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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Lehmann, J. W., Crouch, I. T., Blair, D. J., Trobe, M., Wang, P., Li, J., & Burke, M. (2019). Axial shielding of Pd(II) complexes enables perfect stereoretention in Suzuki-Miyaura cross-coupling of Csp 3 boronic acids Nature communications, 10(1), [1263].

Hillson, N., Caddick, M., Cai, Y., Carrasco, J. A., Chang, M. W., Curach, N. C., ... Freemont, P. S. (2019). Building a global alliance of biofoundries. Nature communications, 10(1), [2040].

Xing, M., Wei, Y., Zhou, Y., Zhang, J., Lin, L., Hu, Y., ... Zhang, Y. (2019). Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nature communications, 10(1), [1609].

Thirawatananond, P., McPherson, R. L., Malhi, J., Nathan, S., Lambrecht, M. J., Brichacek, M., ... Gabelli, S. B. (2019). Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Scientific Reports, 9(1), [5940].

Kondakova, T., Kumar, S., & Cronan, J. E. (2019). A novel synthesis of trans-unsaturated fatty acids by the Gram-positive commensal bacterium Enterococcus faecalis FA2-2. Chemistry and Physics of Lipids, 222, 23-35.

Srinivas, S., & Cronan, J. E. (2019). Coping with inadvertent lysis of Escherichia coli cultures: Strains resistant to lysogeny and infection by the stealthy lysogenic phage Φ80. Biotechnology and bioengineering, 116(7), 1820-1826.

Llabani, E., Hicklin, R. W., Lee, H. Y., Motika, S. E., Crawford, L. A., Weerapana, E., & Hergenrother, P. (2019). Diverse compounds from pleuromutilin lead to a thioredoxin inhibitor and inducer of ferroptosis. Nature Chemistry, 11(6), 521-532.

Aye, Y., & Hergenrother, P. (2019). Editorial overview: From the iceman to modern medicine. Current Opinion in Chemical Biology, 50, A1-A2.

Hegemann, J. D., Bobeica, S. C., Walker, M. C., Bothwell, I. R., & van der Donk, W. A. (2019). Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications. ACS synthetic biology, 8(5), 1204-1214.

Hamedirad, M., Weisberg, S., Chao, R., Lian, J., & Zhao, H. (2019). Highly Efficient Single-Pot Scarless Golden Gate Assembly. ACS synthetic biology, 8(5), 1047-1054.

Sweedler, J. V. (2019). The Periodic Table of Elements at 150. Analytical chemistry, 91(9).

Zhu, L., Zou, Q., Cao, X., & Cronan, J. E. (2019). Enterococcus faecalis encodes an atypical auxiliary acyl carrier protein required for efficient regulation of fatty acid synthesis by exogenous fatty acids. mBio, 10(3), [e00577-19].

Srinivas, S., Hu, Z., & Cronan, J. E. (2019). Escherichia coli vectors having stringently repressible replication origins allow a streamlining of Crispr/Cas9 gene editing. Plasmid, 103, 53-62.

Mothet, J. P., Billard, J. M., Pollegioni, L., Coyle, J. T., & Sweedler, J. V. (2019). Investigating brain d-serine: Advocacy for good practices. Acta Physiologica, 226(1), [e13257].

Neumann, E. K., Comi, T. J., Rubakhin, S., & Sweedler, J. V. (2019). Lipid Heterogeneity between Astrocytes and Neurons Revealed by Single-Cell MALDI-MS Combined with Immunocytochemical Classification. Angewandte Chemie - International Edition, 58(18), 5910-5914.

Petronikolou, N., Ortega, M. A., Borisova, S. A., Nair, S. K., & Metcalf, W. W. (2019). Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin. ACS chemical biology, 14(4), 742-750.

Sweedler, J. V. (2019). Advancing the Fields of Measurement Science with Partnerships and Awards. Analytical chemistry, 91(7).

Shields, R. C., & Jensen, P. A. (2019). The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing. Molecular Oral Microbiology, 34(2), 39-50.

Tang, W., Bobeica, S. C., Wang, L., & van der Donk, W. A. (2019). CylA is a sequence-specific protease involved in toxin biosynthesis. Journal of Industrial Microbiology and Biotechnology, 46(3-4), 537-549.

Muraglia, K. A., Chorghade, R. S., Kim, B. R., Tang, X. X., Shah, V. S., Grillo, A. S., ... Burke, M. (2019). Small-molecule ion channels increase host defences in cystic fibrosis airway epithelia. Nature, 567(7748), 405-408.

Wu, C., Biswas, S., Garcia De Gonzalo, C. V., & van der Donk, W. A. (2019). Investigations into the Mechanism of Action of Sublancin. ACS Infectious Diseases, 5(3), 454-459.

Sweedler, J. V. (2019). Salami Publications and Duplicate Submissions: Put Them on Your List of Things to Avoid. Analytical chemistry, 91(5), 3177-3178.

Zukher, I., Pavlov, M., Tsibulskaya, D., Kulikovsky, A., Zyubko, T., Bikmetov, D., ... Severinova, K. (2019). Reiterative synthesis by the ribosome and recognition of the N-terminal formyl group by biosynthetic machinery contribute to evolutionary conservation of the length of antibiotic microcin c peptide precursor. mBio, 10(2), [e00768-19].

Sweedler, J. V. (2019). The Evolving World of Scientific Publications: From Unethical Behaviors to New Mandates from Funding Agencies. Analytical Chemistry, 91(3), 1673-1674.

