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  Subjects -> COMPUTER SCIENCE (Total: 1992 journals)
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    - COMPUTER SCIENCE (1159 journals)
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COMPUTER SCIENCE (1159 journals)                  1 2 3 4 5 6 | Last

Showing 1 - 200 of 872 Journals sorted alphabetically
3D Printing and Additive Manufacturing     Full-text available via subscription   (Followers: 13)
Abakós     Open Access   (Followers: 4)
ACM Computing Surveys     Hybrid Journal   (Followers: 23)
ACM Journal on Computing and Cultural Heritage     Hybrid Journal   (Followers: 9)
ACM Journal on Emerging Technologies in Computing Systems     Hybrid Journal   (Followers: 13)
ACM Transactions on Accessible Computing (TACCESS)     Hybrid Journal   (Followers: 3)
ACM Transactions on Algorithms (TALG)     Hybrid Journal   (Followers: 16)
ACM Transactions on Applied Perception (TAP)     Hybrid Journal   (Followers: 6)
ACM Transactions on Architecture and Code Optimization (TACO)     Hybrid Journal   (Followers: 9)
ACM Transactions on Autonomous and Adaptive Systems (TAAS)     Hybrid Journal   (Followers: 7)
ACM Transactions on Computation Theory (TOCT)     Hybrid Journal   (Followers: 12)
ACM Transactions on Computational Logic (TOCL)     Hybrid Journal   (Followers: 4)
ACM Transactions on Computer Systems (TOCS)     Hybrid Journal   (Followers: 18)
ACM Transactions on Computer-Human Interaction     Hybrid Journal   (Followers: 14)
ACM Transactions on Computing Education (TOCE)     Hybrid Journal   (Followers: 5)
ACM Transactions on Design Automation of Electronic Systems (TODAES)     Hybrid Journal   (Followers: 1)
ACM Transactions on Economics and Computation     Hybrid Journal  
ACM Transactions on Embedded Computing Systems (TECS)     Hybrid Journal   (Followers: 4)
ACM Transactions on Information Systems (TOIS)     Hybrid Journal   (Followers: 21)
ACM Transactions on Intelligent Systems and Technology (TIST)     Hybrid Journal   (Followers: 8)
ACM Transactions on Interactive Intelligent Systems (TiiS)     Hybrid Journal   (Followers: 3)
ACM Transactions on Multimedia Computing, Communications, and Applications (TOMCCAP)     Hybrid Journal   (Followers: 10)
ACM Transactions on Reconfigurable Technology and Systems (TRETS)     Hybrid Journal   (Followers: 7)
ACM Transactions on Sensor Networks (TOSN)     Hybrid Journal   (Followers: 9)
ACM Transactions on Speech and Language Processing (TSLP)     Hybrid Journal   (Followers: 11)
ACM Transactions on Storage     Hybrid Journal  
ACS Applied Materials & Interfaces     Full-text available via subscription   (Followers: 25)
Acta Automatica Sinica     Full-text available via subscription   (Followers: 3)
Acta Universitatis Cibiniensis. Technical Series     Open Access  
Ad Hoc Networks     Hybrid Journal   (Followers: 11)
Adaptive Behavior     Hybrid Journal   (Followers: 11)
Advanced Engineering Materials     Hybrid Journal   (Followers: 26)
Advanced Science Letters     Full-text available via subscription   (Followers: 9)
Advances in Adaptive Data Analysis     Hybrid Journal   (Followers: 8)
Advances in Artificial Intelligence     Open Access   (Followers: 16)
Advances in Calculus of Variations     Hybrid Journal   (Followers: 2)
Advances in Catalysis     Full-text available via subscription   (Followers: 5)
Advances in Computational Mathematics     Hybrid Journal   (Followers: 15)
Advances in Computer Science : an International Journal     Open Access   (Followers: 14)
Advances in Computing     Open Access   (Followers: 2)
Advances in Data Analysis and Classification     Hybrid Journal   (Followers: 51)
Advances in Engineering Software     Hybrid Journal   (Followers: 26)
Advances in Geosciences (ADGEO)     Open Access   (Followers: 10)
Advances in Human Factors/Ergonomics     Full-text available via subscription   (Followers: 26)
Advances in Human-Computer Interaction     Open Access   (Followers: 20)
Advances in Materials Sciences     Open Access   (Followers: 16)
Advances in Operations Research     Open Access   (Followers: 11)
Advances in Parallel Computing     Full-text available via subscription   (Followers: 7)
Advances in Porous Media     Full-text available via subscription   (Followers: 4)
Advances in Remote Sensing     Open Access   (Followers: 39)
Advances in Science and Research (ASR)     Open Access   (Followers: 6)
Advances in Technology Innovation     Open Access   (Followers: 2)
AEU - International Journal of Electronics and Communications     Hybrid Journal   (Followers: 8)
African Journal of Information and Communication     Open Access   (Followers: 8)
African Journal of Mathematics and Computer Science Research     Open Access   (Followers: 4)
Air, Soil & Water Research     Open Access   (Followers: 9)
AIS Transactions on Human-Computer Interaction     Open Access   (Followers: 6)
