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    1216 results match your criteria Briefings in bioinformatics[Journal]

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    The BioCyc collection of microbial genomes and metabolic pathways.
    Brief Bioinform 2017 Aug 17. Epub 2017 Aug 17.
    BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Read More

    Artificial intelligence in drug combination therapy.
    Brief Bioinform 2018 Feb 9. Epub 2018 Feb 9.
    Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Read More

    Open-source chemogenomic data-driven algorithms for predicting drug-target interactions.
    Brief Bioinform 2018 Feb 6. Epub 2018 Feb 6.
    While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Read More

    Microarray is an efficient tool for circRNA profiling.
    Brief Bioinform 2018 Feb 3. Epub 2018 Feb 3.
    Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. Read More

    Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer.
    Brief Bioinform 2018 Feb 1. Epub 2018 Feb 1.
    It is known that noncoding RNAs (ncRNAs) cover ∼98% of the transcriptome, but do not encode proteins. Among ncRNAs, long noncoding RNAs (lncRNAs) are a large and diverse class of RNA molecules, and are thought to be a gold mine of potential oncogenes, anti-oncogenes and new biomarkers. Although only a minority of lncRNAs is functionally characterized, it is clear that they are important regulators to modulate gene expression and involve in many biological functions. Read More

    Modeling biological problems in computer science: a case study in genome assembly.
    Brief Bioinform 2018 Jan 30. Epub 2018 Jan 30.
    As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. Read More

    Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems.
    Brief Bioinform 2018 Jan 31. Epub 2018 Jan 31.
    In the establishment and maintenance of the interaction between pathogenic or symbiotic bacteria with a eukaryotic organism, protein substrates of specialized bacterial secretion systems called effectors play a critical role once translocated into the host cell. Proteins are also secreted to the extracellular medium by free-living bacteria or directly injected into other competing organisms to hinder or kill. In this work, we explore an approach based on the evolutionary dependence that most of the effectors maintain with their specific secretion system that analyzes the co-occurrence of any orthologous protein group and their corresponding secretion system across multiple genomes. Read More

    How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives.
    Brief Bioinform 2018 Jan 31. Epub 2018 Jan 31.
    The sequencing of the transcriptome of single cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types in heterogeneous cell populations or for the study of stochastic gene expression. In recent years, various experimental methods and computational tools for analysing single-cell RNA-sequencing data have been proposed. However, most of them are tailored to different experimental designs or biological questions, and in many cases, their performance has not been benchmarked yet, thus increasing the difficulty for a researcher to choose the optimal single-cell transcriptome sequencing (scRNA-seq) experiment and analysis workflow. Read More

    Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors.
    Brief Bioinform 2018 Jan 29. Epub 2018 Jan 29.
    Alternative splicing (AS) has shown to play a pivotal role in the development of diseases, including cancer. Specifically, all the hallmarks of cancer (angiogenesis, cell immortality, avoiding immune system response, etc.) are found to have a counterpart in aberrant splicing of key genes. Read More

    Computational prediction of drug-target interactions using chemogenomic approaches: an empirical survey.
    Brief Bioinform 2018 Jan 24. Epub 2018 Jan 24.
    Computational prediction of drug-target interactions (DTIs) has become an essential task in the drug discovery process. It narrows down the search space for interactions by suggesting potential interaction candidates for validation via wet-lab experiments that are well known to be expensive and time-consuming. In this article, we aim to provide a comprehensive overview and empirical evaluation on the computational DTI prediction techniques, to act as a guide and reference for our fellow researchers. Read More

    Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.
    Brief Bioinform 2018 Jan 16. Epub 2018 Jan 16.
    Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Read More

    Recent development of Ori-Finder system and DoriC database for microbial replication origins.
    Brief Bioinform 2018 Jan 9. Epub 2018 Jan 9.
    DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Read More

    SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue.
    Brief Bioinform 2018 Jan 3. Epub 2018 Jan 3.
    Human specifically expressed genes (SEGs) usually serve as potential biomarkers for disease diagnosis and treatment. However, the regulation underlying their specific expression remains to be revealed. In this study, we constructed SEG regulation database (SEGreg; available at http://bioinfo. Read More

    Metabolomics technology and bioinformatics for precision medicine.
    Brief Bioinform 2018 Jan 3. Epub 2018 Jan 3.
    Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Read More

    Drug knowledge bases and their applications in biomedical informatics research.
    Brief Bioinform 2018 Jan 3. Epub 2018 Jan 3.
    Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many drug knowledge bases have been constructed. Read More

    Link synthetic lethality to drug sensitivity of cancer cells.
    Brief Bioinform 2017 Dec 28. Epub 2017 Dec 28.
    Synthetic lethal (SL) interactions occur when alterations in two genes lead to cell death but alteration in only one of them is not lethal. SL interactions provide a new strategy for molecular-targeted cancer therapy. Currently, there are few drugs targeting SL interactions that entered into clinical trials. Read More

    BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches.
    Brief Bioinform 2017 Dec 19. Epub 2017 Dec 19.
    With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typically, predictors based on machine learning techniques contain three main steps: feature extraction, predictor construction and performance evaluation. Read More

    Multi-omics integration-a comparison of unsupervised clustering methodologies.
    Brief Bioinform 2017 Dec 18. Epub 2017 Dec 18.
    With the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these factors is explored when solving the problem of sample classification, by comparing the performances of five unsupervised algorithms: Multiple Canonical Correlation Analysis, Multiple Co-Inertia Analysis, Multiple Factor Analysis, Joint and Individual Variation Explained and Similarity Network Fusion. These methods were applied to three real data sets taken from literature and several ad hoc simulated scenarios to discuss classification performance in different conditions of noise and signal strength across the data types. Read More

    Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes.
    Brief Bioinform 2017 Dec 18. Epub 2017 Dec 18.
    The development of computational methods capable of analyzing -omics data at the individual level is critical for the success of precision medicine. Although unprecedented opportunities now exist to gather data on an individual's -omics profile ('personalome'), interpreting and extracting meaningful information from single-subject -omics remain underdeveloped, particularly for quantitative non-sequence measurements, including complete transcriptome or proteome expression and metabolite abundance. Conventional bioinformatics approaches have largely been designed for making population-level inferences about 'average' disease processes; thus, they may not adequately capture and describe individual variability. Read More

    Bioinformatics for precision oncology.
    Brief Bioinform 2017 Dec 18. Epub 2017 Dec 18.
    Molecular profiling of tumor biopsies plays an increasingly important role not only in cancer research, but also in the clinical management of cancer patients. Multi-omics approaches hold the promise of improving diagnostics, prognostics and personalized treatment. To deliver on this promise of precision oncology, appropriate bioinformatics methods for managing, integrating and analyzing large and complex data are necessary. Read More

    Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains.
    Brief Bioinform 2017 Dec 15. Epub 2017 Dec 15.
    Proteins interact with a variety of molecules including proteins and nucleic acids. We review a comprehensive collection of over 50 studies that analyze and/or predict these interactions. While majority of these studies address either solely protein-DNA or protein-RNA binding, only a few have a wider scope that covers both protein-protein and protein-nucleic acid binding. Read More

    Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.
    Brief Bioinform 2017 Dec 8. Epub 2017 Dec 8.
    Mathematical models can serve as a tool to formalize biological knowledge from diverse sources, to investigate biological questions in a formal way, to test experimental hypotheses, to predict the effect of perturbations and to identify underlying mechanisms. We present a pipeline of computational tools that performs a series of analyses to explore a logical model's properties. A logical model of initiation of the metastatic process in cancer is used as a transversal example. Read More

