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

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 Sequence

Most 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

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

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