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    8141 results match your criteria BMC Bioinformatics [Journal]

    1 OF 163

    Brain medical image diagnosis based on corners with importance-values.
    BMC Bioinformatics 2017 Nov 21;18(1):505. Epub 2017 Nov 21.
    Research center for intelligent information processing, College of Computer Science and Technology, Harbin Engineering University, Harbin, 150001, China.
    Background: Brain disorders are one of the top causes of human death. Generally, neurologists analyze brain medical images for diagnosis. In the image analysis field, corners are one of the most important features, which makes corner detection and matching studies essential. Read More

    Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling.
    BMC Bioinformatics 2017 Nov 21;18(1):506. Epub 2017 Nov 21.
    Department of Computer Architecture and Technology, University of Granada, Periodista Rafael Gómez Montero, 2, Granada, 18014, Spain.
    Background: Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data. Read More

    Swellix: a computational tool to explore RNA conformational space.
    BMC Bioinformatics 2017 Nov 21;18(1):504. Epub 2017 Nov 21.
    , 101 Stephenson Parkway, Norman, OK, 73019, USA.
    Background: The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods. Read More

    bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests.
    BMC Bioinformatics 2017 Nov 18;18(1):503. Epub 2017 Nov 18.
    Department of Statistical Sciences, University of Padova, via C. Battisti, 241, Padova, 35121, Italy.
    Background: Receiver operating characteristic (ROC) surface analysis is usually employed to assess the accuracy of a medical diagnostic test when there are three ordered disease status (e.g. non-diseased, intermediate, diseased). Read More

    GPU-based detection of protein cavities using Gaussian surfaces.
    BMC Bioinformatics 2017 Nov 16;18(1):493. Epub 2017 Nov 16.
    Universidade da Beira Interior, Av. Marques D'Ávila e Bolama, Covilhã, 6200-001, Portugal.
    Background: Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i. Read More

    dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder.
    BMC Bioinformatics 2017 Nov 16;18(1):494. Epub 2017 Nov 16.
    Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, BaYi Road 461, Nanchang, 330006, China.
    Background: Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. Read More

    ANAT 2.0: reconstructing functional protein subnetworks.
    BMC Bioinformatics 2017 Nov 16;18(1):495. Epub 2017 Nov 16.
    School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.
    Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human.

    Results: Here we report on a new version of the tool, ANAT 2. Read More

    TRAVeLer: a tool for template-based RNA secondary structure visualization.
    BMC Bioinformatics 2017 Nov 15;18(1):487. Epub 2017 Nov 15.
    Faculty of Mathematics and Physics, Charles University, Prague, 11800, Czech Republic.
    Background: Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction.

    Results: This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Read More

    Reconstructing cancer karyotypes from short read data: the half empty and half full glass.
    BMC Bioinformatics 2017 Nov 15;18(1):488. Epub 2017 Nov 15.
    Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv-Yafo, Israel.
    Background: During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype. Read More

    SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.
    BMC Bioinformatics 2017 Nov 15;18(1):485. Epub 2017 Nov 15.
    Department of Computer Science, The University of Western Ontario, London, N6A 5B7, Ontario, Canada.
    Background: Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Read More

    Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.
    BMC Bioinformatics 2017 Nov 15;18(1):486. Epub 2017 Nov 15.
    Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
    Background: The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. Read More

    ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.
    BMC Bioinformatics 2017 Nov 14;18(1):480. Epub 2017 Nov 14.
    Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA.
    Background: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e. Read More

    Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs.
    BMC Bioinformatics 2017 Nov 14;18(1):479. Epub 2017 Nov 14.
    Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
    Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Read More

    GFF3sort: a novel tool to sort GFF3 files for tabix indexing.
    BMC Bioinformatics 2017 Nov 14;18(1):482. Epub 2017 Nov 14.
    Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
    Background: The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. Read More

    Analysis of breast cancer subtypes by AP-ISA biclustering.
    BMC Bioinformatics 2017 Nov 14;18(1):481. Epub 2017 Nov 14.
    State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Clinical Research Center for Oral Diseases, Department of Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
    Background: Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment. In the past years, several traditional clustering algorithms have been applied to analyze gene expression profiling. Read More

    BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness.
    BMC Bioinformatics 2017 Nov 13;18(1):477. Epub 2017 Nov 13.
    Nuffield Department of Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
    Background: Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. Solutions to the problem have application to public health (for example, in the detection of possible disease transmission), and as part of divide-and-conquer strategies selecting groups of similar isolates for computationally intensive methods of phylogenetic inference using (for example) maximal likelihood methods. However, the generation and maintenance of distance matrices is computationally intensive, and rapid methods of doing so are needed to allow translation of microbial genomics into public health actions. Read More

    A fragment based method for modeling of protein segments into cryo-EM density maps.
    BMC Bioinformatics 2017 Nov 13;18(1):475. Epub 2017 Nov 13.
    Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany.
    Background: Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. Read More

    Reference-guided de novo assembly approach improves genome reconstruction for related species.
    BMC Bioinformatics 2017 Nov 10;18(1):474. Epub 2017 Nov 10.
    Department of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Zurich, Switzerland.
    Background: The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. Read More

    Sequence-based information-theoretic features for gene essentiality prediction.
    BMC Bioinformatics 2017 Nov 9;18(1):473. Epub 2017 Nov 9.
    Transmission Systems Group, Jacobs University Bremen, Campus Ring 1, Bremen, D-28759, Germany.
    Background: Identification of essential genes is not only useful for our understanding of the minimal gene set required for cellular life but also aids the identification of novel drug targets in pathogens. In this work, we present a simple and effective gene essentiality prediction method using information-theoretic features that are derived exclusively from the gene sequences.

    Results: We developed a Random Forest classifier and performed an extensive model performance evaluation among and within 15 selected bacteria. Read More

    JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.
    BMC Bioinformatics 2017 Nov 6;18(1):469. Epub 2017 Nov 6.
    Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, 59812, MT, USA.
    Background: Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. Read More

    RNA inverse folding using Monte Carlo tree search.
    BMC Bioinformatics 2017 Nov 6;18(1):468. Epub 2017 Nov 6.
    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8561, Japan.
    Background: Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. However, their performance is not satisfactory in complicated cases. Read More

    K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity.
    BMC Bioinformatics 2017 Nov 3;18(1):467. Epub 2017 Nov 3.
    Computational Science Center, IBM T.J. Watson Research, Cambridge, MA, USA.
    Background: De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory. Read More

    Identification of gene pairs through penalized regression subject to constraints.
    BMC Bioinformatics 2017 Nov 3;18(1):466. Epub 2017 Nov 3.
    Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA.
    Background: This article concerns the identification of gene pairs or combinations of gene pairs associated with biological phenotype or clinical outcome, allowing for building predictive models that are not only robust to normalization but also easily validated and measured by qPCR techniques. However, given a small number of biological samples yet a large number of genes, this problem suffers from the difficulty of high computational complexity and imposes challenges to the accuracy of identification statistically.

    Results: In this paper, we propose a parsimonious model representation and develop efficient algorithms for identification. Read More

    Long short-term memory RNN for biomedical named entity recognition.
    BMC Bioinformatics 2017 Oct 30;18(1):462. Epub 2017 Oct 30.
    School of Computer Science, Wuhan University, Wuhan, 430072, Hubei, China.
    Background: Biomedical named entity recognition(BNER) is a crucial initial step of information extraction in biomedical domain. The task is typically modeled as a sequence labeling problem. Various machine learning algorithms, such as Conditional Random Fields (CRFs), have been successfully used for this task. Read More

    Tractable RNA-ligand interaction kinetics.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):424. Epub 2017 Oct 16.
    Department of Computer Science and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstr. 16-18, Leipzig, D-04107, Germany.
    Background: The binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene regulation implemented by a wide variety of riboswitches. The associated refolding processes often cannot be explained by thermodynamic effects alone. Read More

    VAliBS: a visual aligner for bisulfite sequences.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):410. Epub 2017 Oct 16.
    School of Information Science and Engineering, Central South University, Changsha, 410083, China.
    Background: Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfite treatment, traditional mapping tools do not work well with such methylation experimental reads. Read More

    DCJ-RNA - double cut and join for RNA secondary structures.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):427. Epub 2017 Oct 16.
    Imam Mohammad ibn Saud Islamic University, College of Computer and Information Sciences, Riyadh, Saudi Arabia.
    Background: Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minimum number of inversions that are necessary to transform one genome into another; this allows for genome sequence representation in polynomial time. Studies have not been conducted on the topic of rearranging a genome when it is represented as a secondary structure. Read More

