References

Bioinformatics

BioWarehouse: a bioinformatics database warehouse toolkit Lee (2006)

Triad pattern algorithms for predicting strong promoter candidates in bacterial genomes Dekhtyar (2008)

Vector NTI, a balanced all-in-one sequence analysis suite Lu (2004)

E. Coli Metabolic Modelling in Matlab

Deletion

An improved method for deleting large regions of Escherichia coli K-12 chromosome using a combination of Cre/loxP and lambda red Fukiya (2004)

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome Hashimoto (2005)

Construction of consecutive deletions of the Escherichia coli chromosome Kato (2007)

Construction of Escherichia coli K-12 in-frame, single gene knockout mutants: the Keio collection Baba (2006)

Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome Kato (2008)

Emergent properties of reduced genome Escherichia coli Posfai (2006)

Engineering a reduced Escherichia coli genome Kolisnychenko (2002)

Rapid and efficient construction of markerless deletions in the Escherichia coli genome Yu (2008)

DNA Assembly

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium Gibson (2008)

DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine Kelman (1995)

DNA Replication Kornberg (1988)

Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson (2009)

Rebuilding microbial genomes Holt (2007)

Refactoring bacteriophage T7 Chan (2005)

The replication-related organization of bacterial genomes Rocha (2004)

Shear induced assembly of lambda phage DNA Haber (2000)

Structural basis for uracil recognition by archaeal family B DNA polymerases Fogg (2002)

USERTM friendly DNA engineering and cloning method by uracil excision Bitinaite (2007)

E. coli Physiology

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome Hashimoto (2005)

Escherichia coli physiology in Luria-Bertani broth Sezonov (2007)

Fermentation pathways of Escherichia coli, The Clark (1989)

Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110 Hayashi (2006)

The replication-related organization of bacterial genomes Rocha (2004)

Essential Genes

The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame Flower (1986)

Chromosomal Locations of the Genes for rRNA in Escherichia coli K-12t Ellwood (1982)

Construction of Escherichia coli K-12 in-frame, single gene knockout mutants: the Keio collection Baba (2006)

Complete set of ORF clones of Escherichia coli ASKA library (a complete set of Escherichia coli K-12 ORF archive): unique resources for biological research Kitagawa (2005)

Determination of the core of a minimal bacterial gene set Gil (2004)

DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine Kelman (1995)

Experimental determination and systems level analysis of essential genes in Escherichia coli MG1665 Gerdes (2003)

The Heat-Shock-Regulated grpE Gene of Escherichia coli Is Required for Bacterial Growth at All Temperatures but Is Dispensable in Certain Mutant Backgrounds Ang (1989)

Operon Structure of dnaT and dnaC Genes Essential for Normal and Stable DNA Replication of Escherichia coli Chromosome Masai (1988)

Site-directed Mutational Analysis for the ATP Binding of DnaA Protein Mizushima (1998)

Genes, Other

Coding-sequence determinants of gene expression in Escherichia coli Kudla (2009)

Compilation and analysis of Escherichia coli promoter DNA sequences Hawley (1983)

Effect of dna Mutations on the Replication of Plasmid pSC101 in Escherichia coli K-12 Hasunuma (1979)

Genome-wide expression profiling in Escherichia coli K-12 Richmond (1999)

Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110 Hayashi (2006)

Idempotent Vector Design for Standard Assembly of Biobricks Knight 2003

Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli Morgan (1977)

Programming gene expression with combinatorial promoters Cox (2007)

Microfluidics

An inexpensive and portable microchip-based platform for integrated RT–PCR and capillary electrophoresis Kaigala (2008)

Nucleic Acid Properties

Binding of biotinylated DNA to streptavidin-coated polystyrene latex: effects of chain length and particle size Huang (1996)

Dynamic strength of molecular adhesion bonds Evans (1997)

The effect of hydrodynamic shear of DNA from T2 and T4 bacteriophages Davison (1959)

Effect of shear on plasmid DNA in solution Levy (1999)

Folding and unfolding single RNA molecules under tension Folding and unfolding single RNA molecules under tension Woodside (2008)

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays Bernstein (2002)

Shear breakage of DNA Dancis (1978)

Shear degradation of DNA Adam (1977)

Shear-induced degradation of plasmid DNA Lengsfeld (2002)

Shear unzipping of DNA Chakrabarti (2009)

Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions Jendrejack (2002)

Operons

Engineering of bacterial ribosomes: Replacement of all seven Escherichia coli rRNA operons by a single plasmid-encoded operon Nomura (1999)

Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli Morgan (1977)

Operon Structure of dnaT and dnaC Genes Essential for Normal and Stable DNA Replication of Escherichia coli Chromosome Masai (1988)

Recombination

An improved method for deleting large regions of Escherichia coli K-12 chromosome using a combination of Cre/loxP and lambda red Fukiya (2004)

Biochemistry of homologous recombination in Escherichia coli Kowalczykowski (1994)

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome Hashimoto (2005)

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Shizuya (1992)

Conditional-Replication, Integration, Excision, and Retrieval Plasmid-Host Systems for Gene Structure-Function Studies of Bacteria Haldimann (2001)

Construction of consecutive deletions of the Escherichia coli chromosome Kato (2007)

Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome Kato (2008)

DNA cloning by homologous recombination in Escherichia coli Zhang (2000)

Engineering a reduced Escherichia coli genome Kolisnychenko (2002)

Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli Herring (2007)

Gene splicing and mutagenesis by PCR driven overlap extension Heckman (2007)

In vivo transposition of mariner based elements in enteric bacteria and mycobacteria Rubin (1999)

Markerless gene replacement in Escherichia coli stimulated by double strand break in the chromosome Posfai (1999)

One step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome Gibson (2008)

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Datsenko (2000)

Phage integrases: biology and applications Groth (2004)

Rapid and efficient construction of markerless deletions in the Escherichia coli genome Yu (2008)

Recombineering with tolC as a selectable/counter-selectable marker: remodeling the rRNA operons in Escherichia coli DeVito (2007)

Scarless engineering of the Escherichia coli genome Feher (2008)

Shear induced assembly of lambda phage DNA Haber (2000)

Simple and highly efficient BAC recombineering using galK selection Warming (2005)

Techniques: recombinogenic engineering - new options for cloning and manipulating DNA Muyrers (2001)

Synthetic Biology

Engineering BioBrick vectors from BioBrick parts Shetty (2008)

Idempotent Vector Design for Standard Assembly of Biobricks Knight 2003

Refactoring bacteriophage T7 Chan (2005)

Refinement and standardization of synthetic biological parts and devices Canton (2008)

Setting the standard in synthetic biology Arkin (2008)

Transformation

Transformation of Escherichia coli with large DNA molecules by electroporation Sheng (1995)

Vectors

A family of LIC vectors for high through-put cloning and purification of proteins Eschenfeldt (2009)

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Shizuya (1992)

Effect of dna Mutations on the Replication of Plasmid pSC101 in Escherichia coli K-12 Hasunuma (1979)

Engineering BioBrick vectors from BioBrick parts Shetty (2008)

Identification of the mob Genes of Plasmid pSC101 and Characterization of a Hybrid pSC101-R1162 System for Conjugal Mobilization Meyer (2000)

Primary structure of the essential replicon of the plasmid pSC101 Vocke (1983)

Replication of plasmid pSC101 Manen (1991)

Simple and highly efficient BAC recombineering using galK selection Warming (2005)