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    1250 results match your criteria Briefings in bioinformatics[Journal]

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    Accounting for differential variability in detecting differentially methylated regions.
    Brief Bioinform 2017 Aug 18. Epub 2017 Aug 18.
    Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA.
    DNA methylation plays an essential role in cancer. Differential variability (DV) in cancer was recently observed that contributes to cancer heterogeneity and has been shown to be crucial in detecting epigenetic field defects, DNA methylation alterations happening early in carcinogenesis. As neighboring CpG sites are highly correlated, here, we present a new method to detect differentially methylated regions (DMRs) that uses combined signals from differential methylation and DV between sample groups. Read More

    Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity.
    Brief Bioinform 2018 Jun 11. Epub 2018 Jun 11.
    Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057 Rostock, Germany.
    Motivation: Structural connectomics supports understanding aspects of neuronal dynamics and brain functions. Conducting metastudies of tract-tracing publications is one option to generate connectome databases by collating neuronal connectivity data. Meanwhile, it is a common practice that the neuronal connections and their attributes of such retrospective data collations are extracted from tract-tracing publications manually by experts. Read More

    Robust genetic interaction analysis.
    Brief Bioinform 2018 Apr 19. Epub 2018 Apr 19.
    Mengyun Wu and Shuangge Ma, School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China and Yale School of Public Health, New Haven, CT 06520, USA.
    For the risk, progression, and response to treatment of many complex diseases, it has been increasingly recognized that genetic interactions (including gene-gene and gene-environment interactions) play important roles beyond the main genetic and environmental effects. In practical genetic interaction analyses, model mis-specification and outliers/contaminations in response variables and covariates are not uncommon, and demand robust analysis methods. Compared with their nonrobust counterparts, robust genetic interaction analysis methods are significantly less popular but are gaining attention fast. Read More

    iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
    Brief Bioinform 2018 Apr 19. Epub 2018 Apr 19.
    Gordon Life Science Institute, Boston, MA 02478, USA and Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
    Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the accurate prediction of protease-specific substrates and their cleavage sites. Read More

    Regulatory variants: from detection to predicting impact.
    Brief Bioinform 2018 Jun 8. Epub 2018 Jun 8.
    Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain.
    Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Read More

    Microbial genomic island discovery, visualization and analysis.
    Brief Bioinform 2018 Jun 3. Epub 2018 Jun 3.
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
    Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Read More

    In silico clinical trials: concepts and early adoptions.
    Brief Bioinform 2018 Jun 2. Epub 2018 Jun 2.
    Department of Mechanical Engineering, University of Sheffield, Sheffield, UK and INSIGNEO Institute for In Silico Medicine, University of Sheffield, Sheffield, UK.
    Innovations in information and communication technology infuse all branches of science, including life sciences. Nevertheless, healthcare is historically slow in adopting technological innovation, compared with other industrial sectors. In recent years, new approaches in modelling and simulation have started to provide important insights in biomedicine, opening the way for their potential use in the reduction, refinement and partial substitution of both animal and human experimentation. Read More

    A comparison of mechanistic signaling pathway activity analysis methods.
    Brief Bioinform 2018 Jun 3. Epub 2018 Jun 3.
    Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla 41013, Spain.
    Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human traits, whereas conventional pathway enrichment approaches produce only illustrative results of limited practical utility. Recently, a family of new methods has emerged that change the focus from the whole pathways to the definition of elementary subpathways within them that have any mechanistic significance and to the study of their activities. Read More

    Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.
    Brief Bioinform 2018 May 31. Epub 2018 May 31.
    As one of the few irreversible protein posttranslational modifications, proteolytic cleavage is involved in nearly all aspects of cellular activities, ranging from gene regulation to cell life-cycle regulation. Among the various protease-specific types of proteolytic cleavage, cleavages by casapses/granzyme B are considered as essential in the initiation and execution of programmed cell death and inflammation processes. Although a number of substrates for both types of proteolytic cleavage have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remains to be fully characterized. Read More

    Predicting novel microRNA: a comprehensive comparison of machine learning approaches.
    Brief Bioinform 2018 May 23. Epub 2018 May 23.
    sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina.
    Motivation: The importance of microRNAs (miRNAs) is widely recognized in the community nowadays because these short segments of RNA can play several roles in almost all biological processes. The computational prediction of novel miRNAs involves training a classifier for identifying sequences having the highest chance of being precursors of miRNAs (pre-miRNAs). The big issue with this task is that well-known pre-miRNAs are usually few in comparison with the hundreds of thousands of candidate sequences in a genome, which results in high class imbalance. Read More

