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https://www.readbyqxmd.com/read/29036655/mfib-a-repository-of-protein-complexes-with-mutual-folding-induced-by-binding
#1
Erzsébet Fichó, István Reményi, István Simon, Bálint Mészáros
Motivation: It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036643/glass-assisted-and-standardized-assessment-of-gene-variations-from-sanger-sequence-trace-data
#2
Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas
Motivation: Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise. Results: We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in 'curated' or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036627/using-uncertainty-to-link-and-rank-evidence-from-biomedical-literature-for-model-curation
#3
Chrysoula Zerva, Riza Batista-Navarro, Philip Day, Sophia Ananiadou
Motivation: In recent years, there has been great progress in the field of automated curation of biomedical networks and models, aided by text mining methods that provide evidence from literature. Such methods must not only extract snippets of text that relate to model interactions, but also be able to contextualize the evidence and provide additional confidence scores for the interaction in question. Although various approaches calculating confidence scores have focused primarily on the quality of the extracted information, there has been little work on exploring the textual uncertainty conveyed by the author...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036619/the-effects-of-dna-supercoiling-on-g-quadruplex-formation
#4
Doreen A T Sekibo, Keith R Fox
Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036616/deeploc-prediction-of-protein-subcellular-localization-using-deep-learning
#5
José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther
Motivation: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036597/faucet-streaming-de-novo-assembly-graph-construction
#6
Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir
Motivation: We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased. Results: Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036596/delphiforce-web-server-electrostatic-forces-and-energy-calculations-and-visualization
#7
Lin Li, Zhe Jia, Yunhui Peng, Arghya Chakravorty, Lexuan Sun, Emil Alexov
Summary: Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#8
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036584/cgheliparm-analysis-of-dsdna-helical-parameters-for-coarse-grained-martini-molecular-dynamics-simulations
#9
Ignacio Faustino, S J Marrink
Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. Availability and implementation: This package works with Python 2.7 on MacOS and Linux...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036579/hybridsim-vs-a-web-server-for-large-scale-ligand-based-virtual-screening-using-hybrid-similarity-recognition-techniques
#10
Jinling Shang, Xi Dai, Yecheng Li, Marco Pistolozzi, Ling Wang
Summary: Molecular-similarity searches based on two-dimensional (2D) fingerprint and three-dimensional (3D) shape represent two widely used ligand-based virtual screening (VS) methods in computer-aided drug design. 2D fingerprint-based VS utilizes the binary fragment information on a known ligand, whereas 3D shape-based VS takes advantage of geometric information for predefined features from a 3D conformation. Given their different advantages, it would be desirable to hybridize 2D fingerprint and 3D shape molecular-similarity approaches in drug discovery...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036577/biobankuniverse-automatic-matchmaking-between-datasets-for-biobank-data-discovery-and-integration
#11
Chao Pang, Fleur Kelpin, David van Enckevort, Niina Eklund, Kaisa Silander, Dennis Hendriksen, Mark de Haan, Jonathan Jetten, Tommy de Boer, Bart Charbon, Petr Holub, Hans Hillege, Morris A Swertz
Motivation: Biobanks are indispensable for large-scale genetic/epidemiological studies, yet it remains difficult for researchers to determine which biobanks contain data matching their research questions. Results: To overcome this, we developed a new matching algorithm that identifies pairs of related data elements between biobanks and research variables with high precision and recall. It integrates lexical comparison, Unified Medical Language System ontology tagging and semantic query expansion...
August 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036562/nandb-number-and-brightness-in-r-with-a-novel-automatic-detrending-algorithm
#12
Rory Nolan, Luis A J Alvarez, Jonathan Elegheert, Maro Iliopoulou, G Maria Jakobsdottir, Marina Rodriguez-Muñoz, A Radu Aricescu, Sergi Padilla-Parra
Summary: An R package for performing number and brightness image analysis, with the implementation of a novel automatic detrending algorithm. Availability and implementation: Available at https://github.com/rorynolan/nandb for all platforms. Contact: rnolan@well.ox.ac.uk or spadilla@well.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
July 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036558/methrafo-medip-seq-methylation-estimate-using-a-random-forest-regressor
#13
Jun Ding, Ziv Bar-Joseph
Motivation: Profiling of genome wide DNA methylation is now routinely performed when studying development, cancer and several other biological processes. Although Whole genome Bisulfite Sequencing provides high-quality methylation measurements at the resolution of nucleotides, it is relatively costly and so several studies have used alternative methods for such profiling. One of the most widely used low cost alternatives is MeDIP-Seq. However, MeDIP-Seq is biased for CpG enriched regions and thus its results need to be corrected in order to determine accurate methylation levels...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036557/standardizing-biomass-reactions-and-ensuring-complete-mass-balance-in-genome-scale-metabolic-models
#14
Siu H J Chan, Jingyi Cai, Lin Wang, Margaret N Simons-Senftle, Costas D Maranas
Motivation: In a genome-scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol -1 . This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R). Results: We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#15
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#16
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036535/ploc-manimal-predict-subcellular-localization-of-animal-proteins-with-both-single-and-multiple-sites
#17
Xiang Cheng, Shu-Guang Zhao, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou
Motivation: Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036531/spatkin-a-simulator-for-rule-based-modeling-of-biomolecular-site-dynamics-on-surfaces
#18
Marek Kochanczyk, William S Hlavacek, Tomasz Lipniacki
Summary: Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation...
July 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036527/isyte-2-0-a-database-for-expression-based-gene-discovery-in-the-eye
#19
Atul Kakrana, Andrian Yang, Deepti Anand, Djordje Djordjevic, Deepti Ramachandruni, Abhyudai Singh, Hongzhan Huang, Joshua W K Ho, Salil A Lachke
Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036526/dynapho-a-web-platform-for-inferring-the-dynamics-of-time-series-phosphoproteomics
#20
Chia-Lang Hsu, Jian-Kai Wang, Pei-Chun Lu, Hsuan-Cheng Huang, Hsueh-Fen Juan
Summary: Large-scale phosphoproteomics studies have improved our understanding of dynamic cellular signaling, but the downstream analysis of phosphoproteomics data is still a bottleneck. We develop DynaPho, a useful web-based tool providing comprehensive and in-depth analyses of time-course phosphoproteomics data, making analysis intuitive and accessible to non-bioinformatics experts. The tool currently implements five analytic modules, which reveal the transition of biological pathways, kinase activity, dynamics of interaction networks and the predicted kinase-substrate associations...
July 7, 2017: Bioinformatics
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