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Items where Research Group Name is "Jacobs Institute for Molecular Engineering for Medicine"

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Winnett, Alexander Viloria and Akana, Reid and Shelby, Natasha et al. (2023) Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods. PNAS Nexus, 2 (3). Art. No. pgad033. ISSN 2752-6542. PMCID PMC10013338. doi:10.1093/pnasnexus/pgad033.

Carter, Alyssa M. and Winnett, Alexander Viloria and Romano, Anna E. et al. (2023) Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips. Open Forum Infectious Diseases, 10 (1). Art. No. ofac701. ISSN 2328-8957. PMCID PMC9887260. doi:10.1093/ofid/ofac701. (In Press)

Winnett, Alexander Viloria and Porter, Michael K. and Romano, Anna E. et al. (2022) Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking. Microbiology Spectrum, 10 (6). Art. No. e03873-22. ISSN 2165-0497. PMCID PMC9769854. doi:10.1128/spectrum.03873-22.

Anthis, Alexandre H. C. and Abundo, Maria Paulene and Neuer, Anna L. et al. (2022) Modular stimuli-responsive hydrogel sealants for early gastrointestinal leak detection and containment. Nature Communications, 13 . ISSN 2041-1723. PMCID PMC9701692. doi:10.1038/s41467-022-34272-y.

Petrovic, Stefan and Samanta, Dipanjan and Perriches, Thibaud et al. (2022) Architecture of the linker-scaffold in the nuclear pore. Science, 376 (6598). Art. No. abm9798. ISSN 0036-8075. doi:10.1126/science.abm9798.

Pushpawela, Buddhi and Amanatidis, Stavros and Huang, Yuanlong et al. (2022) Variability of the penetration of particles through facemasks. Aerosol Science and Technology, 56 (2). pp. 186-203. ISSN 0278-6826. doi:10.1080/02786826.2021.2003291.

Savela, Emily S. and Winnett, Alexander Viloria and Romano, Anna E. et al. (2022) Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection. Journal of Clinical Microbiology, 60 (2). Art. No. e01785-21. ISSN 0095-1137. PMCID PMC8849374; PMC8043477. doi:10.1128/JCM.01785-21.

Ramachandran, Karthik and Shao, Zixuan and Di Luccio, Tiziana et al. (2022) Tungsten disulfide nanotubes enhance flow-induced crystallization and radio-opacity of polylactide without adversely affecting in vitro toxicity. Acta Biomaterialia, 138 . pp. 313-326. ISSN 1742-7061. doi:10.1016/j.actbio.2021.11.005.

Nichols, Aaron L. and Blumenfeld, Zack and Fan, Chengcheng et al. (2022) Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands. eLife, 11 . Art. No. e74648. ISSN 2050-084X. PMCID PMC8820738. doi:10.7554/eLife.74648.

Wu, Wei-Li and Adame, Mark D. and Liou, Chia-Wei et al. (2021) Microbiota regulate social behaviour via stress response neurons in the brain. Nature, 595 (7867). pp. 409-414. ISSN 0028-0836. PMCID PMC8346519. doi:10.1038/s41586-021-03669-y.

Liu, Zhen and Arnold, Frances H. (2021) New-to-nature chemistry from old protein machinery: carbene and nitrene transferases. Current Opinion in Biotechnology, 69 . pp. 43-51. ISSN 0958-1669. PMCID PMC8225731. doi:10.1016/j.copbio.2020.12.005.

Laccetti, Benjamin and Kornfield, Julia (2021) Ballistic delivery of compounds to inner layers of the cornea is limited by tough mechanical properties of stromal tissue. Journal of the Mechanical Behavior of Biomedical Materials, 115 . Art. No. 104246. ISSN 1751-6161. doi:10.1016/j.jmbbm.2020.104246.

Loffredo, Fausta and Tammaro, Loredana and Di Luccio, Tiziana et al. (2021) Effect of tungsten disulfide nanotubes on crystallization of polylactide under uniaxial deformation and annealing. Functional Composite Materials, 2 (1). Art. No. 3. ISSN 2522-5774. PMCID PMC8198810. doi:10.1186/s42252-021-00016-2.

Dunham, Noah P. and Arnold, Frances H. (2020) Nature’s Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases. ACS Catalysis, 10 (20). pp. 12239-12255. ISSN 2155-5435. PMCID PMC7710332. doi:10.1021/acscatal.0c03606.

Jia, Zhi-Jun and Gao, Shilong and Arnold, Frances H. (2020) Enzymatic Primary Amination of Benzylic and Allylic C(sp³)–H Bonds. Journal of the American Chemical Society, 142 (23). pp. 10279-10283. ISSN 0002-7863. doi:10.1021/jacs.0c03428.

Szablowski, Jerzy and Lee-Gosselin, Audrey and Lue, Brian et al. (2020) Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits. Biological Psychiatry, 87 (9). S95. ISSN 0006-3223. doi:10.1016/j.biopsych.2020.02.263.

Rolando, Justin C. and Jue, Erik and Barlow, Jacob T. et al. (2020) Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification. Nucleic Acids Research, 48 (7). Art. No. e42. ISSN 0305-1048. PMCID PMC7144905. doi:10.1093/nar/gkaa099.

Schoepp, Nathan G. and Liaw, Eric J. and Winnett, Alexander et al. (2020) Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae. PLoS Biology, 18 (3). Art. No. 3000652. ISSN 1545-7885. PMCID PMC7081982.

Savela, Emily S. and Schoepp, Nathan G. and Cooper, Matthew M. et al. (2020) Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae. PLoS Biology, 18 (3). Art. No. 3000651. ISSN 1545-7885. PMCID PMC7081974.

Bogatyrev, Said R. and Rolando, Justin C. and Ismagilov, Rustem F. (2020) Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine. Microbiome, 8 . Art. No. 19. ISSN 2049-2618. PMCID PMC7017497.

Jue, Erik and Witters, Daan and Ismagilov, Rustem F. (2020) Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits. Scientific Reports, 10 . Art. No. 1940. ISSN 2045-2322. PMCID PMC7004994. doi:10.1038/s41598-020-58586-3.

Fasan, Rudi and Kan, S. B. Jennifer and Zhao, Huimin (2019) A Continuing Career in Biocatalysis: Frances H. Arnold. ACS Catalysis, 9 (11). pp. 9775-9788. ISSN 2155-5435. PMCID PMC7390471. doi:10.1021/acscatal.9b02737.

Porter, Michael K. and Steinberg, Asher Preska and Ismagilov, Rustem F. (2019) Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation. Soft Matter, 15 (35). pp. 7071-7079. ISSN 1744-683X. doi:10.1039/c9sm00791a.

Preska Steinberg, Asher and Wang, Zhen-Gang and Ismagilov, Rustem F. (2019) Food Polyelectrolytes Compress the Colonic Mucus Hydrogel by a Donnan Mechanism. Biomacromolecules, 20 (7). pp. 2675-2683. ISSN 1525-7797. doi:10.1021/acs.biomac.9b00442.

Wu, Zachary and Kan, S. B. Jennifer and Lewis, Russell D. et al. (2019) Machine learning-assisted directed protein evolution with combinatorial libraries. Proceedings of the National Academy of Sciences of the United States of America, 116 (18). pp. 8852-8858. ISSN 0027-8424. PMCID PMC6500146. doi:10.1073/pnas.1901979116.

Huang, Xiongyi and Garcia-Borràs, Marc and Miao, Kun et al. (2019) A Biocatalytic Platform for Synthesis of Chiral α-Trifluoromethylated Organoborons. ACS Central Science, 5 (2). pp. 270-276. ISSN 2374-7943. PMCID PMC6396380. doi:10.1021/acscentsci.8b00679.

Preska Steinberg, Asher and Datta, Sujit S. and Naragon, Thomas et al. (2019) High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine. eLife, 8 . Art. No. e40387. ISSN 2050-084X. PMCID PMC6342521.

Rolando, Justin C. and Jue, Erik and Schoepp, Nathan G. et al. (2019) Real-Time, Digital LAMP with Commercial Microfluidic Chips Reveals the Interplay of Efficiency, Speed, and Background Amplification as a Function of Reaction Temperature and Time. Analytical Chemistry, 91 (1). pp. 1034-1042. ISSN 0003-2700. PMCID PMC6322147. doi:10.1021/acs.analchem.8b04324.

