The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Briefings Bioinform.

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bib/bbp054PMID 19906839PMCID PMC2810114
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS

  2009influential reference
• BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

  2009cited by this paper
• Methods for improving simulations of biological systems: systemic computation and fractal proteins

  2009influential reference
• Challenges in the computational design of proteins

  2009cited by this paper
• ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

  2009cited by this paper
• Synthesis of orthogonal transcription-translation networks

  2009cited by this paper
• Model-based redesign of global transcription regulation

  2009cited by this paper
• CellML metadata standards, associated tools and repositories

  2009influential reference
• Towards programming languages for genetic engineering of living cells

  2009cited by this paper
• A systematic design method for robust synthetic biology to satisfy design specifications

  2009cited by this paper
• Robust synthetic biology design: stochastic game theory approach

  2009cited by this paper
• Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

  2009influential reference
• Genetic engineering of carotenoid formation in tomato fruit and the potential application of systems and synthetic biology approaches.

  2009cited by this paper
• A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells.

  2009cited by this paper
• A general map of iron metabolism and tissue-specific subnetworks.

  2009cited by this paper
• The Systems Biology Graphical Notation

  2009cited by this paper
• The second wave of synthetic biology: from modules to systems

  2009influential reference
• Translating biochemical network models between different kinetic formats.

  2009cited by this paper
• Consistent design schematics for biological systems: standardization of representation in biological engineering

  2009cited by this paper
• Biophysical annotation and representation of CellML models

  2009cited by this paper
• Cellular Open Resource (COR): current status and future directions

  2009cited by this paper
• Integrating and annotating the interactome using the MiMI plugin for cytoscape

  2009cited by this paper
• A tunable synthetic mammalian oscillator

  2009cited by this paper
• You're one in a googol: optimizing genes for protein expression

  2009cited by this paper
• Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks

  2009cited by this paper
• RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation

  2009cited by this paper
• Writing DNA with GenoCAD™

  2009cited by this paper
• BMC Systems Biology

  2009cited by this paper
• A synthetic metabolite-based mammalian inter-cell signaling system.

  2009cited by this paper
• Synthetic Gene Networks That Count

  2009cited by this paper
• Designing and encoding models for synthetic biology

  2009cited by this paper
• Synthetic metabolism: engineering biology at the protein and pathway scales.

  2009cited by this paper
• Information theoretical quantification of cooperativity in signalling complexes

  2009cited by this paper
• A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.

  2009cited by this paper
• Optimization in computational systems biology

  2008cited by this paper
• Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

  2008cited by this paper
• Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

  2008cited by this paper
• Recursive construction of perfect DNA molecules from imperfect oligonucleotides

  2008cited by this paper
• Computational design of synthetic gene circuits with composable parts

  2008cited by this paper
• An integrated cell-free metabolic platform for protein production and synthetic biology

  2008cited by this paper
• SynBioSS: the synthetic biology modeling suite

  2008cited by this paper
• Programming biomolecular self-assembly pathways

  2008cited by this paper
• A fast, robust, and tunable synthetic gene oscillator

  2008cited by this paper
• Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels.

  2008influential reference
• Customized signaling with reconfigurable protein scaffolds

  2008cited by this paper
• Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

  2008cited by this paper
• SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

  2008cited by this paper
• A comprehensive modular map of molecular interactions in RB/E2F pathway

  2008cited by this paper
• Ligand-induced conformational changes in a thermophilic ribose-binding protein

  2008cited by this paper
• A synthetic mammalian gene circuit reveals antituberculosis compounds

  2008cited by this paper
• Toward minimal bacterial cells: evolution vs. design

  2008cited by this paper
• Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

  2008cited by this paper
• EcoCyc: A comprehensive view of Escherichia coli biology

  2008cited by this paper
• Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

  2008cited by this paper
• Bottom-up genome assembly using the Bacillus subtilis genome vector

  2008cited by this paper
• Systems Biology Graphical Notation: Process Diagram Level 1

  2008cited by this paper
• Targeted Development of Registries of Biological Parts

  2008cited by this paper
• FERN – a Java framework for stochastic simulation and evaluation of reaction networks

  2008cited by this paper
• Quantification of PRL/Stat5 signaling with a novel pGL4-CISH reporter

  2008cited by this paper
• Refinement and standardization of synthetic biological parts and devices

  2008cited by this paper
• LibSBML: an API Library for SBML

  2008cited by this paper
• The CellML Model Repository

  2008cited by this paper
• Building a Parallel Metabolism within the Cell.

  2008cited by this paper
• A molecular noise generator

  2008cited by this paper
• An Artificial Aptazyme‐Based Riboswitch and its Cascading System in E. coli

  2008cited by this paper
• Toward scalable parts families for predictable design of biological circuits.

  2008cited by this paper
• Engineering microbes with synthetic biology frameworks.

  2008cited by this paper
• DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

  2008cited by this paper
• Dual-In/Out strategy for genes integration into bacterial chromosome: a novel approach to step-by-step construction of plasmid-less marker-less recombinant E. coli strains with predesigned genome structure

  2008cited by this paper
• OptCircuit: An optimization based method for computational design of genetic circuits

  2008cited by this paper
• The iGEM competition: building with biology

  2007influential reference
• Mammalian synthetic biology: engineering of sophisticated gene networks.

  2007cited by this paper
• Biology by design: reduction and synthesis of cellular components and behaviour

  2007influential reference
• MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

  2007cited by this paper
• Integration of biological networks and gene expression data using Cytoscape

  2007cited by this paper
• Towards synthesis of a minimal cell

  2006cited by this paper
• CellML2SBML: conversion of CellML into SBML

  2006cited by this paper
• Synthesizing cellular networks from evolved ribosome-mRNA pairs.

