Review of construction methods for whole-cell computational models

[1]  Nikolaus Sonnenschein,et al.  A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism , 2019, Nature Communications.

[2]  Falk Schreiber,et al.  Editing, validating and translating of SBGN maps , 2010, Bioinform..

[3]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[4]  Edward J. O'Brien,et al.  Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale , 2014, BMC Systems Biology.

[5]  Chris J. Myers,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 , 2018, J. Integr. Bioinform..

[6]  Jason A. Papin,et al.  Functional integration of a metabolic network model and expression data without arbitrary thresholding , 2011, Bioinform..

[7]  Nan Xu,et al.  Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole‐cell model WM_S288C , 2020, Biotechnology and bioengineering.

[8]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[9]  V. Fromion,et al.  Quantitative prediction of genome-wide resource allocation in bacteria. , 2015, Metabolic engineering.

[10]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[11]  I. Nookaew,et al.  Integration of clinical data with a genome-scale metabolic model of the human adipocyte , 2013, Molecular systems biology.

[12]  Antje Chang,et al.  BRENDA in 2019: a European ELIXIR core data resource , 2018, Nucleic Acids Res..

[13]  Astrid Junker,et al.  Visual Analysis of Transcriptome Data in the Context of Anatomical Structures and Biological Networks , 2012, Front. Plant Sci..

[14]  Robert C. Cannon,et al.  LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2 , 2014, Front. Neuroinform..

[15]  Samik Ghosh,et al.  A comprehensive molecular interaction map of the budding yeast cell cycle , 2010, Molecular systems biology.

[16]  K. Struhl,et al.  Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo , 2004, Current protocols in molecular biology.

[17]  Pedro Mendes,et al.  The markup is the model: reasoning about systems biology models in the Semantic Web era. , 2008, Journal of theoretical biology.

[18]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[19]  Jeffrey D. Orth,et al.  In silico method for modelling metabolism and gene product expression at genome scale , 2012, Nature Communications.

[20]  Fengkai Zhang,et al.  SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1 , 2018, J. Integr. Bioinform..

[21]  Aurélien Naldi,et al.  SBML Level 3 package: Qualitative Models, Version 1, Release 1 , 2015, Journal of integrative bioinformatics.

[22]  Christopher J. Rawlings,et al.  Representing and querying disease networks using graph databases , 2016, BioData Mining.

[23]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[24]  Thomas Bernard,et al.  MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks , 2013, Bioinform..

[25]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3 , 2011, J. Integr. Bioinform..

[26]  Chris J. Myers,et al.  Toward community standards and software for whole-cell modeling , 2016, IEEE Transactions on Biomedical Engineering.

[27]  Bumjoon J. Kim,et al.  One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains , 2018, Nature Communications.

[28]  J. Edwards,et al.  Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* , 1999, The Journal of Biological Chemistry.

[29]  Michael Hucka,et al.  SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 , 2015, Journal of integrative bioinformatics.

[30]  Eytan Ruppin,et al.  iMAT: an integrative metabolic analysis tool , 2010, Bioinform..

[31]  Jonathan R. Karr,et al.  A Whole-Cell Computational Model Predicts Phenotype from Genotype , 2012, Cell.

[32]  Yukiko Matsuoka,et al.  Systems Biology Graphical Notation: Process Diagram Level 1 Notes on Typographical Conventions , 2008 .

[33]  Adam M. Feist,et al.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 , 2011, Molecular systems biology.

[34]  Goksel Misirli,et al.  Model annotation for synthetic biology: automating model to nucleotide sequence conversion , 2011, Bioinform..

[35]  D. Wishart,et al.  PathBank: a comprehensive pathway database for model organisms , 2019, Nucleic Acids Res..

[36]  Sang Yup Lee,et al.  From genome sequence to integrated bioprocess for succinic acid production by Mannheimia succiniciproducens , 2008, Applied Microbiology and Biotechnology.

[37]  Oliver A.H. Jones,et al.  Review of recent developments in GC–MS approaches to metabolomics-based research , 2018, Metabolomics.

[38]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[39]  Ronan M. T. Fleming,et al.  Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage , 2012, PloS one.

[40]  N. Price,et al.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis , 2010, Proceedings of the National Academy of Sciences.

[41]  P. Park.  ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[42]  Tommaso Mazza,et al.  Towards a Complete Covering of SBML Functionalities , 2007, Workshop on Membrane Computing.

[43]  Sven Sahle,et al.  The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core , 2015, J. Integr. Bioinform..

[44]  Miguel Rocha,et al.  Integrating data from heterogeneous DNA microarray platforms , 2015, J. Integr. Bioinform..

[45]  L. Bertalanffy.  AN OUTLINE OF GENERAL SYSTEM THEORY , 1950, The British Journal for the Philosophy of Science.