Almhjell, Patrick J. and Boville, Christina E. and Arnold, Frances H. (2018) Engineering enzymes for noncanonical amino acid synthesis. Chemical Society Reviews, 47 (24). pp. 8980-8997. ISSN 0306-0012. PMCID PMC6434697. doi:10.1039/c8cs00665b.

Ramachandran, Karthik and Di Luccio, Tiziana and Ailianou, Artemis et al. (2018) Crimping-induced structural gradients explain the lasting strength of poly L-lactide bioresorbable vascular scaffolds during hydrolysis. Proceedings of the National Academy of Sciences of the United States of America, 115 (41). pp. 10239-10244. ISSN 0027-8424. PMCID PMC6187115. doi:10.1073/pnas.1807347115.

Khazaei, Tahmineh and Barlow, Jacob T. and Schoepp, Nathan G. et al. (2018) RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure. Scientific Reports, 8 . Art. No. 11606. ISSN 2045-2322. PMCID PMC6072703. doi:10.1038/s41598-018-29707-w.

Lu, George J. and Farhadi, Arash and Mukherjee, Arnab et al. (2018) Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging. Current Opinion in Chemical Biology, 45 . pp. 57-63. ISSN 1367-5931. PMCID PMC6076850. doi:10.1016/j.cbpa.2018.02.011.

Boville, Christina E. and Romney, David K. and Almhjell, Patrick J. et al. (2018) Improved synthesis of 4-cyanotryptophan and other tryptophan analogs in aqueous solvent using variants of TrpB from Thermotoga maritima. Journal of Organic Chemistry, 83 (14). pp. 7447-7452. ISSN 0022-3263. PMCID PMC6054569. doi:10.1021/acs.joc.8b00517.

Lewis, Russell D. and Garcia-Borràs, Marc and Chalkley, Matthew J. et al. (2018) Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase. Proceedings of the National Academy of Sciences of the United States of America, 115 (28). pp. 7308-7313. ISSN 0027-8424. PMCID PMC6048479. doi:10.1073/pnas.1807027115.

Szablowski, Jerzy O. and Lee-Gosselin, Audrey and Lue, Brian et al. (2018) Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits. Nature Biomedical Engineering, 2 (7). pp. 475-484. ISSN 2157-846X.

Maresca, David and Lakshmanan, Anupama and Abedi, Mohamad H. et al. (2018) Biomolecular Ultrasound and Sonogenetics. Annual Review of Chemical and Biomolecular Engineering, 9 . pp. 229-252. ISSN 1947-5438. PMCID PMC6086606. doi:10.1146/annurev-chembioeng-060817-084034.

Ramachandran, Karthik and Miscioscia, Riccardo and De Filippo, Giovanni et al. (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. Polymers, 10 (3). Art. No. 288. ISSN 2073-4360. PMCID PMC6415077. doi:10.3390/polym10030288.

Schoepp, Nathan G. and Schlappi, Travis S. and Curtis, Matthew S. et al. (2017) Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples. Science Translational Medicine, 9 (410). Art. No. eaal3693. ISSN 1946-6234. PMCID PMC6765391. doi:10.1126/scitranslmed.aal3693.

Piraner, Dan I. and Farhadi, Arash and Davis, Hunter C. et al. (2017) Going Deeper: Biomolecular Tools for Acoustic and Magnetic Imaging and Control of Cellular Function. Biochemistry, 56 (39). pp. 5202-5209. ISSN 0006-2960. PMCID PMC6058970. doi:10.1021/acs.biochem.7b00443.

Brandenberg, Oliver F. and Fasan, Rudi and Arnold, Frances H. (2017) Exploiting and engineering hemoproteins for abiological carbene and nitrene transfer reactions. Current Opinion in Biotechnology, 47 . pp. 102-111. ISSN 0958-1669. PMCID PMC5617781. doi:10.1016/j.copbio.2017.06.005.

Romney, David K. and Murciano-Calles, Javier and Wehrmüller, Jöri E. et al. (2017) Unlocking Reactivity of TrpB: A General Biocatalytic Platform for Synthesis of Tryptophan Analogues. Journal of the American Chemical Society, 139 (31). pp. 10769-10776. ISSN 0002-7863. PMCID PMC5589443. doi:10.1021/jacs.7b05007.

