The following publications were supported in part by the Jacobs Institute for Molecular Engineering for Medicine:

"High-throughput Screening for Methionyl-tRNA Synthetases that Enable Residue-specific Incorporation of Noncanonical Amino Acids into Recombinant Proteins in Bacterial Cells." T. H. Yoo and D. A. Tirrell. Angew. Chem. Int. Ed. 46: 5340-5343 (2007).

"Site-Specific Incorporation of Tryptophan Analogues into Recombinant Proteins in Bacterial Cells." I. Kwon and D. A. Tirrell. J. Am. Chem. Soc. 129: 10431-10437 (2007).

"Evolution of a Fluorinated Green Fluorescent Protein." T. H. Yoo, A. J. Link and D. A. Tirrell. Proc. Natl. Acad. Sci. USA 104: 13887-13890 (2007).

"Non-Canonical Amino Acids in Protein Polymer Design." R. E. Connor and D. A. Tirrell. J. Macromol. Sci., Part C: Polym. Rev. 47: 9-28 (2007). 

"Lithographic Patterning of Photoreactive Cell-Adhesive Proteins."  I. S. Carrico, S. A. Maskarinec, S.C. Heilshorn, M. Mock, J. C. Liu, P. J. Nowatzki, C. Franck, G. Ravichandran and D. A. Tirrell. J. Am. Chem. Soc. 129: 4874-4875 (2007).

"Processing of N- Terminal Unnatural Amino Acids in Recombinant Human Interferon-b in Escherichia coli."  A. Wang, N. W. Nairn, R. S. Johnson, D. A. Tirrell and K. Grabstein. ChemBioChem 9: 324-330 (2008).

"Mechanically Tunable Thin Films of Photosensitive Artificial Proteins:  Preparation and Characterization by Nanoindentation." P. J. Nowatzki, C. Franck, S. A. Maskarinec, G. Ravichandran and D. A. Tirrell. Macromolecules 41: 1839-1845 (2008).

"Cell Response to RGD Density in Crosslinked Artificial Extracellular Matrix Protein Films." J. C. Liu and D. A. Tirrell. Biomacromolecules 9: 2984-2988 (2008). 

"Reinterpreting the Genetic Code:  Implications for Macromolecular Design, Evolution and Analysis." D. A. Tirrell Physical Biology: From Atoms to Medicine, A. H. Zewail, ed., Imperial College Press, London (2008), p. 165-187

"Two-Color Labeling of Temporally Defined Protein Populations in Mammalian Cells." K. E. Beatty and D. A. TirrellBioorg. Med. Chem. Lett. 18: 5995-5999 (2008).

"Introduction of an Aliphatic Ketone into Recombinant Proteins in a Bacterial Strain that Overexpresses an Editing-Impaired Leucyl-tRNA Synthetase." Y. Tang, P. Wang , J. A. Van Deventer, A. J. Link and D. A. Tirrell. ChemBioChem 10: 2188-2190 (2009).

"Generation of Surface-bound Multicomponent Protein Gradients." K. Zhang, A. Sugawara and D. A. Tirrell. ChemBioChem 10: 2617-2619 (2009).  

"Catalysts On Demand: Selective Oxidations By Laboratory-Evolved Cytochrome P450 BM-3"  J. C. Lewis, F. H. Arnold. Chimia 63, 309-312 (2009).   doi:10.2533/chimia.2009.309.

"Chemoenzymatic Elaboration of Monosaccharides Using Engineered Cytochrome P450BM3 Demethylases"  J. C. Lewis, S. Bastian, C. S. Bennett, Y. Fu, Y. Mitsuda, M. M. Chen, W. A. Greenberg, C. H. Wong, F. H. Arnold. Proc. Natl. Acad. Sci. 106 (39), 16550-16555 (2009).  doi/10.1073/pnas.0908954106.

"A Panel of Cytochrome P450 BM3 Variants to Produce Drug Metabolites and Diversify Lead Compounds"   A. M. Sawayama, M. M. Chen, P. Kulanthaivel, M. S. Kuo, H. Hemmerle, F. H. Arnold. Chemistry, a European Journal 15, 11723-11729 (2009). doi:10.1002/chem.200900643.

"How Proteins Adapt: Lessons From Directed Evolution" F. H. Arnold. Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXIV. (2009) Cold Spring Harbor Laboratory Press 978-087969870-6.

"An In Vitro Intact Globe Expansion Method for Evaluation of Cross-linking Treatments" M. S. Mattson, J. Huynh, M. Wiseman, M. Coassin, J. A. Kornfield and D. M. Schwartz. Invest. Ophthalmol. Vis. Sci. 51(6): 3120-3128 (2010).