Algebras and Representation Theory     Hybrid Journal   (Followers: 1)
Algorithms     Open Access   (Followers: 11)
American Journal of Computational and Applied Mathematics     Open Access   (Followers: 4)
American Journal of Computational Mathematics     Open Access   (Followers: 4)
American Journal of Information Systems     Open Access   (Followers: 5)
American Journal of Sensor Technology     Open Access   (Followers: 4)
Anais da Academia Brasileira de Ciências     Open Access   (Followers: 2)
Analog Integrated Circuits and Signal Processing     Hybrid Journal   (Followers: 7)
Analysis in Theory and Applications     Hybrid Journal   (Followers: 1)
Animation Practice, Process & Production     Hybrid Journal   (Followers: 5)
Annals of Combinatorics     Hybrid Journal   (Followers: 3)
Annals of Data Science     Hybrid Journal   (Followers: 11)
Annals of Mathematics and Artificial Intelligence     Hybrid Journal   (Followers: 7)
Annals of Pure and Applied Logic     Open Access   (Followers: 2)
Annals of Software Engineering     Hybrid Journal   (Followers: 13)
Annual Reviews in Control     Hybrid Journal   (Followers: 6)
Anuario Americanista Europeo     Open Access  
Applicable Algebra in Engineering, Communication and Computing     Hybrid Journal   (Followers: 2)
Applied and Computational Harmonic Analysis     Full-text available via subscription   (Followers: 2)
Applied Artificial Intelligence: An International Journal     Hybrid Journal   (Followers: 14)
Applied Categorical Structures     Hybrid Journal   (Followers: 2)
Applied Clinical Informatics     Hybrid Journal   (Followers: 2)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 12)
Applied Computer Systems     Open Access   (Followers: 1)
Applied Informatics     Open Access  
Applied Mathematics and Computation     Hybrid Journal   (Followers: 33)
Applied Medical Informatics     Open Access   (Followers: 11)
Applied Numerical Mathematics     Hybrid Journal   (Followers: 5)
Applied Soft Computing     Hybrid Journal   (Followers: 16)
Applied Spatial Analysis and Policy     Hybrid Journal   (Followers: 4)
Architectural Theory Review     Hybrid Journal   (Followers: 3)
Archive of Applied Mechanics     Hybrid Journal   (Followers: 5)
Archive of Numerical Software     Open Access  
Archives and Museum Informatics     Hybrid Journal   (Followers: 134)
Archives of Computational Methods in Engineering     Hybrid Journal   (Followers: 4)
Artifact     Hybrid Journal   (Followers: 2)
Artificial Life     Hybrid Journal   (Followers: 7)
Asia Pacific Journal on Computational Engineering     Open Access  
Asia-Pacific Journal of Information Technology and Multimedia     Open Access   (Followers: 1)
Asian Journal of Computer Science and Information Technology     Open Access  
Asian Journal of Control     Hybrid Journal  
Assembly Automation     Hybrid Journal   (Followers: 2)
at - Automatisierungstechnik     Hybrid Journal   (Followers: 1)
Australian Educational Computing     Open Access   (Followers: 1)
Automatic Control and Computer Sciences     Hybrid Journal   (Followers: 4)
Automatic Documentation and Mathematical Linguistics     Hybrid Journal   (Followers: 5)
Automatica     Hybrid Journal   (Followers: 11)
Automation in Construction     Hybrid Journal   (Followers: 6)
Autonomous Mental Development, IEEE Transactions on     Hybrid Journal   (Followers: 8)
Basin Research     Hybrid Journal   (Followers: 5)
Behaviour & Information Technology     Hybrid Journal   (Followers: 52)
Biodiversity Information Science and Standards     Open Access  
Bioinformatics     Hybrid Journal   (Followers: 273)
Biomedical Engineering     Hybrid Journal   (Followers: 16)
Biomedical Engineering and Computational Biology     Open Access   (Followers: 14)
Biomedical Engineering, IEEE Reviews in     Full-text available via subscription   (Followers: 17)
Biomedical Engineering, IEEE Transactions on     Hybrid Journal   (Followers: 33)
Briefings in Bioinformatics     Hybrid Journal   (Followers: 45)
British Journal of Educational Technology     Hybrid Journal   (Followers: 127)
Broadcasting, IEEE Transactions on     Hybrid Journal   (Followers: 10)
c't Magazin fuer Computertechnik     Full-text available via subscription   (Followers: 2)
CALCOLO     Hybrid Journal  
Calphad     Hybrid Journal  
Canadian Journal of Electrical and Computer Engineering     Full-text available via subscription   (Followers: 14)
Capturing Intelligence     Full-text available via subscription  
Catalysis in Industry     Hybrid Journal   (Followers: 1)
CEAS Space Journal     Hybrid Journal   (Followers: 1)
Cell Communication and Signaling     Open Access   (Followers: 1)
Central European Journal of Computer Science     Hybrid Journal   (Followers: 5)
CERN IdeaSquare Journal of Experimental Innovation     Open Access  
Chaos, Solitons & Fractals     Hybrid Journal   (Followers: 3)
