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Wei Lan, Min Li, Kaijie Zhao, Jin Liu, Fang-Xiang Wu, Yi Pan, Jianxin Wang
MOTIVATION: Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. RESULTS: In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources...
October 14, 2016: Bioinformatics
Xingjian Xu, Zhaohua Ji, Zhang Zhang
: Phylogeny reconstruction is fundamentally crucial for molecular evolutionary studies but remains computationally challenging. Here we present CloudPhylo, a tool built on Spark that is capable of processing large-scale datasets for phylogeny reconstruction. As testified on empirical data, CloudPhylo is well suited for big data analysis, achieving high efficiency and good scalability on phylogenetic tree inference. AVAILABILITY: CONTACT: zhangzhang@big...
October 14, 2016: Bioinformatics
Joseph H Marcus, John Novembre
: One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The geographic distribution of a genetic variant can also be of great utility for medical/clinical geneticists and collectively many genetic variants can reveal population structure. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants...
October 14, 2016: Bioinformatics
Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
MOTIVATION: Given a compound, can we predict which ATC (Anatomical Therapeutic Chemical) class/classes it belongs to? It is a challenging problem since the information thus obtained can be used to deduce its possible active ingredients, as well as its therapeutic, pharmacological and chemical properties. And hence the pace of drug development could be substantially expedited. But this problem is by no means an easy one. Particularly, some drugs or compounds may belong to two or more ATC classes...
October 14, 2016: Bioinformatics
Elisa Salviato, Vera Djordjilović, Monica Chiogna, Chiara Romualdi
: In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data-gene expression, RPKM/FPKM or protein abundances-from two conditions, namely, a reference condition and a perturbation of it...
October 14, 2016: Bioinformatics
Ekaterina A Khramtsova, Barbara E Stranger
: Over the last decade, genome-wide association studies (GWAS) have generated vast amounts of analysis results, requiring development of novel tools for data visualization. Quantile-quantile (QQ) plots and Manhattan plots are classical tools which have been utilized to visually summarize GWAS results and identify genetic variants significantly associated with traits of interest. However, static visualizations are limiting in the information that can be shown. Here we present ASSOCPLOTS: , a python package for viewing and exploring GWAS results not only using classic static Manhattan and QQ plots, but also through a dynamic extension which allows to interactively visualize the relationships between GWAS results from multiple cohorts or studies...
October 14, 2016: Bioinformatics
Daniel P Russo, Marlene T Kim, Wenyi Wang, Daniel Pinolini, Sunil Shende, Judy Strickland, Thomas Hartung, Hao Zhu
: We have developed a public Chemical In vitro - In vivo Profiling (CIIPro) portal, which can automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds. For compounds with in vivo target activity data (e.g. animal toxicity testing results), the integrated cheminformatics algorithm will optimize the extracted biological data using in vitro - in vivo correlations. The resulting in vitro biological data for target compounds can be used for read-across risk assessment of target compounds...
October 14, 2016: Bioinformatics
Giacomo Janson, Chengxin Zhang, Maria Giulia Prado, Alessandro Paiardini
MOTIVATION: The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod. RESULTS: The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided...
October 13, 2016: Bioinformatics
Vojtech Bystry, Tomas Reigl, Adam Krejci, Martin Demko, Barbora Hanakova, Andrea Grioni, Henrik Knecht, Max Schlitt, Peter Dreger, Leopold Sellner, Dietrich Herrmann, Marine Pingeon, Myriam Boudjoghra, Jos Rijntjes, Christiane Pott, Anton W Langerak, Patricia J T A Groenen, Frederic Davi, Monika Brüggemann, Nikos Darzentas
MOTIVATION: The study of immunoglobulins and T cell receptors using next-generation sequencing has finally allowed exploring immune repertoires and responses in their immense variability and complexity. Unsurprisingly, their analysis and interpretation is a highly convoluted task. RESULTS: We thus implemented ARResT/Interrogate, a web-based, interactive application. It can organize and filter large amounts of immunogenetic data by numerous criteria, calculate several relevant statistics, and present results in the form of multiple interconnected visualizations...
