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https://www.readbyqxmd.com/read/29684008/diversity-in-binding-regulation-and-evolution-revealed-from-high-throughput-chip
#1
Sneha Mitra, Anushua Biswas, Leelavati Narlikar
Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries...
April 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29669107/dambe7-new-and-improved-tools-for-data-analysis-in-molecular-biology-and-evolution
#2
Xuhua Xia
DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently...
April 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29664927/seedvicious-analysis-of-microrna-target-and-near-target-sites
#3
Antonio Marco
Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation...
2018: PloS One
https://www.readbyqxmd.com/read/29653352/online-molecular-image-repository-and-analysis-system-a-multicenter-collaborative-open-source-infrastructure-for-molecular-imaging-research-and-application
#4
Mahabubur Rahman, Hiroshi Watabe
Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management...
April 4, 2018: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29622804/producing-genome-structure-populations-with-the-dynamic-and-automated-pgs-software
#5
Nan Hua, Harianto Tjong, Hanjun Shin, Ke Gong, Xianghong Jasmine Zhou, Frank Alber
Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments...
May 2018: Nature Protocols
https://www.readbyqxmd.com/read/29618319/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing
#6
Clemens L Weiß, Marina Pais, Liliana M Cano, Sophien Kamoun, Hernán A Burbano
BACKGROUND: Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model...
April 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29608567/parbibit-parallel-tool-for-binary-biclustering-on-modern-distributed-memory-systems
#7
Jorge González-Domínguez, Roberto R Expósito
Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, a parallel tool to accelerate the search of interesting biclusters on binary datasets, which are very popular on different fields such as genetics, marketing or text mining. It is based on the state-of-the-art sequential Java tool BiBit, which has been proved accurate by several studies, especially on scenarios that result on many large biclusters...
2018: PloS One
https://www.readbyqxmd.com/read/29596608/simphospho-a-software-tool-enabling-confident-phosphosite-assignment
#8
Veronika Suni, Tomi Suomi, Tomoya Tsubosaka, Susumu Y Imanishi, Laura L Elo, Garry L Corthals
Motivation: Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments...
March 27, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29594411/recent-advances-in-the-ultrascan-solution-modeller-us-somo-hydrodynamic-and-small-angle-scattering-data-analysis-and-simulation-suite
#9
Emre Brookes, Mattia Rocco
The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release...
March 28, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29572752/development-of-a-smart-mobile-data-module-for-fetal-monitoring-in-e-healthcare
#10
Agathe Houzé de l'Aulnoit, Samuel Boudet, Michaël Génin, Pierre-François Gautier, Jessica Schiro, Denis Houzé de l'Aulnoit, Régis Beuscart
The fetal heart rate (FHR) is a marker of fetal well-being in utero (when monitoring maternal and/or fetal pathologies) and during labor. Here, we developed a smart mobile data module for the remote acquisition and transmission (via a Wi-Fi or 4G connection) of FHR recordings, together with a web-based viewer for displaying the FHR datasets on a computer, smartphone or tablet. In order to define the features required by users, we modelled the fetal monitoring procedure (in home and hospital settings) via semi-structured interviews with midwives and obstetricians...
March 23, 2018: Journal of Medical Systems
https://www.readbyqxmd.com/read/29560826/gxgrare-gene-gene-interaction-analysis-method-for-rare-variants-from-high-throughput-sequencing-data
#11
Minseok Kwon, Sangseob Leem, Joon Yoon, Taesung Park
BACKGROUND: With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it has been shown that only a small proportion of the genetic etiology of complex diseases could be explained by the genetic factors identified from GWAS. This missing heritability could possibly be explained by gene-gene interaction (epistasis) and rare variants. There has been an exponential growth of gene-gene interaction analysis for common variants in terms of methodological developments and practical applications...
March 19, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29547981/nanopack-visualizing-and-processing-long-read-sequencing-data
#12
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven
Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot...
March 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29539389/droids-1-20-a-gui-based-pipeline-for-gpu-accelerated-comparative-protein-dynamics
#13
Gregory A Babbitt, Jamie S Mortensen, Erin E Coppola, Lily E Adams, Justin K Liao
Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures...
March 13, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29525965/step-by-step-construction-of-gene-co-expression-networks-from-high-throughput-arabidopsis-rna-sequencing-data
#14
Orlando Contreras-López, Tomás C Moyano, Daniela C Soto, Rodrigo A Gutiérrez
The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29522192/esatac-an-easy-to-use-systematic-pipeline-for-atac-seq-data-analysis
#15
Zheng Wei, Wei Zhang, Huan Fang, Yanda Li, Xiaowo Wang
Summary: ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines...
March 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29499649/bpwrapper-bioperl-based-sequence-and-tree-utilities-for-rapid-prototyping-of-bioinformatics-pipelines
#16
Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G Vieira, Wei-Gang Qiu
BACKGROUND: Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl ( http://bioperl...
March 2, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29474733/bacmeta-simulator-for-genomic-evolution-in-bacterial-metapopulations
#17
Aleksi Sipola, Pekka Marttinen, Jukka Corander
Summary: The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and microepidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474519/victree-an-automated-framework-for-taxonomic-classification-from-protein-sequences
#18
Sejal Modha, Anil Thanki, Susan F Cotmore, Andrew J Davison, Joseph Hughes
Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29464735/molup-a-vmd-plugin-to-handle-qm-and-oniom-calculations-using-the-gaussian-software
#19
Henrique S Fernandes, Maria J Ramos, Nuno M F S A Cerqueira
The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations...
February 21, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29444236/findgse-estimating-genome-size-variation-within-human-and-arabidopsis-using-k-mer-frequencies
#20
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
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