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List of works by Andreas Dräger

A Padawan Programmer's Guide to Developing Software Libraries

scientific article published on 4 October 2017

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

scientific article published on 01 January 2020

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

scientific article

BowTieBuilder: modeling signal transduction pathways

scientific article published on 30 June 2009

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

Community standards to facilitate development and address challenges in metabolic modeling

scientific article published on 01 August 2020

Computational Model Informs Effective Control Interventions against <i>Y. enterocolitica</i> Co-Infection

scientific article published on 30 November 2020

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

scientific article

Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus

scientific article published in 2021

CySBML: a Cytoscape plugin for SBML ⬇️

scientific article published on 05 July 2012

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

scientific article

FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

scientific article published on 01 December 2020

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

scientific article published on 26 June 2013

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

Improving collaboration by standardization efforts in systems biology.

scientific article

Insights into Dynamic Network States Using Metabolomic Data

scientific article published on 01 January 2019

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

scientific article

JSBML: a flexible Java library for working with SBML.

scientific article

JSBML: a flexible and entirely Java-based library for working with SBML

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

scientific article (publication date: 15 August 2011)

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

scientific article published on 26 November 2020

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

scientific article

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

scientific article published in 2023

Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein.

scientific article

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

scientific article

Precise generation of systems biology models from KEGG pathways

scientific article (publication date: 21 February 2013)

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Qualitative translation of relations from BioPAX to SBML qual

scientific article (publication date: 15 October 2012)

Recon3D enables a three-dimensional view of gene variation in human metabolism.

scientific article published on 19 February 2018

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports

scientific article

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

scientific article published on 18 December 2014

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

scientific article published on 9 October 2015

SBOannotator: a Python tool for the automated assignment of systems biology ontology terms

scientific article published in 2023

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

scientific article published on 01 November 2018

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

scientific article published on 13 June 2019

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

scientific article

Systems biology graphical notation markup language (SBGNML) version 0.3.

scientific article published on 22 June 2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

scientific article published on 06 July 2020

TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors

scientific article

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes

scientific article published on 18 April 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

scientific article published on 20 June 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

scientific article published on 9 March 2018

The systems biology simulation core algorithm

scientific article

Visualizing metabolic network dynamics through time-series metabolomic data

scientific article published on 03 April 2020

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

scientific article

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