Novel systems biology algorithms to analyze Biomedical Big Data--massive and diverse datasets capturing complex biological interactions and are difficult to analyze using conventional data analysis methods.
Multiscale models of metabolism, protein expression, and regulation, and multiscale optimization of bioprocesses.
Antimicrobial strategies using systems biology models and multiple â??omics data (genomics, transcriptomics, proteomics, epigenomics.
Computer-aided microbe design for value-added chemicals, nutrients for animal feed, and therapeutic proteins.
Teaching Interests:
6 years of Teaching Assistant experience for Process Dynamics and Control
Certification for completion of a 15-hour course on teaching university courses (at UCSD)
I make appropriate use of active learning techniques, where student learning is facilitated using in-class clicker (real-time survey) questions on complex concepts that activate existing knowledge, identify misconceptions, and improve knowledge retention. Additional modern pedagogical methods will be used, including the inverted classroom and a balance of formative (ongoing or real-time) assessment and summative (exams, final presentations, etc.) assessment.
Peer-Reviewed Journal Articles
E Brunk, KJ George, J Alonso-Guttierrez, M Thompson, E Baidoo, G Wang, L Yang, D McCloskey, T Baath, C Petzold, J Monk, EJ O'Brien, HG Martin, A Feist, P Adams, JD Keasling, BO Palsson, and TS Lee (2016) Characterizing Strain Variation in Engineered E. coli Using a Multi-omics Based Work ow. Cell Systems 2: 335-346.
L Yang, J Tan, EJ O'Brien, JM Monk, D Kim, HJ Li, P Charusanti, A Ebrahim, CJ Lloyd, JT Yurkovich, B Du, A Drager, A Thomas, Y Sun, MA Saunders, and BO Palsson (2015) A systems biology denition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci USA 112:10810-10815.
L Yang, S Srinivasan, R Mahadevan, and WR Cluett (2015) Characterizing metabolic pathway diversication in the context of perturbation size. Metab Eng 28: 14-122.
K Zhuang, L Yang, WR Cluett, and R Mahadevan (2013) Dynamic strain scanning optimization: an ecient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design. BMC Biotechnol 13:8.
L Yang, WR Cluett, and R Mahadevan (2011) EMILiO: a fast algorithm for genome-scale strain design. Metab Eng 13:272-281.
S Garg, L Yang, and R Mahadevan (2010) Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling. BMC Research Notes, 3:125.
L Yang, R Mahadevan, and WR Cluett (2008) A bilevel optimization algorithm to identify enzymatic capacity constraints in metabolic networks. Comput Chem Eng, 32:2072-2085.
Submitted and pre-print articles
L Yang, D Ma, A Ebrahim, CJ Lloyd, MA Saunders, and BO Palsson. solveME: fast and reliable solution of nonlinear ME models. Under review.
L Yang, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson. dynamicME: Dynamic simulation and renement of integrated models of metabolism and protein expression. Under review.
L Yang, JT Yurkovich, CJ Lloyd, A Ebrahim, MA Saunders, BO Palsson. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Submitted.
D Ma, L Yang, RMT Fleming, I Thiele, BO Palsson, MA Saunders (2016) Quadruple-precision solution of genome-scale models of Metabolism and macromolecular Expression. arXiv Preprint arXiv:1606.00054v1.