Pompano, Rebecca R. and Chiang, Andrew H. and Kastrup, Christian J. et al. (2017) Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. Annual Review of Biochemistry, 86 . pp. 333-356. ISSN 0066-4154. doi:10.1146/annurev-biochem-060815-014207.

Kan, S. B. Jennifer and Lewis, Russell D. and Chen, Kai et al. (2016) Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life. Science, 354 (6315). pp. 1048-1051. ISSN 0036-8075. PMCID PMC5243118. doi:10.1126/science.aah6219.

Murciano-Calles, Javier and Romney, David K. and Brinkmann-Chen, Sabine et al. (2016) A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation. Angewandte Chemie International Edition, 55 (38). pp. 11577-11581. ISSN 1433-7851. PMCID PMC5014574. doi:10.1002/anie.201606242.

Schoepp, Nathan G. and Khorosheva, Eugenia M. and Schlappi, Travis S. et al. (2016) Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure. Angewandte Chemie International Edition in English, 55 (33). pp. 9557-9561. ISSN 0570-0833. PMCID PMC5215780. doi:10.1002/ange.201602763.

Herger, Michael and van Roye, Paul and Romney, David K. et al. (2016) Synthesis of β-Branched Tryptophan Analogues Using an Engineered Subunit of Tryptophan Synthase. Journal of the American Chemical Society, 138 (27). pp. 8388-8391. ISSN 0002-7863. PMCID PMC4948191. doi:10.1021/jacs.6b04836.

Tremblay, Jacob R. and LeBon, Jeanne M. and Luo, Angela et al. (2016) In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas. Journal of Visualized Experiments (112). Art. No. e54016. ISSN 1940-087X. PMCID PMC4927776. doi:10.3791/54016.

Jin, Liang and Gao, Dan and Feng, Tao et al. (2016) Cells with surface expression of CD133^(high)CD71^(low) are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas. Stem Cell Research, 16 (1). pp. 40-53. ISSN 1873-5061. PMCID PMC4762724. doi:10.1016/j.scr.2015.11.015.

Buller, Andrew R. and Brinkmann-Chen, Sabine and Romney, David K. et al. (2015) Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation. Proceedings of the National Academy of Sciences of the United States of America, 112 (47). pp. 14599-14604. ISSN 0027-8424. PMCID PMC4664345. doi:10.1073/pnas.1516401112.

Farwell, Christopher C. and Zhang, Ruijie K. and McIntosh, John A. et al. (2015) Enantioselective Enzyme-Catalyzed Aziridination Enabled by Active-Site Evolution of a Cytochrome P450. ACS Central Science, 1 (2). pp. 89-93. ISSN 2374-7951. PMCID PMC4571169. doi:10.1021/acscentsci.5b00056.

McIntosh, John A. and Coelho, Pedro S. and Farwell, Christopher C. et al. (2013) Enantioselective Intramolecular C-H Amination Catalyzed by Engineered Cytochrome P450 Enzymes In Vitro and In Vivo. Angewandte Chemie International Edition, 52 (35). pp. 9309-9312. ISSN 1433-7851. PMCID PMC3988694. doi:10.1002/anie.201304401.

Brustad, Eric M. and Lelyveld, Victor S. and Snow, Christopher D. et al. (2012) Structure-Guided Directed Evolution of Highly Selective P450-Based Magnetic Resonance Imaging Sensors for Dopamine and Serotonin. Journal of Molecular Biology, 422 (2). pp. 245-262. ISSN 0022-2836. PMCID PMC3418479. doi:10.1016/j.jmb.2012.05.029.

Ting, Christina L. and Wu, Jianzhong and Wang, Zhen-Gang (2011) Thermodynamic basis for the genome to capsid charge relationship in viral encapsidation. Proceedings of the National Academy of Sciences of the United States of America, 108 (41). pp. 16986-16991. ISSN 0027-8424. PMCID PMC3193252. doi:10.1073/pnas.1109307108.

Mattson, Matthew S. and Huynh, Joyce and Wiseman, Meredith et al. (2010) An In Vitro Intact Globe Expansion Method for Evaluation of Cross-linking Treatments. Investigative Ophthalmology and Visual Science, 51 (6). pp. 3120-3128. ISSN 0146-0404. PMCID PMC2891471. doi:10.1167/iovs.09-4001.

