References of "Bioinformatics (Oxford, England)"
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See detailMINERVA API and plugins: opening molecular network analysis and visualization to the community.
Hoksza, David UL; Gawron, Piotr UL; Ostaszewski, Marek UL et al

in Bioinformatics (Oxford, England) (2019)

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and ... [more ▼]

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu. [less ▲]

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See detailFALCON: A Toolbox for the Fast Contextualisation of Logical Networks.
De Landtsheer, Sébastien UL; Trairatphisan, Panuwat UL; Lucarelli, Philippe UL et al

in Bioinformatics (Oxford, England) (2017)

Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer ... [more ▼]

Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results: We have developed a computational approach to contextualise logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualise networks, which includes a pipeline for conducting parameter analysis, knockouts, and easy and fast model investigation. The contextualised models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. Availability and implementation: FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON . FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. Contact: thomas.sauter@uni.lu. Supplementary information: Supplementary data are available at Bioinformatics online. [less ▲]

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See detailSmartR: An open-source platform for interactive visual analytics for translational research data.
Herzinger, Sascha UL; Gu, Wei UL; Satagopam, Venkata UL et al

in Bioinformatics (Oxford, England) (2017)

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre ... [more ▼]

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. Contact: reinhard.schneider@uni.lu. Supplementary information: Supplementary data are available at Bioinformatics online. Availability: : The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. [less ▲]

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See detailmapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
Jonsson, Hakon; Ginolhac, Aurélien UL; Schubert, Mikkel et al

in Bioinformatics (Oxford, England) (2013), 29(13), 1682-4

MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary ... [more ▼]

MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples. RESULTS: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (lambda), nick frequency (nu) and cytosine deamination rates in both double-stranded regions ( ) and overhangs ( ). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. AVAILABILITY: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. [less ▲]

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See detailmapDamage: testing for damage patterns in ancient DNA sequences.
Ginolhac, Aurélien UL; Rasmussen, Morten; Gilbert, M. Thomas P. et al

in Bioinformatics (Oxford, England) (2011), 27(15), 2153-5

SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage ... [more ▼]

SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. AVAILABILITY AND IMPLEMENTATION: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems. [less ▲]

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See detailrBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks.
Thorleifsson, Stefan Gretar; Thiele, Ines UL

in Bioinformatics (Oxford, England) (2011), 27(14), 2009-10

MOTIVATION: Genome-scale metabolic networks are widely used in systems biology. However, to date no freely available tool exists that ensures quality control during the reconstruction process. RESULTS ... [more ▼]

MOTIVATION: Genome-scale metabolic networks are widely used in systems biology. However, to date no freely available tool exists that ensures quality control during the reconstruction process. RESULTS: Here, we present a COBRA toolbox extension, rBioNet, enabling the construction of publication-level biochemical networks while enforcing necessary quality control measures. rBioNet has an intuitive user interface facilitating the reconstruction process for novices and experts. AVAILABILITY: The rBioNet is freely available from http://opencobra.sourceforge.net. [less ▲]

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See detailvon Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Fleming, Ronan MT UL; Thiele, Ines UL

in Bioinformatics (Oxford, England) (2011), 27(1), 142-3

MOTIVATION: In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and ... [more ▼]

MOTIVATION: In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential. RESULTS: This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source. AVAILABILITY: http://opencobra.sourceforge.net. [less ▲]

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See detailModeling RNA loops using sequence homology and geometric constraints.
Schudoma, Christian; May, Patrick UL; Walther, Dirk

in Bioinformatics (Oxford, England) (2010), 26(13), 1671-2

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling ... [more ▼]

SUMMARY: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. AVAILABILITY AND IMPLEMENTATION: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de CONTACT: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de [less ▲]

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See detailA framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors.
de Juan, David; Mellado, Mario; Rodriguez-Frade, Jose Miguel et al

in Bioinformatics (Oxford, England) (2005), 21 Suppl 2

Solving relevant biological problems requires answering complex questions. Addressing such questions traditionally implied the design of time-consuming experimental procedures which most of the time are ... [more ▼]

