Search Results - "Salis, Howard M."

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites by Espah Borujeni, Amin, Channarasappa, Anirudh S, Salis, Howard M

“…The ribosome's interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5' untranslated regions…”
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Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria by LaFleur, Travis L., Hossain, Ayaan, Salis, Howard M.

“…Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear…”
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A portable expression resource for engineering cross-species genetic circuits and pathways by Kushwaha, Manish, Salis, Howard M.

“…Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions…”
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A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation by Farasat, Iman, Salis, Howard M

“…The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type…”
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Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism by Espah Borujeni, Amin, Salis, Howard M

“…RNA folding plays an important role in controlling protein synthesis as well as other cellular processes. Existing models have focused on how RNA folding…”
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Automated design of synthetic ribosome binding sites to control protein expression by Voigt, Christopher A, Salis, Howard M, Mirsky, Ethan A

“…Microbial engineering often requires fine control over protein expression-for example, to connect genetic circuits or control flux through a metabolic pathway…”
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Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration by Ng, Chiam Yu, Farasat, Iman, Maranas, Costas D., Salis, Howard M.

“…NADPH is an essential cofactor for the biosynthesis of several high-value chemicals, including isoprenoids, fatty acid-based fuels, and biopolymers. Tunable…”
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Automated physics-based design of synthetic riboswitches from diverse RNA aptamers by Espah Borujeni, Amin, Mishler, Dennis M, Wang, Jingzhi, Huso, Walker, Salis, Howard M

“…Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it…”
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Efficient search, mapping, and optimization of multi‐protein genetic systems in diverse bacteria by Farasat, Iman, Kushwaha, Manish, Collens, Jason, Easterbrook, Michael, Guido, Matthew, Salis, Howard M

“…Developing predictive models of multi‐protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when…”
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Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system by Vezeau, Grace E., Gadila, Lipika R., Salis, Howard M.

“…Cell-free genetically encoded biosensors have been developed to detect small molecules and nucleic acids, but they have yet to be reliably engineered to detect…”
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Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning by Cetnar, Daniel P., Hossain, Ayaan, Vezeau, Grace E., Salis, Howard M.

“…mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its…”
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Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression by Vezeau, Grace E, Salis, Howard M

“…The composition of cell-free expression systems (TX-TL) is adjusted by adding macromolecular crowding agents and salts. However, the effects of these cosolutes…”
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The ribosome binding site calculator by Salis, Howard M

“…The Ribosome Binding Site (RBS) Calculator is a design method for predicting and controlling translation initiation and protein expression in bacteria. The…”
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Genetic circuitry boosts cell longevity by Salis, Howard M

“…Reprogramming cellular dynamics is used to study and delay the onset of aging in yeast…”
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Autoclaving is at least as effective as gamma irradiation for biotic clearing and intentional microbial recolonization of soil by King, William L, Grandinette, Emily M, Trase, Olivia, Rolon, M Laura, Salis, Howard M, Wood, Harlow, Bell, Terrence H

“…Sterilization is commonly used to remove or reduce the biotic constraints of a soil to allow recolonization by soil-dwelling organisms, with autoclaving and…”
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A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons by Tian, Tian, Salis, Howard M

“…Natural and engineered genetic systems require the coordinated expression of proteins. In bacteria, translational coupling provides a genetically encoded…”
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An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models by Reis, Alexander C, Salis, Howard M

“…Gene expression models greatly accelerate the engineering of synthetic metabolic pathways and genetic circuits by predicting sequence-function relationships…”
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Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays by Reis, Alexander C., Halper, Sean M., Vezeau, Grace E., Cetnar, Daniel P., Hossain, Ayaan, Clauer, Phillip R., Salis, Howard M.

“…Engineering cellular phenotypes often requires the regulation of many genes. When using CRISPR interference, coexpressing many single-guide RNAs (sgRNAs)…”
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Automated design of thousands of nonrepetitive parts for engineering stable genetic systems by Hossain, Ayaan, Lopez, Eriberto, Halper, Sean M., Cetnar, Daniel P., Reis, Alexander C., Strickland, Devin, Klavins, Eric, Salis, Howard M.

“…Engineered genetic systems are prone to failure when their genetic parts contain repetitive sequences. Designing many nonrepetitive genetic parts with desired…”
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Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences by Espah Borujeni, Amin, Cetnar, Daniel, Farasat, Iman, Smith, Ashlee, Lundgren, Natasha, Salis, Howard M

“…A mRNA's translation rate is controlled by several sequence determinants, including the presence of RNA structures within the N-terminal regions of its coding…”
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