Biocomplexity Institute

On December 1st, 2015, the Virginia Bioinformatics Institute (VBI) became the Biocomplexity Institute of Virginia Tech. VBI was created 15 years ago, at a time when the acquisition and analysis of genomics sequences was the new frontier of biology. Today, the new frontier has shifted toward understanding networks of interacting entities from molecules to human […]

Entrainment of a genetic oscillator

This paper from Bill Mather group in the Physics Department at Virginia Tech shows how a genetic oscillator responds to noisy signals. The authors show that the oscillator gets entrained despite the noise affecting the input signal. This is a nice use of an existing oscillator developed in Jeff Hasty’s group. After demonstrating this property […]

Synthetic biology textbooks

synthetic biology books

I recently came across a couple of synthetic biology textbooks that you may find useful if you have not seen them yet. BioBuilder published by O’Reilly in July 2015. The lead author is Natalie Kuldell  who is an Instructor in the Department of Biological Engineering at MIT as well as Founder and President of the […]

Teaching Synthetic Biology with GenoCAD


Teaching synthetic biology can be challenging because it involves concepts from so many fields.  I would like to give credit to two professors who have been teaching synthetic biology using GenoCAD. I was directly involved in the class taught by Massimiliano Pierobon at the University of Nebraska Lincoln. Using video conference, I first gave a seminar […]

Modeling a Minimal CDK Network

This paper reports a computational analysis of the minimal CDK network engineered in fission yeast (doi:10.1038/nature09543). It had been observed that a Cdk-inhibitory mechanism working through tyrosine phosphorylation of the kinase subunit, which is essential for modern fission yeast, is dispensable in the minimal Cdk network. Developing both deterministic and stochastic models of the minimal Cdk […]

Minimal Cell Cycle

This is a great example of a paper where synthetic biology meets systems biology. The authors developed a minimal cell cycle regulatory network by engineering a synthetic CDK. To simplify the cell cycle control machinery, a cassette expressing a fusion of cdc13 and cdc2under the control of the cdc13 regulatory elements was integrated into the genome. They show that oscillation of a […]

Big data reproducibility issues

This piece explains the inherent challenge of providing statistical significant results out of high dimensional data sets. It also suggests a number of strategies to mitigate the problem.

Bacterial tape recorder

This paper describes a bacterial tape recorder. E.coli engineered to be a bacterial tape recorder by allowing it change its genome in response to chemical signals. This is one of these mind-blowing papers that the Lu’s lab is known for. It’s a very nice combination of biology with engineering. This may be a way of using […]

Recent synthetic biology articles

This page helps you find recent synthetic biology articles. All these articles have been mentioned at least once in social media over the last seven days. They are ranked by number of mentions in social media during the last seven days. Click on any of them to know more.

Universal genetic parts for bacteria

This paper describes UBER, a set of universal genetic parts for bacteria.  This gene expression system for bacteria relying on a self-regulated T7 promoter. The advantage of this system is that it can be ported across species. The system is primed by using degenerate promoter sequences that works in many bacteria. The sequences were also […]