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Leyi Wei, Shasha Luan, Luis Augusto Eijy Nagai, Ran Su, Quan Zou
Motivation: As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is recently shown to play crucial roles in restriction-modification systems. For better understanding of their functional mechanisms, it is fundamentally important to identify 4mC modification. Machine learning methods have recently emerged as an effective and efficient approach for the high-throughput identification of 4mC sites, although high predictive error rates are still challenging for existing methods...
September 19, 2018: Bioinformatics
Minoo Ashtiani, Mehdi Mirzaie, Mohieddin Jafari
Availability and implementation: CINNA is available in CRAN, including a tutorial. URL: Supplementary information: Supplementary data are available online.
September 19, 2018: Bioinformatics
Bin Guo, Baolin Wu
Motivation: Many GWAS conducted in the past decade have identified tens of thousands of disease related variants, which in total explained only part of the heritability for most traits. There remain many more genetics variants with small effect sizes to be discovered. This has motivated the development of sequencing studies with larger sample sizes and increased resolution of genotyped variants, e.g., the ongoing NHLBI Trans-Omics for Precision Medicine (TOPMed) whole genome sequencing project...
September 19, 2018: Bioinformatics
E Anatskiy, D P Ryan, B Grüning, L Arrigoni, T Manke, U Bönisch
Motivation: This paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples. Results: Starting with user requests, Parkour allows tracking and assessing samples based on predefined quality criteria through different stages of the sample preparation workflow. Ideally suited for academic core laboratories, the software aims to maximize efficiency and reduce turnaround time by intelligent sample grouping and a clear assignment of staff to work units...
September 19, 2018: Bioinformatics
Junfang Chen, Dietmar Lippold, Josef Frank, William Rayner, Andreas Meyer-Lindenberg, Emanuel Schwarz
Motivation: Genotype imputation is essential for genome-wide association studies (GWAS) to retrieve information of untyped variants and facilitate comparability across studies. However, there is a lack of automated pipelines that perform all required processing steps prior to and following imputation. Results: Based on widely used and freely available tools, we have developed Gimpute, an automated processing and imputation pipeline for genome-wide association data...
September 19, 2018: Bioinformatics
Qiuying Sha, Zhenchuan Wang, Xiao Zhang, Shuanglin Zhang
Summary: There is an increasing interest in joint analysis of multiple phenotypes for genome-wide association studies (GWASs) based on the following reasons. First, cohorts usually collect multiple phenotypes and complex diseases are usually measured by multiple correlated intermediate phenotypes. Second, jointly analyzing multiple phenotypes may increase statistical power for detecting genetic variants associated with complex diseases. Third, there is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases...
September 19, 2018: Bioinformatics
Alejandro Brenes, Angus I Lamond
Summary: The Encyclopedia of Proteome Dynamics (EPD) 'KinoViewer' is an interactive data visualisation tool designed for analysis and exploration of both protein and transcript data, showing expression of kinase genes in either Human or Mouse cells and tissues. The KinoViewer provides a comprehensive, updated graphical display of all human/mouse kinases and an open access analysis tool for the community with a user-friendly graphical interface. Availability and Implementation: The KinoViewer is based on a manually drawn SVG, which is utilised with D3...
September 19, 2018: Bioinformatics
Daniel Wiegreffe, Daniel Alexander, Peter F Stadler, Dirk Zeckzer
Motivation: RNA secondary structure is a useful representation for studying the function of RNA, which captures most of the free energy of RNA folding. Using empirically determined energy parameters, secondary structures of nucleic acids can be efficiently computed by recursive algorithms. Several software packages supporting this task are readily available. As RNA secondary structures are outerplanar graphs, they can be drawn without intersection in the plane. Interpretation by the practitioner is eased when these drawings conform to a series of additional constraints beyond outerplanarity...
September 19, 2018: Bioinformatics
Trang T Le, Ryan J Urbanowicz, Jason H Moore, Brett A McKinney
Motivation: Relief is a family of machine learning algorithms that uses nearest-neighbors to select features whose association with an outcome may be due to epistasis or statistical interactions with other features in high-dimensional data. Relief-based estimators are non-parametric in the statistical sense that they do not have a parameterized model with an underlying probability distribution for the estimator, making it difficult to determine the statistical significance of Relief-based attribute estimates...