Wang, B., Guo, F., Dong, S. H., & Zhao, H. (2019). Activation of silent biosynthetic gene clusters using transcription factor decoys. Nature chemical biology, 15(2), 111-114.

Aguirre, M. Á., Long, K. D., Canals, A., & Cunningham, B. T. (2019). Point-of-use detection of ascorbic acid using a spectrometric smartphone-based system. Food Chemistry, 272, 141-147.

Woodburn, E. V., Long, K. D., & Cunningham, B. T. (2019). Analysis of Paper-Based Colorimetric Assays with a Smartphone Spectrometer. IEEE Sensors Journal, 19(2), 508-514. [8494768].

Bobeica, S. C., Dong, S. H., Huo, L., Mazo, N., McLaughlin, M. I., Jiménez-Osés, G., ... van der Donk, W. A. (2019). Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease. eLife, 8.

Bingham, T. W., Hernandez, L. W., Olson, D. G., Svec, R. L., Hergenrother, P., & Sarlah, D. (2019). Enantioselective Synthesis of Isocarbostyril Alkaloids and Analogs Using Catalytic Dearomative Functionalization of Benzene. Journal of the American Chemical Society, 141(1), 657-670.

Dicaprio, A. J., Firouzbakht, A., Hudson, G. A., & Mitchell, D. A. (2019). Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin. Journal of the American Chemical Society, 141(1), 290-297.

Zhou, Y., Wei, Y., Lin, L., Xu, T., Ang, E. L., Zhao, H., ... Zhang, Y. (2019). Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca. Biochemical Journal, 476(4), 733-746.

Fu, H., Goettge, M. N., & Metcalf, W. W. (2019). Biochemical characterization of the methylmercaptopropionate: Cob(I)alamin Methyltransferase from Methanosarcina acetivorans. Journal of bacteriology, 201(12), [e00130-19].

Mahanta, N., Szantai-Kis, D. M., Petersson, E. J., & Mitchell, D. A. (2019). Biosynthesis and Chemical Applications of Thioamides. ACS chemical biology.

Dong, S. H., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K., & Nair, S. K. (2019). Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor. Chemical Science, 10(8), 2391-2395.

Yeo, W. L., Heng, E., Tan, L. L., Lim, Y. W., Lim, Y. H., Hoon, S., ... Wong, F. T. (2019). Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes. Biotechnology and bioengineering.

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H., & Nair, S. K. (2019). Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098. Organic and Biomolecular Chemistry, 17(6), 1506-1518.

Shi, S., Liang, Y., Ang, E. L., & Zhao, H. (2019). Delta integration CRISPR-Cas (Di-CRISPR) in saccharomyces cerevisiae. In Methods in Molecular Biology (pp. 73-91). (Methods in Molecular Biology; Vol. 1927). Humana Press Inc..

Sabri, L., Huang, Q., Liu, J. N., & Cunningham, B. T. (2019). Design of anapole mode electromagnetic field enhancement structures for biosensing applications. Optics Express, 27(5), 7196-7212.

Neumann, E. K., Do, T. D., Comi, T. J., & Sweedler, J. V. (2019). Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angewandte Chemie - International Edition.

Schlein, L. J., Fadl-Alla, B., Pondenis, H. C., Lezmi, S., Eberhart, C. G., LeBlanc, A. K., ... Fan, T. M. (2019). Immunohistochemical characterization of procaspase-3 overexpression as a druggable target with PAC-1, a procaspase-3 activator, in canine and human brain cancers. Frontiers in Oncology, 9(FEB), [96].

Dong, S. H., Liu, A., Mahanta, N., Mitchell, D. A., & Nair, S. K. (2019). Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS Central Science.

Nayak, D. D., & Metcalf, W. W. (2019). Methylamine-specific methyltransferase paralogs in Methanosarcina are functionally distinct despite frequent gene conversion. ISME Journal.

Bouvier, J. T., Sernova, N. V., Ghasempur, S., Rodionova, I. A., Vetting, M. W., Al-Obaidi, N. F., ... Rodionov, D. A. (2019). Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria. Journal of bacteriology, 201(2), [e00431-18].

Aguirre, M. Á., Long, K. D., & Cunningham, B. T. (2019). Spectrometric Smartphone-Based System for Ibuprofen Quantification in Commercial Dosage Tablets. Journal of Pharmaceutical Sciences.

Jeon, S., Li, Q., Rubakhin, S., Sweedler, J. V., Smith, J. W., Neuringer, M., ... Erdman, J. W. (2019). 13C-lutein is differentially distributed in tissues of an adult female rhesus macaque following a single oral administration: a pilot study. Nutrition Research, 61, 102-108.

Radin, J. N., Zhu, J., Brazel, E. B., McDevitt, C. A., & Kehl-Fie, T. (2019). Synergy between nutritional immunity and independent host defenses contributes to the importance of the MntABC manganese transporter during staphylococcus aureus infection. Infection and immunity, 87(1), [e00642].

Richter, M. F., & Hergenrother, P. (2019). The challenge of converting gram-positive-only compounds into broad-spectrum antibiotics. Annals of the New York Academy of Sciences, 1435(1), 18-38.

Kondakova, T., & Cronan, J. E. (2019). Transcriptional regulation of fatty acid cis–trans isomerization in the solvent-tolerant soil bacterium, Pseudomonas putida F1. Environmental Microbiology.

