User:Jarle Pahr/Articles

Collections and focus issues

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

Nature - COGS focus issue: http://www.nature.com/ng/journal/v45/n4/index.html

"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: http://www.nature.com/msb/focus/systems_technologies/index.html

Pshycology

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

By person

MHM:

A Cost-Effective Solution for the Reliable Determination of Cell Numbers of Microorganisms in Liquid Culture.: http://www.ncbi.nlm.nih.gov/pubmed/23468116

An LED-based fluorometer for chlorophyll quantification in the laboratory and in the field: http://link.springer.com/article/10.1007%2Fs11120-012-9777-y

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

1994

Minimal length requirement of the single-stranded tails for LIC of PCR products: http://genome.cshlp.org/content/4/3/172.full.pdf

1998

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

2005

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome http://www.pnas.org/content/102/44/15971.full

2009

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

A programming language for composable DNA circuits

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

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 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

Back to the kitchen: food-grade agar is a low-cost alternative to bacteriological agar: http://www.ncbi.nlm.nih.gov/pubmed/22809873

Computational Modeling of Synthetic Microbial Biofilms

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

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

January

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies: http://nar.oxfordjournals.org/content/41/1/e1.full?sid=e66b42ac-a309-47cf-8cd1-94e1229a098e

Multiplex Genome Engineering Using CRISPR/Cas Systems: http://www.sciencemag.org/content/339/6121/819.abstract

RNA-Guided Human Genome Engineering via Cas9: http://www.sciencemag.org/content/339/6121/823.abstract

Preparing synthetic biology for the world: http://www.frontiersin.org/Microbiotechnology,_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 : 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

Review - 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

Transferring a synthetic gene circuit from yeast to mammalian cells: http://www.nature.com/ncomms/journal/v4/n2/full/ncomms2471.html

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

Building in biosafety for synthetic biology: http://mic.sgmjournals.org/content/early/2013/03/20/mic.0.066308-0.full.pdf+html

DNA Fragments Assembly Based on Nicking Enzyme System: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590185/

Amplifying Genetic Logic Gates: