ChiamYu is re-engineering cellular metabolism from the bottom-up, and developing new design methods to accelerate that process. She is also an avid photographer and musician.
Alex is developing advanced sequence-to-function biophysical models of gene expression and regulation for prokayotes and eukaryotes. His hobbies include rowing, weight lifting, reading, creative projects, and PC building.
Grace is engineering RNA-based sensors for applications in metabolic engineering, toxicology, medical diagnostics, and environmental remediation. In her free time, she enjoys hiking, skiing, and a good cup of coffee.
Sean is developing next-generation approaches to engineering synthetic metabolic pathways with many enzymes and synthetic genetic circuits with many regulators. In his spare time, Sean enjoys tabletop games, videogames, and sleep.
Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. Automated Physics-based Design of Synthetic Riboswitches from Diverse Aptamers, Nature Biotechnology, in review
Tian T. and H.M. Salis. A Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons, Nucleic Acid Research, in review
Kushwaha M. and H.M. Salis. A Portable Power Supply for Cross-Species Engineering of Genetic Circuits and Metabolic Pathways, Nature Communications, in review
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
Farasat, I., Kushwaha M., Collens J., Easterbrook M., Guido M., and Salis H.M. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria, Molecular Systems Biology, v10 (6)
Espah Borujeni, A., Channarasappa A.S., and Salis H.M. Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites, Nucleic Acid Research, v41 (21)
Salis, H.M. The Ribosome Binding Site Calculator, Methods in Enzymology, v498, pp. 19-42
Salis, H.M., Mirsky, E.A. and Voigt, C.A. Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression, Nature Biotechnology, v27 (10)
Tabor, J.J., Salis, H.M., Simpson, Z.B., Chevalier, A.A., Levskaya, A., Marcotte, E., Voigt, C.A., and Ellington, A.D. A Synthetic Genetic Edge Detection Program, Cell, 137 (7): 1271-1281
Groban, E.S., Clarke, E.J., Salis, H.M, Miller, S.M., and Voigt, C.A. Kinetic Buffering of Crosstalk between Bacterial Two-component Sensors, Journal of Molecular Biology, 390 (3): 380-393.
Salis H.M., Tamsir A., and Voigt C.A. Engineering Bacterial Signals and Sensors, Bacterial Sensing and Signaling, Contributions to Microbiology series, Collin M. and Schuch R. (eds)
Temme, K., Salis, H., Tullman-Ercek, D. Levskaya, A., Hong, S-H., and Voigt, C. A. Induction and Relaxation Dynamics of the Regulatory Network Controlling the Type III Secretion System Encoded within Salmonella Pathogenicity Island 1, Journal of Molecular Biology, 377 (1): 47-61.
H. Salis and Y. Kaznessis. Computer Aided Design of Modular Protein Devices: Logical AND Gene Activation, Physical Biology, v3 (4).
H. Salis, V. Sotiropoulos, and Y. Kaznessis. Multiscale Hy3S: Hybrid Stochastic Simulation for Supercomputers, BMC Bioinformatics, v7. (Highly accessed)
L. Tuttle, H. Salis, J. Tomshine, and Y. Kaznessis. Model-Driven Designs of an Oscillating Gene Network, Biophysical Journal, v89(6).
H. Salis, and 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).
H. Salis, and Y. Kaznessis. Accurate Hybrid Stochastic Simulation of a System of Coupled Chemical or Biochemical Reactions, Journal of Chemical Physics, v122(5).
H. Salis, and Y. Kaznessis. Numerical Simulation of Stochastic Gene Circuits, Computers in Chemical Engineering, v29(3).
H.M. Salis. Simulation of Stochastic Chemical Systems: Applications in the Design and Construction of Synthetic Gene Networks, Ph.D. Thesis, Chemical Engineering, University of Minnesota.
Howard presents the lab's recent work on "Automated Design of Synthetic Riboswitches from Diverse RNA Aptamers" at the International Conference on Biomolecular Engineerign in Austin, TX. It was an excellent conference.
Sean Halper and Alexander Reis have joined the Salis lab as first-year Chemical Engineering graduate students. Welcome!
Tian Tian presented her recent research results at AIChE's Annual Meeting in Atlanta, GA, entitled "Autonomous Control of Metabolism with Synthetic Sensor-Circuits".
ChiamYu Ng presented her recent research results at the AIChE's Annual Meeting in Atlanta, GA, entitled "Design & Optimization of a Synthetic Entner-Doudoroff Pathway for Efficient NADPH Regeneration".
Howard traveled to New Delhi, India and presented the lab's unique, model-oriented approach to engineering synthetic organisms at the NSF-sponsored Indo-US Workshop for Systems and Synthetic Biology.
Howard presented the lab's approach to efficiently engineering metabolic pathways at Genomatica's headquarters in San Diego, CA.
Howard presented an overview of the lab's Synthetic Biology research during the Chemical Engineering seminar series at the California Institute of Technology.
ChiamYu Ng wins the Best Presentation Award at the SynBERC Fall Retreat for her presentation on "Design and Optimization of a Synthetic Entner-Doudoroff Pathway for Improved and Controllable NADPH Regeneration".
The Salis Lab has moved to a new laboratory space in the Wartik building!
Grace Vezeau has joined the Salis lab as a first-year Biological Engineering graduate student. Welcome!
Howard presents the lab's recent research results on "The Design and Optimization of a Synthetic Entner-Doudoroff Pathway for Efficient NADPH Regeneration" at the Society for Industrial Microbiology and Biotechnology's annual meeting in St. Louis, MO.
Howard shared the lab's experiences with translating research results into a user-friendly Software-as-a-Service using AWS' distributing computing system.
The Salis Lab has received a grant from the Air Force Office of Scientific Research to develop a theory-based genetic compiler that designs advanced synthetic genetic circuits.
>Howard shares the lab's recent research on "White-Boxing Genetic Circuit Modeling: Absolute TF Binding Free Energies From Fluorescence Measurements" at the Quantitative-bio Winter conference in Kona Island, HI.
>Amin Espah Borujeni presents his work on the "Riboswitch Calculator: De Novo Design of Synthetic Cis-Acting Riboswitches From Ligand-Binding Aptamers" at the AIChE Annual Meeting in San Francisco.
Iman Farasat presents his work on "White-Boxing Genetic Circuit Modeling: Absolute TF Binding Free Energies From Fluorescence Measurements" at the AIChE Annual Meeting in San Francisco.
Iman Farasat wins the Best Poster Award at the SynBERC Fall Retreat for his work on "Single-pass design of genetic circuits using in vivo measurements of transcription factor binding energies".
The Salis Lab has received a grant from the Office of Naval Research to engineer advanced cellular sensors and signal processing genetic circuits.
Chiam Yu Ng wins the Best Candidacy Exam Award. Congratulations!
Howard presents the lab's research results on the "Efficient Design and Optimization of Genetic Circuits and Metabolic Pathways" at the Society for Industrial Microbiology and Biotechnology in San Diego, CA.
Howard has received the NSF Career Award to develop next-generation approaches for metabolic pathway engineering.
Howard Salis presents an invited talk, "Clone Less, Know More: Efficient Design and Optimization of Genetic Circuits and Metabolic Pathways" at the International Workshop on Bio-design Automation in London.
Long Chen has successfully defended his Masters Thesis on a molecular lock and key system to control DNA replication. Congratulations!
Chiam Yu Ng has joined the Salis lab as a first-year Chemical Engineering graduate student. Welcome!
Tian Tian presents her work on a "Biophysical Model of Translational Coupling to Coordinate Protein Expression" at the SynBERC Fall Retreat.
The Salis lab has received an ONR MURI grant to develop advanced cell-based sensors and signal processing genetic circuits.
Tian Tian has successfully defended her Masters Thesis on a new biophysical model of translational coupling, and will be continuing as a PhD student. Congratulations!
The Salis lab has received a DARPA grant to develop a genetic security system for recombinant DNA.
Tian Tian and Long Chen have joined the Salis lab as first-year Biological Engineering graduate students. Welcome!
Iman Farasat has received the Leighton Riess Graduate Fellowship in Engineering for outstanding work. Congratulations!
Howard has received the DARPA Young Faculty Award for the "Rational Design of Nucleic Acids to Control Metabolism".
Amin Espah Borujeni and Iman Farasat have joined the Salis lab as first-year Chemical Engineering graduate students. Welcome!