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Precise generation of systems biology models from KEGG pathways

Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell
2013 BMC Systems Biology  
In systems biology, two wide-spread formats for modeling and exchanging pathways are the Systems Biology Markup Language (SBML) [5] and Biological Pathway Exchange (BioPAX) [6] .  ...  Thus, a direct conversion into systems biology models would produce incomplete and erroneous models.  ...  We acknowledge support by Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Tuebingen University.  ... 
doi:10.1186/1752-0509-7-15 pmid:23433509 pmcid:PMC3623889 fatcat:wcyr44lh5zeubgryetbreouzua

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch, Andrey Rzhetsky
2014 PLoS Computational Biology  
Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell.  ...  Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships.  ...  One area of systems biology where these computational methods are increasingly applied is for the inference of GRNs [4] [5] [6] [7] [8] [9] .  ... 
doi:10.1371/journal.pcbi.1003666 pmid:24921649 pmcid:PMC4055569 fatcat:thbotdrih5dafieiqvrvpi4h2q

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó, Martin Hofmann-Apitius
2018 npj Systems Biology and Applications  
Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability  ...  We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying  ...  with the Systems Biology Institute  ... 
doi:10.1038/s41540-018-0078-8 pmid:30564458 pmcid:PMC6292919 fatcat:6g5g3xami5b6fhos3npuhki4ei

Path2Models: large-scale generation of computational models from biochemical pathway maps

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating (+14 others)
2013 BMC Systems Biology  
Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions.  ...  Results: To increase the efficiency with which such models can be created, we automatically generated mathematical models from pathway representations using a suite of freely available software.  ...  Generation of SBML Level 3 Core from KEGG metabolic pathways The generation of pathway models from KEGG information was performed with KEGGtranslator [49, 67] .  ... 
doi:10.1186/1752-0509-7-116 pmid:24180668 pmcid:PMC4228421 fatcat:xihw5mql45gpzmiuc4svlr23nm

Pathways on demand: automated reconstruction of human signaling networks

Anna Ritz, Christopher L Poirel, Allison N Tegge, Nicholas Sharp, Kelsey Simmons, Allison Powell, Shiv D Kale, TM Murali
2016 npj Systems Biology and Applications  
Signaling pathways are a cornerstone of systems biology. Several databases store high-quality representations of these pathways that are amenable for automated analyses.  ...  We use PATHLINKER to accurately reconstruct a comprehensive set of signaling pathways from the NetPath and KEGG databases.  ...  We also acknowledge funding from the ICTAS Center for Systems Biology of Engineered Tissues at Virginia Tech (TMM). We thank Brendan Avent and Peter Burnham for their help in preparing the manuscript.  ... 
doi:10.1038/npjsba.2016.2 pmid:28725467 pmcid:PMC5516854 fatcat:rx362tj6s5gund255cbog2gu6e

A Genome-Wide Gene Function Prediction Resource for Drosophila melanogaster

Han Yan, Kavitha Venkatesan, John E. Beaver, Niels Klitgord, Muhammed A. Yildirim, Tong Hao, David E. Hill, Michael E. Cusick, Norbert Perrimon, Frederick P. Roth, Marc Vidal, Nicholas James Provart
2010 PLoS ONE  
Our model predicted GO terms and KEGG pathway memberships for Drosophila melanogaster genes with high accuracy, as affirmed by cross-validation, supporting literature evidence, and large-scale RNAi screens  ...  Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. Here we present a resource for Drosophila melanogaster gene function predictions.  ...  Acknowledgments We thank all members of the Vidal laboratory and the Center for Cancer Systems Biology (CCSB), Dr Chris Bakal, Dr Young Kwon and Dr Mike Boxem for helpful suggestions, Dr Rachel Drysdale  ... 
doi:10.1371/journal.pone.0012139 pmid:20711346 pmcid:PMC2920829 fatcat:o2yowefp25cj7esemzczapu7oi

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
2006 BMC Bioinformatics  
We developed the Genome-based Modeling (GEM) System for the purpose of automatically prototyping simulation models of cell-wide metabolic pathways from genome sequences and other public biological information  ...  Models generated by the GEM System include an entire Escherichia coli metabolism model comprising 968 reactions of 1195 metabolites, achieving 100% coverage when compared with the KEGG database, 92.38%  ...  the 21st Century Center of Excellence (COE) Program entitled "Understanding and Control of Life's Function via Systems Biology (Keio University)".  ... 
doi:10.1186/1471-2105-7-168 pmid:16553966 pmcid:PMC1435936 fatcat:wsuqaqhawnayhifij7xkk7hzs4