    Survey of miRNA-miRNA cooperative regulation principles across cancer types.
    Brief Bioinform 2018 May 25. Epub 2018 May 25.
    College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China.
    Cooperative regulation among multiple microRNAs (miRNAs) is a complex type of posttranscriptional regulation in human; however, the global view of the system-level regulatory principles across cancers is still unclear. Here, we investigated miRNA-miRNA cooperative regulatory landscape across 18 cancer types and summarized the regulatory principles of miRNAs. The miRNA-miRNA cooperative pan-cancer network exhibited a scale-free and modular architecture. Read More

    Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications.
    Brief Bioinform 2018 May 17. Epub 2018 May 17.
    Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China.
    Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the utilization of current computational resources, we first provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. Read More

    Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer.
    Brief Bioinform 2018 May 2. Epub 2018 May 2.
    Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
    With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study. Read More

    Application of Atlas of Cancer Signalling Network in preclinical studies.
    Brief Bioinform 2018 May 3. Epub 2018 May 3.
    Institut Curie, PSL Research University, F-75005 Paris, France, INSERM, U900, F-75005 Paris, France and MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France.
    Cancer initiation and progression are associated with multiple molecular mechanisms. The knowledge of these mechanisms is expanding and should be converted into guidelines for tackling the disease. Here, we discuss the formalization of biological knowledge into a comprehensive resource: the Atlas of Cancer Signalling Network (ACSN) and the Google Maps-based tool NaviCell, which supports map navigation. Read More

    Post genome-wide association analysis: dissecting computational pathway/network-based approaches.
    Brief Bioinform 2018 Apr 26. Epub 2018 Apr 26.
    Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, 7700, Cape Town, South Africa; African Institute for Mathematical Sciences, 7945 Muizenberg, Cape Town, South Africa and Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Anzio Road, Observatory, 7925, Cape Town, South Africa.
    Over thousands of genetic associations to diseases have been identified by genome-wide association studies (GWASs), which conceptually is a single-marker-based approach. There are potentially many uses of these identified variants, including a better understanding of the pathogenesis of diseases, new leads for studying underlying risk prediction and clinical prediction of treatment. However, because of inadequate power, GWAS might miss disease genes and/or pathways with weak genetic or strong epistatic effects. Read More

    Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.
    Brief Bioinform 2018 Apr 24. Epub 2018 Apr 24.
    Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow 117312, Russian Federation.
    The genomes of mammalian species are pervasively transcribed producing as many noncoding as protein-coding RNAs. There is a growing body of evidence supporting their functional role. Long noncoding RNA (lncRNA) can bind both nucleic acids and proteins through several mechanisms. Read More

    Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants.
    Brief Bioinform 2018 Apr 24. Epub 2018 Apr 24.
    Department of Computer Science, Bioinformatics Graduate Program (PPGBIOINFO), Federal University of Technology - Paraná, UTFPR, Campus Cornélio, Procópio, Brazil.
    Motivation: Long noncoding RNAs (lncRNAs) correspond to a eukaryotic noncoding RNA class that gained great attention in the past years as a higher layer of regulation for gene expression in cells. There is, however, a lack of specific computational approaches to reliably predict lncRNA in plants, which contrast the variety of prediction tools available for mammalian lncRNAs. This distinction is not that obvious, given that biological features and mechanisms generating lncRNAs in the cell are likely different between animals and plants. Read More

    Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data.
    Brief Bioinform 2018 Apr 23. Epub 2018 Apr 23.
    Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria. Tel.:+43 316 873 5343; E-mail:
    Integrative analysis aims to identify the driving factors of a biological process by the joint exploration of data from multiple cellular levels. The volume of omics data produced is constantly increasing, and so too does the collection of tools for its analysis. Comparative studies assessing performance and the biological value of results, however, are rare but in great demand. Read More

    Community-driven roadmap for integrated disease maps.
    Brief Bioinform 2018 Apr 23. Epub 2018 Apr 23.
    Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
    The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. Read More

    Navigating the disease landscape: knowledge representations for contextualizing molecular signatures.
    Brief Bioinform 2018 Apr 19. Epub 2018 Apr 19.
    Charles Auffray European Institute for Systems Biology and Medicine, Lyon, France.
    Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes. The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous types of data. In this review, we discuss knowledge representations that can be useful to explore the biological context of molecular signatures, in particular three main approaches, namely, pathway mapping approaches, molecular network centric approaches and approaches that represent biological statements as knowledge graphs. Read More

    Disease prediction by cell-free DNA methylation.
    Brief Bioinform 2018 Apr 16. Epub 2018 Apr 16.
    Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA.
    Disease diagnosis using cell-free DNA (cfDNA) has been an active research field recently. Most existing approaches perform diagnosis based on the detection of sequence variants on cfDNA; thus, their applications are limited to diseases associated with high mutation rate such as cancer. Recent developments start to exploit the epigenetic information on cfDNA, which could have substantially wider applications. Read More

    Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer's disease.
    Brief Bioinform 2018 Apr 17. Epub 2018 Apr 17.
    School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China.
    Increasing evidence has revealed the multiple roles of long noncoding RNAs (lncRNAs) in neurodevelopment, brain function and aging, and their dysregulation was implicated in many types of neurological diseases. However, expression pattern and diagnostic role of lncRNAs in Alzheimer's disease (AD) remain largely unknown and has gained significant attention. In this study, we performed a comparative analysis for lncRNA expression profiles in four brain regions in brain aging and AD. Read More

    Progress in single-access information systems for wheat and rice crop improvement.
    Brief Bioinform 2018 Apr 5. Epub 2018 Apr 5.
    School of Biological Sciences and Institute of Agriculture, University of Western Australia, 6009 Perth, WA, Australia.
    Improving productivity of the staple crops wheat and rice is essential to feed the growing global population, particularly in the context of a changing climate. However, current rates of yield gain are insufficient to support the predicted population growth. New approaches are required to accelerate the breeding process, and many of these are driven by the application of large-scale crop data. Read More

    Molecular subtyping of cancer: current status and moving toward clinical applications.
    Brief Bioinform 2018 Apr 12. Epub 2018 Apr 12.
    Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Academic Medical Center, Amsterdam, The Netherlands.
    Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Read More

    A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data.
    Brief Bioinform 2018 Mar 29. Epub 2018 Mar 29.
    Beijing Institute of Radiation Medicine, Beijing 100850, China.
    The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and discover major cancer-causing genomic alterations with the goal of creating a comprehensive 'atlas' of cancer genomic profiles. The availability of this genome-wide information provides an unprecedented opportunity to expand our knowledge of tumourigenesis. Computational analytics and mining are frequently used as effective tools for exploring this byzantine series of biological and biomedical data. Read More

    Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.
    Brief Bioinform 2018 Apr 2. Epub 2018 Apr 2.
    Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Read More

    Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes.
    Brief Bioinform 2018 Mar 27. Epub 2018 Mar 27.
    College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
    We present here an integrated analysis of structures and functions of genome-scale metabolic networks of 17 microorganisms. Our structural analyses of these networks revealed that the node degree of each network, represented as a (simplified) reaction network, follows a power-law distribution, and the clustering coefficient of each network has a positive correlation with the corresponding node degree. Together, these properties imply that each network has exactly one large and densely connected subnetwork or core. Read More

    Interactive and coordinated visualization approaches for biological data analysis.
    Brief Bioinform 2018 Mar 26. Epub 2018 Mar 26.
    Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Departamento de Engenharia Informática.
    The field of computational biology has become largely dependent on data visualization tools to analyze the increasing quantities of data gathered through the use of new and growing technologies. Aside from the volume, which often results in large amounts of noise and complex relationships with no clear structure, the visualization of biological data sets is hindered by their heterogeneity, as data are obtained from different sources and contain a wide variety of attributes, including spatial and temporal information. This requires visualization approaches that are able to not only represent various data structures simultaneously but also provide exploratory methods that allow the identification of meaningful relationships that would not be perceptible through data analysis algorithms alone. Read More

    Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor.
    Brief Bioinform 2018 Mar 20. Epub 2018 Mar 20.
    Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
    Testicular germ cell tumors (TGCTs) are classified into two main subtypes, seminoma (SE) and non-seminoma (NSE), but their molecular distinctions remain largely unexplored. Here, we used expression data for mRNAs and microRNAs (miRNAs) from The Cancer Genome Atlas (TCGA) to perform a systematic investigation to explain the different telomere length (TL) features between NSE (n = 48) and SE (n = 55). We found that TL elongation was dominant in NSE, whereas TL shortening prevailed in SE. Read More

    Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network.
    Brief Bioinform 2018 Mar 20. Epub 2018 Mar 20.
    Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang 550004, China.
    Helicobacter pylori (H. pylori) infection remains a cause of significant morbidity and mortality worldwide. Comprehensive understanding of the pathogenic mechanism of H. Read More

    Where to search top-K biomedical ontologies?
    Brief Bioinform 2018 Mar 20. Epub 2018 Mar 20.
    Insight Centre for Data Analytics, NUI Galway, Ireland.
    Motivation: Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. Read More

    It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.
    Brief Bioinform 2018 Feb 27. Epub 2018 Feb 27.
    Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. Read More

    Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.
    Brief Bioinform 2018 Feb 21. Epub 2018 Feb 21.
    Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. Read More

    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

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