Systems Biology Perspectives on Minimal and Simpler Cells

The Canonical Network of Autotrophic Intermediary Metabolism: Minimal Metabolome of a Reductive Chemoautotroph

(2016) Vijayasarathy Srinivasan et al.   BIOLOGICAL BULLETIN

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Evolvability Is Inevitable: Increasing Evolvability without the Pressure to Adapt

(2013) Joel Lehman et al.   PLoS One

Availability of public goods shapes the evolution of competing metabolic strategies

(2013) H. Bachmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interfacial assembly of protein–polymer nano-conjugates into stimulus-responsive biomimetic protocells

(2013) Xin Huang et al.   Nature Communications

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

(2013) Maria Lluch-Senar et al.   PLoS Genetics

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Quantitative Real-Time PCR Analysis of ‘Candidatus Phytoplasma mali’ Without External Standard Curves

(2012) Sanja Baric   Erwerbs-Obstbau

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

LUCApedia: a database for the study of ancient life

(2012) Aaron David Goldman et al.   NUCLEIC ACIDS RESEARCH

Coping with complexity in metabolic engineering

(2012) Joerg Mampel et al.   TRENDS IN BIOTECHNOLOGY

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

(2012) Ranjan V. Mannige et al.   PLoS Computational Biology

Minimal cells: Relevance and interplay of physical and biochemical factors

(2011) Pasquale Stano   Biotechnology Journal

The proteomic complexity and rise of the primordial ancestor of diversified life

(2011) Kyung Mo Kim et al.   BMC EVOLUTIONARY BIOLOGY

The minimal genome--a metabolic and environmental comparison

(2011) M. T. DeWall et al.   Briefings in Functional Genomics

Modularity of the Bacterial Cell Cycle Enables Independent Spatial and Temporal Control of DNA Replication

(2011) Kristina Jonas et al.   CURRENT BIOLOGY

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

RcnB Is a Periplasmic Protein Essential for Maintaining Intracellular Ni and Co Concentrations in Escherichia coli

(2011) C. Bleriot et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence of "Candidatus Tremblaya princeps" Strain PCVAL, an Intriguing Translational Machine below the Living-Cell Status

(2011) S. Lopez-Madrigal et al.   JOURNAL OF BACTERIOLOGY

The essential genome of a bacterium

(2011) B. Christen et al.   Molecular Systems Biology

Metabolic modeling of endosymbiont genome reduction on a temporal scale

(2011) K. Yizhak et al.   Molecular Systems Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

(2011) Raul Perez-Jimenez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

OGEE: an online gene essentiality database

(2011) Wei-Hua Chen et al.   NUCLEIC ACIDS RESEARCH

Core Proteome of the Minimal Cell: Comparative Proteomics of Three Mollicute Species

(2011) Gleb Y. Fisunov et al.   PLoS One

The proteome of Mycoplasma pneumoniae, a supposedly “simple” cell

(2011) Ina Catrein et al.   PROTEOMICS

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

(2011) Tom A Mendum et al.   GENOME BIOLOGY

Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry

(2010) Hilal Taymaz-Nikerel et al.   BIOTECHNOLOGY AND BIOENGINEERING

Building the blueprint of life

(2010) Christopher Henry et al.   Biotechnology Journal

Update on designing and building minimal cells

(2010) Michael C Jewett et al.   CURRENT OPINION IN BIOTECHNOLOGY

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

(2010) John P. McCutcheon et al.   Genome Biology and Evolution

Topological network alignment uncovers biological function and phylogeny

(2010) O. Kuchaiev et al.   Journal of the Royal Society Interface

Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications

(2010) Kinga Umenhoffer et al.   Microbial Cell Factories

Genome update: the 1000th genome - a cautionary tale

(2010) K. Lagesen et al.   MICROBIOLOGY-SGM

Cell division in a minimal bacterium in the absence of ftsZ

(2010) Maria Lluch-Senar et al.   MOLECULAR MICROBIOLOGY

A formal test of the theory of universal common ancestry

(2010) Douglas L. Theobald   NATURE

Was the universal common ancestry proved?