Bougioukou, D. J., Ting, C. P., Peck, S. C., Mukherjee, S., & van der Donk, W. A. (2019). Use of the dehydrophos biosynthetic enzymes to prepare antimicrobial analogs of alaphosphin. Organic and Biomolecular Chemistry, 17(4), 822-829.

Howe, G. W., & van der Donk, W. A. (2018). 18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer. Journal of the American Chemical Society, 140(51), 17820-17824.

Rack, J. G. M., Ariza, A., Drown, B. S., Henfrey, C., Bartlett, E., Shirai, T., ... Ahel, I. (2018). (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell chemical biology, 25(12), 1533-1546.e12.

Drown, B. S., Shirai, T., Rack, J. G. M., Ahel, I., & Hergenrother, P. (2018). Monitoring Poly(ADP-ribosyl)glycohydrolase Activity with a Continuous Fluorescent Substrate. Cell Chemical Biology, 25(12), 1562-1570.e19.

Reyes, A. C., Plache, D. C., Koudelka, A. P., Amyes, T. L., Gerlt, J. A., & Richard, J. P. (2018). Enzyme Architecture: Breaking Down the Catalytic Cage that Activates Orotidine 5′-Monophosphate Decarboxylase for Catalysis. Journal of the American Chemical Society, 140(50), 17580-17590.

Jeong, H., Moye, L. S., Southey, B. R., Hernandez, A. G., Dripps, I., Romanova, E. V., ... Rodriguez-Zas, S. L. (2018). Gene network dysregulation in the trigeminal ganglia and nucleus accumbens of a model of chronic migraine-associated hyperalgesia. Frontiers in Systems Neuroscience, 12, [63].

Singh, R. K., Singh, R., Sivakumar, D., Kondaveeti, S., Kim, T., Li, J., ... Lee, J. K. (2018). Insights into Cell-Free Conversion of CO 2 to Chemicals by a Multienzyme Cascade Reaction ACS Catalysis, 8(12), 11085-11093.

Cronan, J. E. (2018). Advances in synthesis of biotin and assembly of lipoic acid. Current Opinion in Chemical Biology, 47, 60-66.

Zallot, R., Oberg, N. O., & Gerlt, J. A. (2018). ‘Democratized’ genomic enzymology web tools for functional assignment. Current Opinion in Chemical Biology, 47, 77-85.

Gerlt, J. A., & Erb, T. J. (2018). Editorial overview: Novel enzymes, coenzymes, and metabolic pathways. Current Opinion in Chemical Biology, 47, A4-A6.

Tapsin, S., Sun, M., Shen, Y., Zhang, H., Lim, X. N., Susanto, T. T., ... Wan, Y. (2018). Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes. Nature communications, 9(1), [1289].

Wang, K. K. A., Ng, T. L., Wang, P., Huang, Z., Balskus, E. P., & van der Donk, W. A. (2018). Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. Nature communications, 9(1), [3687].

Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., ... Zhang, Y. (2018). Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nature communications, 9(1), [4224].

Zhuo, Y., Choi, J. S., Marin, T., Yu, H., Harley, B. A., & Cunningham, B. T. (2018). Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM). Light: Science and Applications, 7(1), [7538].

Svec, R. L., Furiassi, L., Skibinski, C. G., Fan, T. M., Riggins, G. J., & Hergenrother, P. (2018). Tunable Stability of Imidazotetrazines Leads to a Potent Compound for Glioblastoma. ACS chemical biology, 13(11), 3206-3216.

Svec, R. L., & Hergenrother, P. (2018). Oxygen Starvation Unmasks a Killer. Cell chemical biology, 25(11), 1313-1314.

Haley, H. M. S., Hill, A. G., Greenwood, A. I., Woerly, E. M., Rienstra, C., & Burke, M. (2018). Peridinin Is an Exceptionally Potent and Membrane-Embedded Inhibitor of Bilayer Lipid Peroxidation. Journal of the American Chemical Society, 140(45), 15227-15240.

Sweedler, J. V. (2018). Science Research - Looking in the Mirror. Analytical chemistry, 90(21), 12323-12324.

Rodriguez-Zas, S. L., Wu, C., Southey, B. R., O'Connor, J. C., Nixon, S. E., Garcia, R., ... Dantzer, R. (2018). Disruption of microglia histone acetylation and protein pathways in mice exhibiting inflammation-associated depression-like symptoms. Psychoneuroendocrinology, 97, 47-58.

Li, B., Neumann, E. K., Ge, J., Gao, W., Yang, H., Li, P., & Sweedler, J. V. (2018). Interrogation of spatial metabolome of Ginkgo biloba with high-resolution matrix-assisted laser desorption/ionization and laser desorption/ionization mass spectrometry imaging. Plant Cell and Environment, 41(11), 2693-2703.

Lian, J., Mishra, S., & Zhao, H. (2018). Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metabolic Engineering, 50, 85-108.

Dowd, S. E., Mustroph, M. L., Romanova, E. V., Southey, B. R., Pinardo, H., Rhodes, J. S., & Sweedler, J. V. (2018). Exploring Exercise- and Context-Induced Peptide Changes in Mice by Quantitative Mass Spectrometry. ACS Omega, 3(10), 13817-13827.

Neumann, E. K., Comi, T. J., Spegazzini, N., Mitchell, J. W., Rubakhin, S., Gillette, M. L., ... Sweedler, J. V. (2018). Multimodal Chemical Analysis of the Brain by High Mass Resolution Mass Spectrometry and Infrared Spectroscopic Imaging. Analytical chemistry, 90(19), 11572-11580.