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks

J. Schneider, F.-J. Vorh�lter, E. Trost, J. Blom, Y.R. Musa, H. Neuweger, K. Niehaus, S. Schatschneider, A. Tauch, A. Goesmann
2010 Genetics and Molecular Research  
The generated pathways provide automated access to modeling and simulation tools that are compliant with the SBML standard.  ...  The curation of such pathways facilitates enhanced visualization of experimental results, simulations and comparative genomics.  ...  Trost acknowledge the receipt of a scholarship from the CLIB Graduate Cluster Industrial Biotechnology. J. Blom and H.  ... 
doi:10.4238/vol9-3gmr901 pmid:20799163 fatcat:k2wg4agu55godipjfb6wvcyvnu

Combining multiple functional annotation tools increases coverage of metabolic annotation [article]

Marc Griesemer, Jeffrey A Kimbrel, Carol E Zhou, Ali Navid, Patrik D'haeseleer
2017 bioRxiv   pre-print
Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional  ...  These incomplete annotations may be sufficient to derive a model of a core set of well-studied metabolic pathways that support growth in pure culture.  ...  Acknowledgements This work was supported by the Department of Energy through the Genome Sciences Program as part of the LLNL Biofuels SFA (contract SCW1060).  ... 
doi:10.1101/160887 fatcat:qf3bkp5kvnfydeulsa776g5vvm

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Xueyang Feng, You Xu, Yixin Chen, Yinjie J Tang
2012 BMC Systems Biology  
MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites) of~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes) and  ...  The simulation results can be exported in the SBML format (The Systems Biology Markup Language).  ...  In summary, we have developed MicrobesFlux to draft the metabolic models of environmental organisms from the KEGG database and to serve as a high-throughput tool for systems biology.  ... 
doi:10.1186/1752-0509-6-94 pmid:22857267 pmcid:PMC3447728 fatcat:gkxccrx4tndulmfwjpjciizvzq

Metabolic pathway databases and model repositories

Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua, Feng-Biao Guo
2017 Quantitative Biology  
Despite their innumerable use in the fields of systems biology and metabolic engineering, these pathway databases and model repositories are not in harmony with each other due to the inconsistencies in  ...  Besides, the automatically generated metabolic models that can be obtained from the model repositories are not accurate enough for further scientific usage without additional manual curation.  ...  Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua and Feng-Biao Guo declare that they have no conflict of interest.  ... 
doi:10.1007/s40484-017-0108-3 fatcat:j6osebecqjehzj6lkchtldkwke

Concurrent Dynamic Visualizations With Expressive Petri Net Representations to Enrich the Understanding of Biological and Pathological Processes: an Application to Signaling Pathways

F. Ramos, C. Hallal, A. Nieto, D. García, J. Berúmen, D. Escárcega
2012 Journal of Applied Research and Technology  
Dynamic visualizations and expressive representations are needed in systems biology to handle multiple interactionsoccurring during the biological processes of biopathway representations.  ...  with the provided CDV untilthe user generated a personalized pathway.  ...  The generation of a model from a single source, for instance KEGG, supplies an incomplete representation (Figure 5a ).  ... 
doi:10.22201/icat.16656423.2012.10.5.370 fatcat:n4yj65blnfb4tgs7nbgx5njz4y

Combining multiple functional annotation tools increases coverage of metabolic annotation

Marc Griesemer, Jeffrey A. Kimbrel, Carol E. Zhou, Ali Navid, Patrik D'haeseleer
2018 BMC Genomics  
Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional  ...  These incomplete annotations may be sufficient to derive a model of a core set of well-studied metabolic pathways that support growth in pure culture.  ...  Acknowledgements Not applicable Availability of data and materials All data generated or analysed during this study are included in this published article and its supplementary information files.  ... 
doi:10.1186/s12864-018-5221-9 fatcat:trsiwwlqtff3lgspipoq4eucay

An editor for pathway drawing and data visualization in the Biopathways Workbench

Robert W Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam
2009 BMC Systems Biology  
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose.  ...  An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system.  ...  Acknowledgements This work was supported by the National Institutes of Health [1 U54 GM69338].  ... 
doi:10.1186/1752-0509-3-99 pmid:19799790 pmcid:PMC2763869 fatcat:zvjpazjj7fejnkowf5myuedtc4

Selection of an Ideal Machine Learning Framework for Predicting Perturbation Effects on Network Topology of Bacterial KEGG Pathways [article]

Michael Robben, Mohammad Sadegh Nasr, Avishek Das, Manfred Huber, Justyn Jaworski, Jon Weidanz, Jacob M. Luber
2022 bioRxiv   pre-print
To address these issues in the KEGG pathway database, we investigated the ability for machine learning (ML) algorithms to re-annotate bacterial genes based on motif or homology information.  ...  Current methods of gene annotation use homologous alignment to determine orthology, and have been shown to degrade network accuracy in non-model bacterial species.  ...  The authors would also like to express their thanks to Fiza Saeed for her assistance with the curation of data from the KEGG database.  ... 
doi:10.1101/2022.07.21.501034 fatcat:fqu222qznfbzzot42lgi2mgld4
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