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This page lists various sources used in our research organized by topic. Please note that most of the links to articles on this page will take you only to the abstract of the paper.


Includes catalog for restriction endonucleases/other lab products, a resource called NEBcutter that tells you what restriction endonucleases will cut your gene/DNA sequence of interest, and a tool called the Double Digest Finder that will tell you how compatible two restriction endonucleases are by comparing what conditions they work best in.

Contains a complete list of genes in E. coli and their base pair sequences.

Useful for finding gene sequences and functions in E. coli.

A very useful online database for finding research papers and gene sequences.

"collect the annotations of the sRNAs and the regulatory relationship between transcriptional regulator and sRNA, and between sRNA and its target genes. Additionally, more valuable information of sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation."

Small RNAs

An overview of small RNAs that regulate membrane proteins.

Concerns the method regulation of OmpC by the sRNA MicC

An overview on small RNAs and their functions, discussing the roles of Hfq and RNase E, and mentioning advantages to sRNA use.

Discusses various RNA regulators in bacteria, including riboswitches and sRNAs. Gives examples of well-characterized sRNAs and lists advantages of sRNAs over other types of gene regulation.

Documents successful fusions of sRNA target sequences to GFP in order to study regulatory activity of various sRNAs.

Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.

Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.

A paper on GadY, a small RNA in E. coli that acts on the 3' UTR of the acid response gene it regulates.


Provides a basic model and differential equations for sRNA regulation of a gene, and quantitatively compares sRNA regulation with other types of regulation.

Provides a model of small RNA SgrS and its role in the glucose-phosphate stress response in E. coli.

  • 3. An Introduction to Systems Biology: Design Principles of Biological Circuits: Uri Alon, 2007

A book that provides simple models for transcriptional regulation and analyzes natural gene networks to find network motifs. These network motifs are characterized based on advantages in use and robustness. Recommended by Dr. Golding.

A detailed comparison of sRNA regulation and transcription factor regulation, focusing on aspects such as intrinsic noise, gain, filtering, and small-input fidelity.

Discusses and models the threshold-linear nature of trans-encoded sRNA repression.


Useful website for finding protocols online.

A useful and free online resource explaining protocols and the biological relevance of each step. Recommended by Dr. Golding.

Protocol for plasmid purification using the PerfectPrep Spin Mini Kit.

Protocol for plasmid purification using the PureYield Plasmid Miniprep System.

  • Supplementary Material: Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo: Johannes H. Urban and Jörg Vogel, 2007

Includes step-by-step protocols for fusion cloning into a standard plasmid (pXG-10), fusion cloning via 5' RACE (pXG-20), and operon fusion cloning into pXG-30.

Details a modular two-plasmid system that uses GFP to study sRNA regulation in vivo.

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