Mand, T. D., Kulkarni, G., & Metcalf, W. W. (2018). Genetic, biochemical, and molecular characterization of methanosarcina barkeri mutants lacking three distinct classes of hydrogenase. Journal of bacteriology, 200(20), [e00342].

Kelliher, J. L., Radin, J. N., & Kehl-Fie, T. (2018). PhoPR contributes to staphylococcus aureus Growth during phosphate starvation and pathogenesis in an environment- specific manner. Infection and immunity, 86(10), [e00371-18].

Hudson, G. A., & Mitchell, D. A. (2018). RiPP antibiotics: biosynthesis and engineering potential. Current Opinion in Microbiology, 45, 61-69.

An, L., Cogan, D. P., Navo, C. D., Jiménez-Osés, G., Nair, S. K., & van der Donk, W. A. (2018). Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Nature chemical biology, 14(10), 928-933.

Livezey, M., Huang, R., Hergenrother, P., & Shapiro, D. J. (2018). Strong and sustained activation of the anticipatory unfolded protein response induces necrotic cell death. Cell Death and Differentiation, 25(10), 1796-1807.

Si, T., Tian, Q., Min, Y., Zhang, L., Sweedler, J. V., van der Donk, W. A., & Zhao, H. (2018). Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli. Journal of the American Chemical Society, 140(38), 11884-11888.

Tasker, S. Z., Cowfer, A. E., & Hergenrother, P. (2018). Preparation of Structurally Diverse Compounds from the Natural Product Lycorine. Organic Letters, 20(18), 5894-5898.

O'Reilly, M. C., Dong, S. H., Rossi, F. M., Karlen, K. M., Kumar, R. S., Nair, S. K., & Blackwell, H. E. (2018). Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR. Cell chemical biology, 25(9), 1128-1139.e3.

Wang, P., Liang, J., Shi, L. Z., Wang, Y., Zhang, P., Ouyang, M., ... Wang, Y. (2018). Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding. ACS Photonics, 5(9), 3565-3574.

Kapoor, I., & Nair, S. K. (2018). Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin. Biochemistry, 57(36), 5282-5288.

Sweedler, J. V. (2018). Where Do Our Manuscripts Come From? Analytical chemistry, 90(17).

Lian, J., HamediRad, M., & Zhao, H. (2018). Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System. Biotechnology Journal, 13(9), [1700601].

Fine, J. D., Shpigler, H. Y., Ray, A. M., Beach, N. J., Sankey, A. L., Cash-Ahmed, A., ... Robinson, G. E. (2018). Quantifying the effects of pollen nutrition on honey bee queen egg laying with a new laboratory system. PloS one, 13(9), [e0203444].

McLaughlin, M. I., & van der Donk, W. A. (2018). Stereospecific Radical-Mediated B12-Dependent Methyl Transfer by the Fosfomycin Biosynthesis Enzyme Fom3. Biochemistry, 57(33), 4967-4971.

Lim, Y. H., Wong, F. T., Yeo, W. L., Ching, K. C., Lim, Y. W., Heng, E., ... Zhao, H. (2018). Auroramycin: A Potent Antibiotic from Streptomyces roseosporus by CRISPR-Cas9 Activation. ChemBioChem, 19(16), 1716-1719.

Litman, Z. C., Wang, Y., Zhao, H., & Hartwig, J. F. (2018). Cooperative asymmetric reactions combining photocatalysis and enzymatic catalysis. Nature, 560(7718), 355-359.

Peh, J., Boudreau, M. W., Smith, H. M., & Hergenrother, P. (2018). Overcoming Resistance to Targeted Anticancer Therapies through Small-Molecule-Mediated MEK Degradation. Cell chemical biology, 25(8), 996-1005.e4.

Romanova, E. V., & Sweedler, J. V. (2018). Animal Model Systems in Neuroscience. ACS Chemical Neuroscience, 9(8), 1869-1870.

Green, D. J., Huang, R. C., Sudlow, L., Hatcher, N., Potgieter, K., McCrohan, C., ... Gillette, R. (2018). CAMP, Ca2+, pHi, and NO Regulate H-like Cation Channels That Underlie Feeding and Locomotion in the Predatory Sea Slug Pleurobranchaea californica. ACS Chemical Neuroscience, 9(8), 1986-1993.

Atkins, N., Ren, S., Hatcher, N., Burgoon, P. W., Mitchell, J. W., Sweedler, J. V., & Gillette, M. L. (2018). Functional Peptidomics: Stimulus- and Time-of-Day-Specific Peptide Release in the Mammalian Circadian Clock. ACS Chemical Neuroscience, 9(8), 2001-2008.

Zhang, G., Yuan, W. D., Vilim, F. S., Romanova, E. V., Yu, K., Yin, S. Y., ... Jing, J. (2018). Newly Identified Aplysia SPTR-Gene Family-Derived Peptides: Localization and Function. ACS Chemical Neuroscience, 9(8), 2041-2053.

Sweedler, J. V. (2018). Where Is the Data? Analytical chemistry, 90(15).

Schwalen, C. J., Hudson, G. A., Kille, B., & Mitchell, D. A. (2018). Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics. Journal of the American Chemical Society, 140(30), 9494-9501.

Sales, M. J., Herbert, W. G., Du, Y., Sandur, A. S., Stanley, N. M., & Jensen, P. A. (2018). Complete genome sequences of streptococcus sobrinus SL1 (ATCC 33478 DSM 20742), NIDR 6715-7 (ATCC 27351), NIDR 6715-15 (ATCC 27352), and NCTC 10919 (ATCC 33402). Microbiology Resource Announcements, 7(3), [e00804-18].