"Directed Evolution of a MRI Contrast Agent for Noninvasive Imaging of Dopamine"  M. G. Shapiro, G. G. Westmeyer, P. A. Romero, J. O. Szablowski, B. Kuster, A. Shah, C. R. Otey, R. Langer, F. H. Arnold, A. Jasanoff. Nature Biotechnology 28 264-270 (2010).

"Boundary crossing in epithelial wound healing." E. Fong, S. Tzlil and D. A. Tirrell. Proc. Natl. Acad. Sci. USA 107: 19302-19307 (2010). "Collective Cell Migration on Artificial Extracellular Matrix Proteins Containing Full-Length Fibronectin Domains." E. Fong and D. A. Tirrell. Adv. Mater. 22: 5271-5275 (2010).  

"An Asymptotic Analysis of Differential Electrical Mobility Classifiers." A. J. Downard, J. F. Dama and R. C. Flagan. Aerosol Sci. Technol. 45, 727-739 (2011)."Flow-enhanced transient response in whispering gallery mode biosensors." J. M. Gamba and R. C. Flagan. Appl. Phys. Lett. 99, Art. No. 253705 (2011).

"Metal-Substituted Protein MRI Contrast Agents Engineered for Enhanced Relaxivity and Ligand Sensitivity"  V. S. Lelyveld, E. Brustad, F. H. Arnold, A. Jasanoff. Journal of the American Chemical Society 133, 649-651 (2011) .

"Homoisoleucine: A translationally active leucine surrogate of expanded hydrophobic surface area."  J. A. Van Deventer, J. D. Fisk and D. A. Tirrell. ChemBioChem 12: 700-702 (2011)."Measuring shear strength of soft-tissue adhesives" M. Wang and J. A. KornfieldJ. Biomed. Mater. Res. Part B Appl. Biomater. 100B(3): 618-623 (2012).

"Structure-Guided Directed Evolution of Highly Selective P450-based Magnetic Resonance Imaging Sensors for Dopamine and Serotonin"   E. M. Brustad, V. S. Lelyveld, C. D. Snow, N. Crook, S. T. Jung, F. M. Martinez, T. J. Scholl, A. Jasanoff, F. H. Arnold. Journal of Molecular Biology 422, 245-262 (2012).

"The physics of extreme sensitivity in whispering gallery mode optical biosensors." X. Lopez-Yglesias, J. M. Gamba and R. C. Flagan. J. Appl. Phys. 111, Art. No. 084701 (2012).

"Chapter 14. Directed Evolution of Protein-Based Neurotransmitter Sensors for MRI"   P. A. Romero, M. G. Shapiro, F. H. Arnold, A. Jasanoff. In M. R. Banghart (ed.) Chemical Neurobiology: Methods and Protocols - Methods in Molecular Biology, Vol. 995, pp. 193-205 (2013).

"Enantioselective Intramolecular C-H Amination Catalyzed by Engineered Cytochrome P450 Enzymes in vitro and in vivo"   J. A. McIntosh, P. S. Coelho, C. C. Farwell, Z. J. Wang, J. C. Lewis, T. R. Brown, F. H. Arnold. Angewandte Chemie International Edition 52, 9309-9312 (2013).

"Expanding the Enzyme Universe Through a Marriage of Chemistry and Evolution" F. H. Arnold. Solvay Conferences in Chemistry: Expanding the Protein Universe. Brussels, October 2013."Self-Assembly of Elastin-Mimetic Double Hydrophobic Polypeptides." D. H. Le, R. Hanamura, D. H. Pham, M. Kato, D. A. Tirrell, T. Okubo, A. Sugawara-Narutaki. Biomacromolecules 14: 1028-1034 (2013).

"Strain propagation in artificial extracellular matrix proteins can accelerate cell spreading and polarization." S. Tzlil and D. A. Tirrell. Soft Matter 9: 5602-5608 (2013).

"Mutant Methionyl-tRNA Synthetase from Bacteria Enables Site-Selective N-terminal Labeling of Proteins Expressed in Mammalian Cells." C. Kulkarni, T. L. Kinzer-Ursem and D. A. Tirrell. Proc. Natl. Acad. Sci. USA 110: 4992-4997 (2013). 

"Selective Functionalization of the Protein N-Terminus with N-Myristoyl Transferase for Bioconjugation in Cell Lysate." C. Kulkarni, T. L Kinzer-Ursem, D. A Tirrell .ChemBioChem 14: 1958-1962 (2013).  