(2010) Takahiro Yonezawa et al.   NATURE

Theobald reply

(2010) D. L. Theobald   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The metabolic enzyme CTP synthase forms cytoskeletal filaments

(2010) Michael Ingerson-Mahar et al.   NATURE CELL BIOLOGY

Grand Challenge Commentary: Chassis cells for industrial biochemical production

(2010) Claudia E Vickers et al.   Nature Chemical Biology

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

How the insect immune system interacts with an obligate symbiotic bacterium

(2010) A. E. Douglas et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Some considerations on the nature of LUCA, and the nature of life

(2010) Michel Morange   RESEARCH IN MICROBIOLOGY

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

No evidence for elemental-based streamlining of prokaryotic genomes

(2010) Sara Vieira-Silva et al.   TRENDS IN ECOLOGY & EVOLUTION

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Considerations for the design and construction of a synthetic platform cell for biotechnological applications

(2009) P.L. Foley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)

(2009) Roy R Chaudhuri et al.   BMC GENOMICS

Systems Biology: The elements and principles of Life

(2009) Hans V. Westerhoff et al.   FEBS LETTERS

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Mathematical modeling of a minimal protocell with coordinated growth and division

(2009) Ivan V. Surovtsev et al.   JOURNAL OF THEORETICAL BIOLOGY

Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production

(2009) Jun Lee et al.   Microbial Cell Factories

Artificial assembly of a minimal cell

(2009) Giovanni Murtas   Molecular BioSystems

Systems biology and the virtual physiological human

(2009) Peter Kohl et al.   Molecular Systems Biology

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus

(2009) Erik R. Zinser et al.   PLoS One

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EVOLUTIONARY ROOTS: On the Origin of Life on Earth

(2009) C. Zimmer   SCIENCE

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

(2009) E. Yus et al.   SCIENCE

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

The application of flux balance analysis in systems biology

(2009) Erwin P. Gianchandani et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

Proteomic Analysis of Stationary Phase in the Marine Bacterium "Candidatus Pelagibacter ubique"

(2008) S. M. Sowell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'

(2008) Michael Kube et al.   BMC GENOMICS

Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis

(2008) T. Morimoto et al.   DNA RESEARCH

Superpositioning of Deletions Promotes Growth of Escherichia coli with a Reduced Genome

(2008) H. Mizoguchi et al.   DNA RESEARCH

The genomics of LUCA

(2008) Wai-Kin Mat   Frontiers in Bioscience-Landmark

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

(2008) N. Gupta et al.   GENOME RESEARCH

Evolution and self-assembly of protocells

(2008) Ricard V. Solé   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

The Striking Case of Tryptophan Provision in the Cedar Aphid Cinara cedri

(2008) M. J. Gosalbes et al.   JOURNAL OF BACTERIOLOGY

Large-scale transposon mutagenesis ofMycoplasma pulmonis

(2008) Christopher T. French et al.   MOLECULAR MICROBIOLOGY

An integrated cell-free metabolic platform for protein production and synthetic biology

(2008) Michael C Jewett et al.   Molecular Systems Biology

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

(2008) Véronique de Berardinis et al.   Molecular Systems Biology

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

Hydrothermal vents and the origin of life

(2008) William Martin et al.   NATURE REVIEWS MICROBIOLOGY

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

(2008) R. Zhang et al.   NUCLEIC ACIDS RESEARCH

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

(2008) Stephen J. Callister et al.   PLoS One

A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae

(2008) D. E. Cameron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome

(2008) J. Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE

The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus

(2008) Claudia Steglich et al.   PLoS Genetics

Knowledge-making distinctions in synthetic biology

(2007) Maureen A. O'Malley et al.   BIOESSAYS