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Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
Thomas O McDonald, Franziska Michor
Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own...
March 16, 2017: Bioinformatics
Robert Stewart, Mick Watson
Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs. Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets...
March 9, 2017: Bioinformatics
Xiuwen Zheng, Stephanie M Gogarten, Michael Lawrence, Adrienne Stilp, Matthew P Conomos, Bruce S Weir, Cathy Laurie, David Levine
Motivation: Whole-genome sequencing (WGS) data is being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package "SeqArray" for storing variant calls in an arrayoriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing...
March 16, 2017: Bioinformatics
Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Motivation: While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia. Results: To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem...
February 22, 2017: Bioinformatics
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
Denis Agniel, Boris P Hejblum
As gene expression measurement technology is shifting from microarrays to sequencing, the statistical tools available for their analysis must be adapted since RNA-seq data are measured as counts. It has been proposed to model RNA-seq counts as continuous variables using nonparametric regression to account for their inherent heteroscedasticity. In this vein, we propose tcgsaseq, a principled, model-free, and efficient method for detecting longitudinal changes in RNA-seq gene sets defined a priori. The method identifies those gene sets whose expression varies over time, based on an original variance component score test accounting for both covariates and heteroscedasticity without assuming any specific parametric distribution for the (transformed) counts...
March 10, 2017: Biostatistics
Raziur Rahman, John Otridge, Ranadip Pal
Summary: IntegratedMRF is an open-source R implementation for integrating drug response predictions from various genomic characterizations using univariate or multivariate random forests that includes various options for error estimation techniques. The integrated framework was developed following superior performance of random forest based methods in NCI-DREAM drug sensitivity prediction challenge. The computational framework can be applied to estimate mean and confidence interval of drug response prediction errors based on ensemble approaches with various combinations of genetic and epigenetic characterizations as inputs...
February 6, 2017: Bioinformatics
Panagiota Filippou, Giampiero Marra, Rosalba Radice
This article proposes a penalized likelihood method to estimate a trivariate probit model, which accounts for several types of covariate effects (such as linear, nonlinear, random, and spatial effects), as well as error correlations. The proposed approach also addresses the difficulty in estimating accurately the correlation coefficients, which characterize the dependence of binary responses conditional on covariates. The parameters of the model are estimated within a penalized likelihood framework based on a carefully structured trust region algorithm with integrated automatic multiple smoothing parameter selection...
March 4, 2017: Biostatistics
Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei
Motivation: Over the past decade, there has been a remarkable improvement in our understanding of the role of genetic variation in complex human diseases, especially via genome-wide association studies. However, the underlying molecular mechanisms are still poorly characterized, impending the development of therapeutic interventions. Identifying genetic variants that influence the expression level of a gene, i.e. expression quantitative trait loci (eQTLs), can help us understand how genetic variants influence traits at the molecular level...
March 11, 2017: Bioinformatics
Daniel Schlauch, Heide Fier, Christoph Lange
Motivation: In order to minimize the effects of genetic confounding on the analysis of high-throughput genetic association studies, e.g. (whole-genome) sequencing (WGS) studies, genome-wide association studies (GWAS), etc., we propose a general framework to assess and to test formally for genetic heterogeneity among study subjects. As the approach fully utilizes the recent ancestor information captured by rare variants, it is especially powerful in WGS studies. Even for relatively moderate sample sizes, the proposed testing framework is able to identify study subjects that are genetically too similar, e...
February 22, 2017: Bioinformatics
Michal Sharabi-Schwager, Etti Or, Ron Ophir
Summary: A prerequisite to clustering noisy data, such as gene-expression data, is the filtering step. As an alternative to this step, the ctsGE R-package applies a sorting step in which all of the data are divided into small groups. The groups are divided according to how the time points are related to the time-series median. Then clustering is performed separately on each group. Thus, the clustering is done in two steps. First, an expression index (i.e., a sequence of 1, -1, and 0) is defined and genes with the same index are grouped together, and then each group of genes is clustered by k-means to create subgroups...