Kim, Jin-Hong and Kushiro, Keiichiro and Graham, Nicholas A. et al. (2009) Tunable interplay between epidermal growth factor and cell–cell contact governs the spatial dynamics of epithelial growth. Proceedings of the National Academy of Sciences of the United States of America, 106 (27). pp. 11149-11153. ISSN 0027-8424. PMCID PMC2708686. doi:10.1073/pnas.0812651106.

Beisel, Chase L. and Smolke, Christina D. (2009) Design principles for riboswitch function. PLoS Computational Biology, 5 (4). Art. No. e1000363. ISSN 1553-734X. PMCID PMC2666153. doi:10.1371/journal.pcbi.1000363.

Giurumescu, Claudiu A. and Sternberg, Paul W. and Asthagiri, Anand R. (2009) Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions. PLoS Computational Biology, 5 (4). Art. No. e1000354. ISSN 1553-734X. PMCID PMC2661366. doi:10.1371/journal.pcbi.1000354.

Rentmeister, Andrea and Arnold, Frances H. and Fasan, Rudi (2009) Chemo-enzymatic fluorination of unactivated organic compounds. Nature Chemical Biology, 5 (1). pp. 26-28. ISSN 1552-4450. PMCID PMC2713661. doi:10.1038/nchembio.128.

Beatty, Kimberly E. and Tirrell, David A. (2008) Two-color labeling of temporally defined protein populations in mammalian cells. Bioorganic and Medicinal Chemistry Letters, 18 (22). pp. 5995-5999. ISSN 0960-894X. PMCID PMC3182832. doi:10.1016/j.bmcl.2008.08.046.

Book Section

Breunig, Stephanie L. and Tirrell, David A. (2021) Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. In: Synthetic and Enzymatic Modifications of the Peptide Backbone. Methods in Enzymology. No.656. Academic Press , Cambridge, MA, pp. 545-571. ISBN 978-0-12-821253-0.

Report or Paper

Xiong, Lealia L. and Garrett, Michael A. and Kornfield, Julia A. et al. (2023) Self-regulating living material with temperature-dependent light absorption. . doi:10.1101/2023.03.11.532239. (Unpublished)

Ji, Jenny and Winnett, Alexander Viloria and Shelby, Natasha et al. (2023) Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types. . doi:10.1101/2023.03.09.23286855. (Unpublished)

Wang, Grace Z. and Warren, Elizabeth A. and Haas, Allison L. et al. (2023) Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa. . doi:10.1101/2023.01.29.526047. (Unpublished)

Winnett, Alexander Viloria and Akana, Reid and Shelby, Natasha et al. (2022) Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods. . doi:10.1101/2022.07.13.22277113. (Unpublished)

Winnett, Alexander Viloria and Akana, Reid and Shelby, Natasha et al. (2022) Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals. . doi:10.1101/2022.07.13.22277513. (Unpublished)

Poceviciute, Roberta and Bogatyrev, Said R. and Romano, Anna E. et al. (2022) Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa. . doi:10.1101/2022.06.17.496478. (Unpublished)

Winnett, Alexander Viloria and Porter, Michael K. and Romano, Anna E. et al. (2022) Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking. . doi:10.1101/2022.03.02.22271724. (Unpublished)

Mondragón-Palomino, Octavio and Poceviciute, Roberta and Lignell, Antti et al. (2021) 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa. . doi:10.1101/2021.10.07.463215. (Unpublished)

Li, Hongyi and Heath, John E and Trippett, James S. et al. (2021) Engineering Viral Vectors for Acoustically Targeted Gene Delivery. . doi:10.1101/2021.07.26.453904. (Unpublished)

Winnett, Alexander and Cooper, Matthew M. and Shelby, Natasha et al. (2020) SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans. . doi:10.1101/2020.12.09.20239467. (Unpublished)

Jue, Erik and Ismagilov, Rustem F. (2020) Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays. . doi:10.1101/2020.04.28.20077602. (Unpublished)

Bogatyrev, Said R. and Ismagilov, Rustem F. (2020) Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding. . doi:10.1101/2020.01.22.914705. (Unpublished)

Cho, Inha and Jia, Zhi-Jun and Arnold, Frances H. (2019) Genetically Tunable Enzymatic C‒H Amidation for Lactam Synthesis. . (Unpublished)

This list was generated on Thu Jun 1 19:05:12 2023 UTC.