Howard Salis, Ph.D.
- Associate Professor of Biological and Chemical Engineering
- Synthetic Biology
Agricultural Engineering Building, Rm. 244
University Park, PA 16802
- Email salis@psu.edu
- Office 814-865-1931
Areas of Expertise
- Synthetic Biology
- Metabolic Engineering
- Biophysics
- Molecular Biology and Biochemistry
- Modeling & Optimization
Websites
Education
- Ph.D. Chemical Engineering, University of Minnesota, 2007
- B.S. Chemical Engineering, Rutgers University, 2002
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
Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements
ACS Synthetic Biology, Hossain, Ayaan, Cetnar, Daniel P., LaFleur, Travis L., McLellan, James R., Salis, Howard M., 2024
Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning
Nature Communications, Cetnar, Daniel P., Hossain, Ayaan, Vezeau, Grace E., Salis, Howard M., 2024
An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil
Nature Communications, Essington, Erin A., Vezeau, Grace E., Cetnar, Daniel P., Grandinette, Emily, Bell, Terrence, Salis, Howard M., 2024
Autoclaving is at least as effective as gamma irradiation for biotic clearing and intentional microbial recolonization of soil
mSphere, King, William L., Grandinette, Emily M., Trase, Olivia, Rolon, M. Laura, Salis, Howard M., Wood, Harlow, Bell, Terrence H., 2024
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
Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression
ACS Synthetic Biology, Vezeau, Grace E., Salis, Howard M., 2021
Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons
ACS Synthetic Biology, Cetnar, Daniel P., Salis, Howard M., 2021
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
An automated pipeline for engineering many-enzyme pathways: Computational sequence design, pathway expression-flux mapping, and scalable pathway optimization, Halper, Sean M., Cetnar, Daniel P., Salis, Howard 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 Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation
PLoS Computational Biology, Farasat, Iman, 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
A predictive biophysical model of translationalcoupling to coordinate and control protein expressionin bacterial operons
Nucleic Acids Research, Tian, Tian, Salis, Howard M., 2015
Scalable system-wide design of TF - And dCas9-based genetic circuits, Salis, Howard, 2015
