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BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks

M. Sirava, T. Schafer, M. Eiglsperger, M. Kaufmann, O. Kohlbacher, E. Bornberg-Bauer, H. P. Lenhof
2002 Bioinformatics  
BioMiner is based on a new comprehensive, extensible and reusable data model-BioCore-which can be used to model biochemical pathways and networks.  ...  No integrated and easy to use software tool for this purpose exists as yet. Results: We present a new software system-BioMinerfor analyzing and visualizing biochemical pathways and networks.  ...  We are further grateful to Hans Werner Adolph, Vicki Kelly and Michaela Falb for support in biochemical questions.  ... 
doi:10.1093/bioinformatics/18.suppl_2.s219 pmid:12386006 fatcat:ty2kffkvdfddxh6mtwhz2cb3se

BioMiner: Paving the Way for Personalized Medicine

Chris Bauer, Karol Stec, Alexander Glintschert, Kristina Gruden, Christian Schichor, Michal Or-Guil, Joachim Selbig, Johannes Schuchhardt
2015 Cancer Informatics  
It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities.  ...  BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer.  ...  Acknowledgments We thank Sergio Grimbs and Matjaz Hren for helpful discussions.  ... 
doi:10.4137/cin.s20910 pmid:26005322 pmcid:PMC4406277 fatcat:irm5eg4invdwxnggbfir54slke

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications

Miguel A. Campodonico, Daniela Vaisman, Jean F. Castro, Valeria Razmilic, Francesca Mercado, Barbara A. Andrews, Adam M. Feist, Juan A. Asenjo
2016 Metabolic Engineering Communications  
for A. ferrooxidans and enables the understanding and engineering of Acidithiobacillus and similar species from a comprehensive model-driven perspective for biomining applications.  ...  A total of 587 metabolic and transport/exchange reactions, 507 genes and 573 metabolites organized in over 42 subsystems were incorporated into the model.  ...  Flux Balance Analysis (FBA) (Orth et al., 2010) was utilized for predicting growth and analyzing the reaction flux (v j ) through the metabolic network.  ... 
doi:10.1016/j.meteno.2016.03.003 pmid:29468116 pmcid:PMC5779729 fatcat:jd22z6crejgh3ikhs6vgfvs3le

Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities

María Sofía Urbieta, Nicolás Rascovan, Martín P. Vázquez, Edgardo Donati
2017 BMC Genomics  
Results: In this work we analyzed the genome of Acidianus copahuensis and describe the genetic pathways involved in biomining processes.  ...  as an experimental model to further understand the fascinating biology of thermoacidophilic biomining archaea.  ...  Camila Castro and Marcela Hipperdinger for the assistance with A. copahuensis cultures.  ... 
doi:10.1186/s12864-017-3828-x pmid:28587624 pmcid:PMC5461723 fatcat:jjb4ouh32ncwjmnljpwxfllx6y

Using Gene networks to drug target identification

Zhenran Jiang, Yanhong Zhou, BieColl, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Bielefeld University, Publikationsdienste.Ub@Uni-Bielefeld.De
2007 Journal of Integrative Bioinformatics  
Gene network technique holds the promise of providing a conceptual framework for analysis of the profusion of biological data being generated on potential drug targets and providing insights to understand  ...  In addition, some of the relevant data resources and computational tools are given.  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (Grants No. 90203011 and 30370354), the Ministry of Education of China (Grants No. 505010 and CG2003-GA002).  ... 
doi:10.2390/biecoll-jib-2005-14 dblp:journals/jib/JiangZ05 fatcat:j57ctcfy7rc6djeji52lnf3qxm

Using gene networks to drug target identification

Zhenran Jiang, Yanhong Zhou
2005 Journal of Integrative Bioinformatics  
Gene network technique holds the promise of providing a conceptual framework for analysis of the profusion of biological data being generated on potential drug targets and providing insights to understand  ...  In addition, some of the relevant data resources and computational tools are given.  ...  for network modeling [63] Path Finder http://bibiserv.techfak.uni-bielefeld.de/pathfinder/ Tool for biochemical pathways reconstruction and dynamic visualization [64] Pathway Miner http://www.biorag.org  ... 
doi:10.1515/jib-2005-14 fatcat:osugzd6pbvhl7egnsdv7wrfma4

PathCase: pathways database system

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. Meral Ozsoyoglu
2008 Bioinformatics  
Results: In this article, we present the new features of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of genetic, molecular, biochemical and organismal  ...  , (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) two distinct querying capabilities  ...  This way, the system can dynamically visualize, query and analyze any subsection of the larger pathways network, or even show how pathways themselves are interconnected at a higher level.  ... 
doi:10.1093/bioinformatics/btn459 pmid:18728044 fatcat:25jn4wwelzahlp235bygmz2hha

VANTED: a system for advanced data analysis and visualization in the context of biological networks