Cao, X., Zhu, L., Song, X., Hu, Z., & Cronan, J. E. (2018). Protein moonlighting elucidates the essential human pathway catalyzing lipoic acid assembly on its cognate enzymes. Proceedings of the National Academy of Sciences of the United States of America, 115(30), E7063-E7072.

Gerlt, J. A. (2018). The Need for Manuscripts to Include Database Identifiers for Proteins. Biochemistry, 57(29), 4239-4240.

Cao, X., Koch, T., Steffens, L., Finkensieper, J., Zigann, R., Cronan, J. E., & Dahl, C. (2018). Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor. eLife, 7, [e37439].

Petronikolou, N., & Nair, S. K. (2018). Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters. ACS Catalysis, 8(7), 6334-6344.

Movassaghi, M., & van der Donk, W. A. (2018). Synthesis of Antibiotics and Related Molecules. Journal of Organic Chemistry, 83(13), 6826-6828.

Estrada, P., Morita, M., Hao, Y., Schmidt, E. W., & Nair, S. K. (2018). A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases. Journal of the American Chemical Society, 140(26), 8124-8127.

Weir, W. B., Fred, L. Y., Pike, M., Rubakhin, S., Ludwig, T. J., Shar, A. M., ... Sweedler, J. V. (2018). Expired Epinephrine Maintains Chemical Concentration and Sterility. Prehospital Emergency Care, 22(4), 414-418.

Kulkarni, G., Mand, T. D., & Metcalf, W. W. (2018). Energy conservation via hydrogen cycling in the methanogenic archaeon Methanosarcina barkeri. mBio, 9(4), [e01256-18].

Carter, M. S., Zhang, X., Huang, H., Bouvier, J. T., Francisco, B. S., Vetting, M. W., ... Gerlt, J. A. (2018). Functional assignment of multiple catabolic pathways for d-apiose article. Nature chemical biology, 14(7), 696-705.

Bao, Z., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., ... Zhao, H. (2018). Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nature Biotechnology, 36(6), 505-508.

Shi, S., Ang, E. L., & Zhao, H. (2018). In vivo biosensors: mechanisms, development, and applications. Journal of Industrial Microbiology and Biotechnology, 45(7), 491-516.

Katz, L., Chen, Y. Y., Gonzalez, R., Peterson, T. C., Zhao, H., & Baltz, R. H. (2018). Synthetic biology advances and applications in the biotechnology industry: a perspective. Journal of Industrial Microbiology and Biotechnology, 45(7), 449-461.

Shen, M., Qu, Z., Deslaurier, J., Welle, T. M., Sweedler, J. V., & Chen, R. (2018). Single Synaptic Observation of Cholinergic Neurotransmission on Living Neurons: Concentration and Dynamics. Journal of the American Chemical Society, 140(25), 7764-7768.

Drown, B. S., & Hergenrother, P. (2018). Going on offense against the gram-negative defense. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6530-6532.

Ongpipattanakul, C., & Nair, S. K. (2018). Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides. Biochemistry, 57(23), 3201-3209.

Li, B., Dunham, S. J. B., Ellis, J. F., Lange, J. D., Smith, J. R., Yang, N., ... Sweedler, J. V. (2018). A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms. Analytical chemistry, 90(11), 6725-6734.

Gerlt, J. A. (2018). Special Issue: Current Topics in Mechanistic Enzymology. Biochemistry, 57(22), 3085-3086.

Aguirre, M. Á., Long, K. D., Li, N., Manoto, S. L., & Cunningham, B. T. (2018). Detection and digital resolution counting of nanoparticles with optical resonators and applications in biosensing. Chemosensors, 6(2), [13].

Lian, J., Bao, Z., Hu, S., & Zhao, H. (2018). Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains. Biotechnology and bioengineering, 115(6), 1630-1635.

HamediRad, M., Lian, J., Li, H., & Zhao, H. (2018). RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization. Biotechnology and bioengineering, 115(6), 1552-1560.

Do, T. D., Ellis, J. F., Neumann, E. K., Comi, T. J., Tillmaand, E. G., Lenhart, A. E., ... Sweedler, J. V. (2018). Optically Guided Single Cell Mass Spectrometry of Rat Dorsal Root Ganglia to Profile Lipids, Peptides and Proteins. ChemPhysChem, 19(10), 1180-1191.

Checco, J. W., Zhang, G., Yuan, W. D., Yu, K., Yin, S. Y., Roberts-Galbraith, R. H., ... Sweedler, J. V. (2018). Molecular and Physiological Characterization of a Receptor for d -Amino Acid-Containing Neuropeptides. ACS chemical biology, 13(5), 1343-1352.

Morita, M., Hao, Y., Jokela, J. K., Sardar, D., Lin, Z., Sivonen, K., ... Schmidt, E. W. (2018). Post-Translational Tyrosine Geranylation in Cyanobactin Biosynthesis. Journal of the American Chemical Society, 140(19), 6044-6048.

Anapindi, K. D. B., Romanova, E. V., Southey, B. R., & Sweedler, J. V. (2018). Peptide identifications and false discovery rates using different mass spectrometry platforms. Talanta, 182, 456-463.

