Howard M. Salis, Ph.D. - Publications

2007 University of Minnesota, Twin Cities, Minneapolis, MN 
Chemical Engineering, Mathematics, Genetics

25 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
2020 Reis AC, Salis HM. An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models. Acs Synthetic Biology. PMID 33054181 DOI: 10.1021/acssynbio.0c00394  0.72
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  0.84
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  0.84
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  0.84
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  0.84
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  1
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  1
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  1
2016 Soo VW, McAnulty MJ, Tripathi A, Zhu F, Zhang L, Hatzakis E, Smith PB, Agrawal S, Nazem-Bokaee H, Gopalakrishnan S, Salis HM, Ferry JG, Maranas CD, Patterson AD, Wood TK. Reversing methanogenesis to capture methane for liquid biofuel precursors. Microbial Cell Factories. 15: 11. PMID 26767617 DOI: 10.1186/s12934-015-0397-z  0.56
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  0.56
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  1
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  0.96
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  1
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  1
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  1
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  0.56
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  1
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  1
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