Björn H Junker, Christian Klukas, Falk Schreiber
2006 BMC Bioinformatics  
Visualization and navigation methods support the visual exploration of the data-enriched networks.  ...  We present VANTED, a tool for the visualization and analysis of networks with related experimental data.  ...  Acknowledgements This work was partly supported by the German Ministry of Education and Research (BMBF) under grants 0312706A and 0313115. We would like to thank Franz J.  ... 
doi:10.1186/1471-2105-7-109 pmid:16519817 pmcid:PMC1413562 fatcat:5w3sxs4pafeediwraseaojjdam

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot, Fabien Jourdan
2007 BMC Systems Biology  
Metabolic network visualization eliminating node redundance and preserving metabolic pathways.  ...  Results: We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways.  ...  Acknowledgements The work presented in this paper was funded in part by the ACI Nouvelles Interfaces des Mathématiques (project p-vert) of the French Ministry of Research, by the ARC (project IBN) from the INRIA and  ... 
doi:10.1186/1752-0509-1-29 pmid:17608928 pmcid:PMC1934383 fatcat:7bm57u4rujeobhwjscmucht52a

Network Visualization for Integrative Bioinformatics [chapter]

Andreas Kerren, Falk Schreiber
2013 Approaches in Integrative Bioinformatics  
Fields such as (information) visualization, visual analytics and automatic layout of networks are highlighted and illustrated by a number of examples.  ...  Due to their size and complexity, their growth and continuous change, as well as their compilation from databases on demand, researchers very often request novel network visualization, interaction and  ...  of dynamic approaches is visualizing the evolution of biochemical networks [112] , for instance).  ... 
doi:10.1007/978-3-642-41281-3_7 fatcat:reo437khrndrvmpjs4o5s5rt6m

Text mining biomedical literature for constructing gene regulatory networks

Yong-Ling Song, Su-Shing Chen
2009 Interdisciplinary Sciences Computational Life Sciences  
(Krishnamurthy et al., 2003) ; VitaPad: visualization tools for the analysis of pathway data -http://bioinformatics.med.yale.edu (Holford et al., 2005) ; BioMiner-modeling, analyzing, and visualizing  ...  biochemical pathways and networks-http://www.zbi.uni-saarland.de/chair/projects/BioMiner (Sirava et al., 2002) ; The Pathway Tools Software (Karp et al., 2002) ; Graphical interface to the gene network  ... 
doi:10.1007/s12539-009-0028-7 pmid:20640836 fatcat:5bnptxze4vfk3gck2wywg4zeum

Gene-Gene Interaction Analysis In Alzheimer

Rishi Yadav
2018 Zenodo  
Then we filter the output files using probe set filtering attributes p-value and fold count and draw a gene-gene interaction network. Then we analyze the interaction network using GeneMania software.  ...  Past researches prove that neuro diseases damage the brain network interaction, protein- protein interaction and gene-gene interaction.  ...  Sirava et al., [2] developed a tool for modeling, analyzing and visualizing biochemical pathways and networks of genomes and array data.  ... 
doi:10.5281/zenodo.1406824 fatcat:ombs7t5bvnffnmg7zu7zbxxu6e

Effects of Deoxynivalenol and Fumonisins Fed in Combination to Beef Cattle: Immunotoxicity and Gene Expression

Heaven L. Roberts, Massimo Bionaz, Duo Jiang, Barbara Doupovec, Johannes Faas, Charles T. Estill, Dian Schatzmayr, Jennifer M. Duringer
2021 Toxins  
Comparative profiles of CD4+ and CD8+ T cells, along with bactericidal capacity of circulating neutrophils and monocytes were evaluated at 0, 7, 14, 21 and 35 days.  ...  We evaluated the effects of a treatment diet contaminated with 1.7 mg deoxynivalenol and 3.5 mg fumonisins (B1, B2 and B3) per kg ration on immune status and peripheral blood gene expression profiles in  ...  Swanson and Kari Carola for their assistance with sampling; Gita Cherian for the use of her laboratory space; and Allison Ehrlich for assistance with flow cytometry troubleshooting.  ... 
doi:10.3390/toxins13100714 pmid:34679007 pmcid:PMC8541374 fatcat:iuy2apffifaedhkpaugg2ts32m

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized  ...  handling, sharing, and data archiving.  ...  interaction and miRNA-target gene network https://sourceforge.net/projects/netclassr/ Cun & Fröhlich (2014) BioMiner Web Easy BioMiner incorporates transcriptomic and cross-omics high-throughput data  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N. Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira (+4 others)
2018 PLoS Computational Biology  
Data Availability Statement: The complete datasets used for the reconstruction of the four metabolic networks (genome, proteome, metabolic network and proteome for the template models, seeds and targets  ...  This process is not straightforward and choices are made along the way, for example, which data is analyzed, with what tools.  ...  Dittami (Station Biologique de Roscoff) for the expertise and analysis support in the reconstruction process of Ectocarpus siliculosus metabolic network and Caroline Baroukh, Elodie Nicolau and Bruno Saint-Jean  ... 
doi:10.1371/journal.pcbi.1006146 pmid:29791443 pmcid:PMC5988327 fatcat:6tpm6fqgqbcubinvhrlvqso5u4
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