Hegemann, J. D., & van der Donk, W. A. (2018). Investigation of Substrate Recognition and Biosynthesis in Class IV Lanthipeptide Systems. Journal of the American Chemical Society, 140(17), 5743-5754.

Sweedler, J. V. (2018). A Resource for Our Reagents: ACS Reagent Chemicals. Analytical Chemistry, 90(9).

Li, L., Andrén, P. E., & Sweedler, J. V. (2018). Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry—Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS. Journal of the American Society for Mass Spectrometry, 29(5), 801-806.

Monroe, E. B., Annangudi, S. P., Wadhams, A. A., Richmond, T. A., Yang, N., Southey, B. R., ... Sweedler, J. V. (2018). Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 29(5), 923-934.

Hu, Z., Dong, H., Ma, J. C., Yu, Y., Li, K. H., Guo, Q. Q., ... Wang, H. (2018). Novel Xanthomonas campestris long-chain-specific 3-oxoacyl- acyl carrier protein reductase involved in diffusible signal factor synthesis. mBio, 9(3), [e00596-18].

Dunham, S. J. B., Ellis, J. F., Baig, N. F., Morales-Soto, N., Cao, T., Shrout, J. D., ... Sweedler, J. V. (2018). Quantitative SIMS Imaging of Agar-Based Microbial Communities. Analytical chemistry, 90(9), 5654-5663.

Greenwood, M. P., Greenwood, M., Romanova, E. V., Mecawi, A. S., Paterson, A., Sarenac, O., ... Murphy, D. (2018). The effects of aging on biosynthetic processes in the rat hypothalamic osmoregulatory neuroendocrine system. Neurobiology of Aging, 65, 178-191.

Hetrick, K. J., Walker, M. C., & van der Donk, W. A. (2018). Development and Application of Yeast and Phage Display of Diverse Lanthipeptides. ACS Central Science, 4(4), 458-467.

Parkinson, E. I., Tryon, J. H., Goering, A. W., Ju, K. S., McClure, R. A., Kemball, J. D., ... Metcalf, W. W. (2018). Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. ACS chemical biology, 13(4), 1029-1037.

Kakkar, N., Perez, J. G., Liu, W. R., Jewett, M. C., & van der Donk, W. A. (2018). Incorporation of Nonproteinogenic Amino Acids in Class i and II Lantibiotics. ACS chemical biology, 13(4), 951-957.

Limsakul, P., Peng, Q., Wu, Y., Allen, M. E., Liang, J., Remacle, A. G., ... Wang, Y. (2018). Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface. Cell chemical biology, 25(4), 370-379.e4.

Petronikolou, N., Hollatz, A. J., Schuler, M. A., & Nair, S. K. (2018). Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside. ChemBioChem, 19(8), 784-788.

Trobe, M., & Burke, M. (2018). The Molecular Industrial Revolution: Automated Synthesis of Small Molecules. Angewandte Chemie - International Edition, 57(16), 4192-4214.

Yang, N., Anapindi, K. D. B., Rubakhin, S., Wei, P., Yu, Q., Li, L., ... Sweedler, J. V. (2018). Neuropeptidomics of the Rat Habenular Nuclei. Journal of Proteome Research, 17(4), 1463-1473.

Yang, X., Lennard, K. R., He, C., Walker, M. C., Ball, A. T., Doigneaux, C., ... van der Donk, W. A. (2018). A lanthipeptide library used to identify a protein-protein interaction inhibitor article. Nature chemical biology, 14(4), 375-380.

Sun, H., Zhang, H., Ang, E. L., & Zhao, H. (2018). Biocatalysis for the synthesis of pharmaceuticals and pharmaceutical intermediates. Bioorganic and Medicinal Chemistry, 26(7), 1275-1284.

Wei, Y., Ang, E. L., & Zhao, H. (2018). Recent developments in the application of P450 based biocatalysts. Current Opinion in Chemical Biology, 43, 1-7.

Della Ripa, L. A., Petros, Z. A., Cioffi, A. G., Piehl, D. W., Courtney, J. M., Burke, M. D., & Rienstra, C. M. (2018). Solid-State NMR of highly 13 C-enriched cholesterol in lipid bilayers Methods, 138-139, 47-53.

Repka, L. M., Hetrick, K. J., Chee, S. H., & van der Donk, W. A. (2018). Characterization of Leader Peptide Binding during Catalysis by the Nisin Dehydratase NisB. Journal of the American Chemical Society, 140(12), 4200-4203.

Mahanta, N., Liu, A., Dong, S., Nair, S. K., & Mitchell, D. A. (2018). Enzymatic reconstitution of ribosomal peptide backbone thioamidation. Proceedings of the National Academy of Sciences of the United States of America, 115(12), 3030-3035.

Davis, R. G., Park, H. M., Kim, K., Greer, J. B., Fellers, R. T., Leduc, R. D., ... Kelleher, N. L. (2018). Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms between Mouse Strains. Analytical chemistry, 90(6), 3802-3810.

Ulrich, E. C., Bougioukou, D. J., & van der Donk, W. A. (2018). Investigation of Amide Bond Formation during Dehydrophos Biosynthesis. ACS chemical biology, 13(3), 537-541.

Eriksen, D. T., Chao, R., & Zhao, H. (2018). Applying advanced dna assembly methods to generate pathway libraries. In Synthetic Biology: Parts, Devices and Applications (pp. 331-347). Wiley-VCH Verlag.

Sweedler, J. V. (2018). Who Are Your Coauthors? Make Sure to Follow Appropriate Practices. Analytical chemistry, 90(5), 2977-2978.