    A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years.
    Brief Bioinform 2017 Dec 8. Epub 2017 Dec 8.
    Background: The long-term availability of online Web services is of utmost importance to ensure reproducibility of analytical results. However, because of lack of maintenance following acceptance, many servers become unavailable after a short period of time. Our aim was to monitor the accessibility and the decay rate of published Web services as well as to determine the factors underlying trends changes. Read More

    A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.
    Brief Bioinform 2017 Dec 6. Epub 2017 Dec 6.
    Motivation: Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. Read More

    Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine.
    Brief Bioinform 2017 Dec 5. Epub 2017 Dec 5.
    Systems medicine holds many promises, but has so far provided only a limited number of proofs of principle. To address this road block, possible barriers and challenges of translating systems medicine into clinical practice need to be identified and addressed. The members of the European Cooperation in Science and Technology (COST) Action CA15120 Open Multiscale Systems Medicine (OpenMultiMed) wish to engage the scientific community of systems medicine and multiscale modelling, data science and computing, to provide their feedback in a structured manner. Read More

    Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates.
    Brief Bioinform 2017 Dec 5. Epub 2017 Dec 5.
    High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. Read More

    Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis.
    Brief Bioinform 2017 Nov 29. Epub 2017 Nov 29.
    The development of disease involves a systematic disturbance inside cells and is associated with changes in the interactions or regulations among genes forming biological networks. The bridges inside a network are critical in shortening the distances between nodes. We observed that, inside the human gene regulatory network, one strongly connected core bridged the whole network. Read More

    Computer-aided biomarker discovery for precision medicine: data resources, models and applications.
    Brief Bioinform 2017 Nov 29. Epub 2017 Nov 29.
    Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. Read More

    Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. Read More

    A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. Read More

    Resources and tools for the high-throughput, multi-omic study of intestinal microbiota.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. Read More

    Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using a bottom-up approach as in systems biology with a data-driven top-down approach as in bioinformatics. The advent of omics technologies has provided the stepping-stone for the emergence of Systems Bioinformatics. Read More

    Construction of a hierarchical gene regulatory network centered around a transcription factor.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    We have modified a multitude of transcription factors (TFs) in numerous plant species and some animal species, and obtained transgenic lines that exhibit phenotypic alterations. Whenever we observe phenotypic changes in a TF's transgenic lines, we are always eager to identify its target genes, collaborative regulators and even upstream high hierarchical regulators. This issue can be addressed by establishing a multilayered hierarchical gene regulatory network (ML-hGRN) centered around a given TF. Read More

    Translational bioinformatics in mental health: open access data sources and computational biomarker discovery.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    Mental illness is increasingly recognized as both a significant cost to society and a significant area of opportunity for biological breakthrough. As -omics and imaging technologies enable researchers to probe molecular and physiological underpinnings of multiple diseases, opportunities arise to explore the biological basis for behavioral health and disease. From individual investigators to large international consortia, researchers have generated rich data sets in the area of mental health, including genomic, transcriptomic, metabolomic, proteomic, clinical and imaging resources. Read More

    Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
    Brief Bioinform 2017 Nov 27. Epub 2017 Nov 27.
    In the course of infecting their hosts, pathogenic bacteria secrete numerous effectors, namely, bacterial proteins that pervert host cell biology. Many Gram-negative bacteria, including context-dependent human pathogens, use a type IV secretion system (T4SS) to translocate effectors directly into the cytosol of host cells. Various type IV secreted effectors (T4SEs) have been experimentally validated to play crucial roles in virulence by manipulating host cell gene expression and other processes. Read More

    RNA methylation and diseases: experimental results, databases, Web servers and computational models.
    Brief Bioinform 2017 Nov 18. Epub 2017 Nov 18.
    Ribonucleic acid (RNA) methylation is a type of posttranscriptional modifications occurring in all kingdoms of life. It is strongly related to important biological process, thus making it linked to a number of human diseases. Owing to the development of high-throughput sequencing technology, plenty of achievement had been obtained in RNA methylation research recently. Read More