Chemometrics and Intelligent Laboratory Systems     Hybrid Journal   (Followers: 15)
ChemSusChem     Hybrid Journal   (Followers: 7)
China Communications     Full-text available via subscription   (Followers: 7)
Chinese Journal of Catalysis     Full-text available via subscription   (Followers: 2)
CIN Computers Informatics Nursing     Full-text available via subscription   (Followers: 12)
Circuits and Systems     Open Access   (Followers: 16)
Clean Air Journal     Full-text available via subscription   (Followers: 2)
CLEI Electronic Journal     Open Access  
Clin-Alert     Hybrid Journal   (Followers: 1)
Cluster Computing     Hybrid Journal   (Followers: 1)
Cognitive Computation     Hybrid Journal   (Followers: 4)
COMBINATORICA     Hybrid Journal  
Combustion Theory and Modelling     Hybrid Journal   (Followers: 13)
Communication Methods and Measures     Hybrid Journal   (Followers: 12)
Communication Theory     Hybrid Journal   (Followers: 20)
Communications Engineer     Hybrid Journal   (Followers: 1)
Communications in Algebra     Hybrid Journal   (Followers: 3)
Communications in Partial Differential Equations     Hybrid Journal   (Followers: 3)
Communications of the ACM     Full-text available via subscription   (Followers: 54)
Communications of the Association for Information Systems     Open Access   (Followers: 18)
COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering     Hybrid Journal   (Followers: 3)
Complex & Intelligent Systems     Open Access  
Complex Adaptive Systems Modeling     Open Access  
Complex Analysis and Operator Theory     Hybrid Journal   (Followers: 2)
Complexity     Hybrid Journal   (Followers: 6)
Complexus     Full-text available via subscription  
Composite Materials Series     Full-text available via subscription   (Followers: 9)
Computación y Sistemas     Open Access  
Computation     Open Access  
Computational and Applied Mathematics     Hybrid Journal   (Followers: 2)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2)
Computational and Mathematical Organization Theory     Hybrid Journal   (Followers: 2)
Computational and Structural Biotechnology Journal     Open Access   (Followers: 2)
Computational and Theoretical Chemistry     Hybrid Journal   (Followers: 9)
Computational Astrophysics and Cosmology     Open Access   (Followers: 1)
Computational Biology and Chemistry     Hybrid Journal   (Followers: 12)
Computational Chemistry     Open Access   (Followers: 2)
Computational Cognitive Science     Open Access   (Followers: 2)
Computational Complexity     Hybrid Journal   (Followers: 4)
Computational Condensed Matter     Open Access  
Computational Ecology and Software     Open Access   (Followers: 9)
Computational Economics     Hybrid Journal   (Followers: 9)
Computational Geosciences     Hybrid Journal   (Followers: 15)
Computational Linguistics     Open Access   (Followers: 23)
Computational Management Science     Hybrid Journal  
Computational Mathematics and Modeling     Hybrid Journal   (Followers: 8)
Computational Mechanics     Hybrid Journal   (Followers: 4)
Computational Methods and Function Theory     Hybrid Journal  
Computational Molecular Bioscience     Open Access   (Followers: 2)
Computational Optimization and Applications     Hybrid Journal   (Followers: 7)
Computational Particle Mechanics     Hybrid Journal   (Followers: 1)
Computational Research     Open Access   (Followers: 1)
Computational Science and Discovery     Full-text available via subscription   (Followers: 2)
Computational Science and Techniques     Open Access  
Computational Statistics     Hybrid Journal   (Followers: 13)
Computational Statistics & Data Analysis     Hybrid Journal   (Followers: 31)
Computer     Full-text available via subscription   (Followers: 87)
Computer Aided Surgery     Hybrid Journal   (Followers: 3)
Computer Applications in Engineering Education     Hybrid Journal   (Followers: 7)
Computer Communications     Hybrid Journal   (Followers: 10)
Computer Engineering and Applications Journal     Open Access   (Followers: 5)
Computer Journal     Hybrid Journal   (Followers: 8)
Computer Methods in Applied Mechanics and Engineering     Hybrid Journal   (Followers: 21)
Computer Methods in Biomechanics and Biomedical Engineering     Hybrid Journal   (Followers: 10)
Computer Methods in the Geosciences     Full-text available via subscription   (Followers: 1)
Computer Music Journal     Hybrid Journal   (Followers: 16)
Computer Physics Communications     Hybrid Journal   (Followers: 6)
Computer Science - Research and Development     Hybrid Journal   (Followers: 7)
Computer Science and Engineering     Open Access   (Followers: 17)
Computer Science and Information Technology     Open Access   (Followers: 12)
Computer Science Education     Hybrid Journal   (Followers: 13)
Computer Science Journal     Open Access   (Followers: 20)

