All Stories

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