User:Jarle Pahr/Articles

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See also: Rejected paper repository:



Collections and focus issues


PLOS Comp. Biol. Ten Simple Rules:

PLOS ONE synthetic biology collection:

Microbial Cell Factories - Systems biotechnology and metabolic engineering:

Nature - COGS focus issue:

"The iCOGS Focus highlights 13 papers in genetic epidemiology from the COGS consortium, representing a significant advance in our understanding of genetic susceptibility to breast, ovarian and prostate cancer. "

Molecular Systems Biology - Systems biology technologies series January 2013:

Article series- Applications of next-generation sequencing:

Focus issues:

IET Synthetic Biology:

ACS Synthetic Biology IWBDA 2012 Special Issue:



Negativland - a home for all findings in psychology:

By person


A Cost-Effective Solution for the Reliable Determination of Cell Numbers of Microorganisms in Liquid Culture.:

An LED-based fluorometer for chlorophyll quantification in the laboratory and in the field:

By topic

By year

Enzymes used in molecular biology:


Low-copy-number plasmid-cloning vectors amplifiable by derepression of an inserted foreign promoter


T4 DNA Polymerase Exonuclease:


Minimal length requirement of the single-stranded tails for LIC of PCR products:


Purification of DNA from soil:


Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome


Design Parameters to Control Synthetic Gene Expression in Escherichia coli:

A programming language for composable DNA circuits


Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome:

Automated seamless DNA co-transformation cloning with direct expression vectors applying positive or negative insert selection:

Reports the use of Seamless Enzyme-Free Cloning (or in their words, "Co-transformation cloning" to produce a large library. "The E.coli strain Mach1 yields most colonies, but a few other strains like DH5alpha and Top10 work also."

"Co-transformation employs chemically competent cells [7] yielding 107 or more colonies per μg plasmid. Per co-transformation 200 ng of vector plus 50-500 ng of insert were mixed and the competent cells added to the DNA mixture which was less than 10% of the cell volume (50 μL cells)."


Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement


Review: Engineering genes for predictable protein expression. Gustafsson et al. 2012. Protein expression and purification.

Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

A Data-Driven Framework for Identifying Nonlinear Dynamic Models of Genetic Parts

A novel PCR-based method for high throughput prokaryotic expression of antimicrobial peptide genes

A Whole-Cell Computational Model Predicts Phenotype from Genotype:

Estimation and Discrimination of Stochastic Biochemical Circuits from Time-Lapse Microscopy Data:;jsessionid=E644941045A1954B020570C9A0135584

Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices:;jsessionid=E644941045A1954B020570C9A0135584

Back to the kitchen: food-grade agar is a low-cost alternative to bacteriological agar:

Computational Modeling of Synthetic Microbial Biofilms


TREX: A Universal Tool for the Transfer and Expression of Biosynthetic Pathways in Bacteria -


Shared control of gene expression in bacteria by transcription factors and global physiology of the cell:


Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies:

Multiplex Genome Engineering Using CRISPR/Cas Systems:

RNA-Guided Human Genome Engineering via Cas9:

Preparing synthetic biology for the world:,_Ecotoxicology_and_Bioremediation/10.3389/fmicb.2013.00005/abstract

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology :

Nutrient timing revisited: is there a post-exercise anabolic window?

Review - Genome-scale engineering for systems and synthetic biology:

High-throughput sequencing for biology and medicine:

Cultivation conditions and the diffusion of oxygen into culture media: The rationale for the flask-to-medium ratio in microbiology:

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective:

Can simple biological systems be built from standardized interchangeable parts? Negotiating biology and engineering in a synthetic biology competition:

Engineering biology? Exploring rhetoric, practice, constraints and collaborations within a synthetic biology research centre:

Propellers and promoters: emerging engineering knowledge in aeronautics and synthetic biology:

Identifying Personal Genomes by Surname Inference -


Multiplex Genome Engineering Using CRISPR/Cas Systems. ("Genetic surgery"):

Synthetic circuits integrating logic and memory in living cells:

The Bacterial Nanorecorder: Engineering E. coli to Function as a Chemical Recording Device:

Growth-rate-dependent dynamics of a bacterial genetic oscillator:

Understanding and Exploiting Feedback in Synthetic Biology:

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli:

Artificial repressors for controlling gene expression in bacteria:

Programming biological models in Python using PySB:

Modeling the effect of cell division on genetic oscillators:

Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology:

A new method to customize protein expression vectors for fast, efficient and background free parallel cloning:

Transferring a synthetic gene circuit from yeast to mammalian cells:


Quantitative estimation of activity and quality for collections of functional genetic elements:

Precise and reliable gene expression via standard transcription and translation initiation elements:

Lentini et al. Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology. ACS Synthetic Biology

Building in biosafety for synthetic biology:

DNA Fragments Assembly Based on Nicking Enzyme System:

Amplifying Genetic Logic Gates: