Howard Salis, Ph.D.

Teaching

• BE 496 - Independent Studies
  
• CHE 340 - Introduction to Biomolecular Engineering
• CHE 410 - Mass Transfer and Separation Processes

For information about courses please visit the LionPATH Course Catalog.

Research Summary

Research in the Salis laboratory focuses on the development of rational design methods for engineering synthetic biological systems - metabolic pathways, genetic circuits, and genomes. Our goal is to make engineering biology as reliable as building planes, trains, and automobiles. We develop biophysical models of genetic regulation and experimentally test their predictions in industrially and medically useful microorganisms to gain a quantitative understanding of genetic function.

We combine these models with optimization algorithms to automatically design synthetic DNA sequences with desired biological functions — we call them DNA compilers. We have used our methodology to program synthetic microorganisms to sense chemicals, such as environmental toxins or explosives, and to manufacture valuable chemicals for bioenergy applications. Our approach to engineering genetic systems has eliminated trial-and-error, while helping to decipher the physical rules that govern biological function.

Our models and algorithms have become widely used by over 6000 academic and industrial biotechnology researchers, who have designed over 100,000 synthetic DNA sequences using our user-friendly web interface (http://salislab.net/software).

Publications

• Farasat I. and H.M. Salis. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation, PLoS Computational Biology, 2016
• Valerie Soo, Michael McAnulty, Arti Tripathi, Fayin Zhu, Limin Zhang, Emmanuel Hatzakis, Philip Smith, Saumya Agrawal, Hadi Nazem-Bokaee, Saratram Gopalakrishnan, Howard Salis, James Ferry, Costas Maranas, Andrew Patterson and Thomas Wood. Reversing methanogenesis to capture methane for liquid biofuel precursors. Microbial Cell Factories. v15(1):1, (2016).
• Breakthrough Article: Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. Automated Physics-based Design of Synthetic Riboswitches from Diverse RNA Aptamers, Nucleic Acids Research, 0.1093/nar/gkv1289, (2015).
• Tian T. and H.M. Salis. A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons, Nucleic Acids Research, 43 (14), p7137-7151, (2015).
• Kushwaha M. and H.M. Salis. A Portable Expression Resource for Engineering Cross-species Genetic Circuits and Pathways, Nature Communications, v6, (2015).
• Ng C.Y., I. Farasat, C. Maranas, and H.M. Salis. Rational Design of a Synthetic Entner-Doudoroff pathway for Improved and Controllable NADPH Regeneration, Metabolic Engineering, v29, (2015).
• Farasat, I., Kushwaha M., Collens J., Easterbrook M., Guido M., and H.M. Salis. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria, Molecular Systems Biology, v10 (6), (2014).
• Espah Borujeni, A., Channarasappa A.S., and H.M. Salis. Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites, Nucleic Acids Research, v41 (21), (2013).
• H.M. Salis. The Ribosome Binding Site Calculator, Methods in Enzymology, (2011)
• H.M. Salis, E. Mirsky, C.A. Voigt, "Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression", Nature Biotechnology, (2009)
• J.J. Tabor, H.M. Salis, Z. B. Simpson, A.A. Chevalier, A. Levskaya, E.M. Marcotte, C.A. Voigt, A.D. Ellington, "A Synthetic Genetic Edge Detection Program", Cell, v137(1), (2009)
• E.S. Groban, E.J. Clarke, H.M. Salis, S. Miller, and C.A. Voigt, "Kinetic Buffering of Crosstalk between Bacterial Two-Component Sensors", Journal of Molecular Biology, v390(3), (2009)
• H.M. Salis, A. Tamsir, C.A. Voigt, "Engineering Bacterial Signals and Sensors", Contributions to Microbiology book series, 2009 (16), editors: Mattias Collin and Raymond Schuch
• K. Temme, H.M. Salis, D. Tullman-Ercek, A. Levskaya, S.H. Hong, C.A. Voigt, "Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island 1", Journal of Molecular Biology, v377(1), (2008)
• H.M. Salis, Y. Kaznessis, "Computer aided design of modular protein devices: Logical AND gene activation", Physical Biology, v3(4), (2006)
• H.M. Salis, V. Sotiropoulos, Y. Kaznessis, "Multiscale Hy3S: Hybrid stochastic simulation for supercomputers", BMC Bioinformatics, v7, (2006)
• L. Tuttle, H.M. Salis, J. Tomshine, and Y. Kaznessis, "Model-driven designs of an oscillating gene network", Biophysical Journal, v89(6), (2005)
• H.M. Salis, Y. Kaznessis, "An equation-free probabilistic steady state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks", Journal of Chemical Physics, v123 (21), p214106 (2005)
• H.M. Salis, Y. Kaznessis "Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions", Journal of Chemical Physics, v122(5), (2005)
• H.M. Salis, Y. Kaznessis, "Numerical simulation of stochastic gene circuits" Computers in Chemical Engineering, v29(3), (2005)