Edinburgh Research Explorer

Dr Yizhi Cai

(Former employee or visitor)

Education/Academic qualification

Doctor of Philosophy (PhD), Virginia Tech
GenoCAD: linguistic approaches to synthetic biology
Master of Science, University of Edinburgh
Simulating the Interferon Response Pathway
Bachelor of Engineering, Central South University
Active Object Tracking based on Snake Model

Professional Qualifications

Postdoc Fellowship, Johns Hopkins University

Willingness to take PhD students: Yes

Computer Assisted Design: CAD tools are instrumental in any engineering fields; however synthetic biology as an engineering field is lagging behind in this regard.

We are collaborating with the world’s best CAD company, Autodesk, Inc., to develop a cutting edge design tool named Autogene. We developed Autogene 1.0 as a proof of principle, and it won the best software award in the International Genetically Engineered Machine Competition (iGEM) 2012 (http://2012.igem.org/Team:Johns_Hopkins-Software). We are now looking for motivated students with strong computational background to continue this project and take it to the next level.

The philosophy of Autogene is: Scan, Modify and Print. On the Scan level, we will partner with BGI, the world largest sequencing center, to develop a comprehensive biological sequence feature database, and will continue leveraging Autodesk's cloud computing power to develop state of the art feature finding algorithms. On the Modify/Design level, we will focus on design of novel pathways to be integrated into our NeoChromosome (a synthetic yeast chromosome). And on the Print/Synthesis level, we are hoping to connect Autogene directly to our DNA synthesis automation platform so that a designer DNA sequence can be quickly fabricated and characterised.

Area of Expertise

Research expertisesynthetic biology, bioinformatics, genomics, yeast genetics

Research activities & awards

  1. ACS Synthetic Biology (Journal)

    Activity: Publication peer-review and editorial work typesEditorial activity

  2. School of Biological Sciences Symposium

    Activity: Academic talk or presentation typesInvited talk

  3. Seminar at MD Andersen Cancer Research Center

    Activity: Academic talk or presentation typesInvited talk

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