        1 2 3 4 5 6 | Last

Journal Cover Briefings in Bioinformatics
  [SJR: 4.086]   [H-I: 73]   [45 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1467-5463 - ISSN (Online) 1477-4054
   Published by Oxford University Press Homepage  [370 journals]
  • Editorial
    • Authors: Martin B.
      Abstract: Briefings in Bioinformatics will move to online-only publication from January 2018. The last printed issue will be in November 2017. The editors and publishers of Briefings in Bioinformatics have taken this decision in the light of the extensive online usage of the journal and that fact that we are now supplying very few print subscribers with copies of the journal. Online-only journals are more environmentally friendly, eliminating the need for paper, shipping materials and transportation and thus significantly reducing the journal’s carbon footprint. Journal articles are available to you instantly on the day of publication, rather than you having to wait for printing and despatch to be completed.
      PubDate: 2017-10-24
       
  • Systematic bias of correlation coefficient may explain negative accuracy
           of genomic prediction
    • Authors: Zhou Y; Isabel Vales M, Wang A, et al.
      Abstract: Briefings in Bioinformatics 2017. https://doi.org/10.1093/bib/bbw064.
      PubDate: 2017-10-06
       
  • Next-generation sequencing data analysis
    • Authors: Christian T K.-H S.
      Abstract: Briefings in Bioinformatics 2017. doi: 10.1093/bib/bbx038
      PubDate: 2017-09-14
       
  • Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and
           expansion around genomes and protein structures
    • Authors: De Las Rivas J; Bonavides-Martínez C, Campos-Laborie F.
      Abstract: Briefings in Bioinformatics 2017. doi: 10.1093/bib/bbx064.
      PubDate: 2017-09-02
       
  • Critical evaluation of bioinformatics tools for the prediction of protein
           crystallization propensity
    • Authors: Wang H; Feng L, Webb G, et al.
      Abstract: Briefings in Bioinformatics 2017. doi: 10.1093/bib/bbx018.
      PubDate: 2017-06-22
       
  • The genetic architecture of heterochrony as a quantitative trait: lessons
           from a computational model
    • Authors: Sun L; Sang M, Zheng C, et al.
      Abstract: Briefings in Bioinformatics 2017. doi: 10.1093/bib/bbx056
      PubDate: 2017-06-22
       
  • What is the probability of replicating a statistically significant
           association in genome-wide association studies'
    • Authors: Jiang W; Xue J, Yu W.
      Abstract: The goal of genome-wide association studies (GWASs) is to discover genetic variants associated with diseases/traits. Replication is a common validation method in GWASs. We regard an association as true finding when it shows significance in both primary and replication studies. A question worth pondering is what is the probability of a primary association (i.e. a statistically significant association in the primary study) being validated in the replication study' This article systematically reviews the answers to this question from different points of view. As Bayesian methods can help us integrate out the uncertainty about the underlying effect of the primary association, we will mainly focus on the Bayesian view in this article. We refer the Bayesian replication probability as the replication rate (RR). We further describe an estimation method for RR, which makes use of the summary statistics from the primary study. We can use the estimated RR to determine the sample size of the replication study and to check the consistency between the results of the primary study and those of the replication study. We describe an R-package to estimate and apply RR in GWASs. Simulation and real data experiments show that the estimated RR has good prediction and calibration performance. We also use these data to demonstrate the usefulness of RR. The R-package is available at http://bioinformatics.ust.hk/RRate.html.
      PubDate: 2016-09-28
       
  • Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq
           bioinformatics pipeline
    • Authors: Smith D; Sanitá Lima M.
      Abstract: Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains massive amounts of organelle RNA-Seq data that are just waiting to be downloaded and analyzed. Recently, a team of scientists designed an open-source bioinformatics program called ChloroSeq, which systemically analyzes an organelle transcriptome using RNA-Seq. The ChloroSeq pipeline uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for further analysis and for generating graphical representations of the data. In addition to providing data on expression levels via coverage statistics, ChloroSeq can examine splicing efficiency and RNA editing profiles. Ultimately, ChloroSeq provides a well-needed avenue for researchers of all stripes to start exploring organelle transcription and could be a key step toward a more thorough understanding of organelle gene expression.
      PubDate: 2016-09-26
       
