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Howard M. Salis, Ph.D. - Publications

Affiliations: 
Agricultural and Biological Engineering Pennsylvania State University, State College, PA, United States 
 2007 University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Chemical Engineering, Mathematics, Genetics
Website:
https://abe.psu.edu/directory/hms17
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 LaFleur TL, Hossain A, Salis HM. Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nature Communications. 13: 5159. PMID 36056029 DOI: 10.1038/s41467-022-32829-5  0.664
2021 Vezeau GE, Salis HM. Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression. Acs Synthetic Biology. PMID 34498860 DOI: 10.1021/acssynbio.1c00136  0.325
2021 Korwar AM, Hossain A, Lee TJ, Shay AE, Basrur V, Conlon K, Smith PB, Carlson BA, Salis HM, Patterson AD, Prabhu KS. Selenium-dependent metabolic reprogramming during inflammation and resolution. The Journal of Biological Chemistry. 100410. PMID 33581115 DOI: 10.1016/j.jbc.2021.100410  0.536
2021 Cetnar DP, Salis HM. Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. Acs Synthetic Biology. PMID 33464822 DOI: 10.1021/acssynbio.0c00471  0.355
2020 Hossain A, Lopez E, Halper SM, Cetnar DP, Reis AC, Strickland D, Klavins E, Salis HM. Automated design of thousands of nonrepetitive parts for engineering stable genetic systems. Nature Biotechnology. PMID 32661437 DOI: 10.1038/S41587-020-0584-2  0.665
2020 Halper SM, Hossain A, Salis HM. The Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning. Acs Synthetic Biology. PMID 32559378 DOI: 10.1021/Acssynbio.9B00460  0.61
2020 Manzano I, Vezeau G, Salis H, Zydney AL. RNA size and 3-dimensional structure determine ultrafiltration behavior of small RNA molecules Separation and Purification Technology. 237: 116372. DOI: 10.1016/J.Seppur.2019.116372  0.322
2019 Reis AC, Halper SM, Vezeau GE, Cetnar DP, Hossain A, Clauer PR, Salis HM. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nature Biotechnology. PMID 31591552 DOI: 10.1038/S41587-019-0286-9  0.668
2019 Tamiev D, Lantz A, Vezeau G, Salis H, Reuel NF. Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Spores for Time-Delayed Protein Expression Applications. Acs Synthetic Biology. 8: 2336-2346. PMID 31490060 DOI: 10.1021/Acssynbio.9B00163  0.366
2018 Halper SM, Cetnar DP, Salis HM. An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization. Methods in Molecular Biology (Clifton, N.J.). 1671: 39-61. PMID 29170952 DOI: 10.1007/978-1-4939-7295-1_4  0.338
2017 Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Research. PMID 28158713 DOI: 10.1093/Nar/Gkx061  0.742
2016 Espah Borujeni A, Salis HM. Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism. Journal of the American Chemical Society. PMID 27199273 DOI: 10.1021/Jacs.6B01453  0.759
2016 Farasat I, Salis HM. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. Plos Computational Biology. 12: e1004724. PMID 26824432 DOI: 10.1371/Journal.Pcbi.1004724  0.443
2015 Espah Borujeni A, Mishler DM, Wang J, Huso W, Salis HM. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Research. PMID 26621913 DOI: 10.1093/Nar/Gkv1289  0.76
2015 Kushwaha M, Salis HM. A portable expression resource for engineering cross-species genetic circuits and pathways. Nature Communications. 6: 7832. PMID 26184393 DOI: 10.1038/Ncomms8832  0.4
2015 Tian T, Salis HM. A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons. Nucleic Acids Research. 43: 7137-51. PMID 26117546 DOI: 10.1093/Nar/Gkv635  0.501
2015 Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering. 29: 86-96. PMID 25769287 DOI: 10.1016/J.Ymben.2015.03.001  0.37
2014 Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology. 10: 731. PMID 24952589 DOI: 10.15252/Msb.20134955  0.421
2014 Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research. 42: 2646-59. PMID 24234441 DOI: 10.1093/Nar/Gkt1139  0.755
2011 Salis HM. The ribosome binding site calculator. Methods in Enzymology. 498: 19-42. PMID 21601672 DOI: 10.1016/B978-0-12-385120-8.00002-4  0.439
2009 Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology. 27: 946-50. PMID 19801975 DOI: 10.1038/Nbt.1568  0.767
2009 Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. A synthetic genetic edge detection program. Cell. 137: 1272-81. PMID 19563759 DOI: 10.1016/J.Cell.2009.04.048  0.732
2009 Salis H, Tamsir A, Voigt C. Engineering bacterial signals and sensors Contributions to Microbiology. 16: 194-225. PMID 19494587 DOI: 10.1159/000219381  0.762
2009 Groban ES, Clarke EJ, Salis HM, Miller SM, Voigt CA. Kinetic buffering of cross talk between bacterial two-component sensors. Journal of Molecular Biology. 390: 380-93. PMID 19445950 DOI: 10.1016/J.Jmb.2009.05.007  0.744
2008 Temme K, Salis H, Tullman-Ercek D, Levskaya A, Hong SH, Voigt CA. Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island 1. Journal of Molecular Biology. 377: 47-61. PMID 18242639 DOI: 10.1016/J.Jmb.2007.12.044  0.727
2006 Salis H, Kaznessis YN. Computer-aided design of modular protein devices: Boolean AND gene activation Physical Biology. 3: 295-310. PMID 17200605 DOI: 10.1088/1478-3975/3/4/007  0.643
2006 Salis H, Sotiropoulos V, Kaznessis YN. Multiscale Hy3S: hybrid stochastic simulation for supercomputers. Bmc Bioinformatics. 7: 93. PMID 16504125 DOI: 10.1186/1471-2105-7-93  0.769
2005 Salis H, Kaznessis YN. An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks. The Journal of Chemical Physics. 123: 214106. PMID 16356038 DOI: 10.1063/1.2131050  0.607
2005 Tuttle LM, Salis H, Tomshine J, Kaznessis YN. Model-driven designs of an oscillating gene network. Biophysical Journal. 89: 3873-83. PMID 16183880 DOI: 10.1529/Biophysj.105.064204  0.78
2005 Salis H, Kaznessis Y. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. The Journal of Chemical Physics. 122: 54103. PMID 15740306 DOI: 10.1063/1.1835951  0.587
2005 Salis H, Kaznessis Y. Numerical simulation of stochastic gene circuits Computers and Chemical Engineering. 29: 577-588. DOI: 10.1016/J.Compchemeng.2004.08.017  0.636
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