Howard Salis
Associate Professor of Chemical Engineering; Associate Professor of Agricultural and Biological Engineering

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224 Ag Engineering
University Park, PA - hms17@psu.edu
- 814-863-1931
Research Summary
Engineering microorganisms for applications in synthetic biology and metabolic engineering.
Huck Affiliations
- Bioinformatics and Genomics
- Molecular, Cellular, and Integrative Biosciences
- Center for Biorenewables
Links
Publication Tags
Genes Proteins Gene Expression Messenger Rna Rna Bacteria Machine Learning Dna Kinetics Escherichia Coli Genome Enzymes Ribosomes Synthetic Biology Transcription Biosynthesis Protein Guide Rna Biofuels Ultrafiltration Methane Metabolic Engineering Application Dna SequenceMost Recent Publications
Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria
Travis L. LaFleur, Ayaan Hossain, Howard M. Salis, 2022, Nature Communications
Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression
Grace E. Vezeau, Howard M. Salis, 2021, ACS Synthetic Biology on p. 2508-2519
Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons
Daniel P. Cetnar, Howard M. Salis, 2021, ACS Synthetic Biology on p. 318-332
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems
Ayaan Hossain, Eriberto Lopez, Sean M. Halper, Daniel P. Cetnar, Alexander C. Reis, Devin Strickland, Eric Klavins, Howard M. Salis, 2020, Nature Biotechnology on p. 1466-1475
Purification of Cas9—RNA complexes by ultrafiltration
Ivan Manzano, Neil Taylor, Matthew Csordas, Grace E. Vezeau, Howard M. Salis, Andrew L. Zydney, 2020, Biotechnology Progress
An automated model test system for systematic development and improvement of gene expression models
Alexander C. Reis, Howard M. Salis, 2020, ACS Synthetic Biology on p. 3145-3156
Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning
Sean M. Halper, Ayaan Hossain, Howard M. Salis, 2020, ACS Synthetic Biology on p. 1563-1571
RNA size and 3-dimensional structure determine ultrafiltration behavior of small RNA molecules
Ivan Manzano, Grace Vezeau, Howard Salis, Andrew L. Zydney, 2020, Gas Separation and Purification
Convolutional neural net learns promoter sequence features driving transcription strength
Nicholas Leiby, Ayaan Hossain, Howard M. Salis, 2020, EPiC Series in Computing on p. 163-172
A massively parallel COVID-19 diagnostic assay for simultaneous testing of 19200 patient samples
Ayaan Hossain, Alexander Reis, Sarthok Rahman, Howard Salis, 2020, on p. 22
Most-Cited Papers
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
Amin Espah Borujeni, Anirudh S. Channarasappa, Howard M. Salis, 2014, Nucleic Acids Research on p. 2646-2659
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, Howard M. Salis, 2014, Molecular Systems Biology
Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration
Chiam Yu Ng, Iman Farasat, Costas D. Maranas, Howard M. Salis, 2015, Metabolic Engineering on p. 86-96
Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
Amin Espah Borujeni, Dennis M. Mishler, Jingzhi Wang, Walker Huso, Howard M. Salis, 2016, Nucleic Acids Research on p. 1-13
Reversing methanogenesis to capture methane for liquid biofuel precursors
Valerie W.C. Soo, Michael J. McAnulty, Arti Tripathi, Fayin Zhu, Limin Zhang, Emmanuel Hatzakis, Philip B. Smith, Saumya Agrawal, Hadi Nazem-Bokaee, Saratram Gopalakrishnan, Howard M. Salis, James G. Ferry, Costas D. Maranas, Andrew D. Patterson, Thomas K. Wood, 2016, Microbial Cell Factories on p. 11
A portable expression resource for engineering cross-species genetic circuits and pathways
Manish Kushwaha, Howard M. Salis, 2015, Nature Communications
Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism
Amin Espah Borujeni, Howard M. Salis, 2016, Journal of the American Chemical Society on p. 7016-7023
Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays
Alexander C. Reis, Sean M. Halper, Grace E. Vezeau, Daniel P. Cetnar, Ayaan Hossain, Phillip R. Clauer, Howard M. Salis, 2019, Nature Biotechnology on p. 1294-1301
A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation
Iman Farasat, Howard M. Salis, 2016, PLoS Computational Biology on p. e1004724
Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences
Amin Espah Borujeni, Daniel Cetnar, Iman Farasat, Ashlee Smith, Natasha Lundgren, Howard M. Salis, 2017, Nucleic Acids Research on p. 5437-5448
News Articles Featuring Howard Salis
Jul 21, 2020
Researchers offer solution for one of synthetic biology's biggest problems
A team of Penn State and University of Washington researchers recently developed a new algorithm to help prevent the failure of engineered genetic systems, or organisms engineered to have new capabilities.
Full Article