User:Jarle Pahr/Articles
See also: Rejected paper repository: http://emlab.rose2.brandeis.edu/rejections
Reviews
Favorites
Collections and focus issues
Collections:
PLOS ONE synthetic biology collection: 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
Article series- Applications of next-generation sequencing: http://www.nature.com/nrg/series/nextgeneration/index.html
Focus issues:
IET Synthetic Biology: http://digital-library.theiet.org/content/journals/iet-stb/1/1-2
ACS Synthetic Biology IWBDA 2012 Special Issue: http://pubs.acs.org/toc/asbcd6/2/5
Nutrition
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 topic
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
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 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: http://www.nature.com/msb/journal/v9/n1/full/msb201270.html
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
Lentini et al. Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology. ACS Synthetic Biology
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:
