Publications by authors named "Howard Salis"

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Quantifying the impact of genetic mutations on enhancer dynamics.
Maitreya Das, Deepro Banerjee, Ayaan Hossain, Matthew Jensen, Saie Mogre, Howard M Salis

bioRxiv· October 2025

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Microcapillary Array-Based High Throughput Screening for Protein Biomanufacturability.
Khushank Singhal, Harry E Adamson, Thomas M Baer, Howard M Salis, Melik C Demirel

ACS Synth Biol· June 2025

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An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil.
Erin A Essington, Grace E Vezeau, Daniel P Cetnar, Emily Grandinette, Terrence H Bell, Howard M Salis

Nat Commun· December 2024

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Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.
Ayaan Hossain, Daniel P Cetnar, Travis L LaFleur, James R McLellan, Howard M Salis

ACS Synth Biol· December 2024

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Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.
Daniel P Cetnar, Ayaan Hossain, Grace E Vezeau, Howard M Salis

Nat Commun· November 2024

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Autoclaving is at least as effective as gamma irradiation for biotic clearing and intentional microbial recolonization of soil.
William L King, Emily M Grandinette, Olivia Trase, M Laura Rolon, Howard M Salis

mSphere· July 2024

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Genetic circuitry boosts cell longevity.
Howard M Salis

Science· April 2023

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

Nat Commun· April 2023

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

Nat Commun· September 2022

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Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression.
Grace E Vezeau, Howard M Salis

ACS Synth Biol· October 2021

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Selenium-dependent metabolic reprogramming during inflammation and resolution.
Arvind M Korwar, Ayaan Hossain, Tai-Jung Lee, Ashley E Shay, Venkatesha Basrur, Howard M Salis

J Biol Chem· August 2021

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Purification of Cas9-RNA complexes by ultrafiltration.
Ivan Manzano, Neil Taylor, Matthew Csordas, Grace E Vezeau, Howard M Salis

Biotechnol Prog· March 2021

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Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons.
Daniel P Cetnar, Howard M Salis

ACS Synth Biol· February 2021

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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, Howard M Salis

Nat Biotechnol· December 2020

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An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models.
Alexander C Reis, Howard M Salis

ACS Synth Biol· November 2020

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

ACS Synth Biol· July 2020

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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, Howard M Salis

Nat Biotechnol· November 2019

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

ACS Synth Biol· October 2019

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An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.
Sean M Halper, Daniel P Cetnar, Howard M Salis

Methods Mol Biol· July 2018

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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

Nucleic Acids Res· May 2017

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Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism.
Amin Espah Borujeni, Howard M Salis

J Am Chem Soc· June 2016

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

Nucleic Acids Res· January 2016

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Reversing methanogenesis to capture methane for liquid biofuel precursors.
Valerie W C Soo, Michael J McAnulty, Arti Tripathi, Fayin Zhu, Limin Zhang, Howard M Salis

Microb Cell Fact· January 2016

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A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.
Iman Farasat, Howard M Salis

PLoS Comput Biol· January 2016

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

Nat Commun· July 2015

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