Publications

On Deck

Tian T. and Salis, H.M., Biophysical Modeling of Translational Coupling Reveals Contributions from Ribosome Re-initiation and De Novo Initiation in Multi-Protein Operons, editing

Collens, J., Emerson, D., and Salis, H.M., Rational Design and Characterization of a Furfural Catabolic Pathway for Removing Microbial Furan Inhibitors, editing

Farasat I. and Salis, H.M., Automated Global Optimization of a Synthetic Metabolic Module using Coupled Biophysical Models that Link Sequence, Expression, Pathway Activity, and Host Growth Rate, editing

2013

Espah Borujeni, A., Channarasappa A.S., and Salis H.M., (2013) 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)

Farasat, I., Collens J., Guido M., and Salis H.M., (2013) Efficient Search for Optimal Expression Levels in Multi-protein Genetic Systems, submitted

2011

Salis, H.M. (2011) The Ribosome Binding Site Calculator, Methods in Enzymology, v498, pp. 19-42, Voigt C.A. (editor)

2009

Salis, H.M., Mirsky, E.A. & Voigt, C.A. (2009) 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., & Ellington, A.D. (2009) A Synthetic Genetic Edge Detection Program, Cell, 137 (7): 1271-1281

Groban, E.S., Clarke, E.J., Salis, H.M, Miller, S.M., & Voigt, C.A. (2009) Kinetic Buffering of Crosstalk between Bacterial Two-component Sensors, Journal of Molecular Biology, 390 (3): 380-393.

Salis H.M., Tamsir A., Voigt C.A. (2009) Engineering Bacterial Signals and Sensors, Bacterial Sensing and Signaling, Contributions to Microbiology series, Collin M. and Schuch R. (eds)

2008

Temme, K., Salis, H., Tullman-Ercek, D. Levskaya, A., Hong, S-H., & Voigt, C. A. (2008) 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.

2006

H. Salis, Y. Kaznessis. (2006) Computer Aided Design of Modular Protein Devices: Logical AND Gene Activation, Physical Biology, v3 (4).

H. Salis, V. Sotiropoulos, Y. Kaznessis. (2006) Multiscale Hy3S: Hybrid Stochastic Simulation for Supercomputers, BMC Bioinformatics, v7. (Highly accessed)

2005

L. Tuttle, H. Salis, J. Tomshine, and Y. Kaznessis. (2005) Model-Driven Designs of an Oscillating Gene Network, Biophysical Journal, v89(6).

H. Salis, Y. Kaznessis. (2005) 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, Y. Kaznessis. (2005) Accurate Hybrid Stochastic Simulation of a System of Coupled Chemical or Biochemical Reactions, Journal of Chemical Physics, v122(5).

H. Salis, Y. Kaznessis. (2005) Numerical Simulation of Stochastic Gene Circuits, Computers in Chemical Engineering, v29(3).


H.M. Salis. (2007) Simulation of Stochastic Chemical Systems: Applications in the Design and Construction of Synthetic Gene Networks, Ph.D. Thesis, Chemical Engineering, University of Minnesota.