    A new method for enhancer prediction based on deep belief network.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):418. Epub 2017 Oct 16.
    Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China.
    Background: Studies have shown that enhancers are significant regulatory elements to play crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation and distance to their target genes, it is a challenging mission for scholars and researchers to accurately predicting distal enhancers. In the past years, with the high-throughout ChiP-seq technologies development, several computational techniques emerge to predict enhancers using epigenetic or genomic features. Read More

    Detecting large deletions at base pair level by combining split read and paired read data.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):413. Epub 2017 Oct 16.
    Department of Computer Science, Tennessee State University, 3500 John A. Merritt Blvd., Nashville, 37221, Tennessee, USA.
    Background: Genomic structural variants (SV) play a significant role in the onset and progression of cancer. Genomic deletions can create oncogenic fusion genes or cause the loss of tumor suppressing gene function which can lead to tumorigenesis by downregulating these genes. Detecting these variants has clinical importance in the treatment of diseases. Read More

    MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):408. Epub 2017 Oct 16.
    Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong.
    Background: The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other assembly methods. Xander, as a pilot study, indeed has a lot of room for improvement. Apart from its slow speed, Xander uses only 1 k-mer size for graph construction and whatever choice of k will compromise either sensitivity or accuracy. Read More

    Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):422. Epub 2017 Oct 16.
    Institute of Informatics, University of Warsaw, Banacha 2, Warsaw, 02097, Poland.
    Background: The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest. Read More

    A sensitive short read homology search tool for paired-end read sequencing data.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):414. Epub 2017 Oct 16.
    Department of Computer Science and Engineering, Michigan State University, East Lansing, 48824, MI, USA.
    Background: Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. Read More

    NemoProfile as an efficient approach to network motif analysis with instance collection.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):423. Epub 2017 Oct 16.
    Division of Computing and Software Systems, School of Science, Technology, Engineering, and Mathematics (STEM), University of Washington Bothell, 18115 Campus Way NE, Bothell, 98011-8246, WA, USA.
    Background: A network motif is defined as a statistically significant and recurring subgraph pattern within a network. Most existing instance collection methods are not feasible due to high memory usage issues and provision of limited network motif information. They require a two-step process that requires network motif identification prior to instance collection. Read More

    Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):420. Epub 2017 Oct 16.
    Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 220 Handan Road, Shanghai, 200433, China.
    Background: Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting lncRNA-protein interactions (lncRPIs) is an important way to study the functions of lncRNA. Up to now, there have been a few works that exploit protein-protein interactions (PPIs) to help the prediction of new lncRPIs. Read More

    Predicting combinative drug pairs towards realistic screening via integrating heterogeneous features.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):409. Epub 2017 Oct 16.
    Department of Computer Science, the University of Hong Kong, Hong Kong, China.
    Background: Drug Combination is one of the effective approaches for treating complex diseases. However, determining combinative drug pairs in clinical trials is still costly. Thus, computational approaches are used to identify potential drug pairs in advance. Read More

    An effective approach to detecting both small and large complexes from protein-protein interaction networks.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):419. Epub 2017 Oct 16.
    Department of Computer Science and Technology, Tongji University, 4800 Cao'an Road, Shanghai, 201804, China.
    Background: Predicting protein complexes from protein-protein interaction (PPI) networks has been studied for decade. Various methods have been proposed to address some challenging issues of this problem, including overlapping clusters, high false positive/negative rates of PPI data and diverse complex structures. It is well known that most current methods can detect effectively only complexes of size ≥3, which account for only about half of the total existing complexes. Read More

    Detection and quantification of mitochondrial DNA deletions from next-generation sequence data.
    BMC Bioinformatics 2017 Oct 16;18(Suppl 12):407. Epub 2017 Oct 16.
    Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
    Background: Chromosomal deletions represent an important class of human genetic variation. Various methods have been developed to mine "next-generation" sequencing (NGS) data to detect deletions and quantify their clonal abundances. These methods have focused almost exclusively on the nuclear genome, ignoring the mitochondrial chromosome (mtDNA). Read More

    riboviz: analysis and visualization of ribosome profiling datasets.
    BMC Bioinformatics 2017 Oct 25;18(1):461. Epub 2017 Oct 25.
    Department of Genetics, Rutgers University, Piscataway, NJ, USA.
    Background: Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption.