"Ion Mobility-Mass Spectrometry with a Radial Opposed Migration Ion and Aerosol Classifier (ROMIAC)." W. Mui, D. A. Thomas, A. J. Downard, J. L. Beauchamp, J. H. Seinfeld and R. C. Flagan. Anal. Chem., 85, 6319-6326 (2013).

"Expanding P450 Catalytic Reaction Space Through Evolution and Engineering"   J. A. McIntosh, C. C. Farwell, F. H. Arnold. Current Opinion in Chemical Biology 19, 126-134 (2014).

"Chapter 9.15. Synthetic Biology Approaches for Organic Synthesis"   P. S Coelho, F. H. Arnold, J. C. Lewis. In Gary A. Molander and Paul Knochel (eds.), Comprehensive Organic Synthesis, 2nd edition, Vol 9, pp. 390-420 (2014).

"Enantioselective Imidation of Sulfides via Enzyme-Catalyzed Intermolecular Nitrogen-Atom Transfer"   C. C. Farwell, J. A. McIntosh, T. K. Hyster, Z. J. Wang, F. H. Arnold. Journal of the American Chemical Society 136, 8766-8771 (2014).

"Enzyme-Controlled Nitrogen-Atom Transfer Enables Regiodivergent C-H Amination"   T. K. Hyster, C. C. Farwell, A. R. Buller, J. A. McIntosh, F. H. Arnold. Journal of the American Chemical Society 136, 15505-15508 (2014)

"Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture."J. Bagert, Y. Xie, M. Sweredoski, Y. Qi, S. Hess, E. Schuman and D. A. Tirrell. Mol. Cell Proteomics 13: 1352-1358 (2014).

"Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications." C. Kulkarni, M. Lo, J. G. Fraseur, D. A. Tirrell, T. L. Kinzer-Ursem. Bioconjug Chem., 26(10): 2153-60 (2015).

"P450 BM3-Axial Mutations: A Gateway to Non-Natural Reactivity"   T. K. Hyster, F. H. Arnold. Israel Journal of Chemistry 55, 14-20 (2015).

"Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution" H. Renata, Z. J. Wang, F. H. Arnold. Angewandte Chemie Int. Ed. 54, 3351-3367 (2015).

"Enantioselective Enzyme-Catalyzed Aziridination Enabled by Active-Site Evolution of a Cytochrome P450"   C. C. Farwell, R. K. Zhang, J. A. McIntosh, T. K. Hyster, F. H. Arnold. ACS Central Science 1, 89-93 (2015).

"The Nature of Chemical Innovation: New Enzymes by Evolution" F. H. Arnold. Quarterly Reviews of Biophysics Discovery — The Nobel Workshop Issue (2015).

"Directed Evolution of the Tryptophan Synthase β-Subunit for Stand-Alone Function Recapitulates Allosteric Activation," A. R. Buller, S. Brinkmann-Chen, D. K. Romney, M. Herger, J. Murciano-Calles, F. H. Arnold. Proceedings of the National Academy of Sciences 112, 14599-14604 (2015).

"Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas." L. Jin, D. Gao, T. Feng, J. R. Tremblay, N. Ghazalli, A. Luo, J. Rawson, J. C. Quijano, J. Chai, L. Wedeken, J. Hsu, J. LeBon, S. Walker, H. P. Shih, A. Mahdavi, D. A. Tirrell, A. D. Riggs, H. T. Ku. Stem Cell Res., 16(1): 40-53 (2016).

"In vitro colony assays for characterizing tri-potent progenitor cells isolated from the adult murine pancreas." J. R. Tremblay, J. LeBon, A. Luo, J. C. Quijano, L. Wedeken, K. Jou, A. D. Riggs, D. A. Tirrell, H. T. Ku. J. Vis. Exp. 112, e54016 (2016).

"Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells." S. H. Ho, D. A. Tirrell, Journal of the American Chemical Society, 138(46): 15098-15101 (2016)."Synthesis of β-Branched Tryptophan Analogues Using an Engineered SubUnit of Tryptophan Synthase," M. Herger, P. van Roye, D. K. Romney, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold. Journal of the American Chemical Society 138, 8388-8391 (2016).

"A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation,"  J. Murciano-Calles, D. K. Romney, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold. Angewandte Chemie Int. Ed. 55, 11577-11581 (2016).

"Directed Evolution of Cytochrome c for Carbon-Silicon Bond Formation: Bringing Silicon to Life"  S.B. J. Kan, R. D. Lewis, K. Chen, F. H. ArnoldScience 354, 1048-1051 (2016).

"Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility After Only 15 Minutes of Antibiotic Exposure." N. G. Schoepp, E. M. Khorosheva, T. S. Schlappi, R. M. Humphries, J. A. Hindler, R. F. IsmagilovAngewandte Chemie Int. Ed. 55(33):9557–9561. (2016)

"Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore"  L. Herwig, A. J. Rice, C. N. Bedbrook, R. K. Zhang, A. Lignell, J. K. B. Cahn, H. Renata, S. C. Dodani, I. Cho, L. Cai, V. Gradinaru, F. H. ArnoldCell Chemical Biology 24, 415-425 (2017).

"Exploiting and Engineering Hemoproteins for Abiological Carbene and Nitrene Transfer Reactions" O. F. Brandenberg, R. Fasan, F. H. Arnold. Current Opinion in Biotechnology (2017)

"Chapter 5. Directed Evolution of Artificial Metalloenzymes: Bridging Synthetic Chemistry and Biology," R. K. Zhang, D. K. Romney, S. B. J. Kan, F. H. Arnold.  Artificial Metalloenzymes and MetalloDNAzymes in Catalysis. From Design to Applications.  Wiley-VCH. "Design and Evolution of Enzymes for Non-Natural Chemistry" S. C. Hammer, A. M. Knight, F. H. Arnold. Current Opinion in Green Sustainable Chemistry 7:23-30 (2017)

"Unlocking Reactivity of TrpB: A General Biocatalytic Platform for Synthesis of Tryptophan Analogs" D. Romney, J. Murciano-Calles, J. Wehrmüller, F. H. Arnold. Journal of the American Chemical Society (2017) 

"Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples." N. G. Schoepp, T. S. Schlappi, M. S. Curtis, S. S. Butkovich, S. Miller, R. M. Humphries, R. F. IsmagilovScience Translational Medicine (2017).

"Genetically Programmed Chiral Organoborane Synthesis," S. B. J. Kan, X. Huang, Y. Gumulya, K. Chen, F. H. Arnold. Nature 552, 132-136 (2017).

"Design, simulation, and characterization of a radial opposed migration ion and aerosol classifier (ROMIAC)." W. Mui, H. Mai, A. J. Downard, J. H. Seinfeld, and R. C. Flagan. Aerosol Science and Technology (2017)

"Acoustically targeted chemogenetics for noninvasive control of neural circuits." J. O. Szablowski, B. Lue, A. Lee-Gosselin, D. Malounda, M. G. ShapiroNature Biomedical Engineering (2018) 

"Polyelectrolyte chain structure and solution phase behavior." K. Shen and Z.-G. WangMacromolecules  (2018)

"RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure. T. Khazaei, J. T. Barlow, N. G. Schoepp and R. F. IsmagilovScientific Reports (2018) 

"Tube Expansion Deformation Enables In Situ Synchrotron X-ray Scattering Measurements during Extensional Flow-Induced Crystallization of Poly l-Lactide Near the Glass Transition." K. Ramachandran, R. Miscioscia, G. De Filippo, G. Landolfi, T. Di Luccio and J. A. Kornfield. Polymers (2018) 10: 288 (2018).

"Crimping-induced structural gradients explain the lasting strength of poly l-lactide bioresorbable vascular scaffolds during hydrolysis." K. Ramachandran, T. Di Luccio, A. Ailianou, M. B. Kossuth, J. P. Oberhauser and J. A. Kornfield. Proc. of the Nat. Academy of Sci. of the U.S.A. (2018) 

"Chapter 5. Directed Evolution of Artificial Metalloenzymes: Bridging Synthetic Chemistry and Biology," R. K. Zhang, D. K. Romney, S. B. J. Kan, F. H. Arnold. In M. Dieguez, J.-E. Backvall, O. Pamies (Eds.), Artificial Metalloenzyme and MetalloDNAzymes in Catalysis. From Design to Applications. (2018)

"Improved Synthesis of 4-Cyanotryptophan and Other Tryptophan Analogs in Aqueous Solvent Using Variants of TrpB from Thermotoga maritime," C. E. Boville, D. K. Romney, P. J. Almhjell, M. Sieben, F. H. Arnold. The Journal of Organic Chemistry 83, 7447-7452 (2018).

"Catalytic Iron-Carbene Intermediate Revealed in a Cytochrome c Carbene Transferase" R. D. Lewis, M. Garcia-Borràs, M. J. Chalkley, A. R. Buller, K. N. Houk, S. B. J. Kan, F. H. Arnold. Proceedings of the National Academy of Sciences 115, 7308-7313 (2018).