October 13, 2016: Bioinformatics
Iakov I Davydov, Marc Robinson-Rechavi, Nicolas Salamin
MOTIVATION: Codon models are widely used to identify the signature of selection at the molecular level and to test for changes in selective pressure during the evolution of genes encoding proteins. The large size of the state space of the Markov processes used to model codon evolution makes it difficult to use these models with large biological datasets. We propose here to use state aggregation to reduce the state space of codon models and, thus, improve the computational performance of likelihood estimation on these models...
October 2, 2016: Bioinformatics
Stefan Canzar, Karlynn E Neu, Qingming Tang, Patrick C Wilson, Aly A Khan
MOTIVATION: The B-cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-seq have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-seq (scRNA-seq) in B cells has been largely unstudied. RESULTS: We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single cell resolution...
October 2, 2016: Bioinformatics
Sufang Wang, Michael Gribskov
MOTIVATION: With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo transcriptome assemblies and how the assembly quality influences downstream analysis. RESULTS: We used two authentic RNA-Seq datasets from Arabidopsis thaliana, and produced transcriptome assemblies using eight programs with a series of k-mer sizes (from 25 to 71), including BinPacker, Bridger, IDBA-tran, Oases-Velvet, SOAPdenovo-Trans, SSP, Trans-ABySS and Trinity...
September 30, 2016: Bioinformatics
Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y Yip, Ting-Fung Chan
MOTIVATION: Optical mapping is a technique for capturing fluorescent signal patterns of long DNAmolecules (in the range of 0.1 Mbp to 1 Mbp). Recently, it has been complementing the widely-used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations. Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping...
September 30, 2016: Bioinformatics
Dmytro Guzenko, Sergei V Strelkov
MOTIVATION: Modern algorithms for de novo prediction of protein structures typically output multiple full-length models (decoys) rather than a single solution. Subsequent clustering of such decoys is used both to gauge the success of the modelling and to decide on the most native-like conformation. At the same time, partial protein models are sufficient for some applications such as crystallographic phasing by molecular replacement (MR) in particular, provided these models represent a certain part of the target structure with reasonable accuracy...
September 30, 2016: Bioinformatics
Ilham Ayub Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, Vladimir B Bajic
MOTIVATION: The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ(70) promoters in Escherichia coli Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E...
September 30, 2016: Bioinformatics
Zhi-Yong Liang, Hong-Yan Lai, Huan Yang, Chang-Jian Zhang, Hui Yang, Huan-Huan Wei, Xin-Xin Chen, Ya-Wei Zhao, Zhen-Dong Su, Wen-Chao Li, En-Ze Deng, Hua Tang, Wei Chen, Hao Lin
: In prokaryotes, the σ(54) promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on σ(54) promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for σ(54) promoter, a free and easy accessed database called Pro54DB (σ(54) promoter database) was built to collect information of σ(54) promoter...
September 30, 2016: Bioinformatics
Christopher Barrett, Fenix W Huang, Christian M Reidys
MOTIVATION: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. RESULTS: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures...
September 30, 2016: Bioinformatics
Monther Alhamdoosh, Milica Ng, Nicholas J Wilson, Julie M Sheridan, Huy Huynh, Michael J Wilson, Matthew E Ritchie
MOTIVATION: Gene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular data set. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions...
September 30, 2016: Bioinformatics
Krishna Choudhary, Luyao Ruan, Fei Deng, Nathan Shih, Sharon Aviran
: To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approaches continues to emerge, a universal framework is needed to quantitatively ensure consistent and high-quality data. We present SE-Qualyzer, a visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure profiling experiments...
September 30, 2016: Bioinformatics
Jonathan W Nelson, Jiri Sklenar, Anthony P Barnes, Jessica Minnier
: Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful methodology to quantify global gene expression patterns in various contexts from single cells to whole tissues. The tremendous amount of data generated by this profiling technology presents a daunting challenge in terms of effectively visualizing and interpreting results. Convenient and intuitive data interfaces are critical for researchers to easily upload, analyze, and visualize their RNAseq data. We designed the START (Shiny Transcriptome Analysis Resource Tool) App with these requirements in mind...
September 30, 2016: Bioinformatics
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