Howard Salis

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

Howard Salis

Research Summary

Engineering microorganisms for applications in synthetic biology and metabolic engineering.

Huck Affiliations


Publication Tags

Proteins Genes Kinetics Dna Rna Gene Expression Machine Learning Bacteria Messenger Rna Genome Ribosomes Binding Sites Enzymes Synthetic Biology Biosynthesis Transcription Plasmids Guide Rna Riboswitch Methane Biofuels Ultrafiltration Escherichia Coli Engineering Networks (Circuits)

Most Recent Papers

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

Selenium-dependent metabolic reprogramming during inflammation and resolution

Arvind M. Korwar, Ayaan Hossain, Tai Jung Lee, Ashley E. Shay, Venkatesha Basrur, Kevin Conlon, Philip B. Smith, Bradley A. Carlson, Howard M. Salis, Andrew D. Patterson, K. Sandeep Prabhu, 2021, Journal of Biological Chemistry

Purification of Cas9-RNA complexes by ultrafiltration

Ivan Manzano, Neil Taylor, Matthew Csordas, Grace Vezeau, Howard Salis, Andrew Zydney, 2020, Biotechnology Progress

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

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

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, Separation and Purification Technology

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

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

Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Bacillus subtilis Spores for Time-Delayed Protein Expression Applications

Denis Tamiev, Alyssa Lantz, Grace Vezeau, Howard Salis, Nigel F. Reuel, 2019, ACS Synthetic Biology on p. 2336-2346

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

The ribosome binding site calculator

Howard M. Salis, 2011, Methods in enzymology on p. 19-42

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

A portable expression resource for engineering cross-species genetic circuits and pathways

Manish Kushwaha, Howard M. Salis, 2015, Nature Communications

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 predictive biophysical model of translationalcoupling to coordinate and control protein expressionin bacterial operons

Tian Tian, Howard M. Salis, 2015, Nucleic Acids Research on p. 7137-7151

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

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

Iman Farasat, Howard Salis, 2016, PLoS Computational Biology on p. e1004724