  • A novel computational method for inferring competing endogenous
           interactions
    • Authors: Sardina D; Alaimo S, Ferro A, et al.
      Abstract: Posttranscriptional cross talk and communication between genes mediated by microRNA response element (MREs) yield large regulatory competing endogenous RNA (ceRNA) networks. Their inference may improve the understanding of pathologies and shed new light on biological mechanisms. A variety of RNA: messenger RNA, transcribed pseudogenes, noncoding RNA, circular RNA and proteins related to RNA-induced silencing complex complex interacting with RNA transfer and ribosomal RNA have been experimentally proved to be ceRNAs. We retrace the ceRNA hypothesis of posttranscriptional regulation from its original formulation [Salmena L, Poliseno L, Tay Y, et al. Cell 2011;146:353–8] to the most recent experimental and computational validations. We experimentally analyze the methods in literature [Li J-H, Liu S, Zhou H, et al. Nucleic Acids Res 2013;42:D92–7; Sumazin P, Yang X, Chiu H-S, et al. Cell 2011;147:370–81; Sarver AL, Subramanian S. Bioinformation 2012;8:731–3] comparing them with a general machine learning approach, called ceRNA predIction Algorithm, evaluating the performance in predicting novel MRE-based ceRNAs.
      PubDate: 2016-09-26
       
  • Rare variant association test in family-based sequencing studies
    • Authors: Wang X; Zhang Z, Morris N, et al.
      Abstract: The objective of this article is to introduce valid and robust methods for the analysis of rare variants for family-based exome chips, whole-exome sequencing or whole-genome sequencing data. Family-based designs provide unique opportunities to detect genetic variants that complement studies of unrelated individuals. Currently, limited methods and software tools have been developed to assist family-based association studies with rare variants, especially for analyzing binary traits. In this article, we address this gap by extending existing burden and kernel-based gene set association tests for population data to related samples, with a particular emphasis on binary phenotypes. The proposed approach blends the strengths of kernel machine methods and generalized estimating equations. Importantly, the efficient generalized kernel score test can be applied as a mega-analysis framework to combine studies with different designs. We illustrate the application of the proposed method using data from an exome sequencing study of autism. Methods discussed in this article are implemented in an R package ‘gskat’, which is available on CRAN and GitHub.
      PubDate: 2016-09-26
       
  • AlloMap6: an R package for genetic linkage analysis in allohexaploids
    • Authors: Zhu X; Li H, Ye M, et al.
      Abstract: Allopolyploids are a group of polyploids with more than two sets of chromosomes derived from different species. Previous linkage analysis of allopolyploids is based on the assumption that different chromosomes pair randomly during meiosis. A more sophisticated model to relax this assumption has been developed for allotetraploids by incorporating the preferential pairing behavior of homologous over homoeologous chromosomes. Here, we show that the basic principle of this model can be extended to perform linkage analysis of higher-ploidy allohexaploids, where multiple preferential pairing factors are used to characterize chromosomal-pairing meiotic features between different constituent species. We implemented the extended model into an R package, called AlloMap6, allowing the recombination fractions and preferential pairing factors to be estimated simultaneously. Allomap6 has two major functionalities, computer simulation and real-data analysis. By analyzing a real data from a full-sib family of allohexaploid persimmon, we tested and validated the usefulness and utility of this package. AlloMap6 lays a foundation for allohexaploid genetic mapping and provides a new horizon to explore the chromosomal kinship of allohexaploids.
      PubDate: 2016-09-17
       
  • RNAEditor: easy detection of RNA editing events and the introduction of
           editing islands
    • Authors: John D; Weirick T, Dimmeler S, et al.
      Abstract: RNA editing of adenosine residues to inosine (‘A-to-I editing’) is the most common RNA modification event detectible with RNA sequencing (RNA-seq). While not directly detectable, inosine is read by next-generation sequencers as guanine. Therefore, mapping RNA-seq reads to their corresponding reference genome can detect potential editing events by identifying ‘A-to-G’ conversions. However, one must exercise caution when searching for editing sites, as A-to-G conversions also arise from sequencing errors as well as mutations. To address these complexities, several algorithms and software products have been developed to accurately identify editing events. Here, we survey currently available methods to analyze RNA editing events and introduce a new easy-to-use bioinformatics tool ‘RNAEditor’ for the detection of RNA editing events. During the development of RNAEditor, we noticed editing often happened in clusters, which we named ‘editing islands’. We developed a clustering algorithm to find editing islands and included it in RNAEditor. RNAEditor is freely available at http://rnaeditor.uni-frankfurt.de. We anticipate that RNAEditor will provide biologists with an easy-to-use tool for studying RNA editing events and the newly defined editing islands.
      PubDate: 2016-09-17
       
