The Salis Lab develops biophysical models and optimization methods
to predict, control, and design the function of synthetic genetic systems.

We engineer metabolic pathways, genetic circuits, and genomes to manufacture products and solve diverse problems.

Design your genetic systems using the Salis Lab DNA Compiler @

Our software has designed over 50,000 synthetic DNA sequences for biotech researchers around the world.


Predictive Biophysical Models
of Gene Expression and Regulation

Automated Optimization Methods
for Genetic Parts and Systems

Thermodynamic model of translation initiation
Optimization of metabolic pathways


A Furan Biodetoxification Pathway
to Harness Lignocellulose Feedstock
Advanced Cellular Sensors
with Signal Amplifying Circuits
A Genetic Security System to Prevent Unauthorized DNA Replication


  • September 2014 -- The Salis Lab has moved to a bigger and better laboratory space in the Wartik building!
  • August 2014 -- Grace Vezeau has joined the Salis lab as a first-year graduate student. Welcome!
  • June 2014 -- The Salis Lab has received an AFOSR grant to develop a theory-based genetic compiler to design synthetic genetic circuits with environmental and evolutionary robustness.
  • May 2014 -- Long Chen has successfully defended his PhD candidacy examination. Congratulations!
  • November 2013 -- 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.
  • November 2013 -- 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.
  • August 2013 -- Tian Tian has successfully passed her PhD candidacy examination. Congratulations!
  • August 2013 -- Chiam Yu Ng won the Best Candidacy Exam Award. Congratulations!
  • July 2013 -- 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.
  • March 2013 -- Howard has received the NSF Career Award to develop next-generation approaches for metabolic pathway engineering, applied to a synthetic biodetoxification pathway for harnessing lignocellulosic feedstock.
  • March 2013 -- Iman Farasat won the SynBERC Best Poster award at the Spring retreat for his work on "White-Boxing Genetic Circuit Modeling: Absolute TF Binding Free Energies From Fluorescence Measurements".
  • November 2012 -- Long Chen has successfully defended his Masters Thesis on a molecular lock and key system to control DNA replication, and will be continuing as a PhD student. Congratulations!
  • October 2012 -- Chiam Yu Ng has joined the Salis lab as a first-year graduate student. Welcome!
  • September 2012 -- Tian Tian presents her work on a "Biophysical Model of Translational Coupling to Coordinate Protein Expression" at the SynBERC Fall Annual Retreat in Cambridge.
  • August 2012 -- The Salis lab has received an ONR MURI grant to develop advanced cell-based sensors and signal processing genetic circuits.
  • July 2012 -- 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!
  • November 2011 -- Howard presents "Myth-busting dogma with synthetic biology", an invited talk at "The 8th International Conference on Bioinformatics" in Atlanta, GA.
  • October 2011 -- The Salis lab has received a DARPA grant to develop a genetic security system for recombinant DNA.
  • December 2010 -- Tian Tian and Long Chen have joined the Salis lab as first-year graduate students. Welcome!
  • June 2010 -- Iman Farasat has received the Leighton Riess Graduate Fellowship in Engineering for outstanding work! Congratulations!
  • April 2010 -- Howard has received the DARPA Young Faculty Award for the "Rational Design of Nucleic Acids to Control Metabolism and Kill Pathogens".
  • January 2010 -- Amin Espah Borujeni and Iman Farasat have joined the Salis lab as first-year graduate students. Welcome!


Howard's picture

Howard M. Salis
Principle Investigator
salis at
Manish's picture
Manish Kushwaha
Post-doctoral Fellow
manish.kushwaha at
Amin's picture
Amin Espah Borujeni
Graduate Student
aue130 at
Iman's picture
Iman Farasat
Graduate Student
izf101 at
Tian's picture
Tian Tian
Graduate Student
tit5090 at
Long's picture
Long Chen
Graduate Student
luc161 at
ChiamYu's picture
Chiam Yu Ng
Graduate Student (co-advised with Costas Maranas)
cun121 at

Undergraduate Student Researchers

Ani Channarasappa
asc5131 at
Ashlee Smith
aes5433 at
Michael Easterbrook
mee5135 at
Victoria Heasly
vheas01 at
Sam Krug
sam.krug11 at
Lauren Brethauer
lbrethauer0818 at
Patrick Gannon
pgannon421 at
Clay Swackhamer
swackhamerclay at
Walker Huso
wdh126 at
Justin Miller
jbm5300 at
Matthew Guido
mrg5220 at


Elizabeth Houston
B.S. Chemical Engineering 2011
David Emerson
B.S. Chemical Engineering 2012
Natasha Lundgren
B.S. Chemical Engineering 2012
Emily Dong
B.S. Chemical Engineering 2013
Andrew Kirk
B.S. Biological Engineering 2013
Capitol One


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., Kushwaha M., Collens J., Easterbrook M., Guido M., and Salis H.M., (2014) 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., (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)


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


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)


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.


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)


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.


Undergraduate-Level Courses

BE 302: Transport Processes for Biological Systems

The fundamentals of fluid mechanics, heat transfer, and mass transfer are applied to biological systems at scales ranging from microbial to ecological. This course includes a weekly 2-hour lab. Past lecture notes are available here.

ChE 340: Introduction to Biomolecular Engineering

Design principles for engineering biological systems are introduced, with a focus on biotechnology and pharmaceutical applications. This course covers the engineering of proteins, metabolism, and genetic circuits using kinetics, thermodynamics, bioinformatics, and genetic engineering techniques.

ChE 410: Mass Transfer and Separations

Introduction to principles and applications of mass transfer with a focus on the design of equilibrium staged and continuously contacting separation processes.

BE 297 | ChE 297: Introduction to Synthetic Biology and Genetic Engineering

An introductory course on designing and modeling small genetic systems -- sensors, regulators, and enzymes -- that reprogram an organism's behavior towards making cellular decisions and manufacturing chemical products.

Graduate-Level Courses

BE 597 | ChE 597: Synthetic Biology. Programming Life.

An advanced course on designing and modeling synthetic genetic circuits to carry out Boolean decision-making, analog feedback control, and programmed decision-making. Several literature examples are discussed. Stochastic and deterministic modeling approaches are reviewed and applied to example systems.

Undergraduate Research Projects

3 undergraduate student co-authorships on recent publications

International Genetically Engineered Machine Contest (iGEM). 2010-present.

NSF Research Experience for Undergraduates: Chemical Energy Storage and Conversion. 2010-2013.

NSF Research Experience for Undergraduates: Biologically Inspired Catalytic Materials. 2014-present.


We are currently recruiting graduate students from the Biological Engineering and Chemical Engineering departments. Please apply to their respective graduate programs, and contact Howard for more information on research topics.


Lab Address

113 Tyson Hall
Pennsylvania State University
University Park, PA 16802

Correspondence Mailing Address

210 Agricultural Engineering Building
Pennsylvania State University
University Park, PA 16802

Phone Numbers

Howard Salis's office: (814) 865-1931
Fax number: (814) 863-1031
Lab number: (814) 865-2402


Howard Salis: salis at

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