A5065854572- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Metabolomics and Mass Spectrometry Studies
- Computational Drug Discovery Methods
- Biofuel production and bioconversion
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Distributed and Parallel Computing Systems
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Microbial Natural Products and Biosynthesis
- Bacterial Genetics and Biotechnology
- Pharmacological Effects of Natural Compounds
- Viral Infectious Diseases and Gene Expression in Insects
- Gut microbiota and health
- COVID-19 Clinical Research Studies
- RNA and protein synthesis mechanisms
- Yersinia bacterium, plague, ectoparasites research
- Protein Structure and Dynamics
- Endoplasmic Reticulum Stress and Disease
- Semantic Web and Ontologies
University of Tübingen
2015-2024
German Center for Infection Research
2019-2024
VenatoRx Pharmaceuticals (United States)
2024
Martin Luther University Halle-Wittenberg
2024
Luther University
2024
Biology of Infection
2020-2023
Bernstein Center for Computational Neuroscience Tübingen
2007-2021
University of California, San Diego
2013-2016
La Jolla Bioengineering Institute
2013-2016
University of California, Berkeley
2014
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict pathway usage and growth phenotypes. Furthermore, they generate test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories high-quality must established, adhere established standards model components linked relevant databases. Tools for visualization further enhance their utility. meet needs, we present BiGG Models...
Escher is a web application for visualizing data on biological pathways. Three key features make uniquely effective tool pathway visualization. First, users can rapidly design new maps. provides suggestions based user and genome-scale models, so draw pathways in semi-automated way. Second, visualize related to genes or proteins the associated reactions pathways, using rules that define which enzymes catalyze each reaction. Thus, identify trends common genomic types (e.g. RNA-Seq, proteomics,...
Abstract Summary: BioJava is a mature open-source project that provides framework for processing of biological data. contains powerful analysis and statistical routines, tools parsing common file formats packages manipulating sequences 3D structures. It enables rapid bioinformatics application development in the Java programming language. Availability: an distributed under Lesser GPL (LGPL). can be downloaded from website (http://www.biojava.org). requires 1.5 or higher. Contact:...
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational in declarative form that different software systems exchange. SBML oriented towards describing processes of the sort common research on number topics, including metabolic pathways, cell signaling many others. By supporting as an input/output format, tools all operate...
Abstract The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, website has allowed users to browse and search Within this update, we detail new content features in repository, continuing original effort connect each model genome annotations external databases as well standardization of reactions metabolites. We describe addition 31 models that expand portion phylogenetic tree covered by Models....
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models reconstructions. However, the majority these are still created de novo , based on literature mining manual processing data. Results To increase efficiency model creation, Path2Models project has automatically generated mathematical from representations using suite freely available software. Data sources include KEGG, BioCarta, MetaCyc SABIO-RK. Depending source data,...
Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, well-suited for studies large While numerous groups have developed specific computational tools provide original methods analyse qualitative models, a standard format exchange models has been missing. We present Systems Biology Markup Language (SBML)...
Abstract Transcriptional regulation enables cells to respond environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods used fully characterize only a few dozen. Identifying these remaining TFs is key improving our knowledge of E. transcriptional regulatory network (TRN). Here, we developed an integrated workflow for computational prediction and comprehensive experimental...
We need to effectively combine the knowledge from surging literature with complex datasets propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets intervention. Here, we describe a large-scale community effort build an open access, interoperable computable repository COVID-19 molecular mechanisms. The Disease Map (C19DMap) is graphical, interactive representation disease-relevant mechanisms linking many sources. Notably, it computational...
Abstract Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models biological processes in text files. In order to perform model simulations, graphical visualizations other software manipulations, an in-memory representation SBML is required. We developed JSBML this purpose. contrast prior implementations APIs, has been designed from ground up Java™ programming language, can therefore be used on all platforms...
Abstract Several studies have shown that neither the formal representation nor functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability across groups software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source containing community-maintained, standardized set me tabolic mo del te sts. The tests cover range aspects from...
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational in declarative form that different software systems exchange. SBML oriented towards describing processes of the sort common research on number topics, including metabolic pathways, cell signaling many others. By supporting as an input/output format, tools all operate...
Abstract Motivation The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. number of infections increases daily, without any approved antiviral therapy. recently released viral nucleotide sequence enables identification therapeutic targets, e.g. by analyzing integrated human-virus metabolic models. Investigations changed processes after virus and effect knock-outs on host can reveal new potential targets. Results We generated an host–virus genome-scale...
Commentary26 August 2020Open Access Community standards to facilitate development and address challenges in metabolic modeling Maureen A Carey orcid.org/0000-0003-2890-5445 Division of Infectious Diseases International Health, Department Medicine, University Virginia, Charlottesville, VA, USA Search for more papers by this author Andreas Dräger orcid.org/0000-0002-1240-5553 Computational Systems Biology Infection Antimicrobial-Resistant Pathogens, Institute Biomedical Informatics (IBMI),...
The development of complex biochemical models has been facilitated through the standardization machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by ongoing human-readable diagrammatic representation SBGN Graphical Notation). graphical editor CellDesigner allows direct translation into SBML, and vice versa. For assignment kinetic rate laws, however, this process not straightforward, as it often requires manual assembly specific knowledge...