive process with high attrition rates at each stage. Given the safety hurdles drugs must pass due to increased regulatory scrutiny, it is essential for pharmaceutical companies to maximize their return on investment by effectively extending drug life cycles. There have been many effective techniques, such as phenotypic screening and compound profiling, which identify new indications for existing drugs, often referred to as drug repurposing or drug repositioning. This chapter explores the use of text mining leveraging several publicly available knowledge resources a...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news

Integrative Literature and Data Mining to Rank Disease Candidate Genes
While the genomics-derived discoveries promise benefits to basic research and health care, the speed and affordability of sequencing following recent technological advances has further aggravated the data deluge. Seamless integration of the ever-increasing clinical, genomic, and experimental data and efficient mining for knowledge extraction, delivering actionable insight and generating testable hypotheses are therefore critical for the needs of biomedical research. For instance, high-throughput techniques are frequently applied to detect disease candidate genes. Experimental validation of these candidates however is both ...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news

Role of Text Mining in Early Identification of Potential Drug Safety Issues
Drugs are an important part of today’s medicine, designed to treat, control, and prevent diseases; however, besides their therapeutic effects, drugs may also cause adverse effects that range from cosmetic to severe morbidity and mortality. To identify these potential drug safety issues early, surveillance must be conducted for each drug throughout its life cycle, from drug development to different phases of clinical trials, and continued after market approval. A major aim of pharmacovigilance is to identify the potential drug–event associations that may be novel in nature, severity, and/or frequency. Currently,...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news

Mining Emerging Biomedical Literature for Understanding Disease Associations in Drug Discovery
Systematically evaluating the exponentially growing body of scientific literature has become a critical task that every drug discovery organization must engage in in order to understand emerging trends for scientific investment and strategy development. Developing trends analysis uses the number of publications within a 3-year window to determine concepts derived from well-established disease and gene ontologies to aid in recognizing and predicting emerging areas of scientific discoveries relevant to that space. In this chapter, we describe such a method and use obesity and psoriasis as use-case examples by analyzing the f...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news

Mining Biological Networks from Full-Text Articles
The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein–protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present pract...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news