Wang, Y., Ren, H., & Zhao, H. (2018). Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Critical Reviews in Biochemistry and Molecular Biology, 53(2), 115-129.

Sweedler, J. V. (2018). The ACS Measurement Journals, the Analytical Division, and Pittcon 2018: A Busy Four Days. Analytical chemistry, 90(4).

Race, C. M., Kwon, L. E., Foreman, M. T., Huang, Q., Inan, H., Kesiraju, S., ... Cunningham, B. T. (2018). An Automated Microfluidic Assay for Photonic Crystal Enhanced Detection and Analysis of an Antiviral Antibody Cancer Biomarker in Serum. IEEE Sensors Journal, 18(4), 1464-1473. [8119803].

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., ... Zhang, B. (2018). How many human proteoforms are there? Nature chemical biology, 14(3), 206-214.

Liu, J. N., Huang, Q., Liu, K. K., Singamaneni, S., & Cunningham, B. T. (2018). Nanoantenna-microcavity hybrid resonators with highly cooperative plasmonic-photonic coupling. In 2017 IEEE Photonics Conference (IPC) Part II (Vol. 2018-January, pp. 1-2). Institute of Electrical and Electronics Engineers Inc..

Wan, Y., Carlson, J. A., Al-Mulla, S. A., Peng, W., Long, K. D., Kesler, B. A., ... Cunningham, B. T. (2018). Integrated spectroscopic analysis system with low vertical height for measuring liquid or solid assays. Sensors and Actuators, B: Chemical, 255, 935-943.

Besold, A. N., Gilston, B. A., Radin, J. N., Ramsoomair, C., Culbertson, E. M., Li, C. X., ... Culotta, V. C. (2018). Role of calprotectin in withholding zinc and copper from Candida albicans. Infection and immunity, 86(2), [e00779-17].

Calhoun, S., Korczynska, M., Wichelecki, D. J., San Francisco, B., Zhao, S., Rodionov, D. A., ... Sali, A. (2018). Prediction of enzymatic pathways by integrative pathway mapping. eLife, 7, [e31097].

Cao, X., Hong, Y., Zhu, L., Hu, Y., & Cronan, J. E. (2018). Development and retention of a primordial moonlighting pathway of protein modification in the absence of selection presents a puzzle. Proceedings of the National Academy of Sciences of the United States of America, 115(4), 647-655.

Qi, M., Philip, M. C., Yang, N., & Sweedler, J. V. (2018). Single Cell Neurometabolomics. ACS Chemical Neuroscience, 9(1), 40-50.

Cunningham, B. T., Long, K. D., Yu, H., Chen, W., Sun, F., Ornob, A., ... Bashir, R. (2018). Mobile biosensing using the sensing capabilities of smartphone cameras. In 2017 IEEE MTT-S International Microwave Workshop Series on Advanced Materials and Processes for RF and THz Applications, IMWS-AMP 2017 (pp. 1-3). (2017 IEEE MTT-S International Microwave Workshop Series on Advanced Materials and Processes for RF and THz Applications, IMWS-AMP 2017; Vol. 2018-January). Institute of Electrical and Electronics Engineers Inc..

Manandhar, M., & Cronan, J. E. (2018). A canonical biotin synthesis enzyme, 8-amino-7- oxononanoate synthase (BioF), utilizes different acyl chain donors in Bacillus subtilis and Escherichia coli. Applied and environmental microbiology, 84(1), [e02084-17].

Sun, H., Zhao, H., & Ang, E. L. (2018). A coupled chlorinase-fluorinase system with a high efficiency of trans -halogenation and a shared substrate tolerance. Chemical Communications, 54(68), 9458-9461.

Kelliher, J. L., Radin, J. N., Grim, K. P., Solórzano, P. K. P., Degnan, P., & Kehl-Fie, T. (2018). Acquisition of the phosphate transporter NptA enhances Staphylococcus aureus pathogenesis by improving phosphate uptake in divergent environments. Infection and immunity, 86(1), [e00631-17].

Welle, T. M., Alanis, K., Colombo, M. L., Sweedler, J. V., & Shen, M. (2018). A high spatiotemporal study of somatic exocytosis with scanning electrochemical microscopy and nanoITIES electrodes. Chemical Science, 9(22), 4937-4941.

Checco, J. W., Zhang, G., Yuan, W. D., Le, Z. W., Jing, J., & Sweedler, J. V. (2018). Aplysia allatotropin-related peptide and its newly identified D-amino acid-containing epimer both activate a receptor and a neuronal target. Journal of Biological Chemistry, 293(43), 16862-16873.

Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L., & Sweedler, J. V. (2018). Bioinformatics for prohormone and neuropeptide discovery. In Methods in Molecular Biology (pp. 71-96). (Methods in Molecular Biology; Vol. 1719). Humana Press Inc..

Do, T. D., Checco, J. W., Tro, M., Shea, J. E., Bowers, M. T., & Sweedler, J. V. (2018). Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of: Aplysia californica involved in the feeding circuit. Physical Chemistry Chemical Physics, 20(34), 22047-22057.

Jensen, P. A. (2018). Coupling fluxes, enzymes, and regulation in genome-scale metabolic models. In Methods in Molecular Biology (pp. 337-351). (Methods in Molecular Biology; Vol. 1716). Humana Press Inc..

Tasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., ... Zhao, H. (2018). CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic acids research, 46(17), [e100].

Storm, A. J., & Jensen, P. A. (2018). Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites. Biotechnology Journal, 13(1), [1700326].