[46]  Philip Miller,et al.  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models , 2015, Nucleic Acids Res..

[47]  D. Fell,et al.  A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties1[C][W] , 2009, Plant Physiology.

[48]  Ugur Dogrusoz,et al.  Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 , 2019, J. Integr. Bioinform..

[49]  Jens Nielsen,et al.  Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma , 2018, Front. Physiol..

[50]  S. Matsuoka,et al.  Simulation of ATP metabolism in cardiac excitation-contraction coupling. , 2004, Progress in biophysics and molecular biology.

[51]  P. R. ten Wolde,et al.  Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space. , 2005, The Journal of chemical physics.

[52]  Ugur Dogrusoz,et al.  Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps , 2020, Bioinform..

[53]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Entity Relationship language Level 1 , 2010 .

[54]  Benjamín J. Sánchez,et al.  Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints , 2017, Molecular systems biology.

[55]  Ronan M. T. Fleming,et al.  Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..

[56]  H. Kitano,et al.  LimeMap: a comprehensive map of lipid mediator metabolic pathways , 2021, NPJ systems biology and applications.

[57]  Kim Marriott,et al.  Conversion of KEGG metabolic pathways to SBGN maps including automatic layout , 2013, BMC Bioinformatics.

[58]  Satoshi Matsuoka,et al.  Role of individual ionic current systems in ventricular cells hypothesized by a model study. , 2003, The Japanese journal of physiology.

[59]  H. Kitano,et al.  Computational systems biology , 2002, Nature.

[60]  Ugur Dogrusoz,et al.  Systems biology graphical notation markup language (SBGNML) version 0.3 , 2020, J. Integr. Bioinform..

[61]  Gi Bae Kim,et al.  Current status and applications of genome-scale metabolic models , 2019, Genome Biology.

[62]  Masaru Tomita,et al.  Toward large-scale modeling of the microbial cell for computer simulation. , 2004, Journal of biotechnology.

[63]  Zachary A. King,et al.  Constraint-based models predict metabolic and associated cellular functions , 2014, Nature Reviews Genetics.

[64]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[65]  Edda Klipp,et al.  Parameter Balancing in Kinetic Models of Cell Metabolism , 2010, The journal of physical chemistry. B.

[66]  Michael Hucka,et al.  MOCCASIN: converting MATLAB ODE models to SBML , 2016, Bioinform..

[67]  A. Goldbeter.  A model for circadian oscillations in the Drosophila period protein (PER) , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[68]  Alexander Mazein,et al.  STON: exploring biological pathways using the SBGN standard and graph databases , 2016, BMC Bioinformatics.

[69]  A. Pradhan,et al.  Thyroid hormone: sex-dependent role in nervous system regulation and disease , 2021, Biology of Sex Differences.

[70]  Margaret Werner-Washburne,et al.  A system for generating transcription regulatory networks with combinatorial control of transcription , 2008, Bioinform..

[71]  Michael Hucka,et al.  SBML Level 3 package: Groups, Version 1 Release 1 , 2016, J. Integr. Bioinform..

[72]  Stephen W. Gilroy,et al.  SBML: a user interface mark-up language based on interaction style , 2008, Int. J. Web Eng. Technol..

[73]  Miguel Rocha,et al.  Modeling formalisms in Systems Biology , 2011, AMB Express.

[74]  Markus J. Herrgård,et al.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.

[75]  Feng He,et al.  Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms , 2018, npj Systems Biology and Applications.

[76]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 , 2015, J. Integr. Bioinform..

[77]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[78]  Reinhard Schneider,et al.  Using graph theory to analyze biological networks , 2011, BioData Mining.

[79]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2 , 2015, Journal of integrative bioinformatics.

[80]  M. A. de Menezes,et al.  Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity , 2007, Proceedings of the National Academy of Sciences.

[81]  Chris J. Myers,et al.  SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 , 2015, J. Integr. Bioinform..

[82]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Activity Flow language Level 1 , 2009 .

[83]  Amy K. Schmid,et al.  A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell , 2007, Cell.

[84]  Edward J. O'Brien,et al.  Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation , 2017, Proceedings of the National Academy of Sciences.

[85]  Falk Schreiber,et al.  Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. , 2015, Journal of integrative bioinformatics.

[86]  Xinjian Qi,et al.  DORMAN: Database of Reconstructed MetAbolic Networks , 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[87]  B. Palsson,et al.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.

[88]  Henning Hermjakob,et al.  BioModels—15 years of sharing computational models in life science , 2019, Nucleic Acids Res..

[89]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[90]  Inna Kuperstein,et al.  Signalling maps in cancer research: construction and data analysis , 2018, Database J. Biol. Databases Curation.

