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Briefings in Bioinformatics

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https://www.readbyqxmd.com/read/28679163/network-approaches-to-systems-biology-analysis-of-complex-disease-integrative-methods-for-multi-omics-data
#1
Jingwen Yan, Shannon L Risacher, Li Shen, Andrew J Saykin
In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of biological interconnections, and much success has been achieved using systems biology approaches. However, because of the typical focus on one single omics layer at a time, existing systems biology findings explain only a modest portion of complex disease. Recent advances in multi-omics data collection and sharing present us new opportunities for studying complex diseases in a more comprehensive fashion, and yet simultaneously create new challenges considering the unprecedented data dimensionality and diversity...
June 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28673025/alignment-free-inference-of-hierarchical-and-reticulate-phylogenomic-relationships
#2
Guillaume Bernard, Cheong Xin Chan, Yao-Ban Chan, Xin-Yi Chua, Yingnan Cong, James M Hogan, Stefan R Maetschke, Mark A Ragan
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA...
June 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28651335/critical-evaluation-of-bioinformatics-tools-for-the-prediction-of-protein-crystallization-propensity
#3
Huilin Wang, Liubin Feng, Geoffrey I Webb, Lukasz Kurgan, Jiangning Song, Donghai Lin
No abstract text is available yet for this article.
June 22, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28645151/the-genetic-architecture-of-heterochrony-as-a-quantitative-trait-lessons-from-a-computational-model
#4
Lidan Sun, Mengmeng Sang, Chenfei Zheng, Dongyang Wang, Hexin Shi, Kaiyue Liu, Yanfang Guo, Tangren Cheng, Qixiang Zhang, Rongling Wu
No abstract text is available yet for this article.
June 22, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#5
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28633390/investigating-microrna-mediated-regulation-of-the-nascent-nuclear-transcripts-in-plants-a-bioinformatics-workflow
#6
Dongliang Yu, Zhonghai Tang, Chaogang Shao, Xiaoxia Ma, Taihe Xiang, Zhihong Fan, Huizhong Wang, Yijun Meng
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs...
June 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28633401/biomedical-text-mining-for-research-rigor-and-integrity-tasks-challenges-directions
#7
Halil Kilicoglu
An estimated quarter of a trillion US dollars is invested in the biomedical research enterprise annually. There is growing alarm that a significant portion of this investment is wasted because of problems in reproducibility of research findings and in the rigor and integrity of research conduct and reporting. Recent years have seen a flurry of activities focusing on standardization and guideline development to enhance the reproducibility and rigor of biomedical research. Research activity is primarily communicated via textual artifacts, ranging from grant applications to journal publications...
June 13, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28605404/recent-computational-developments-on-clip-seq-data-analysis-and-microrna-targeting-implications
#8
Silvia Bottini, David Pratella, Valerie Grandjean, Emanuela Repetto, Michele Trabucchi
Cross-Linking Immunoprecipitation associated to high-throughput sequencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell or tissue samples. Recent technological and computational advances permit the analysis of many CLIP-seq samples simultaneously, allowing us to reveal the comprehensive network of RNA-protein interaction and to integrate it to other genome-wide analyses. Therefore, the design and quality management of the CLIP-seq analyses are of critical importance to extract clean and biological meaningful information from CLIP-seq experiments...
June 12, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28605403/power-and-sample-size-calculations-for-high-throughput-sequencing-based-experiments
#9
Chung-I Li, David C Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo
Power/sample size (power) analysis estimates the likelihood of successfully finding the statistical significance in a data set. There has been a growing recognition of the importance of power analysis in the proper design of experiments. Power analysis is complex, yet necessary for the success of large studies. It is important to design a study that produces statistically accurate and reliable results. Power computation methods have been well established for both microarray-based gene expression studies and genotyping microarray-based genome-wide association studies...
June 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575155/dynamic-bm-multispecies-dynamic-bodymap-database-from-temporal-rna-seq-data
#10
Ya Cui, Xiaowei Chen, Yiwei Niu, Dongpeng Wang, Huaxia Luo, Zhen Fan, Dan Wang, Wei Wu, Xueyi Teng, Shunmin He, Jianjun Luo, Runsheng Chen
Biological processes, especially developmental processes, are often dynamic. Previous BodyMap projects for human and mouse have provided researchers with portals to tissue-specific gene expression, but these efforts have not included dynamic gene expression patterns. Over the past few years, substantial progress in our understanding of the molecular mechanisms of protein-coding and long noncoding RNA (lncRNA) genes in development processes has been achieved through numerous time series RNA sequencing (RNA-seq) studies...
June 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575146/a-comprehensive-evaluation-of-popular-proteomics-software-workflows-for-label-free-proteome-quantification-and-imputation
#11
Tommi Välikangas, Tomi Suomi, Laura L Elo
Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them...
May 31, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575183/the-genetic-architecture-of-heterochronsy-as-a-quantitative-trait-lessons-from-a-computational-model
#12
Lidan Sun, Mengmeng Sang, Chenfei Zheng, Dongyang Wang, Hexin Shi, Kaiyue Liu, Yanfang Guo, Tangren Cheng, Qixiang Zhang, Rongling Wu
Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes...
May 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575144/cernas-in-plants-computational-approaches-and-associated-challenges-for-target-mimic-research
#13
Alexandre Rossi Paschoal, Irma Lozada-Chávez, Douglas Silva Domingues, Peter F Stadler
The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions...
May 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575143/seeing-the-wood-for-the-trees-a-forest-of-methods-for-optimization-and-omic-network-integration-in-metabolic-modelling
#14
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees. Driven by this analogy, we here present a 'forest' of principal methods used for constraint-based modelling in systems biology. This provides a tree-based view of methods available to prospective modellers, also available in interactive version at http://modellingmetabolism...
May 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28575140/optimizing-drug-development-in-oncology-by-clinical-trial-simulation-why-and-how
#15
Jocelyn Gal, Gérard Milano, Jean-Marc Ferrero, Esma Saâda-Bouzid, Julien Viotti, Sylvie Chabaud, Paul Gougis, Christophe Le Tourneau, Renaud Schiappa, Agnes Paquet, Emmanuel Chamorey
In therapeutic research, the safety and efficacy of pharmaceutical products are necessarily tested on humans via clinical trials after an extensive and expensive preclinical development period. Methodologies such as computer modeling and clinical trial simulation (CTS) might represent a valuable option to reduce animal and human assays. The relevance of these methods is well recognized in pharmacokinetics and pharmacodynamics from the preclinical phase to postmarketing. However, they are barely used and are poorly regarded for drug approval, despite Food and Drug Administration and European Medicines Agency recommendations...
May 29, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28535295/bioinformatic-analysis-of-bacteria-and-host-cell-dual-rna-sequencing-experiments
#16
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
#17
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
#18
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
#19
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
#20
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
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