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BMC Bioinformatics

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https://www.readbyqxmd.com/read/29792161/a-website-to-identify-shared-genes-in-saccharomyces-cerevisiae-homozygous-deletion-library-screens
#1
Mark D Temple
BACKGROUND: The homozygous yeast deletion library includes approximately 4800 diploid strains each containing one deleted non-essential gene. Hundreds of publications have arisen through experimentation using this genome-wide biological resource. As part of this work over 677 genesets have been collated from these experiments representing the phenotypic responses of the library to a diverse set of chemical and physical challenges. DESCRIPTION: A website called the Saccharomyces cerevisiae Homozygous Deletion Library Tools (ScHo DeLiTo-96) has been developed with the primary goal of browsing and identifying genes shared between these responsive phenotypes (available at yeastdb...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#2
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29788930/npbss-a-new-pacbio-sequencing-simulator-for-generating-the-continuous-long-reads-with-an-empirical-model
#3
Ze-Gang Wei, Shao-Wu Zhang
BACKGROUND: PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of subsequent analysis tools. Although there are several available simulators (e...
May 22, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29783945/samsa2-a-standalone-metatranscriptome-analysis-pipeline
#4
Samuel T Westreich, Michelle L Treiber, David A Mills, Ian Korf, Danielle G Lemay
BACKGROUND: Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms. RESULTS: SAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster...
May 21, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29783926/neural-networks-for-link-prediction-in-realistic-biomedical-graphs-a-multi-dimensional-evaluation-of-graph-embedding-based-approaches
#5
Gamal Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen
BACKGROUND: Link prediction in biomedical graphs has several important applications including predicting Drug-Target Interactions (DTI), Protein-Protein Interaction (PPI) prediction and Literature-Based Discovery (LBD). It can be done using a classifier to output the probability of link formation between nodes. Recently several works have used neural networks to create node representations which allow rich inputs to neural classifiers. Preliminary works were done on this and report promising results...
May 21, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29776330/robust-joint-score-tests-in-the-application-of-dna-methylation-data-analysis
#6
Xuan Li, Yuejiao Fu, Xiaogang Wang, Weiliang Qiu
BACKGROUND: Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW's method seems to be quite conservative and has not been fully compared with existing joint tests...
May 18, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29769044/visualizing-histopathologic-deep-learning-classification-and-anomaly-detection-using-nonlinear-feature-space-dimensionality-reduction
#7
Kevin Faust, Quin Xie, Dominick Han, Kartikay Goyle, Zoya Volynskaya, Ugljesa Djuric, Phedias Diamandis
BACKGROUND: There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies highlight expert-level performance of convolutional neural networks (CNNs) on focused classification tasks, most studies rely on probability distribution scores with empirically defined cutoff values based on post-hoc analysis. More generalizable tools that allow humans to visualize histology-based deep learning inferences and decision making are scarce...
May 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29769032/live-neighbor-joining
#8
Guilherme P Telles, Graziela S Araújo, Maria E M T Walter, Marcelo M Brigido, Nalvo F Almeida
BACKGROUND: In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. RESULTS: We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa...
May 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29764362/gpu-accelerated-iterative-reconstruction-for-limited-data-tomography-in-cbct-systems
#9
Claudia de Molina, Estefania Serrano, Javier Garcia-Blas, Jesus Carretero, Manuel Desco, Monica Abella
BACKGROUND: Standard cone-beam computed tomography (CBCT) involves the acquisition of at least 360 projections rotating through 360 degrees. Nevertheless, there are cases in which only a few projections can be taken in a limited angular span, such as during surgery, where rotation of the source-detector pair is limited to less than 180 degrees. Reconstruction of limited data with the conventional method proposed by Feldkamp, Davis and Kress (FDK) results in severe artifacts. Iterative methods may compensate for the lack of data by including additional prior information, although they imply a high computational burden and memory consumption...
May 15, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29751737/correction-to-hicomet-a-high-throughput-comet-analysis-tool-for-large-scale-dna-damage-assessment
#10
Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min, Sungroh Yoon
After publication of the original article [1], it has been found that the author affiliations have been accidentally left out in the PDF. The full affiliations can be found in this correction.
May 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29743010/an-automatic-method-to-calculate-heart-rate-from-zebrafish-larval-cardiac-videos
#11
Chia-Pin Kang, Hung-Chi Tu, Tzu-Fun Fu, Jhe-Ming Wu, Po-Hsun Chu, Darby Tien-Hao Chang
BACKGROUND: Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafish is powerful in modeling mammalian cardiac physiology and pathology as well as in large-scale high throughput screening. However, an economical and convenient tool for rapid evaluation of fish cardiac function is still in need...
