Research graph
References from Process bigraphs and the architecture of compositional systems biology. Local targets link to admitted publications; unresolved targets remain external evidence.
On the origins of approximations for stochastic chemical kinetics
10.1063/1.2062048 · 2005 · External reference
Dynamic flux balance analysis of diauxic growth in Escherichia coli
10.1016/s0006-3495(02)73903-9 · 2002 · External reference
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
10.1093/bioinformatics/btn352 · 2008 · External reference
Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
10.1371/journal.pcbi.1005236 · 2016 · External reference
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
10.1038/s41596-021-00593-3 · 2021 · External reference
A whole-cell computational model predicts phenotype from genotype
10.1016/j.cell.2012.05.044 · 2012 · External reference
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
10.1126/science.aav3751 · 2020 · External reference
Building Structural Models of a Whole Mycoplasma Cell
10.1016/j.jmb.2021.167351 · 2022 · External reference
Fundamental behaviors emerge from simulations of a living minimal cell
10.1016/j.cell.2021.12.025 · 2022 · External reference
Molecular dynamics simulation of an entire cell
10.3389/fchem.2023.1106495 · 2023 · External reference
10.21203/rs.3.rs-55125/v1
10.21203/rs.3.rs-55125/v1 · External reference
Multiscale computational models of complex biological systems
10.1146/annurev-bioeng-071811-150104 · 2013 · External reference
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
10.1371/journal.pcbi.1005991 · 2018 · External reference
Multi-scale modeling of tissues using CompuCell3D
10.1016/b978-0-12-388403-9.00013-8 · 2012 · External reference
SBML Level 3: an extensible format for the exchange and reuse of biological models
10.15252/msb.20199110 · 2020 · External reference
CellML: its future, present and past
10.1016/j.pbiomolbio.2004.01.004 · 2004 · External reference
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
10.1186/1752-0509-5-198 · 2011 · External reference
BioSimulators: a central registry of simulation engines and services for recommending specific tools
10.1093/nar/gkac331 · 2022 · External reference
Vivarium: an interface and engine for integrative multiscale modeling in computational biology
10.1093/bioinformatics/btac049 · 2022 · External reference
Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses
10.1371/journal.pcbi.1011232 · 2023 · External reference
A Multi-Scale Approach to Modeling E. coli Chemotaxis
10.3390/e22101101 · 2020 · External reference
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy
10.1016/j.cels.2024.03.004 · 2024 · External reference
10.1017/cbo9780511626661
10.1017/cbo9780511626661 · 2009 · External reference
Unresolved reference
2000 · External reference
Multiscale representation of simulated time
10.1177/0037549717726868 · 2017 · External reference
The growth of bacterial cultures
10.1016/b978-0-12-460482-7.50020-8 · 1978 · External reference
SBML level 3 package: spatial processes, version 1, release 1
10.1515/jib-2022-0054 · 2023 · External reference
The Virtual Cell: a software environment for computational cell biology
10.1016/s0167-7799(01)01740-1 · 2001 · External reference
Seven challenges in the multiscale modeling of multicellular tissues
2022 · External reference
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
10.1093/nar/gkj092 · 2006 · External reference
Integration from proteins to organs: the Physiome Project
10.1038/nrm1054 · 2003 · External reference
Multi-scale modeling of tissues using CompuCell3D
10.1016/b978-0-12-388403-9.00013-8 · 2012 · External reference
Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry
2022 · External reference
Detailed simulations of cell biology with Smoldyn 2.1
10.1371/journal.pcbi.1000705 · 2010 · External reference
10.1007/978-1-4939-3389-1_2
10.1007/978-1-4939-3389-1_2 · External reference
The MARTINI force field: coarse grained model for biomolecular simulations
10.1021/jp071097f · 2007 · External reference
Fast Parallel Algorithms for Short-Range Molecular Dynamics
10.1006/jcph.1995.1039 · 1995 · External reference
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
10.1038/s41586-019-1629-x · 2019 · External reference
The BioCyc collection of microbial genomes and metabolic pathways
10.1093/bib/bbx085 · 2019 · External reference
The reactome pathway knowledgebase
2020 · External reference