Solving relevant biological problems requires answering complex questions. Addressing such questions traditionally implied the design of time-consuming experimental procedures which most of the time are not accessible to average-sized laboratories. The current trend is to move towards a multidisciplinary approach integrating both theoretical knowledge and experimental work. This combination creates a powerful tool for shedding light on biological problems. To illustrate this concept, we present here a descriptive example of where computational methods were shown to be a key aspect in detecting crucial players in an important biological problem: the dimerization of chemokine receptors. Using evolutionary based sequence analysis in combination with structural predictions two CCR5 residues were selected as important for dimerization and further validated experimentally. The experimental validation of computational procedures demonstrated here provides a wealth of valuable information not obtainable by any of the individual approaches alone. [less ▲]

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See detailTopology of small-world networks of protein-protein complex structures.
del Sol Mesa, Antonio UL; Fujihashi, Hirotomo; O'Meara, Paul

in Bioinformatics (Oxford, England) (2005), 21(8), 1311-5

The majority of real examples of small-world networks exhibit a power law distribution of edges among the nodes, therefore not fitting into the wiring model proposed by Watts and Strogatz. However ... [more ▼]

The majority of real examples of small-world networks exhibit a power law distribution of edges among the nodes, therefore not fitting into the wiring model proposed by Watts and Strogatz. However, protein structures can be modeled as small-world networks, with a distribution of the number of links decaying exponentially as in the case of this wiring model. We approach the protein-protein interaction mechanism by viewing it as a particular rewiring occurring in the system of two small-world networks represented by the monomers, where a re-arrangement of links takes place upon dimerization leaving the small-world character in the dimer network. Due to this rewiring, the most central residues at the complex interfaces tend to form clusters, which are not homogenously distributed. We show that these highly central residues are strongly correlated with the presence of hot spots of binding free energy. CONTACT: ao-mesa@fujirebio.co.jp SUPPLEMENTARY INFORMATION: http://www.fujirebio.co.jp/support/index.php (under construction). [less ▲]

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See detailPTGL--a web-based database application for protein topologies.
May, Patrick UL; Barthel, Stefan; Koch, Ina

in Bioinformatics (Oxford, England) (2004), 20(17), 3277-9

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary ... [more ▼]

Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary structure level. Different views on protein topology are given by four linear notations for their characterization. Protein topologies can be derived at different description levels considering alpha- and beta-structures. The on-line search tool is based on an object-relational database and provides a query browser for data interrogation by string patterns, keyword queries and sequence similarity. Protein topologies are represented both as schematic diagrams and as three-dimensional images. [less ▲]

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See detailA comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Krause, Roland UL; von Mering, Christian; Bork, Peer

in Bioinformatics (Oxford, England) (2003), 19(15), 1901-8

MOTIVATION: The analysis of protein-protein interactions allows for detailed exploration of the cellular machinery. The biochemical purification of protein complexes followed by identification of ... [more ▼]

MOTIVATION: The analysis of protein-protein interactions allows for detailed exploration of the cellular machinery. The biochemical purification of protein complexes followed by identification of components by mass spectrometry is currently the method, which delivers the most reliable information--albeit that the data sets are still difficult to interpret. Consolidating individual experiments into protein complexes, especially for high-throughput screens, is complicated by many contaminants, the occurrence of proteins in otherwise dissimilar purifications due to functional re-use and technical limitations in the detection. A non-redundant collection of protein complexes from experimental data would be useful for biological interpretation, but manual assembly is tedious and often inconsistent. RESULTS: Here, we introduce a measure to define similarity within collections of purifications and generate a set of minimally redundant, comprehensive complexes using unsupervised clustering. AVAILABILITY: Programs and results are freely available from http://www.bork.embl-heidelberg.de/Docu/purclust/ [less ▲]

Detailed reference viewed: 75 (2 UL)