May 9, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745866/astral-iii-polynomial-time-species-tree-reconstruction-from-partially-resolved-gene-trees
#12
Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
BACKGROUND: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. RESULTS: We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k)...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745865/on-the-rank-distance-median-of-3-permutations
#13
Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidanis
BACKGROUND: Recently, Pereira Zanetti, Biller and Meidanis have proposed a new definition of a rearrangement distance between genomes. In this formulation, each genome is represented as a matrix, and the distance d is the rank distance between these matrices. Although defined in terms of matrices, the rank distance is equal to the minimum total weight of a series of weighted operations that leads from one genome to the other, including inversions, translocations, transpositions, and others...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745863/generation-and-comparative-genomics-of-synthetic-dengue-viruses
#14
Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller
BACKGROUND: Synthetic virology is an important multidisciplinary scientific field, with emerging applications in biotechnology and medicine, aiming at developing methods to generate and engineer synthetic viruses. In particular, many of the RNA viruses, including among others the Dengue and Zika, are widespread pathogens of significant importance to human health. The ability to design and synthesize such viruses may contribute to exploring novel approaches for developing vaccines and virus based therapies...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745861/computing-the-family-free-dcj-similarity
#15
Diego P Rubert, Edna A Hoshino, Marília D V Braga, Jens Stoye, Fábio V Martinez
BACKGROUND: The genomic similarity is a large-scale measure for comparing two given genomes. In this work we study the (NP-hard) problem of computing the genomic similarity under the DCJ model in a setting that does not assume that the genes of the compared genomes are grouped into gene families. This problem is called family-free DCJ similarity. RESULTS: We propose an exact ILP algorithm to solve the family-free DCJ similarity problem, then we show its APX-hardness and present four combinatorial heuristics with computational experiments comparing their results to the ILP...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745853/a-new-method-to-measure-the-semantic-similarity-from-query-phenotypic-abnormalities-to-diseases-based-on-the-human-phenotype-ontology
#16
Xiaofeng Gong, Jianping Jiang, Zhongqu Duan, Hui Lu
BACKGROUND: Although rapid developed sequencing technologies make it possible for genotype data to be used in clinical diagnosis, it is still challenging for clinicians to understand the results of sequencing and make correct judgement based on them. Before this, diagnosis based on clinical features held a leading position. With the establishment of the Human Phenotype Ontology (HPO) and the enrichment of phenotype-disease annotations, there throws much more attention to the improvement of phenotype-based diagnosis...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745849/pathway-based-approach-using-hierarchical-components-of-rare-variants-to-analyze-multiple-phenotypes
#17
Sungyoung Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang, Taesung Park
BACKGROUND: As one possible solution to the "missing heritability" problem, many methods have been proposed that apply pathway-based analyses, using rare variants that are detected by next generation sequencing technology. However, while a number of methods for pathway-based rare-variant analysis of multiple phenotypes have been proposed, no method considers a unified model that incorporate multiple pathways. RESULTS: Simulation studies successfully demonstrated advantages of multivariate analysis, compared to univariate analysis, and comparison studies showed the proposed approach to outperform existing methods...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745848/automated-transition-analysis-of-activated-gene-regulation-during-diauxic-nutrient-shift-in-escherichia-coli-and-adipocyte-differentiation-in-mouse-cells
#18
Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda
BACKGROUND: Comprehensively understanding the dynamics of biological systems is among the biggest current challenges in biology and medicine. To acquire this understanding, researchers have measured the time-series expression profiles of cell lines of various organisms. Biological technologies have also drastically improved, providing a huge amount of information with support from bioinformatics and systems biology. However, the transitions between the activation and inactivation of gene regulations, at the temporal resolution of single time points, are difficult to extract from time-course gene expression profiles...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745843/hierarchical-structural-component-modeling-of-microrna-mrna-integration-analysis
#19
Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Jin-Young Jang, Taesung Park
BACKGROUND: Identification of multi-markers is one of the most challenging issues in personalized medicine era. Nowadays, many different types of omics data are generated from the same subject. Although many methods endeavor to identify candidate markers, for each type of omics data, few or none can facilitate such identification. RESULTS: It is well known that microRNAs affect phenotypes only indirectly, through regulating mRNA expression and/or protein translation...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29745837/cnnh_pss-protein-8-class-secondary-structure-prediction-by-convolutional-neural-network-with-highway
#20
Jiyun Zhou, Hongpeng Wang, Zhishan Zhao, Ruifeng Xu, Qin Lu
BACKGROUND: Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches for protein secondary structure prediction is becoming increasingly urgent. RESULTS: We present a novel deep learning based model, referred to as CNNH_PSS, by using multi-scale CNN with highway. In CNNH_PSS, any two neighbor convolutional layers have a highway to deliver information from current layer to the output of the next one to keep local contexts...
May 8, 2018: BMC Bioinformatics
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