    Description: We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. Read More

    QuaDMutEx: quadratic driver mutation explorer.
    BMC Bioinformatics 2017 Oct 24;18(1):458. Epub 2017 Oct 24.
    Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA.
    Background: Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. Read More

    A heuristic model for computational prediction of human branch point sequence.
    BMC Bioinformatics 2017 Oct 24;18(1):459. Epub 2017 Oct 24.
    School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China.
    Background: Pre-mRNA splicing is the removal of introns from precursor mRNAs (pre-mRNAs) and the concurrent ligation of the flanking exons to generate mature mRNA. This process is catalyzed by the spliceosome, where the splicing factor 1 (SF1) specifically recognizes the seven-nucleotide branch point sequence (BPS) and the U2 snRNP later displaces the SF1 and binds to the BPS. In mammals, the degeneracy of BPS motifs together with the lack of a large set of experimentally verified BPSs complicates the task of BPS prediction in silico. Read More

    An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm.
    BMC Bioinformatics 2017 Oct 24;18(1):460. Epub 2017 Oct 24.
    Computational Sciences Division, Saha Institute of Nuclear Physics, Kolkata, 700064, WB, India.
    Background: Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and structural unit of DNA. The computation of gene prediction is, therefore, very essential for detailed genome annotation. Read More

    A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).
    BMC Bioinformatics 2017 Oct 23;18(1):457. Epub 2017 Oct 23.
    Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada.
    Background: An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. Read More

    LCS-TA to identify similar fragments in RNA 3D structures.
    BMC Bioinformatics 2017 Oct 23;18(1):456. Epub 2017 Oct 23.
    Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
    Background: In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. Read More

    Mapping eQTL by leveraging multiple tissues and DNA methylation.
    BMC Bioinformatics 2017 Oct 18;18(1):455. Epub 2017 Oct 18.
    Program in Computational Biology and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA.
    Background: DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variation and gene expression, and this relationship can be exploited while mapping multi-tissue expression quantitative trait loci (eQTL). Current multi-tissue eQTL mapping techniques are limited to only exploiting gene expression patterns across multiple tissues either in a joint tissue or tissue-by-tissue frameworks. Read More

    chngpt: threshold regression model estimation and inference.
    BMC Bioinformatics 2017 Oct 16;18(1):454. Epub 2017 Oct 16.
    Human Vaccine Institute, Duke University Medical Center, 2 Genome Court, Durham, USA.
    Background: Threshold regression models are a diverse set of non-regular regression models that all depend on change points or thresholds. They provide a simple but elegant and interpretable way to model certain kinds of nonlinear relationships between the outcome and a predictor.

    Results: The R package chngpt provides both estimation and hypothesis testing functionalities for four common variants of threshold regression models. Read More

    A strategy for evaluating pathway analysis methods.
    BMC Bioinformatics 2017 Oct 13;18(1):453. Epub 2017 Oct 13.
    Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Fort Detrick, MD, 21702, USA.
    Background: Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Read More

    LiverWiki: a wiki-based database for human liver.
    BMC Bioinformatics 2017 Oct 13;18(1):452. Epub 2017 Oct 13.
    Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, Beijing, 102206, China.
    Background: Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. Read More

    A method for named entity normalization in biomedical articles: application to diseases and plants.
    BMC Bioinformatics 2017 Oct 13;18(1):451. Epub 2017 Oct 13.
    School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 123 Chemdangwagi-ro, Buk-gu, Gwangju, Republic of Korea.
    Background: In biomedical articles, a named entity recognition (NER) technique that identifies entity names from texts is an important element for extracting biological knowledge from articles. After NER is applied to articles, the next step is to normalize the identified names into standard concepts (i.e. Read More

    Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.
    BMC Bioinformatics 2017 Oct 12;18(1):449. Epub 2017 Oct 12.
    Anacleto Lab - Dipartimento di Informatica, Universitá degli Studi di Milano, Via Comelico 39, Milan, 20135, Italy.
    Background: The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this context the Human Phenotype Ontology (HPO) provides a standard categorization of the abnormalities associated with human diseases. While the problem of the prediction of gene-disease associations has been widely investigated, the related problem of gene-phenotypic feature (i. Read More

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