4.0 Review

Hybrid computational modeling methods for systems biology

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Mathematical & Computational Biology

Formalizing Metabolic-Regulatory Networks by Hybrid Automata

Lin Liu et al.

ACTA BIOTHEORETICA (2020)

Article Biochemistry & Molecular Biology

BioModels-15 years of sharing computational models in life science

Rahuman S. Malik-Sheriff et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Robustness and lethality in multilayer biological molecular networks

Xueming Liu et al.

NATURE COMMUNICATIONS (2020)

Review Biochemical Research Methods

Agent-based modeling of morphogenetic systems: Advantages and challenges

Chad M. Glen et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemical Research Methods

PlantSimLab-a modeling and simulation web tool for plant biologists

S. Ha et al.

BMC BIOINFORMATICS (2019)

Article Biochemical Research Methods

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

Ahmadreza Ghaffarizadeh et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Review Biochemistry & Molecular Biology

Systems biology primer: the basic methods and approaches

Iman Tavassoly et al.

SYSTEMS BIOLOGY (2018)

Article Mathematical & Computational Biology

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

Michael Hucka et al.

JOURNAL OF INTEGRATIVE BIOINFORMATICS (2018)

Article Mathematical & Computational Biology

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Frank T. Bergmann et al.

JOURNAL OF INTEGRATIVE BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Use of CellNetAnalyzer in biotechnology and metabolic engineering

Axel von Kamp et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Mathematical & Computational Biology

Integrating transcriptional activity in genome-scale models of metabolism

Daniel Trejo Banos et al.

BMC SYSTEMS BIOLOGY (2017)

Article Mathematical & Computational Biology

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models

Mostafa Herajy et al.

BMC SYSTEMS BIOLOGY (2017)

Review Computer Science, Information Systems

Agent Based Modelling and Simulation tools: A review of the state-of-art software

Sameera Abar et al.

COMPUTER SCIENCE REVIEW (2017)

Review Mathematical & Computational Biology

Hybrid Modelling in Biology: a Classification Review

A. Stephanou et al.

MATHEMATICAL MODELLING OF NATURAL PHENOMENA (2016)

Review Multidisciplinary Sciences

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

Jesper Tegner et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2016)

Review Biochemical Research Methods

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ezio Bartocci et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Computer Science, Interdisciplinary Applications

Hybrid Simulations of Heterogeneous Biochemical Models in SBML

Hui Ju K. Chiang et al.

ACM TRANSACTIONS ON MODELING AND COMPUTER SIMULATION (2015)

Article Mathematical & Computational Biology

FlexFlux: combining metabolic flux and regulatory network analyses

Lucas Marmiesse et al.

BMC SYSTEMS BIOLOGY (2015)

Review Genetics & Heredity

Quantitative and logic modelling of molecular and gene networks

Nicolas Le Novere

NATURE REVIEWS GENETICS (2015)

Review Cell & Tissue Engineering

Strategies for Efficient Numerical Implementation of Hybrid Multi-scale Agent-Based Models to Describe Biological Systems

Nicholas A. Cilfone et al.

CELLULAR AND MOLECULAR BIOENGINEERING (2015)

Article Biochemistry & Molecular Biology

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

Faiz M. Khan et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2014)

Article Multidisciplinary Sciences

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

Matthew B. Biggs et al.

PLOS ONE (2013)

Article Biochemical Research Methods

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Natalie Berestovsky et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Mathematical & Computational Biology

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm

Gautier Stoll et al.

BMC SYSTEMS BIOLOGY (2012)

Article Biology

Nested Canalyzing Depth and Network Stability

Lori Layne et al.

BULLETIN OF MATHEMATICAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Jonathan R. Karr et al.

Article Biochemical Research Methods

Hybrid Models and Biological Model Reduction with PyDSTool

Robert Clewley

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Mathematical & Computational Biology

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath et al.

BMC SYSTEMS BIOLOGY (2011)

Review Genetics & Heredity

Software for systems biology: from tools to integrated platforms

Samik Ghosh et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemical Research Methods

A Hybrid Model of Mammalian Cell Cycle Regulation

Rajat Singhania et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Review Biotechnology & Applied Microbiology

Modeling formalisms in Systems Biology

Daniel Machado et al.

AMB EXPRESS (2011)

Article Biochemical Research Methods

SBRML: a markup language for associating systems biology data with models

Joseph O. Dada et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BoolNet-an R package for generation, reconstruction and analysis of Boolean networks

Christoph Muessel et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

An overview of the CellML API and its implementation

Andrew K. Miller et al.

BMC BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Sriram Chandrasekaran et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biotechnology & Applied Microbiology

The Systems Biology Graphical Notation

Nicolas Le Novere et al.

NATURE BIOTECHNOLOGY (2009)

Article Physiology

Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language

Yoshiyuki Asai et al.

JOURNAL OF PHYSIOLOGICAL SCIENCES (2008)

Article Mathematical & Computational Biology

Boolean network simulations for life scientists

Istvan Albert et al.

SOURCE CODE FOR BIOLOGY AND MEDICINE (2008)

Article Mathematical & Computational Biology

Structural and functional analysis of cellular networks with CellNetAnalyzer

Steffen Klamt et al.

BMC SYSTEMS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

The response of human epithelial cells to TNF involves an inducible autocrine cascade

KA Janes et al.

Article Biochemical Research Methods

A compendium of signals and responses triggered by prodeath and prosurvival cytokines

S Gaudet et al.

MOLECULAR & CELLULAR PROTEOMICS (2005)

Review Cell Biology

Integrative analysis of cell cycle control in budding yeast

KC Chen et al.

MOLECULAR BIOLOGY OF THE CELL (2004)

Article Biochemistry & Molecular Biology

CeIIML: its future, present and past

CM Lloyd et al.

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2004)

Article Biotechnology & Applied Microbiology

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

B Schoeberl et al.

NATURE BIOTECHNOLOGY (2002)