    A survey of software tools for microRNA discovery and characterization using RNA-seq.
    Brief Bioinform 2017 Nov 6. Epub 2017 Nov 6.
    Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in the most studied model organisms, and many researchers are using sRNA-seq in studies with different aims in biomedicine, fundamental research and in applied animal sciences. We review several miRNA discovery and characterization software tools that implement different strategies, providing a useful guide for researchers to select the programs best suiting their study objectives and data. Read More

    Privacy-preserving techniques of genomic data-a survey.
    Brief Bioinform 2017 Nov 7. Epub 2017 Nov 7.
    Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regarding the collection, storage and analysis of such sensitive human data. Read More

    Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma.
    Brief Bioinform 2017 Nov 3. Epub 2017 Nov 3.
    Motivation: One of the main challenges in machine learning (ML) is choosing an appropriate normalization method. Here, we examine the effect of various normalization methods on analyzing FPKM upper quartile (FPKM-UQ) RNA sequencing data sets. We collect the HTSeq-FPKM-UQ files of patients with colon adenocarcinoma from TCGA-COAD project. Read More

    Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems.
    Brief Bioinform 2017 Nov 3. Epub 2017 Nov 3.
    Owing to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets (ColPNs) have been successfully applied to multilevel, multiscale and multidimensional modelling of some biological systems, addressing many of these challenges. In this article, we first review the basics of ColPNs and some popular extensions, and then their applications for multilevel, multiscale and multidimensional modelling of biological systems. Read More

    Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.
    Brief Bioinform 2017 Nov 3. Epub 2017 Nov 3.
    Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. Read More

    Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.
    Brief Bioinform 2017 Nov 3. Epub 2017 Nov 3.
    Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. Read More

    Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.
    Brief Bioinform 2017 Jun 30. Epub 2017 Jun 30.
    EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia's capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. Read More

    A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia.
    Brief Bioinform 2017 Jul 3. Epub 2017 Jul 3.
    The growing number of modalities (e.g. multi-omics, imaging and clinical data) characterizing a given disease provides physicians and statisticians with complementary facets reflecting the disease process but emphasizes the need for novel statistical methods of data analysis able to unify these views. Read More

    CircView: a visualization and exploration tool for circular RNAs.
    Brief Bioinform 2017 Jun 30. Epub 2017 Jun 30.
    Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. Read More

    An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies.
    Brief Bioinform 2017 Nov 2. Epub 2017 Nov 2.
    Functionally annotating genetic variations is an essential yet challenging topic in human genetics research. As large consortia including ENCODE and Roadmap Epigenomics Project continue to generate high-throughput transcriptomic and epigenomic data, many computational frameworks have been developed to integrate these experimental data to predict functionality of genetic variations in both protein-coding and noncoding regions. Here, we compare a number of recently developed annotation frameworks for noncoding regions through enrichment analysis on genome-wide association studies (GWASs). Read More

    Bioinformatics on a national scale: an example from Switzerland.
    Brief Bioinform 2017 Jul 4. Epub 2017 Jul 4.
    Switzerland has been a pioneer in the field of bioinformatics since the early 1980s. As time passed, the need for one entity to gather and represent bioinformatics on a national scale was felt and, in 1998, the SIB Swiss Institute of Bioinformatics was created. Hence, 2018 marks the Institute's 20th anniversary. Read More

    A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.
    Brief Bioinform 2017 Oct 30. Epub 2017 Oct 30.
    Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Read More

    Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures.
    Brief Bioinform 2017 Oct 30. Epub 2017 Oct 30.
    How chromosomes fold and how distal genomic elements interact with one another at a genomic scale have been actively pursued in the past decade following the seminal work describing the Chromosome Conformation Capture (3C) assay. Essentially, 3C-based technologies produce two-dimensional (2D) contact maps that capture interactions between genomic fragments. Accordingly, a plethora of analytical methods have been proposed to take a 2D contact map as input to recapitulate the underlying whole genome three-dimensional (3D) structure of the chromatin. Read More

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