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Briefings in Bioinformatics

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https://www.readbyqxmd.com/read/28535295/bioinformatic-analysis-of-bacteria-and-host-cell-dual-rna-sequencing-experiments
#1
James W Marsh, Regan J Hayward, Amol C Shetty, Anup Mahurkar, Michael S Humphrys, Garry S A Myers
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell...
May 23, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#2
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28520909/large-scale-data-driven-integrative-framework-for-extracting-essential-targets-and-processes-from-disease-associated-gene-data-sets
#3
Gaston K Mazandu, Emile R Chimusa, Kayleigh Rutherford, Elsa-Gayle Zekeng, Zoe Z Gebremariam, Maryam Y Onifade, Nicola J Mulder
Populations worldwide currently face several public health challenges, including growing prevalence of infections and the emergence of new pathogenic organisms. The cost and risk associated with drug development make the development of new drugs for several diseases, especially orphan or rare diseases, unappealing to the pharmaceutical industry. Proof of drug safety and efficacy is required before market approval, and rigorous testing makes the drug development process slow, expensive and frequently result in failure...
May 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28498882/mutational-signatures-and-mutable-motifs-in-cancer-genomes
#4
Igor B Rogozin, Youri I Pavlov, Alexander Goncearenco, Subhajyoti De, Artem G Lada, Eugenia Poliakov, Anna R Panchenko, David N Cooper
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts...
May 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#5
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28481991/deep-learning-for-healthcare-review-opportunities-and-challenges
#6
Riccardo Miotto, Fei Wang, Shuang Wang, Xiaoqian Jiang, Joel T Dudley
Gaining knowledge and actionable insights from complex, high-dimensional and heterogeneous biomedical data remains a key challenge in transforming health care. Various types of data have been emerging in modern biomedical research, including electronic health records, imaging, -omics, sensor data and text, which are complex, heterogeneous, poorly annotated and generally unstructured. Traditional data mining and statistical learning approaches typically need to first perform feature engineering to obtain effective and more robust features from those data, and then build prediction or clustering models on top of them...
May 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28475767/advances-in-computational-approaches-in-identifying-synergistic-drug-combinations
#7
Zhen Sheng, Yi Sun, Zuojing Yin, Kailin Tang, Zhiwei Cao
Accumulated empirical clinical experience, supported by animal or cell line models, has initiated efforts of predicting synergistic combinatorial drugs with more-than-additive effect compared with the sum of the individual agents. Aiming to construct better computational models, this review started from the latest updated data resources of combinatorial drugs, then summarized the reported mechanism of the known synergistic combinations from aspects of drug molecular and pharmacological patterns, target network properties and compound functional annotation...
May 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28472242/bridging-semantics-and-syntax-with-graph-algorithms-state-of-the-art-of-extracting-biomedical-relations
#8
Yuan Luo, Özlem Uzuner, Peter Szolovits
No abstract text is available yet for this article.
May 2, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28460068/in-silico-polypharmacology-of-natural-products
#9
Jiansong Fang, Chuang Liu, Qi Wang, Ping Lin, Feixiong Cheng
Natural products with polypharmacological profiles have demonstrated promise as novel therapeutics for various complex diseases, including cancer. Currently, many gaps exist in our knowledge of which compounds interact with which targets, and experimentally testing all possible interactions is infeasible. Recent advances and developments of systems pharmacology and computational (in silico) approaches provide powerful tools for exploring the polypharmacological profiles of natural products. In this review, we introduce recent progresses and advances of computational tools and systems pharmacology approaches for identifying drug targets of natural products by focusing on the development of targeted cancer therapy...
April 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28453640/pioneering-topological-methods-for-network-based-drug-target-prediction-by-exploiting-a-brain-network-self-organization-theory
#10
Claudio Durán, Simone Daminelli, Josephine M Thomas, V Joachim Haupt, Michael Schroeder, Carlo Vittorio Cannistraci
The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared-using standard and innovative validation frameworks-with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks...
April 26, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28449042/long-noncoding-rna-a-crosslink-in-biological-regulatory-network
#11
Yuwei Zhang, Yang Tao, Qi Liao
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil...
April 24, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430873/bioinformatics-in-germany-toward-a-national-level-infrastructure
#12
Andreas Tauch, Arwa Al-Dilaimi
The German Network for Bioinformatics Infrastructure (de.NBI) is a national initiative funded by the German Federal Ministry of Education and Research (BMBF). The mission of de.NBI is (i) to provide high-quality bioinformatics services to users in basic and applied life sciences research from academia, industry and biomedicine; (ii) to offer bioinformatics training to users in Germany and Europe through a wide range of workshops and courses; and (iii) to foster the cooperation of the German bioinformatics community with international network structures such as the European life-sciences Infrastructure for biological Information (ELIXIR)...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#13
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28419324/improving-data-workflow-systems-with-cloud-services-and-use-of-open-data-for-bioinformatics-research
#14
Md Rezaul Karim, Audrey Michel, Achille Zappa, Pavel Baranov, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted...
April 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#15
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28398567/bioinformatics-tools-for-the-identification-of-gene-clusters-that-biosynthesize-specialized-metabolites
#16
Arvind K Chavali, Seung Y Rhee
Specialized metabolites (also called natural products or secondary metabolites) derived from bacteria, fungi, marine organisms and plants constitute an important source of antibiotics, anti-cancer agents, insecticides, immunosuppressants and herbicides. Many specialized metabolites in bacteria and fungi are biosynthesized via metabolic pathways whose enzymes are encoded by clustered genes on a chromosome. Metabolic gene clusters comprise a group of physically co-localized genes that together encode enzymes for the biosynthesis of a specific metabolite...
April 7, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28387809/the-anatomy-of-phenotype-ontologies-principles-properties-and-applications
#17
Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies...
April 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28387786/cash-a-constructing-comprehensive-splice-site-method-for-detecting-alternative-splicing-events
#18
Wenwu Wu, Jie Zong, Ning Wei, Jian Cheng, Xuexia Zhou, Yuanming Cheng, Dai Chen, Qinghua Guo, Bo Zhang, Ying Feng
RNA-sequencing (RNA-seq) can generate millions of reads to provide clues for analyzing novel or abnormal alternative splicing (AS) events in cells. However, current methods for exploring AS events are still far from being satisfactory. Here, we present Comprehensive AS Hunting (CASH), which constructs comprehensive splice sites including known and novel AS sites in cells, and identifies differentially AS events between cells. We illuminated the versatility of CASH on RNA-seq data from a wide range of species and also on simulated in silico data, validated the advantages of CASH over other AS predictors and exhibited novel differentially AS events...
April 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28379479/experimental-design-and-data-analysis-of-ago-rip-seq-experiments-for-the-identification-of-microrna-targets
#19
Diana Tichy, Julia Maria Anna Pickl, Axel Benner, Holger Sültmann
The identification of microRNA (miRNA) target genes is crucial for understanding miRNA function. Many methods for the genome-wide miRNA target identification have been developed in recent years; however, they have several limitations including the dependence on low-confident prediction programs and artificial miRNA manipulations. Ago-RNA immunoprecipitation combined with high-throughput sequencing (Ago-RIP-Seq) is a promising alternative. However, appropriate statistical data analysis algorithms taking into account the experimental design and the inherent noise of such experiments are largely lacking...
March 31, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28369159/context-based-retrieval-of-functional-modules-in-protein-protein-interaction-networks
#20
Maria Pamela Dobay, Silke Stertz, Mauro Delorenzi
Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein-protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods...
March 27, 2017: Briefings in Bioinformatics
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