References of "Gawron, Piotr 50001830"
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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 detailClosing the gap between formats for storing layout information in systems biology.
Hoksza, David UL; Gawron, Piotr UL; Ostaszewski, Marek UL et al

in Briefings in bioinformatics (2019)

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no ... [more ▼]

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology. [less ▲]

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See detailThe Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
Noronha, Alberto UL; Modamio Chamarro, Jennifer UL; Jarosz, Yohan UL et al

in Nucleic Acids Research (2018)

A multitude of factors contribute to complex diseases and can be measured with ‘omics’ methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic ... [more ▼]

A multitude of factors contribute to complex diseases and can be measured with ‘omics’ methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources ‘Human metabolism’, ‘Gut microbiome’, ‘Disease’, ‘Nutrition’, and ‘ReconMaps’. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH’s unique features are (i) the hosting of the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; (ii) seven human metabolic maps for data visualization; (iii) a nutrition designer; (iv) a user-friendly webpage and application-programming interface to access its content; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community. [less ▲]

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See detailMolArt: a molecular structure annotation and visualization tool
Hoksza, David UL; Gawron, Piotr UL; Ostaszewski, Marek UL et al

in Bioinformatics (2018)

Summary MolArt fills the gap between sequence and structure visualization by providing a light-weight, interactive environment enabling exploration of sequence annotations in the context of available ... [more ▼]

Summary MolArt fills the gap between sequence and structure visualization by providing a light-weight, interactive environment enabling exploration of sequence annotations in the context of available experimental or predicted protein structures. Provided a UniProt ID, MolArt downloads and displays sequence annotations, sequence-structure mapping and relevant structures. The sequence and structure views are interlinked, enabling sequence annotations being color overlaid over the mapped structures, thus providing an enhanced understanding and interpretation of the available molecular data. Availability and implementation MolArt is released under the Apache 2 license and is available at https://github.com/davidhoksza/MolArt. The project web page https://davidhoksza.github.io/MolArt/ features examples and applications of the tool. [less ▲]

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See detailSystems medicine disease maps: community-driven comprehensive representation of disease mechanisms.
Mazein, Alexander; Ostaszewski, Marek UL; Kuperstein, Inna et al

in NPJ systems biology and applications (2018), 4

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context ... [more ▼]

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes. [less ▲]

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See detailCommunity-driven roadmap for integrated disease maps.
Ostaszewski, Marek UL; Gebel, Stephan UL; Kuperstein, Inna et al

in Briefings in bioinformatics (2018)

The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated ... [more ▼]

The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. The involvement of domain experts ensures that the key disease hallmarks are covered and relevant, up-to-date knowledge is adequately represented. Expert-curated and computer readable, disease maps may serve as a compendium of knowledge, allow for data-supported hypothesis generation or serve as a scaffold for the generation of predictive mathematical models. This article summarizes the 2nd Disease Maps Community meeting, highlighting its important topics and outcomes. We outline milestones on the roadmap for the future development of disease maps, including creating and maintaining standardized disease maps; sharing parts of maps that encode common human disease mechanisms; providing technical solutions for complexity management of maps; and Web tools for in-depth exploration of such maps. A dedicated discussion was focused on mathematical modeling approaches, as one of the main goals of disease map development is the generation of mathematically interpretable representations to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions. [less ▲]

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See detailReconMap: An interactive visualisation of human metabolism
Noronha, Alberto UL; Danielsdóttir, Anna Dröfn; Jóhannsson, Freyr et al

in Bioinformatics (2016)

A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew ... [more ▼]

A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0, that is consistent with the content of Recon 2. We present it within a web interface that allows content query, visualization of custom datasets and submission of feedback to manual curators. ReconMap can be accessed via http://vmh.uni.lu, with network export in a Systems Biology Graphical Notation compliant format. A Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox. [less ▲]

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See detailVizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
Laczny, Cedric Christian UL; Sternal, Tomasz; Plugaru, Valentin UL et al

in Microbiome (2015)

Background Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent ... [more ▼]

Background Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge. Results We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented. Conclusions VizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux. [less ▲]

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See detailG-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
Gawron, Piotr UL; Frohmberg, W; Kierzynka, M et al

in Bulletin of the Polish Academy of Sciences. Technical Sciences (2014)

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See detailResearch on DNA sequence assembly using graph approach
Gawron, Piotr UL

Doctoral thesis (2013)

Detailed reference viewed: 111 (18 UL)