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Briefings in Bioinformatics

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https://www.readbyqxmd.com/read/28077405/vrprofile-gene-cluster-detection-based-profiling-of-virulence-and-antibiotic-resistance-traits-encoded-within-genome-sequences-of-pathogenic-bacteria
#1
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077404/high-throughput-sequencing-of-the-t-cell-receptor-repertoire-pitfalls-and-opportunities
#2
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077403/gene-co-expression-analysis-for-functional-classification-and-gene-disease-predictions
#3
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077402/elemental-metabolomics
#4
Ping Zhang, Constantinos A Georgiou, Vladimir Brusic
Elemental metabolomics is quantification and characterization of total concentration of chemical elements in biological samples and monitoring of their changes. Recent advances in inductively coupled plasma mass spectrometry have enabled simultaneous measurement of concentrations of > 70 elements in biological samples. In living organisms, elements interact and compete with each other for absorption and molecular interactions. They also interact with proteins and nucleotide sequences. These interactions modulate enzymatic activities and are critical for many molecular and cellular functions...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#5
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069635/evaluating-approaches-to-find-exon-chains-based-on-long-reads
#6
Anna Kuosmanen, Tuukka Norri, Veli Mäkinen
: Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069634/a-review-of-connectivity-map-and-computational-approaches-in-pharmacogenomics
#7
Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina Galzko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28065918/exploiting-next-generation-sequencing-to-solve-the-haplotyping-puzzle-in-polyploids-a-simulation-study
#8
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species...
January 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28065917/transformation-and-model-choice-for-rna-seq-co-expression-analysis
#9
Andrea Rau, Cathy Maugis-Rabusseau
Although a large number of clustering algorithms have been proposed to identify groups of co-expressed genes from microarray data, the question of if and how such methods may be applied to RNA sequencing (RNA-seq) data remains unaddressed. In this work, we investigate the use of data transformations in conjunction with Gaussian mixture models for RNA-seq co-expression analyses, as well as a penalized model selection criterion to select both an appropriate transformation and number of clusters present in the data...
January 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28062411/mapping-morphological-shape-as-a-high-dimensional-functional-curve
#10
Guifang Fu, Mian Huang, Wenhao Bo, Han Hao, Rongling Wu
Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits...
January 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28062413/survey-of-local-and-global-biological-network-alignment-the-need-to-reconcile-the-two-sides-of-the-same-coin
#11
Pietro Hiram Guzzi, Tijana Milenković
Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments...
January 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28062412/plant-genome-and-transcriptome-annotations-from-misconceptions-to-simple-solutions
#12
Marie E Bolger, Borjana Arsova, Björn Usadel
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources...
January 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28049135/design-of-rnas-comparing-programs-for-inverse-rna-folding
#13
Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures...
January 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28049134/mirandb-a-resource-of-online-services-for-mirna-research
#14
Seyed Hamid Aghaee-Bakhtiari, Ehsan Arefian, Pierre Lau
Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available. However, the increasing number and diversity of bioinformatics tools, each covering a specific and specialized area, as well as their redundancies, represent potential sources of complication for end users...
January 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28040748/how-the-strengths-of-lisp-family-languages-facilitate-building-complex-and-flexible-bioinformatics-applications
#15
Bohdan B Khomtchouk, Edmund Weitz, Peter D Karp, Claes Wahlestedt
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28040747/statistical-method-evaluation-for-differentially-methylated-cpgs-in-base-resolution-next-generation-dna-sequencing-data
#16
Yun Zhang, Saurabh Baheti, Zhifu Sun
High-throughput bisulfite methylation sequencing such as reduced representation bisulfite sequencing (RRBS), Agilent SureSelect Human Methyl-Seq (Methyl-seq) or whole-genome bisulfite sequencing is commonly used for base resolution methylome research. These data are represented either by the ratio of methylated cytosine versus total coverage at a CpG site or numbers of methylated and unmethylated cytosines. Multiple statistical methods can be used to detect differentially methylated CpGs (DMCs) between conditions, and these methods are often the base for the next step of differentially methylated region identification...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28040746/sixty-five-years-of-the-long-march-in-protein-secondary-structure-prediction-the-final-stretch
#17
Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip Paliwal, Yaoqi Zhou
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28028006/identification-and-analysis-of-the-human-sex-biased-genes
#18
Sisi Guo, Yuan Zhou, Pan Zeng, Guoheng Xu, Guoqing Wang, Qinghua Cui
Tremendous differences between human sexes are universally observed. Therefore, identifying and analyzing the sex-biased genes are becoming basically important for uncovering the mystery of sex differences and personalized medicine. Here, we presented a computational method to identify sex-biased genes from public gene expression databases. We obtained 1407 female-biased genes (FGs) and 1096 male-biased genes (MGs) across 14 different tissues. Bioinformatics analysis revealed that compared with MGs, FGs have higher evolutionary rate, higher single-nucleotide polymorphism density, less homologous gene numbers and smaller phyletic age...
December 27, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28025179/measuring-the-diversity-of-the-human-microbiota-with-targeted-next-generation-sequencing
#19
Francesca Finotello, Eleonora Mastrorilli, Barbara Di Camillo
The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples...
December 26, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28025178/mtgipick-allows-robust-identification-of-genomic-islands-from-a-single-genome
#20
Qi Dai, Chaohui Bao, Yabing Hai, Sheng Ma, Tao Zhou, Cong Wang, Yunfei Wang, Wenwen Huo, Xiaoqing Liu, Yuhua Yao, Zhenyu Xuan, Min Chen, Michael Q Zhang
Genomic islands (GIs) that are associated with microbial adaptations and carry sequence patterns different from that of the host are sporadically distributed among closely related species. This bias can dominate the signal of interest in GI detection. However, variations still exist among the segments of the host, although no uniform standard exists regarding the best methods of discriminating GIs from the rest of the genome in terms of compositional bias. In the present work, we proposed a robust software, MTGIpick, which used regions with pattern bias showing multiscale difference levels to identify GIs from the host...
December 26, 2016: Briefings in Bioinformatics
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