  • Exploring and visualizing multidimensional data in translational research
           platforms
    • Authors: Dunn W; Jr, Burgun A, Krebs M, et al.
      Abstract: The unprecedented advances in technology and scientific research over the past few years have provided the scientific community with new and more complex forms of data. Large data sets collected from single groups or cross-institution consortiums containing hundreds of omic and clinical variables corresponding to thousands of patients are becoming increasingly commonplace in the research setting. Before any core analyses are performed, visualization often plays a key role in the initial phases of research, especially for projects where no initial hypotheses are dominant. Proper visualization of data at a high level facilitates researcher’s abilities to find trends, identify outliers and perform quality checks. In addition, research has uncovered the important role of visualization in data analysis and its implied benefits facilitating our understanding of disease and ultimately improving patient care. In this work, we present a review of the current landscape of existing tools designed to facilitate the visualization of multidimensional data in translational research platforms. Specifically, we reviewed the biomedical literature for translational platforms allowing the visualization and exploration of clinical and omics data, and identified 11 platforms: cBioPortal, interactive genomics patient stratification explorer, Igloo-Plot, The Georgetown Database of Cancer Plus, tranSMART, an unnamed data-cube-based model supporting heterogeneous data, Papilio, Caleydo Domino, Qlucore Omics, Oracle Health Sciences Translational Research Center and OmicsOffice® powered by TIBCO Spotfire. In a health sector continuously witnessing an increase in data from multifarious sources, visualization tools used to better grasp these data will grow in their importance, and we believe our work will be useful in guiding investigators in similar situations.
      PubDate: 2016-09-01
       
  • Opportunities for community awareness platforms in personal genomics and
           bioinformatics education
    • Authors: Bianchi L; Liò P.
      Abstract: Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analysis. Being on the Internet poses constant threats to security and privacy. While we are connected and we share information, websites and internet services collect various types of personal data with or without the user consent. It is likely that genomics will merge with the internet culture of connectivity. This process will increase incidental findings, exposure and vulnerability. Here we discuss the social vulnerability owing to the genome and Internet combined security and privacy weaknesses. This urges more efforts in education and social awareness on how biomedical data are analysed and transferred through the internet and how inferential methods could integrate information from different sources. We propose that digital social platforms, used for raising collective awareness in different fields, could be developed for collaborative and bottom-up efforts in education. In this context, bioinformaticians could play a meaningful role in mitigating the future risk of digital-genomic divide.
      PubDate: 2016-08-30
       
  • Protein side-chain packing problem: is there still room for
           improvement'
    • Authors: Colbes J; Corona R, Lezcano C, et al.
      Abstract: The protein side-chain packing problem (PSCPP) is an important subproblem of both protein structure prediction and protein design. During the past two decades, a large number of methods have been proposed to tackle this problem. These methods consist of three main components: a rotamer library, a scoring function and a search strategy. The average overall accuracy level obtained by these methods is approximately 87%. Whether a better accuracy level could be achieved remains to be answered. To address this question, we calculated the maximum accuracy level attainable using a simple rotamer library, independently of the energy function or the search method. Using 2883 different structures from the Protein Data Bank, we compared this accuracy level with the accuracy level of five state-of-the-art methods. These comparisons indicated that, for buried residues in the protein, we are already close to the best possible accuracy results. In addition, for exposed residues, we found that a significant gap exists between the possible improvement and the maximum accuracy level achievable with current methods. After determining that an improvement is possible, the next step is to understand what limitations are preventing us from obtaining such an improvement. Previous works on protein structure prediction and protein design have shown that scoring function inaccuracies may represent the main obstacle to achieving better results for these problems. To show that the same is true for the PSCPP, we evaluated the quality of two scoring functions used by some state-of-the-art algorithms. Our results indicate that neither of these scoring functions can guide the search method correctly, thereby reinforcing the idea that efforts to solve the PSCPP must also focus on developing better scoring functions.
      PubDate: 2016-08-26
       
  • Recent advances in sequence-based protein structure prediction
    • Authors: KC D.
      Abstract: The most accurate characterizations of the structure of proteins are provided by structural biology experiments. However, because of the high cost and labor-intensive nature of the structural experiments, the gap between the number of protein sequences and solved structures is widening rapidly. Development of computational methods to accurately model protein structures from sequences is becoming increasingly important to the biological community. In this article, we highlight some important progress in the field of protein structure prediction, especially those related to free modeling (FM) methods that generate structure models without using homologous templates. We also provide a short synopsis of some of the recent advances in FM approaches as demonstrated in the recent Computational Assessment of Structure Prediction competition as well as recent trends and outlook for FM approaches in protein structure prediction.
      PubDate: 2016-08-25
       
