Virginia Tech announces GenoCAD transition

GenoCAD_Logo

Virginia Tech issued a press-release announcing the transformation of GenoCAD into a commercial product. GenoCAD started as a NSF-funded research project. In 2010, we released the application open-source using the Apache 2.0 license. Open source licensing appeared to be the most favorable way of ensuring the long-term sustainability of this infrasture. After we created GenoFAB, […]

Scholar of the week

graduate student silhouette

Thank you to whoever nominated me for the “Scholar of the Week” award. The goals of the Scholar of the Week are to recognize individuals while also telling people about research and scholarly activities at the university. Recognition is based on research and/or scholarship.  

Undergraduate Internship Experimental Cell Biology

internship

We are looking for an undergraduate student for an internship in experimental cell biology. Interested candidates should send me their resume. Project Cell division is the basis of life and requires a tightly regulated series of events coordinated cell growth and division with chromosome duplication and segregation. Not surprisingly, the central cell division control mechanisms […]

Undergraduate Internship Scientific Communication

internship

We are looking for an undergraduate student for an internship in scientific communication. Interested candidates should send me their resume. Project Communication is an important aspect of the scientific process. We are looking for a student who is enthusiastic about scientific communication. The student primary responsibilities will include editing the Wikipedia pages related to synthetic […]

Undergraduate Internship Bioinformatics

internship

We are looking for an undergraduate student to participate in a bioinformatics project. Interested candidates should send me their resume. Project Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone […]

Computational Biology Position

Hiring sign blackboard. "we are hiring!" written on black chalkb

Our collaborator John Tyson has an open computational biology position for a postdoc with background in computational biology. The postdoctoral associate’s primary responsibility will be to construct, analyze, simulate and optimize models of cell cycle checkpoints based on elementary reaction networks suitable for investigation by Gillespie’s stochastic simulation algorithm. Success will require close attention to experimental […]

Single Cell Imaging Position

Hiring sign blackboard. "we are hiring!" written on black chalkb

We have a single cell imaging position open to work on our project exploring the molecular basis of cell cycle checkpoints in budding yeast. The emphasis of this position will be on the collection and analysis of experimental data to build stochastic model of the spindle assembly checkpoint and the DNA damage checkpoint in Saccharomyces […]

Design of plant expression vectors

design of plant expression vectors

An article describing the rule-based design of plant expression vectors was published in PLoS ONE. This plant synthetic biology paper is a collaboration with Anna Coll and Kristina Gruden from the National Institute of Biology in Ljubljana. The GenoCAD file available in the online supplement is preloaded in the GenoCAD platform. Give it a try and let us know how it could […]

Plant Synthetic Biology

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software that can be used for plant synthetic biology. It includes a library of plant biological parts […]

Synthetic Biology Informatics

Bioinformatics Conceptual

Overview I lead the Synthetic Biology Informatics Group at the Virginia Bioinformatics Institute (VBI). VBI is a research institute of Virginia Tech.   My group combines experimental and computational approaches to understand how complex phenotypes are encoded natural and synthetic genomes. We develop software to design DNA molecules and analyze the phenotype of individual cells. Recently, we […]