Howard Salis, Ph.D.

Howard Salis, Ph.D.

  • Associate Professor of Biological and Chemical Engineering
  • Synthetic Biology
244 Agricultural Engineering Building
Shortlidge Road

University Park, PA 16802

Areas of Expertise

  • Synthetic Biology
  • Metabolic Engineering
  • Biophysics
  • Molecular Biology and Biochemistry
  • Modeling & Optimization


  • Ph.D. Chemical Engineering, University of Minnesota, 2007
  • B.S. Chemical Engineering, Rutgers University, 2002


  • 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 (


Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system
Nature Communications, Vezeau, Grace E., Gadila, Lipika R., Salis, Howard M., 2023

Genetic circuitry boosts cell longevity
Science, Salis, Howard M., 2023

Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria
Nature Communications, LaFleur, Travis L., Hossain, Ayaan, Salis, Howard M., 2022

Selenium-dependent metabolic reprogramming during inflammation and resolution
Journal of Biological Chemistry, Korwar, A, Hossain, A, Lee, T, Shay, Ashley, Basrur, V, Conlon, K, Smith, Philip B., Carlson, B, Salis, Howard M., Patterson, Andrew D., Prabhu, K. Sandeep, 2021

Automated design of thousands of nonrepetitive parts for engineering stable genetic systems
Nature Biotechnology, Hossain, Ayaan, Lopez, Eriberto, Halper, Sean M., Cetnar, Daniel P., Reis, Alexander C., Strickland, Devin, Klavins, Eric, Salis, Howard M., 2020

Purification of Cas9—RNA complexes by ultrafiltration
Biotechnology Progress, Manzano, Ivan, Taylor, Neil, Csordas, Matthew, Vezeau, Grace E., Salis, Howard M., Zydney, Andrew L., 2020

An automated model test system for systematic development and improvement of gene expression models
ACS Synthetic Biology, Reis, Alexander C., Salis, Howard M., 2020

Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning
ACS Synthetic Biology, Halper, Sean M., Hossain, Ayaan, Salis, Howard M., 2020

RNA size and 3-dimensional structure determine ultrafiltration behavior of small RNA molecules
Gas Separation and Purification, Manzano, Ivan, Vezeau, Grace, Salis, Howard, Zydney, Andrew L., 2020

Convolutional neural net learns promoter sequence features driving transcription strength
EPiC Series in Computing, Leiby, Nicholas, Hossain, Ayaan, Salis, Howard M., 2020

A massively parallel COVID-19 diagnostic assay for simultaneous testing of 19200 patient samples, Hossain, Ayaan, Reis, Alexander, Rahman, Sarthok, Salis, Howard, 2020

Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays
Nature Biotechnology, Reis, Alexander C., Halper, Sean M., Vezeau, Grace E., Cetnar, Daniel P., Hossain, Ayaan, Clauer, Phillip R., Salis, Howard M., 2019

Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Bacillus subtilis Spores for Time-Delayed Protein Expression Applications
ACS Synthetic Biology, Tamiev, Denis, Lantz, Alyssa, Vezeau, Grace, Salis, Howard, Reuel, Nigel F., 2019

Engineering Biology: A Research Roadmap for the Next-Generation Bioeconomy, Aurand, Emily, Keasling, Jay, Friedman, Dan, Salis, Howard, 2019

A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions
Scientific Reports, Leistra, A. N., Gelderman, G., Sowa, S. W., Moon-Walker, A., Salis, H. M., Contreras, L. M., 2018

Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences
Nucleic Acids Research, Borujeni, Amin Espah, Cetnar, Daniel, Farasat, Iman, Smith, Ashlee, Lundgren, Natasha, Salis, Howard M., 2017

Towards the automated design of bacterial genomes for tailored applications, Salis, H., 2017

Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism
Journal of the American Chemical Society, Espah Borujeni, Amin, Salis, Howard M., 2016

Reversing methanogenesis to capture methane for liquid biofuel precursors
Microbial Cell Factories, Soo, Valerie W.C., McAnulty, Michael J., Tripathi, Arti, Zhu, Fayin, Zhang, Limin, Hatzakis, Emmanuel, Smith, Philip B., Agrawal, Saumya, Nazem-Bokaee, Hadi, Gopalakrishnan, Saratram, Salis, Howard M., Ferry, James G., Maranas, Costas D., Patterson, Andrew D., Wood, Thomas K., 2016

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
Nucleic Acids Research, Espah Borujeni, Amin, Mishler, Dennis M., Wang, Jingzhi, Huso, Walker, Salis, Howard M., 2016

A portable expression resource for engineering cross-species genetic circuits and pathways
Nature Communications, Kushwaha, Manish, Salis, Howard M., 2015

Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration
Metabolic Engineering, Ng, Chiam Yu, Farasat, Iman, Maranas, Costas D., Salis, Howard M., 2015

Scalable system-wide design of TF - And dCas9-based genetic circuits, Salis, Howard, 2015

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
Nucleic Acids Research, Espah Borujeni, Amin, Channarasappa, Anirudh S., Salis, Howard M., 2014

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Molecular Systems Biology, Farasat, Iman, Kushwaha, Manish, Collens, Jason, Easterbrook, Michael, Guido, Matthew, Salis, Howard M., 2014