"Engineering Enzymes for Noncanonical Amino Acid Synthesis: Convincing Classic Amino Acids to Create their Noncanonical Counterparts" P. J. Almhjell, C. E. Boville, F. H. Arnold. Chemical Society Reviews 47, 8980-8997 (2018).

"High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine." A.P. Steinberg, S. S. Datta, T. Naragon, J.C, Rolando, S. R. Bogatyrev, and R. F. Ismagilov. eLife. 8:e40387 (2018).

"A Biocatalytic Platform for Synthesis of Chiral α-Trifluoromethylated Organoborons" X. Huang, M. Garcia-Borras, K. Miao, S. B. Kan, A. Zutshi, K. N. Houk, F. H. Arnold. ACS Central Science 5(2), 270-276 (2019).

"Machine-Learning-Assisted Directed Protein Evolution with Combinatorial Libraries" Z. Wu, S. B. J. Kan, R. D. Lewis, B. J. Wittmann, F. H. Arnold. Proceedings of the National Academy of Sciences 116(18), 8852-8858 (2019).

"Food polyelectrolytes compress the colonic mucus hydrogel by a Donnan mechanism." A.P. Steinberg, Z.-G. Wang, and R. F. Ismagilov. Biomacromolecules. 20(7):2675-2683 (2019).

"Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation." M. Porter, A. P. Steinberg, and R. F. Ismagilov. Soft Matter. 15:7071-7079 (2019).

"Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells." S.H. Ho, D.A. Tirrell. ACS Cent Sci.,5(12): 1911-1919 (2019).

"Enzymatic Primary Amination of Benzylic and Allylic C(sp3)-H Bonds" Z.-J. Jia, S. Gao, F. H. Arnold. Journal of the American Chemical Society 142(23), 10279-10283 (2020).

"New-to-Nature Carbene and Nitrene Transformations Catalyzed By Hemoproteins" Z. Liu, F. H. Arnold. Current Opinion in Biotechnology, submitted.

"Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae. E. S. Savela*, N. G. Schoepp*, M. M. Cooper, J. C. Rolando, J. D. Klausner, O. O. Soge, and R. F. Ismagilov. " PLoS Biology.

"Differential DNA Accessibility to Polymerase during Nucleic Acid Amplification Enables 30-Minute Phenotypic Beta-lactam Antibiotic Susceptibility Testing of Carbapenem-resistant Enterobacteriaceae (CRE)." N. G. Schoepp, E. J. Liaw, A. Winnett, E. S. Savela, O. B. Garner, and R. F. Ismagilov. PLoS Biology. (2020)

"Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and nonspecific amplification." J. C. Rolando, E. Jue, J. T. Barlow, and R. F. Ismagilov. Nucleic Acids Research. gkaa099 (2020).

"Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine." S. R. Bogatyrev, J. C. Rolando, and R. F. Ismagilov. Microbiome. 8(19):1-22 (2020).

"Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits." E. Jue, D. Witters, and R. F. Ismagilov. Scientific Reports. 10(1940) (2020).

"Ultrasound Technologies for Imaging and Modulating Neural Activity." Rabut C, Yoo S, Hurt RC, Jin Z, Li H, Guo H, Ling B, Shapiro MG. Neuron, 108(1): 93-110. (2020).

"Enzymatic Primary Amination of Benzylic and Allylic C(sp3)-H Bonds." Z.-J. Jia, S. Gao, and F. H. Arnold. Journal of the American Chemical Society 142(23), 10279-10283 (2020).

"Nature's Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases." N. P. Dunham and F. H. Arnold, ACS Catalysis 10(20), 12239-12255 (2020).

"Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection." E.S. Savela, A. Viloria Winnett, A.E. Romano, M.K. Porter, N. Shelby, R. Akana, J. Ji, M.M. Cooper, N.W. Schlenker, J.A. Reyes, A.M. Carter, J.T. Barlow, C. Tognazzini, M. Feaster, Y-Y Goh, R.F. Ismagilov. Journal of Clinical Microbiology doi:10.1128/JCM.01785-21 (2021).

"Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome." J.T. Barlow, G. Leite, A.E. Romano, R. Sedighi, C. Chang, S. Celly, A. Rezaie, R. Muthur, M. Pimentel, R.F. Ismagilov. Microbiome 9:214 (2021).

"New-to-Nature Carbene and Nitrene Transformations Catalyzed By Hemoproteins." Z. Liu, F. H. Arnold, Current Opinion in Biotechnology 69, 43-51 (2021).

"Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa." O. Mondragón-Palomino, R. Poceviciute, A. Lignell, J.A. Griffiths, H. Takko, R.F. Ismagilov. PNAS 10.1073/pnas.2118483119 (2022).