Hegemann, J. D., Schwalen, C. J., Mitchell, D. A., & van der Donk, W. A. (2018). Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin. Chemical Communications, 54(65), 9007-9010.

Yien, Y. Y., Shi, J., Chen, C., Cheung, J. T. M., Grillo, A. S., Shrestha, R., ... Paw, B. H. (2018). FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity. Journal of Biological Chemistry, 293(51), 19797-19811.

Nayak, D. D., & Metcalf, W. W. (2018). Genetic techniques for studies of methyl-coenzyme M reductase from Methanosarcina acetivorans C2A. In F. Armstrong (Ed.), Methods in Enzymology (pp. 325-347). (Methods in Enzymology; Vol. 613). Academic Press Inc..

Dutta, D., Lai, K. Y., Reyes-Ordoñez, A., Chen, J., & van der Donk, W. A. (2018). Lanthionine synthetase C-like protein 2 (LanCL2) is important for adipogenic differentiation. Journal of Lipid Research, 59(8), 1433-1445.

Schultz, C., Lian, J., & Zhao, H. (Accepted/In press). Metabolic Engineering of Saccharomyces cerevisiae Using a Trifunctional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion. Methods in Enzymology.

Ongpipattanakul, C., & Nair, S. K. (Accepted/In press). Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chemical Biology.

Tai, H. C., Checco, J. W., & Sweedler, J. V. (2018). Non-targeted identification of d-amino acid-containing peptides through enzymatic screening, chiral amino acid analysis, and LC-MS. In Methods in Molecular Biology (pp. 107-118). (Methods in Molecular Biology; Vol. 1719). Humana Press Inc..

Garcia-Ruiz, E., HamediRad, M., & Zhao, H. (2018). Pathway design, engineering, and optimization. In Advances in Biochemical Engineering/Biotechnology (Advances in Biochemical Engineering/Biotechnology; Vol. 162). Springer Science and Business Media Deutschland GmbH.

Goettge, M. N., Cioni, J. P., Ju, K. S., Pallitsch, K., & Metcalf, W. W. (2018). PcxL and HpxL are flavin-dependent, oxime-forming N-oxidases in phosphonocystoximic acid biosynthesis in Streptomyces. Journal of Biological Chemistry, 293(18), 6859-6868.

Cunningham, B. T., Liu, J. N., Huang, Q., Canady, T., Long, K. D., Li, N., ... Singamaneni, S. (2018). Photonic crystal resonant coupling to nanoantennas and applications for digital resolution biosensing. In Microscopy Histopathology and Analytics, MICROSCOPY 2018 (Vol. Part F89-MICROSCOPY 2018). OSA - The Optical Society.

Zhuo, Y., Choi, J. S., Marin, T., Yu, H., Harley, B. A., & Cunningham, B. T. (2018). Photonic resonator outcoupler microscopy (PROM) for quantitative monitoring of stem cell focal adhesion area. In Frontiers in Optics, FIO 2018 (Vol. Part F114-FIO 2018). OSA - The Optical Society.

Ren, H., Biswas, S., Ho, S., van der Donk, W. A., & Zhao, H. (Accepted/In press). Rapid Discovery of Glycocins through Pathway Refactoring in Escherichia coli. ACS Chemical Biology.

Liu, J. N., Huang, Q., Liu, K. K., Singamaneni, S., & Cunningham, B. T. (2018). Resonant coupling from photonic crystal surfaces to plasmonic nanoantennas: Principles, detection instruments, and applications in digital resolution biosensing. In S. He, E-H. Lee, & S. He (Eds.), Smart Photonic and Optoelectronic Integrated Circuits XX (Vol. 10536). [105361O] SPIE.

Cunningham, B. T., Long, K. D., Woodburn, E., Wan, Y., Carlson, J., Su, P., ... Dallesasse, J. M. (2018). Smartphone spectroscopy for mobile health diagnostics with laboratory-equivalent capabilities. In M. A. Druy, S. M. Barnett, L. T. M. Profeta, R. A. Crocombe, & A. K. Azad (Eds.), Next-Generation Spectroscopic Technologies XI (Vol. 10657). [1065702] SPIE.

Morales-Soto, N., Dunham, S. J. B., Baig, N. F., Ellis, J. F., Madukoma, C. S., Bohn, P. W., ... Shrout, J. D. (2018). Spatially dependent alkyl quinolone signaling responses to antibiotics in Pseudomonas aeruginosa swarms. Journal of Biological Chemistry, 293(24), 9544-9552.

Cogan, D. P., Baraquet, C., Harwood, C. S., & Nair, S. K. (2018). Structural basis of transcriptional regulation by cour, a repressor of coumarate catabolism, in rhodopseudomonas palustris. Journal of Biological Chemistry, 293(30), 11727-11735.

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P., ... Shapiro, D. J. (2018). Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response. Oncotarget, 9(19), 14741-14753.

Gu, W., Dong, S. H., Sarkar, S., Nair, S. K., & Schmidt, E. W. (2018). The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis. In B. S. Moore (Ed.), Methods in Enzymology (pp. 113-163). (Methods in Enzymology; Vol. 604). Academic Press Inc..

Bobeica, S. C., & van der Donk, W. A. (2018). The Enzymology of Prochlorosin Biosynthesis. In B. S. Moore (Ed.), Methods in Enzymology (pp. 165-203). (Methods in Enzymology; Vol. 604). Academic Press Inc..

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