  • Characterization of MinION nanopore data for resequencing analyses
    • Authors: Magi A; Giusti B, Tattini L.
      Abstract: The Oxford Nanopore Technologies MinION is a new device, based on nanopore sequencing that is able to generate reads of tens of kilobases in length with faster sequencing time with respect to other platforms. To evaluate the capability of nanopore data to be exploited for resequencing analyses we used the largest MinION data set to date and we compared with Illumina and Pacific Biosciences technologies. By using five different mapping approaches we estimated that the global sequencing error rate of MinION reads, mainly caused by inserted and deleted bases, is around 11%. The study of error distribution showed that substituted, inserted and deleted bases are not randomly distributed along the reads, but mainly occur in specific nucleotide patterns, generating a significant number of genomic loci that can be misclassified as false-positive variants. With 40× sequencing coverage, MinION data can produce at best around one false substitution and insertion every 10–50 kb, and one false deletion every 1000 bp, making use of this technology still challenging for small-sized variant discovery. We also analyzed depth of coverage distribution and we demonstrated that nanopore sequencing is a uniform process that generates sequences randomly and independently without classical sources of bias such as GC-content and mappability. Owing to these properties, the MinION data can be readily used to detect genomic regions involved in copy number variants with high accuracy, outperforming other state-of-the-art sequencing methods in terms of both sensitivity and specificity.
      PubDate: 2016-08-24
       
  • miRNA–miRNA crosstalk: from genomics to phenomics
    • Authors: Xu J; Shao T, Ding N, et al.
      Abstract: The discovery of microRNA (miRNA)–miRNA crosstalk has greatly improved our understanding of complex gene regulatory networks in normal and disease-specific physiological conditions. Numerous approaches have been proposed for modeling miRNA–miRNA networks based on genomic sequences, miRNA–mRNA regulation, functional information and phenomics alone, or by integrating heterogeneous data. In addition, it is expected that miRNA–miRNA crosstalk can be reprogrammed in different tissues or specific diseases. Thus, transcriptome data have also been integrated to construct context-specific miRNA–miRNA networks. In this review, we summarize the state-of-the-art miRNA–miRNA network modeling methods, which range from genomics to phenomics, where we focus on the need to integrate heterogeneous types of omics data. Finally, we suggest future directions for studies of crosstalk of noncoding RNAs. This comprehensive summarization and discussion elucidated in this work provide constructive insights into miRNA–miRNA crosstalk.
      PubDate: 2016-08-20
       
  • Robust logistic regression to narrow down the winner’s curse for rare
           and recessive susceptibility variants
    • Authors: Kesselmeier M; Lorenzo Bermejo J.
      Abstract: Logistic regression is the most common technique used for genetic case-control association studies. A disadvantage of standard maximum likelihood estimators of the genotype relative risk (GRR) is their strong dependence on outlier subjects, for example, patients diagnosed at unusually young age. Robust methods are available to constrain outlier influence, but they are scarcely used in genetic studies. This article provides a non-intimidating introduction to robust logistic regression, and investigates its benefits and limitations in genetic association studies. We applied the bounded Huber and extended the R package ‘robustbase’ with the re-descending Hampel functions to down-weight outlier influence. Computer simulations were carried out to assess the type I error rate, mean squared error (MSE) and statistical power according to major characteristics of the genetic study and investigated markers. Simulations were complemented with the analysis of real data. Both standard and robust estimation controlled type I error rates. Standard logistic regression showed the highest power but standard GRR estimates also showed the largest bias and MSE, in particular for associated rare and recessive variants. For illustration, a recessive variant with a true GRR=6.32 and a minor allele frequency=0.05 investigated in a 1000 case/1000 control study by standard logistic regression resulted in power=0.60 and MSE=16.5. The corresponding figures for Huber-based estimation were power=0.51 and MSE=0.53. Overall, Hampel- and Huber-based GRR estimates did not differ much. Robust logistic regression may represent a valuable alternative to standard maximum likelihood estimation when the focus lies on risk prediction rather than identification of susceptibility variants.
      PubDate: 2016-08-20
       
  • Comprehensive characterization of tissue-specific circular RNAs in the
           human and mouse genomes
    • Authors: Xia S; Feng J, Lei L, et al.
      Abstract: Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and mouse tissue-specific (TS) circRNAs. We identified in total 302 853 TS circRNAs in the human and mouse genome, and showed that the brain has the highest abundance of TS circRNAs. We further confirmed the existence of circRNAs by reverse transcription polymerase chain reaction (RT-PCR). We also characterized the genomic location and conservation of these TS circRNAs and showed that the majority of TS circRNAs are generated from exonic regions. To further understand the potential functions of TS circRNAs, we identified microRNAs and RNA binding protein, which might bind to TS circRNAs. This process suggested their involvement in development and organ differentiation. Finally, we constructed an integrated database TSCD (Tissue-Specific CircRNA Database: http://gb.whu.edu.cn/TSCD) to deposit the features of TS circRNAs. This study is the first comprehensive view of TS circRNAs in human and mouse, which shed light on circRNA functions in organ development and disorders.
      PubDate: 2016-08-20
       
