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Briefings in Bioinformatics

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https://www.readbyqxmd.com/read/28334282/comprehensive-assessment-of-flexible-ligand-docking-algorithms-current-effectiveness-and-challenges
#1
Sheng-You Huang
Protein-ligand docking has been playing an important role in modern drug discovery. To model drug-target binding in real systems, a number of flexible-ligand docking algorithms with different sampling strategies and scoring methods have been subsequently developed over the past three decades, while rigid-ligand docking is still being used because of its compelling computational efficiency. Here, a comprehensive assessment has been conducted to investigate the effectiveness of flexible-ligand docking versus rigid-ligand docking for three representative docking algorithms (global optimization, incremental construction and multi-conformer docking) in virtual screening and pose prediction on the Directory of Useful Decoys...
March 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334239/comparison-of-the-general-co-expression-landscapes-between-human-and-mouse
#2
Di Liu, Linna Zhao, Yang Chen, Zhaoyang Wang, Jing Xu, Ying Li, Changgui Lei, Simeng Hu, Miaomiao Niu, Yongshuai Jiang
The murine model serves as an important experimental system in biomedical science because of its high degree of similarities at the sequence level with human. Recent studies have compared the transcriptional landscapes between human and mouse, but the general co-expression landscapes have not been characterized. Here, we calculated the general co-expression coefficients and constructed the general co-expression maps for human and mouse. The differences and similarities of the general co-expression maps between the two species were compared in detail...
March 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334354/methodological-implementation-of-mixed-linear-models-in-multi-locus-genome-wide-association-studies
#3
Yang-Jun Wen, Hanwen Zhang, Yuan-Li Ni, Bo Huang, Jin Zhang, Jian-Ying Feng, Shi-Bo Wang, Jim M Dunwell, Yuan-Ming Zhang, Rongling Wu
No abstract text is available yet for this article.
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334273/gwas-summary-based-pathway-analysis-correcting-for-the-genetic-confounding-impact-of-environmental-exposures
#4
Qianrui Fan, Feng Zhang, Wenyu Wang, Jiawen Xu, Jingcan Hao, Awen He, Yan Wen, Ping Li, Xiao Liang, Yanan Du, Li Liu, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo
Genome-wide association study (GWAS)-based pathway association analysis is a powerful approach for the genetic studies of human complex diseases. However, the genetic confounding effects of environment exposure-related genes can decrease the accuracy of GWAS-based pathway association analysis of target diseases. In this study, we developed a pathway association analysis approach, named Mendelian randomization-based pathway enrichment analysis (MRPEA), which was capable of correcting the genetic confounding effects of environmental exposures, using the GWAS summary data of environmental exposures...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#5
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334228/a-survey-of-the-approaches-for-identifying-differential-methylation-using-bisulfite-sequencing-data
#6
Adib Shafi, Cristina Mitrea, Tin Nguyen, Sorin Draghici
DNA methylation is an important epigenetic mechanism that plays a crucial role in cellular regulatory systems. Recent advancements in sequencing technologies now enable us to generate high-throughput methylation data and to measure methylation up to single-base resolution. This wealth of data does not come without challenges, and one of the key challenges in DNA methylation studies is to identify the significant differences in the methylation levels of the base pairs across distinct biological conditions. Several computational methods have been developed to identify differential methylation using bisulfite sequencing data; however, there is no clear consensus among existing approaches...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334258/review-and-comparative-assessment-of-sequence-based-predictors-of-protein-binding-residues
#7
Jian Zhang, Lukasz Kurgan
Understanding of molecular mechanisms that govern protein-protein interactions and accurate modeling of protein-protein docking rely on accurate identification and prediction of protein-binding partners and protein-binding residues. We review over 40 methods that predict protein-protein interactions from protein sequences including methods that predict interacting protein pairs, protein-binding residues for a pair of interacting sequences and protein-binding residues in a single protein chain. We focus on the latter methods that provide residue-level annotations and that can be broadly applied to all protein sequences...
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334200/mirandb-a-resource-of-online-services-for-mirna-research
#8
(no author information available yet)
No abstract text is available yet for this article.
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334156/how-the-strengths-of-lisp-family-languages-facilitate-building-complex-and-flexible-bioinformatics-applications
#9
Bohdan B Khomtchouk, Edmund Weitz, Peter D Karp, Claes Wahlestedt
No abstract text is available yet for this article.