  2006cited by this paper
• Systems biology as a foundation for genome-scale synthetic biology.

  2006influential reference
• Cell‐free translation systems for protein engineering

  2006cited by this paper
• Production of isoprenoid pharmaceuticals by engineered microbes

  2006influential reference
• Synthetic biology projects in vitro.

  2006cited by this paper
• Model storage, exchange and integration

  2006cited by this paper
• A network of orthogonal ribosome·mRNA pairs

  2005cited by this paper
• Subnets of scale-free networks are not scale-free: sampling properties of networks.

  2005cited by this paper
• Complex networks and simple models in biology

  2005influential reference
• Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX

  2005cited by this paper
• BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

  2005cited by this paper
• Minimum information requested in the annotation of biochemical models (MIRIAM)

  2005cited by this paper
• Uniform Resource Identifier (URI): Generic Syntax

  2005cited by this paper
• PAX of mind for pathway researchers.

  2005cited by this paper
• Gaining confidence in high-throughput protein interaction networks

  2004cited by this paper
• Unraveling protein interaction networks with near-optimal efficiency

  2004cited by this paper
• Global Mapping of the Yeast Genetic Interaction Network

  2004cited by this paper
• CellML: its future, present and past.

  2004cited by this paper
• Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

  2004cited by this paper
• Idempotent Vector Design for Standard Assembly of Biobricks

  2003influential reference
• The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

  2003cited by this paper
• CellDesigner: a process diagram editor for gene-regulatory and biochemical networks

  2003cited by this paper
• Assembly of Cell Regulatory Systems Through Protein Interaction Domains

  2003cited by this paper

• Weak ties in scientific cooperation contribute to scientific innovation

  2026cites this paper
• SeqImprove: Machine-Learning-Assisted Curation of Genetic Circuit Sequence Information.

  2024cites this paper
• The emergence of entrepreneurial ecosystems based on enabling technologies: Evidence from synthetic biology

  2022cites this paper
• Design of artificial cells: artificial biochemical systems, their thermodynamics and kinetics properties

  2022influential citation
• Curation Principles Derived from the Analysis of the SBOL iGEM Data Set.

  2021cites this paper
• Genome Engineering Tools in Plant Synthetic Biology

  2019cites this paper
• Human Digital Immortality: Where Human Old Dreams and New Technologies meet

  2019cites this paper
• Design automation in synthetic biology : a dual evolutionary strategy

  2019cites this paper
• Current challenges facing one-step production of l-ascorbic acid.

  2018cites this paper
• Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms.

  2017cites this paper
• Synthetic Biology: Culture and Bioethical Considerations

  2016cites this paper
• Emerging Synthetic Biology Techniques: Synthetic DNA, Metabolic Pathways, and Life

  2016cites this paper
• Standardised Genetic Output Measurement

  2016cites this paper
• Plant synthetic biology.

  2015cites this paper
• Synthetic biology: A control engineering perspective

  2014cites this paper
• G protein-coupled receptors revisited: therapeutic applications inspired by synthetic biology.

  2014cites this paper
• Protein Subcellular Localization Feature of Essential/Nonessential Genes in 28 Prokaryotes

  2014cites this paper
• Synthetic Biology and Microdevices: A Powerful Combination

  2013cites this paper
• Digital 'faces' of synthetic biology.

  2013cites this paper
• Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology.

  2013cites this paper
• Synthetic biology & microdevices : a powerful combination

  2013cites this paper
• Boosting forward-time population genetic simulators through genotype compression

  2013cites this paper
• Translational cross talk in gene networks.

  2013cites this paper
• Design and Application of Synthetic Biology Devices for Therapy

  2013cites this paper
• Performing Collective Tasks with Flagellated Bacteria Acting as Natural and Hybrid Microrobots

  2013cites this paper
• Embodied artificial evolution

  2012cites this paper
• Rise and Demise of Bioinformatics? Promise and Progress

  2012cites this paper
• Genetic design automation: engineering fantasy or scientific renewal?

  2012cites this paper
• Automated selection of synthetic biology parts for genetic regulatory networks.

  2012cites this paper
• Synthetic Biology: Mapping the Scientific Landscape

  2012cites this paper
• Bio-informational capitalism

  2012cites this paper
• A statistical feature of Hurst exponents of essential genes in bacterial genomes.

  2012cites this paper
• Artificial evolutionary systems in the 21st Century

  2012cites this paper
• Aims and Scope

  2011cites this paper
• Robot Companions: Technology for Humans

  2011cites this paper
• Living Technology Artificial Systems Embodied Evolution Fet Consultation Workshop @bullet@bullet@bullet Future and Emerging Technologies Fet Consultation Meeting: Living Technology – Artificial Systems – Embodied Evolution Fet Consultation Meeting: Living Technology – Artificial Systems – Embodied E

  2011cites this paper
• On Three Challenges of Artificial Living Systems and Embodied Evolution

  2011cites this paper
• Evolution of Things

  2011cites this paper
• Can we grow buildings? Concepts and requirements for automated nano- to meter-scale building

  2011cites this paper
• Methods for and results from the study of design principles in molecular systems.

  2011cites this paper
• Synthetic biology: From the first synthetic cell to see its current situation and future development

  2011cites this paper
• Techniken der Überschreitung. Fertigungsmechanismen ‹verlässlich lebensfähiger› biologischer Entitäten

  2011cites this paper
• Cross-Platform Microarray Data Normalisation for Regulatory Network Inference

  2010cites this paper
• Confidence from uncertainty - A multi-target drug screening method from robust control theory

  2010cites this paper