September 18, 2018: Bioinformatics
Yuan Luo, Chengsheng Mao, Yiben Yang, Fei Wang, Faraz S Ahmad, Donna Arnett, Marguerite R Irvin, Sanjiv J Shah
Motivation: Hypertension is a heterogeneous syndrome in need of improved subtyping using phenotypic and genetic measurements with the goal of identifying subtypes of patients who share similar pathophysiologic mechanisms and may respond more uniformly to targeted treatments. Existing machine learning approaches often face challenges in integrating phenotype and genotype information and presenting to clinicians an interpretable model. We aim to provide informed patient stratification based on phenotype and genotype features...
September 15, 2018: Bioinformatics
Jaroslav Budis, Juraj Gazdarica, Jan Radvanszky, Gabor Szucs, Marcel Kucharik, Lucia Strieskova, Iveta Gazdaricova, Maria Harsanyova, Frantisek Duris, Gabriel Minarik, Martina Sekelska, Balint Nagy, Jan Turna, Tomas Szemes
Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test...
September 14, 2018: Bioinformatics
Nengjun Yi, Zaixiang Tang, Xinyan Zhang, Boyi Guo
Summary: BhGLM is a freely available R package that implements Bayesian hierarchical modeling for high-dimensional clinical and genomic data. It consists of functions for setting up various Bayesian hierarchical models, including generalized linear models (GLMs) and Cox survival models, with four types of prior distributions for coefficients, i.e. double-exponential, Student-t, mixture double-exponential, and mixture Student-t. These functions adapt fast and stable algorithms to estimate parameters...
September 13, 2018: Bioinformatics
Albert Casanovas, Óscar Gallardo, Montserrat Carrascal, Joaquin Abian
Motivation: Protein function is regulated by post-translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross-talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented towards the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs co-exist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides...
September 13, 2018: Bioinformatics
Patrick V Holec, Joseph Berleant, Mark Bathe, Michael E Birnbaum
Motivation: The study of T cell receptor repertoires has generated new insights into immune system recognition. However, the ability to robustly characterize these populations has been limited by technical barriers and an inability to reliably infer heterodimeric chain pairings for T cell receptors. Results: Here, we describe a novel analytical approach to an emerging immune repertoire sequencing method, improving the resolving power of this low-cost technology...
September 12, 2018: Bioinformatics
Tuan Trieu, Oluwatosin Oluwadare, Julia Wopata, Jianlin Cheng
Motivation: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization. Results: We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models, and the integration of these models with functional genomics data...
September 12, 2018: Bioinformatics
Kevin Y X Wang, Alexander M Menzies, Ines P Silva, James S Wilmott, Yibing Yan, Matthew Wongchenko, Richard F Kefford, Richard A Scolyer, Georgina V Long, Garth Tarr, Samuel Mueller, Jean Y H Yang
Motivation: Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes are important tools in Gene Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome...
September 12, 2018: Bioinformatics
Xian Liu, Mingfei Han, Chen Zhao, Cheng Chang, Yunping Zhu, Changhui Ge, Ronghua Yin, Yiqun Zhan, Changyan Li, Miao Yu, Fuchu He, Xiaoming Yang
Summary: Effective visualization is important for knowledge discovery when analysing expression profile data. However, existing tools for visually integrating expression profile data with KEGG pathway maps lack extensive interactive visualization operations. KeggExp simultaneously presents the pathway map of one pathway, dendrogram & heatmap of the genes in the pathway, and scatter map of one gene; and also provides interactive operations for highlighting specific genes on the pathway map, including differentially-expressed genes, co-expressed genes selected from the heatmap, and user-input genes...
September 10, 2018: Bioinformatics
Raffaele Giancarlo, Simona E Rombo, Filippo Utro
Motivation: Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy...
September 10, 2018: Bioinformatics
Oana M Enache, David L Lahr, Ted E Natoli, Lev Litichevskiy, David Wadden, Corey Flynn, Joshua Gould, Jacob K Asiedu, Rajiv Narayan, Aravind Subramanian
Motivation: Facilitated by technological improvements, pharmacologic and genetic perturbational datasets have grown in recent years to include millions of experiments. Sharing these diverse data creates many opportunities for discovery, but the unprecedented size of data generated and its complex associated metadata have created data storage and integration challenges. Results: We present the GCTx file format and a suite of open-source packages for the efficient storage, serialization, and analysis of dense two-dimensional matrices...
September 10, 2018: Bioinformatics
Jaroslav Budiš, Marcel Kucharík, František Duriš, Juraj Gazdarica, Michaela Zrubcová, Andrej Ficek, Tomáš Szemes, Brona Brejová, Jan Radvanszky
Motivation: Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays...
September 8, 2018: Bioinformatics
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