March 3, 2017: Bioinformatics
Yun Zhang, David J Topham, Juilee Thakar, Xing Qiu
Motivation: Gene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements; and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing...
February 21, 2017: Bioinformatics
Grete Lottrup, Kirstine Belling, Henrik Leffers, John E Nielsen, Marlene D Dalgaard, Anders Juul, Niels E Skakkebæk, Søren Brunak, Ewa Rajpert-De Meyts
STUDY QUESTION: Do human adult Leydig cells (ALCs) within hyperplastic micronodules display characteristics of foetal LCs (FLCs)? SUMMARY ANSWER: The gene expression profiles of FLCs and all ALC subgroups were clearly different, but there were no significant differences in expressed genes between the normally clustered and hyperplastic ALCs. WHAT IS KNOWN ALREADY: LCs are the primary androgen producing cells in males throughout development and appear in chronologically distinct populations; FLCs, neonatal LCs and ALCs...
March 17, 2017: Molecular Human Reproduction
Stephen R Bond, Karl E Keat, Sofia N Barreira, Andreas D Baxevanis
The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction...
February 25, 2017: Molecular Biology and Evolution
Lois W Choi-Kain, Ellen F Finch, Sara R Masland, James A Jenkins, Brandon T Unruh
PURPOSE OF THE REVIEW: This review summarizes advances in treatments for adults with borderline personality disorder (BPD) in the last 5 years. RECENT FINDINGS: Evidence-based advances in the treatment of BPD include a delineation of generalist models of care in contrast to specialist treatments, identification of essential effective elements of dialectical behavioral therapy (DBT), and the adaptation of DBT treatment to manage post-traumatic stress disorder (PTSD) and BPD...
2017: Current Behavioral Neuroscience Reports
Filipa Tomé, Karel Jansseune, Bernadette Saey, Jack Grundy, Korneel Vandenbroucke, Matthew A Hannah, Henning Redestig
BACKGROUND: Growth is an important parameter to consider when studying the impact of treatments or mutations on plant physiology. Leaf area and growth rates can be estimated efficiently from images of plants, but the experiment setup, image analysis, and statistical evaluation can be laborious, often requiring substantial manual effort and programming skills. RESULTS: Here we present rosettR, a non-destructive and high-throughput phenotyping protocol for the measurement of total rosette area of seedlings grown in plates in sterile conditions...
2017: Plant Methods
S B Choudhary, M Kumar, I Chowdhury, R K Singh, S P Pandey, H K Sharma, P G Karmakar
Tossa jute is an important natural fiber crop of Southeast Asian countries including India, Bangladesh, China, Thailand, Myanmar etc. Traditional industrial application of jute fiber is limited to the packaging products like hessians, sacks, etc. and the fiber found unsuitable for textile industries largely due to significantly high lignin content. Therefore, understanding genetic factors underlying lignin biosynthesis in tossa jute holds promise for jute based product diversification. The major limiting factor in undertaking such study is unavailability of efficient protocol for RNA extraction at secondary growth active stage of tossa jute...
June 2016: 3 Biotech
Andreas Kuehnapfel, Fabian Schwarzenberger, Markus Scholz
Conditional power of survival endpoints at interim analyses can support decisions on continuing a trial or stopping it for futility. When a cure fraction becomes apparent, conditional power cannot be calculated accurately using simple survival models, e.g. the exponential model. Non-mixture models consider such cure fractions. In this paper, we derive conditional power functions for non-mixture models, namely the non-mixture exponential, the non-mixture Weibull, and the non-mixture Gamma models. Formulae were implemented in the R package CP...
March 17, 2017: International Journal of Biostatistics
Debalin Sarangi, Andrew J Tyre, Eric L Patterson, Todd A Gaines, Suat Irmak, Stevan Z Knezevic, John L Lindquist, Amit J Jhala
Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate...
March 22, 2017: Scientific Reports
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