User:Jarle Pahr/Articles

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http://www.ploscollections.org/article/browse/issue/info%3Adoi%2F10.1371%2Fissue.pcol.v02.i18

Microbial Cell Factories - Systems biotechnology and metabolic engineering: http://www.microbialcellfactories.com/series/Systemsbiotech

Pshycology

Negativland - a home for all findings in psychology: http://www.biomedcentral.com/2050-7283/1/2

By year

Enzymes used in molecular biology: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/

1984

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

1985

T4 DNA Polymerase Exonuclease: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC341235/pdf/nar00303-0272.pdf

1998

Purification of DNA from soil: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140122/

2009

Design Parameters to Control Synthetic Gene Expression in Escherichia coli: http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0007002

2010

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome: http://www.sciencemag.org/content/329/5987/52.abstract

Automated seamless DNA co-transformation cloning with direct expression vectors applying positive or negative insert selection: http://www.biomedcentral.com/1472-6750/10/56

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)."

2011

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

2012

A novel PCR-based method for high throughput prokaryotic expression of antimicrobial peptide genes http://www.biomedcentral.com/1472-6750/12/10

http://onlinelibrary.wiley.com/doi/10.1002/biot.201200002/abstract

A Whole-Cell Computational Model Predicts Phenotype from Genotype: http://www.cell.com/abstract/S0092-8674%2812%2900776-3

Estimation and Discrimination of Stochastic Biochemical Circuits from Time-Lapse Microscopy Data: http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047151;jsessionid=E644941045A1954B020570C9A0135584

Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices: http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039407;jsessionid=E644941045A1954B020570C9A0135584

September

TREX: A Universal Tool for the Transfer and Expression of Biosynthetic Pathways in Bacteria - http://pubs.acs.org/doi/abs/10.1021/sb3000657

2013

January

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology : http://nar.oxfordjournals.org/content/early/2013/01/31/nar.gkt052.full

Nutrient timing revisited: is there a post-exercise anabolic window? http://www.jissn.com/content/10/1/5

Genome-scale engineering for systems and synthetic biology: http://www.nature.com/msb/journal/v9/n1/full/msb201266.html

High-throughput sequencing for biology and medicine: http://www.nature.com/msb/journal/v9/n1/full/msb201261.html

Cultivation conditions and the diffusion of oxygen into culture media: The rationale for the flask-to-medium ratio in microbiology: http://www.biomedcentral.com/1471-2180/13/9

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective: http://www.ncbi.nlm.nih.gov/pubmed/23341769

Can simple biological systems be built from standardized interchangeable parts? Negotiating biology and engineering in a synthetic biology competition: http://www.tandfonline.com/doi/pdf/10.1080/19378629.2013.764881

Engineering biology? Exploring rhetoric, practice, constraints and collaborations within a synthetic biology research centre: http://www.tandfonline.com/doi/abs/10.1080/19378629.2013.763811

Propellers and promoters: emerging engineering knowledge in aeronautics and synthetic biology: http://www.tandfonline.com/doi/abs/10.1080/19378629.2012.762651

Identifying Personal Genomes by Surname Inference - http://www.sciencemag.org/content/339/6117/321.abstract

February

Multiplex Genome Engineering Using CRISPR/Cas Systems. ("Genetic surgery"): http://www.sciencemag.org/content/339/6121/819.full

Synthetic circuits integrating logic and memory in living cells: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2510.html

The Bacterial Nanorecorder: Engineering E. coli to Function as a Chemical Recording Device: http://www.ncbi.nlm.nih.gov/pubmed/22132112

Growth-rate-dependent dynamics of a bacterial genetic oscillator: http://pre.aps.org/abstract/PRE/v87/i1/e012726

Understanding and Exploiting Feedback in Synthetic Biology: http://www.sciencedirect.com/science/article/pii/S0009250913001097

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli: http://www.nature.com/msb/journal/v9/n1/full/msb201276.html

Artificial repressors for controlling gene expression in bacteria: http://pubs.rsc.org/en/content/articlepdf/2013/cc/c2cc37107c

Programming biological models in Python using PySB: http://www.nature.com/msb/journal/v9/n1/full/msb20131.html

Modeling the effect of cell division on genetic oscillators: http://www.sciencedirect.com/science/article/pii/S0022519313000593

Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology: http://www.la-press.com/a-unifying-mathematical-framework-for-genetic-robustness-environmental-article-a3561

A new method to customize protein expression vectors for fast, efficient and background free parallel cloning: http://www.biomedcentral.com/1472-6750/13/12

March

Quantitative estimation of activity and quality for collections of functional genetic elements: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2403.html

Precise and reliable gene expression via standard transcription and translation initiation elements: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2404.html