Systems biology and cell engineering

Living systems have classically been studied in-depth one gene at a time. However, each gene and protein exists and functions within complex matrices consisting of a vast array of biomolecules, ranging from small metabolites to large macromolecules. Thus, in vivo, the thousands of other unique molecules and their interactions will influence the function and evolution of each individual protein. Systems-engineering principles are now being applied to elucidate how the cellular context influences each protein and how each protein influences cellular phenotype. This can be accomplished by treating each enzyme as a component in a vast network of proteins, and then modeling their interactions, as if the system were a chemical plant or electrical circuit. We develop novel algorithms to integrate genome-scale data with these models to gain insight into how the network context influences how each protein contributes to phenotypes, such as disease. We also leverage this knowledge to guide cell engineering efforts for biotherapeutic development.

Jan 2017 - Congrats to Anne Richelle for being selected as a Lilly Innovation Fellow.

Jan 2017 - Congrats to Austin Chiang for winning the best poster award at the PepTalk conference.

Nov 2016 - Check out our recent paper on the genome-scale metabolic network for CHO cells at Cell Systems.

May 2016 - Congrats to Shangzhong Li for receiving the best poster award at the Cell Culture Engineering conference.

Jan 2016 – Check out a commentary on our CHO research highlighted in Genetic Engineering & Biotechnology News!

Nov 2015 - Check out our new paper on predictive glycoengineering in Metabolic Engineering

Oct, 2015 – Alex Thomas and Vanessa Thomas both successfully defended their theses!

Sept, 2015 – Philipp Spahn won the poster award at the 2015 Peace Conference!

Aug, 2015 – Anders Bech Bruntse did amazing at his master's thesis defense. Congrats!

Feb, 2015 – Shangzhong Li and Joanne Liu were both awarded FISP fellowships!

Dec 2014 - Anders Bech Bruntse was awarded a Novo Scholarship for his Masters studies!

Nov 2014 - See a recent podcast describing our work on CHO cells

Nov 2014 - Check out our new paper on our 4-day neuron stem cell differentiation in Molecular Systems Biology

Oct 2014 - Jahir Gutierrez won the international Roche & OBR: Game Changing Innovation competition. Congrats!

July 2014 - Jahir Gutierrez was awarded a CONACYT fellowship for his PhD studies!

Feb, 2014 – Congratulations to Shangzhong Li and Jahir Gutierrez for passing their quals and joining the UCSD bioengineering PhD program! Alex Thomas also advanced to PhD candidacy!

Dec, 2013 – Sources of error in next-gen sequencing, and how replicates may help… our work in Nature Reviews Genetics.