  • Recording negative results of protein–protein interaction assays: an
           easy way to deal with the biases and errors of interactomic data sets
    • Authors: Alvarez-Ponce D.
      Abstract: In recent years, it has become increasingly common to use assays that can test whether two proteins interact, such as yeast two-hybrid and tandem affinity purification followed by mass spectrometry. Such techniques, particularly when applied at a large scale, suffer from high rates of false positives and false negatives. In addition, interactomic data sets are subjected to a number of biases, which limits considerably their usefulness to address biological questions. Interactomic databases only keep track of the positive results of protein interaction assays (those indicating that the tested proteins interact). Despite their importance, negative results (those indicating that the tested proteins do not interact) are not recorded in interactomic databases. Indeed, current interactomic databases do not support negative results. Here, I argue that systematically recording not only positive but also negative results of protein interaction assays would help scientists identify errors and deal with biases, thus enormously increasing the value of interactomic data sets. The challenges of implementing this change, along with potential solutions, are discussed.
      PubDate: 2016-08-18
       
  • A protein network descriptor server and its use in studying protein,
           disease, metabolic and drug targeted networks
    • Authors: Zhang P; Tao L, Zeng X, et al.
      Abstract: The genetic, proteomic, disease and pharmacological studies have generated rich data in protein interaction, disease regulation and drug activities useful for systems-level study of the biological, disease and drug therapeutic processes. These studies are facilitated by the established and the emerging computational methods. More recently, the network descriptors developed in other disciplines have become more increasingly used for studying the protein–protein, gene regulation, metabolic, disease networks. There is an inadequate coverage of these useful network features in the public web servers. We therefore introduced upto 313 literature-reported network descriptors in PROFEAT web server, for describing the topological, connectivity and complexity characteristics of undirected unweighted (uniform binding constants and molecular levels), undirected edge-weighted (varying binding constants), undirected node-weighted (varying molecular levels), undirected edge-node-weighted (varying binding constants and molecular levels) and directed unweighted (oriented process) networks. The usefulness of the PROFEAT computed network descriptors is illustrated by their literature-reported applications in studying the protein–protein, gene regulatory, gene co-expression, protein–drug and metabolic networks. PROFEAT is accessible free of charge at http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi.
      PubDate: 2016-08-18
       
  • Benchmarking computational tools for polymorphic transposable element
           detection
    • Authors: Rishishwar L; Mariño-Ramírez L, Jordan I.
      Abstract: Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become increasingly important as the pace of human genome sequencing accelerates. For this report, we performed a comparative benchmarking and validation analysis of polyTE detection tools in an effort to inform their selection and use by the TE research community. We analyzed a core set of seven tools with respect to ease of use and accessibility, polyTE detection performance and runtime parameters. An experimentally validated set of 893 human polyTE insertions was used for this purpose, along with a series of simulated data sets that allowed us to assess the impact of sequence coverage on tool performance. The recently developed tool MELT showed the best overall performance followed by Mobster and then RetroSeq. PolyTE detection tools can best detect Alu insertion events in the human genome with reduced reliability for L1 insertions and substantially lowered performance for SVA insertions. We also show evidence that different polyTE detection tools are complementary with respect to their ability to detect a complete set of insertion events. Accordingly, a combined approach, coupled with manual inspection of individual results, may yield the best overall performance. In addition to the benchmarking results, we also provide notes on tool installation and usage as well as suggestions for future polyTE detection algorithm development.
      PubDate: 2016-08-12
       
  • Indel detection from RNA-seq data: tool evaluation and strategies for
           accurate detection of actionable mutations
    • Authors: Sun Z; Bhagwate A, Prodduturi N, et al.
      Abstract: Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Although single-nucleotide variants (SNVs) can be easily identified from RNA-seq, intermediate long insertions/deletions (indels  > 2 bases and less than sequence reads) cause significant challenges and are ignored by most RNA-seq analysis tools. This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known indels. The aim is to develop strategies for accurate indel detection. Our results show that the RNA-seq alignment is the most important step for indel identification and the evaluated programs have a wide range of sensitivity to map sequence reads with indels, from not at all to decently sensitive. The sensitivity is impacted by sequence read lengths. Most variant calling programs rely on hard evidence indels marked in the alignment and the programs with realignment may use soft-clipped reads for indel inferencing. Based on the observations, we have provided practical recommendations for indel detection when different RNA-seq aligners are used and demonstrated the best option with highly reliable results. With careful customization of bioinformatics algorithms, RNA-seq can be reliably used for both SNV and indel mutation detection that can be used for clinical decision-making.
      PubDate: 2016-07-26
       
 
 
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