H. Salis

发表

Engineering bacterial signals and sensors.

Christopher A. Voigt, C. Voigt, H. Salis, 2009, Contributions to microbiology.

Automated design of synthetic ribosome binding sites to control protein expression

Christopher A. Voigt, C. Voigt, H. Salis, 2016 .

The ribosome binding site calculator.

H. Salis, 2011, Methods in enzymology.

A Synthetic Genetic Edge Detection Program

Christopher A. Voigt, Jeffrey J. Tabor, Anselm Levskaya, 2009, Cell.

A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons

H. Salis, T. Tian, 2015, Nucleic acids research.

Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Many-Enzyme Heterologous Pathways

Sean M. Halper, H. Salis, Iman Farasat, 2017, bioRxiv.

Automated Design of Synthetic Ribosome Binding Sites to Precisely Control Protein Expression

Christopher A. Voigt, C. Voigt, H. Salis, 2009, Nature Biotechnology.

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

H. Salis, Amin Espah Borujeni, Anirudh S. Channarasappa, 2013, Nucleic acids research.

Efficient search, mapping, and optimization of multi‐protein genetic systems in diverse bacteria

H. Salis, Iman Farasat, Manish Kushwaha, 2014 .

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

H. Salis, Walker Huso, Amin Espah Borujeni, 2015, Nucleic acids research.

Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays

Sean M. Halper, Daniel P. Cetnar, Alexander C. Reis, 2019, Nature Biotechnology.

Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration.

Chiam Yu Ng, Costas D Maranas, Iman Farasat, 2015, Metabolic engineering.

Title : Efficient search , mapping , and optimization of multiprotein genetic systems in diverse bacteria

H. Salis, Iman Farasat, Manish Kushwaha, 2014 .

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

H. Salis, Iman Farasat, Manish Kushwaha, 2014, bioRxiv.

Precise Quantification of Translation Inhibition by mRNA Structures that Overlap with the Ribosomal Footprint in N-terminal Coding Sequences

Daniel P. Cetnar, H. Salis, Amin Espah Borujeni, 2016, bioRxiv.

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

H. Salis, N. Reuel, Grace E. Vezeau, 2019, bioRxiv.

Reversing methanogenesis to capture methane for liquid biofuel precursors

Howard M. Salis, Limin Zhang, Michael J. McAnulty, 2016, Microbial Cell Factories.

Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons

Daniel P. Cetnar, H. Salis, 2020, bioRxiv.

Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression.

H. Salis, Grace E. Vezeau, 2021, ACS synthetic biology.

Tuning Cell-free Composition Controls the Time-delay, Dynamics, and Productivity of TX-TL Expression

H. Salis, Grace E. Vezeau, 2021, bioRxiv.

Computer-aided design of modular protein devices: Boolean AND gene activation

H. Salis, Y. Kaznessis, Y N Kaznessis, 2006, Physical biology.

Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons.

Daniel P. Cetnar, H. Salis, 2021, ACS synthetic biology.

Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria

H. Salis, Ayaan Hossain, Travis L. LaFleur, 2021, Nature Communications.

Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism.

Amin Espah Borujeni, H. Salis, Amin Espah Borujeni, 2016, Journal of the American Chemical Society.

An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models.

Alexander C. Reis, Alexander C Reis, Howard M Salis, 2020, ACS synthetic biology.

An automated model test system for systematic development and improvement of gene expression models

Howard M. Salis, Alexander C. Reis, Alexander C. Reis, 2017, bioRxiv.

Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences

Howard M. Salis, Daniel P. Cetnar, Amin Espah Borujeni, 2016, bioRxiv.

The Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning.

Sean M. Halper, Ayaan Hossain, Sean M Halper, 2020, ACS synthetic biology.

Purification of Cas9—RNA complexes by ultrafiltration

H. Salis, A. Zydney, Grace E. Vezeau, 2020, Biotechnology progress.

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

Howard M. Salis, Iman Farasat, H. Salis, 2016, PLoS Comput. Biol..

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

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

Computational design to efficiently search, map, and optimize multi-protein genetic systems in gram-negative and gram-positive bacteria

Howard M. Salis, Manish Kushwaha, Iman Farasat, 2013 .

Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Vassilios Sotiropoulos, Howard M. Salis, Yiannis N. Kaznessis, 2006, BMC Bioinformatics.

Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island 1.

Christopher A. Voigt, Danielle Tullman-Ercek, Christopher A Voigt, 2008, Journal of molecular biology.

Kinetic buffering of cross talk between bacterial two-component sensors.

Christopher A. Voigt, Christopher A Voigt, Eli S Groban, 2009, Journal of molecular biology.

Automated design of thousands of nonrepetitive parts for engineering stable genetic systems

Eric Klavins, Ayaan Hossain, Eriberto Lopez, 2020, Nature Biotechnology.

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

H. Salis, N. Reuel, Grace E. Vezeau, 2019, ACS synthetic biology.

Model-driven designs of an oscillating gene network.

Yiannis N Kaznessis, Howard Salis, Jonathan R. Tomshine, 2005, Biophysical journal.

Numerical simulation of stochastic gene circuits

Howard M. Salis, Yiannis N. Kaznessis, H. Salis, 2005, Comput. Chem. Eng..

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, Sean M Halper, 2018, Methods in molecular biology.

Selenium-dependent metabolic reprogramming during inflammation and resolution

H. Salis, B. Carlson, K. S. Prabhu, 2021, bioRxiv.

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions.

Yiannis Kaznessis, Howard Salis, H. Salis, 2005, The Journal of chemical physics.

Automated design of thousands of nonrepetitive parts for engineering stable genetic systems

Sean M. Halper, Daniel P. Cetnar, Alexander C. Reis, 2020, Nature Biotechnology.

A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions

H. Salis, L. Contreras, A. Moon-Walker, 2018, Scientific Reports.

Genetic circuitry boosts cell longevity

H. Salis, 2023, Science.

Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system

H. Salis, Grace E. Vezeau, Lipika R Gadila, 2023, Nature communications.

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

H. Salis, Manish Kushwaha, 2015, Nature Communications.

RNA size and 3-dimensional structure determine ultrafiltration behavior of small RNA molecules

H. Salis, A. Zydney, Grace E. Vezeau, 2020 .

A Synthetic Genetic Edge Detection Program

Christopher A. Voigt, Jeffrey J. Tabor, Anselm Levskaya, 2009, Cell.

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

H. Salis, Iman Farasat, Manish Kushwaha, 2014, bioRxiv.

Numerical simulation of stochastic gene circuits

H. Salis, Y. Kaznessis, 2005, Comput. Chem. Eng..

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

Yiannis N Kaznessis, Howard Salis, H. Salis, 2005, The Journal of chemical physics.

The Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning

Howard M. Salis, Sean M. Halper, Ayaan Hossain, 2020, bioRxiv.