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BMC Bioinformatics

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https://www.readbyqxmd.com/read/29145826/gpu-based-detection-of-protein-cavities-using-gaussian-surfaces
#1
Sérgio E D Dias, Ana Mafalda Martins, Quoc T Nguyen, Abel J P Gomes
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...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29145823/dbmdega-a-database-for-meta-analysis-of-differentially-expressed-genes-in-autism-spectrum-disorder
#2
Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan
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. METHODS: Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples)...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29145805/anat-2-0-reconstructing-functional-protein-subnetworks
#3
Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan
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 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29141608/traveler-a-tool-for-template-based-rna-secondary-structure-visualization
#4
Richard Elias, David Hoksza
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...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29141589/reconstructing-cancer-karyotypes-from-short-read-data-the-half-empty-and-half-full-glass
#5
Rami Eitan, Ron Shamir
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. Using high-throughput technologies of deep sequencing and microarrays it is possible to interrogate a cancer genome and produce chromosomal copy number profiles and a list of breakpoints ("jumps") relative to the normal genome...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29141584/sprint-ultrafast-protein-protein-interaction-prediction-of-the-entire-human-interactome
#6
Yiwei Li, Lucian Ilie
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. Many computational methods have been proposed among which sequence-based ones are very promising. However, so far no such method is able to predict effectively the entire human interactome: they require too much time or memory. RESULTS: We present SPRINT (Scoring PRotein INTeractions), a new sequence-based algorithm and tool for predicting protein-protein interactions...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29141580/usability-of-human-infinium-methylationepic-beadchip-for-mouse-dna-methylation-studies
#7
Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic
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. RESULTS: In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#8
Oluwatosin Oluwadare, Jianlin Cheng
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., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137601/random-walks-on-mutual-microrna-target-gene-interaction-network-improve-the-prediction-of-disease-associated-micrornas
#9
Duc-Hau Le, Lieven Verbeke, Le Hoang Son, Dinh-Toi Chu, Van-Huy Pham
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. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137598/gff3sort-a-novel-tool-to-sort-gff3-files-for-tabix-indexing
#10
Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang
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. RESULTS: We developed GFF3sort, a script to sort GFF3 files for tabix indexing...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137596/analysis-of-breast-cancer-subtypes-by-ap-isa-biclustering
#11
Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang, Jianhua Wei
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. However, accurate identification of breast cancer subtypes, especially within highly variable LuminalA subtype, remains a challenge. Furthermore, the relationship between DNA methylation and expression level in different breast cancer subtypes is not clear...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29132318/bugmat-and-findneighbour-command-line-and-server-applications-for-investigating-bacterial-relatedness
#12
Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W Eyre, Anthony Underwood, Derrick Crook, David H Wyllie
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...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29132296/a-fragment-based-method-for-modeling-of-protein-segments-into-cryo-em-density-maps
#13
Jochen Ismer, Alexander S Rose, Johanna K S Tiemann, Peter W Hildebrand
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. RESULTS: Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit)...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29132292/flps-fast-discovery-of-compositional-biases-for-the-protein-universe
#14
Paul M Harrison
BACKGROUND: Proteins often contain regions that are compositionally biased (CB), i.e., they are made from a small subset of amino-acid residue types. These CB regions can be functionally important, e.g., the prion-forming and prion-like regions that are rich in asparagine and glutamine residues. RESULTS: Here I report a new program fLPS that can rapidly annotate CB regions. It discovers both single-residue and multiple-residue biases. It works through a process of probability minimization...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29126390/reference-guided-de-novo-assembly-approach-improves-genome-reconstruction-for-related-species
#15
Heidi E L Lischer, Kentaro K Shimizu
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. However, previous methods mostly focused on the assembly of other genotypes within the same species...
November 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29121868/sequence-based-information-theoretic-features-for-gene-essentiality-prediction
#16
Dawit Nigatu, Patrick Sobetzko, Malik Yousef, Werner Henkel
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...
November 9, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29110634/js-ms-a-cross-platform-modular-javascript-viewer-for-mass-spectrometry-signals
#17
Jebediah Rosen, Kyle Handy, André Gillan, Rob Smith
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. RESULTS: We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data...
November 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29110632/rna-inverse-folding-using-monte-carlo-tree-search
#18
Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda
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. RESULT: We present a new inverse folding algorithm called MCTS-RNA, which uses Monte Carlo tree search (MCTS), a technique that has shown exceptional performance in Computer Go recently, to represent and discover the essential part of the sequence space...
November 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29100493/k-mer-clustering-algorithm-using-a-mapreduce-framework-application-to-the-parallelization-of-the-inchworm-module-of-trinity
#19
Chang Sik Kim, Martyn D Winn, Vipin Sachdeva, Kirk E Jordan
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. RESULTS: We introduce a novel approach that clusters k-mers as the first step...
November 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29100492/identification-of-gene-pairs-through-penalized-regression-subject-to-constraints
#20
Rex Shen, Lan Luo, Hui Jiang
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...
November 3, 2017: BMC Bioinformatics
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