[91]  Daogang Guan,et al.  An integrative method to decode regulatory logics in gene transcription , 2017, Nature Communications.

[92]  Edda Klipp,et al.  Automatically generated model of a metabolic network. , 2007, Genome informatics. International Conference on Genome Informatics.

[93]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[94]  S. Soliman,et al.  A Unique Transformation from Ordinary Differential Equations to Reaction Networks , 2010, PloS one.

[95]  Chris J. Myers,et al.  Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions , 2015, J. Integr. Bioinform..

[96]  N. Kikuchi,et al.  CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks , 2008, Proceedings of the IEEE.

[97]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[98]  Michael Hucka,et al.  SBML Level 3 package: Groups, Version 1 Release 1 , 2016, J. Integr. Bioinform..

[99]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[100]  Sven Sahle,et al.  SBML Level 3 package: Render, Version 1, Release 1 , 2018, J. Integr. Bioinform..

[101]  Tim Clark,et al.  Pain Research Forum: application of scientific social media frameworks in neuroscience , 2014, Front. Neuroinform..

[102]  Chris J. Myers,et al.  JSBML 1.0: providing a smorgasbord of options to encode systems biology models , 2015, Bioinform..

[103]  Chris T. A. Evelo,et al.  The systems biology format converter , 2016, BMC Bioinformatics.

[104]  Michael Hucka,et al.  SBMLToolbox: an SBML toolbox for MATLAB users , 2006, Bioinform..

[105]  Nicolas Le Novère,et al.  Supporting SBML as a model exchange format in software applications. , 2013, Methods in molecular biology.

[106]  C. Kiel,et al.  Repository of proposed pathways and protein–protein interaction networks in age-related macular degeneration , 2020, npj Aging and Mechanisms of Disease.

[107]  Zhiyong Lu,et al.  Database resources of the National Center for Biotechnology Information , 2020, Nucleic Acids Res..

[108]  Masaru Tomita,et al.  A general computational model of mitochondrial metabolism in a whole organelle scale , 2004, Bioinform..

[109]  Byung-Gee Kim,et al.  Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica , 2018, BMC Systems Biology.

[110]  R. Haw,et al.  Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 , 2015, J. Integr. Bioinform..

[111]  Lincoln Stein,et al.  Reactome pathway analysis to enrich biological discovery in proteomics data sets , 2011, Proteomics.

[112]  B. Palsson,et al.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[113]  Julio Saez-Rodriguez,et al.  CySBGN: A Cytoscape plug-in to integrate SBGN maps , 2012, BMC Bioinformatics.

[114]  Frank T. Bergmann,et al.  The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core , 2015, J. Integr. Bioinform..

[115]  Elena Kutumova,et al.  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data , 2019, Nucleic Acids Res..

[116]  Matthias König,et al.  Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1 , 2020, J. Integr. Bioinform..

[117]  Jian Li,et al.  OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling , 2019, PLoS Comput. Biol..

[118]  J. Ecker,et al.  Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). , 2016, Current protocols in plant biology.

[119]  Enrica Calura,et al.  The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways , 2011, Bioinform..

[120]  C. Kiel,et al.  Repository of proposed pathways and protein–protein interaction networks in age-related macular degeneration , 2020, npj Aging and Mechanisms of Disease.

[121]  Masaru Tomita,et al.  E-Cell 2: Multi-platform E-Cell simulation system , 2003, Bioinform..

[122]  Ugur Dogrusoz,et al.  SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps , 2015, PloS one.

[123]  Frank T. Bergmann,et al.  SBML Level 3 Package: Flux Balance Constraints version 2 , 2018, J. Integr. Bioinform..

[124]  Axel Kowald,et al.  Systems biology standards—the community speaks , 2007, Nature Biotechnology.

[125]  Edward J. O'Brien,et al.  COBRAme: A computational framework for genome-scale models of metabolism and gene expression , 2017, bioRxiv.

[126]  Peter J. Hunter,et al.  An Overview of CellML 1.1, a Biological Model Description Language , 2003, Simul..

[127]  Fangfang Xia,et al.  Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli , 2016, PLoS Comput. Biol..

[128]  Nagasuma R. Chandra,et al.  Flux balance analysis of biological systems: applications and challenges , 2009, Briefings Bioinform..

[129]  Eytan Ruppin,et al.  Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model , 2010, Bioinform..

[130]  Michael Hucka,et al.  LibSBML: an API Library for SBML , 2008, Bioinform..

[131]  Vassily Hatzimanikatis,et al.  The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models , 2020, Nature Communications.

[132]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[133]  Lars Keld Nielsen,et al.  Plant genome-scale metabolic reconstruction and modelling. , 2013, Current opinion in biotechnology.