All Stories

  1. Integrating fed‐batch pulse feeding and flux balance analysis for PHB production by Cupriavidus necator from cassava‐based dextrose
  2. Systems biology graphical notation: process description language level 1 version 2.1
  3. MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology
  4. MCC: automated mass and charge curation at the genome scale applied to C. tuberculostearicum
  5. Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions
  6. MCC: Automated Mass and Charge Curation at Genome-Scale Applied toC. tuberculostearicum
  7. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling
  8. Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities
  9. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
  10. Perspectives on computational modeling of biological systems and the significance of the SysMod community
  11. Genome-scale metabolic model ofStaphylococcus epidermidisATCC 12228 matchesin vitroconditions
  12. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
  13. Genome-Scale Modeling ofRothia mucilaginosaReveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis
  14. Exploring the metabolic profiling ofA. baumanniifor antimicrobial development using genome-scale modelling
  15. Advancements in computational modelling of biological systems: seventh annual SysMod meeting
  16. SBOannotator: a Python tool for the automated assignment of systems biology ontology terms
  17. Genome-scale metabolic models consistently predictin vitrocharacteristics ofCorynebacterium striatum
  18. standard-GEM: standardization of open-source genome-scale metabolic models
  19. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
  20. SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms
  21. Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
  22. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
  23. Hierarchical modelling of microbial communities
  24. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
  25. Computational modelling in health and disease: highlights of the 6th annual SysMod meeting
  26. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
  27. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
  28. A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice
  29. COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms
  30. High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
  31. SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
  32. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
  33. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
  34. The systems biology simulation core library
  35. SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
  36. 114 highly specific computer models of the threatening pathogen Staphylococcus aureus
  37. The community for data-driven computational modelling and multi-scale analysis of biological systems
  38. Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms GK1 as Potential Antiviral Target
  39. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target
  40. Genome-scale modeling ofPseudomonas aeruginosaPA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation
  41. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
  42. <span data-preserver-spaces="true">Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of <em><span data-preserver-spaces="true">Staphylococcus aureus</em>
  43. An updated genome-scale metabolic network reconstruction ofPseudomonas aeruginosaPA14 to characterize mucin-driven shifts in bacterial metabolism
  44. Overview: Standards for Modeling in Systems Medicine
  45. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine
  46. Clinical Applications of Metabolic Models in SBML Format
  47. The Systems Biology Simulation Core Library
  48. A computer model identifies a human enzyme as a potential target to treat COVID-19
  49. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
  50. Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection
  51. Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications
  52. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
  53. A Computational Model to Inform Effective Control Interventions against Yersinia enterocolitica Coinfection
  54. Model-based prediction of bacterial population dynamics in gastrointestinal infection
  55. SBML Level 3: an extensible format for the exchange and reuse of biological models
  56. Community standards to facilitate development and address challenges in metabolic modeling
  57. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
  58. Visualizing metabolic network dynamics through time-series metabolomic data
  59. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
  60. A file format to store and distribute maps of biological processes.
  61. We want to collaborate on exchanging what we know on how the new coronavirus works
  62. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
  63. MEMOTE for standardized genome-scale metabolic model testing
  64. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
  65. Community standards to facilitate development and address challenges in metabolic modeling
  66. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
  67. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
  68. The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
  69. Insights into Dynamic Network States Using Metabolomic Data
  70. Harmonizing semantic annotations for computational models in biology
  71. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
  72. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
  73. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
  74. Recon3D enables a three-dimensional view of gene variation in human metabolism
  75. Harmonizing semantic annotations for computational models in biology
  76. A Padawan Programmer’s Guide to Developing Software Libraries
  77. Visualization and creation of biochemical networks with Escher
  78. Evaluation of rate law approximations in bottom-up kinetic models of metabolism
  79. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii
  80. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis
  81. Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling
  82. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
  83. Do genome-scale models need exact solvers or clearer standards?
  84. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
  85. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
  86. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
  87. JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.
  88. Cooperative development of logical modelling standards and tools with CoLoMoTo
  89. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology
  90. Improving Collaboration by Standardization Efforts in Systems Biology
  91. Controlled vocabularies and semantics in systems biology
  92. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors
  93. Parkinson’s disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein
  94. GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML
  95. Path2Models: large-scale generation of computational models from biochemical pathway maps
  96. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
  97. Metabolic Networks
  98. Parameter Estimation, Metabolic Network Modeling
  99. Precise generation of systems biology models from KEGG pathways
  100. The systems biology simulation core algorithm
  101. Qualitative translation of relations from BioPAX to SBML qual
  102. CySBML: a Cytoscape plugin for SBML
  103. ProDGe: investigating protein-protein interactions at the domain level
  104. Inferring statin-induced gene regulatory relationships in primary human hepatocytes
  105. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
  106. JSBML: a flexible Java library for working with SBML
  107. Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization
  108. Automating Mathematical Modeling of Biochemical Reaction Networks
  109. ModuleMaster: A new tool to decipher transcriptional regulatory networks
  110. BowTieBuilder: modeling signal transduction pathways
  111. SBML2LATEX: Conversion of SBML files into human-readable reports
  112. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
  113. BioJava: an open-source framework for bioinformatics
  114. SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
  115. Benchmarking evolutionary algorithms on convenience kinetics models of the valine and leucine biosynthesis in C. glutamicum
  116. Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum
  117. INFERRING GENE REGULATORY NETWORKS BY MACHINE LEARNING METHODS