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334140/circular-rna-identification-based-on-multiple-seed-matching
#10
Yuan Gao, Jinyang Zhang, Fangqing Zhao
Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage...
February 28, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334202/selecting-between-sample-rna-seq-normalization-methods-from-the-perspective-of-their-assumptions
#11
Ciaran Evans, Johanna Hardin, Daniel M Stoebel
RNA-Seq is a widely used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An underemphasized feature of normalization is the assumptions on which the methods rely and how the validity of these assumptions can have a substantial impact on the performance of the methods...
February 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334201/critical-evaluation-of-bioinformatics-tools-for-the-prediction-of-protein-crystallization-propensity
#12
Huilin Wang, Liubin Feng, Geoffrey I Webb, Lukasz Kurgan, Jiangning Song, Donghai Lin
X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-throughput X-ray crystallography. The attrition rate of these efforts can be improved by selection of proteins that are potentially easier to be crystallized...
February 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334136/a-review-of-network-based-approaches-to-drug-repositioning
#13
Maryam Lotfi Shahreza, Nasser Ghadiri, Sayed Rasoul Mousavi, Jaleh Varshosaz, James R Green
Experimental drug development is time-consuming, expensive and limited to a relatively small number of targets. However, recent studies show that repositioning of existing drugs can function more efficiently than de novo experimental drug development to minimize costs and risks. Previous studies have proven that network analysis is a versatile platform for this purpose, as the biological networks are used to model interactions between many different biological concepts. The present study is an attempt to review network-based methods in predicting drug targets for drug repositioning...
February 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334173/a-review-of-connectivity-map-and-computational-approaches-in-pharmacogenomics
#14
(no author information available yet)
No abstract text is available yet for this article.
February 23, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334118/individualized-analysis-of-differentially-expressed-mirnas-with-application-to-the-identification-of-mirnas-deregulated-commonly-in-lung-cancer-tissues
#15
Haidan Yan, Hao Cai, Qingzhou Guan, Jun He, Juan Zhang, You Guo, Haiyan Huang, Xiangyu Li, Yawei Li, Yunyan Gu, Lishuang Qi, Zheng Guo
Identifying differentially expressed microRNAs (DE miRNAs) between cancer samples and normal controls is a common way to investigate carcinogenesis mechanisms. However, for a DE miRNA detected at the population-level, we do not know whether it is DE in a particular cancer sample. Here, based on the finding that the within-sample relative expression orderings of miRNA pairs are highly stable in a particular type of normal tissues but widely disrupted in the corresponding cancer tissues, we proposed a method, called RankMiRNA, to identify DE miRNAs in each cancer tissue compared with its own normal state...
February 23, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334151/strategies-for-processing-and-quality-control-of-illumina-genotyping-arrays
#16
Shilin Zhao, Wang Jing, David C Samuels, Quanghu Sheng, Yu Shyr, Yan Guo
Illumina genotyping arrays have powered thousands of large-scale genome-wide association studies over the past decade. Yet, because of the tremendous volume and complicated genetic assumptions of Illumina genotyping data, processing and quality control (QC) of these data remain a challenge. Thorough QC ensures the accurate identification of single-nucleotide polymorphisms and is required for the correct interpretation of genetic association results. By processing genotyping data on > 100 000 subjects from >10 major Illumina genotyping arrays, we have accumulated extensive experience in handling some of the most peculiar scenarios related to the processing and QC of Illumina genotyping data...
February 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334084/molecular-dynamics-recipes-for-genome-research
#17
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334070/detection-of-drug-drug-interactions-through-data-mining-studies-using-clinical-sources-scientific-literature-and-social-media
#18
Santiago Vilar, Carol Friedman, George Hripcsak
Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to the population are a primary aim of drug safety researchers. Here, we review different methodologies and recent advances using data mining to detect DDIs with impact on patients. We focus on data mining of different pharmacovigilance sources, such as the US Food and Drug Administration Adverse Event Reporting System and electronic health records from medical institutions, as well as on the diverse data mining studies that use narrative text available in the scientific biomedical literature and social media...
February 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#19
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28203720/hpqtl-a-geometric-morphometric-platform-to-compute-the-genetic-architecture-of-heterophylly
#20
Lidan Sun, Jing Wang, Xuli Zhu, Libo Jiang, Kirk Gosik, Mengmeng Sang, Fengsuo Sun, Tangren Cheng, Qixiang Zhang, Rongling Wu
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
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