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( 1.) *Hillman, A.S.; *Hyland, S.N.; *Wodzanowski, K.A.; Moore, D.L.; Ratna, S.; Jemas, A.;Sandles, L.M.; Chaya, T.; Ghosh, A.; Fox, J.M.; Grimes, C.L.; Minimalist Tetrazine N-Acetyl Muramic Acid Proes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion. JACS ASAP 2024


(1) Fu, Q, Lee, Y.S., Green, E.A., Wang, Y, Park, S.Y., Polanco, A, Lee, K.H., Betenbaugh, M, McNally, D, Yoon, S. Design space determination to optimize DNA complexation and full capsid formation in transient rAAV manufacturing. Biotechnology and Bioengineering,120,11, 3148-3162 (2023).

(2) Green, E.A., Hamaker, N.K. & Lee, K.H. Comparison of vector elements and process conditions in transient and stable suspension HEK293 platforms using SARS-CoV-2 receptor binding domain as a model protein. BMC Biotechnology, 23, 7 (2023).

(3) Irvin-Choy, N’dea S.*, Katherine M. Nelson*, Jason P. Gleghorn, and Emily S. Day. Delivery and short-term maternal and fetal safety of vaginally administered PEG-PLGA nanoparticles. Drug Deliv. and Transl. Res. 13, 3003–3013 (2023). *indicates co-first author

(4) D’Oliviera, Angel. Dai, Xuhang. Mottaghinia, Saba. Geissler, Evan. Etienne, Lucie. Zhang, Yingkai. Mugridge, Jeffrey. (2023). Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. eLife.

(5) Rasool RU, O’Connor C, Das CK, Alhusayan M, Verma BK, Frohner IE, Deng Q, Mitchell-Velasquez E, Sangodkar J, Ahmed A, Islam S, Linauer S, Mudrak I, Rainey J, Zawacki KP, Suhan TK, Rebernick R, Natesan R, Siddiqui J, Sauter G, Thomas D, Wang S, Taylor DJ, Simon R, Cieslik M, Busino L, Chinnaiyan AM, Ogris E, Narla G, Asangani IA. “Loss of LCMT1 and biased protein phosphatase 2A heterotrimerization drive prostate cancer progression and therapy resistance.” Nature Communications 14, 5253 (2023).

(6) Sudduth E. R. , Trautmann-Rodriguez M, Gill N, Bomb K, Fromen CA. Aerosol pulmonary immune engineering. Advanced Drug Delivery Reviews. (2023);199:114831. doi: PMCID: PMC10527166

 (7) Sudduth E. R., Kolewe EL, Graf J, Yu Y, Somma J, Fromen CA. Nebulization of model hydrogel nanoparticles to macrophages at the air-liquid interface. Frontiers in Chemical Engineering. (2023);4. doi: 10.3389/fceng.2022.1086031. PMCID: PMC10586456

(8) Bria Garcia, Jessica Sampson, Mary P. Watson, Dipannita Kalyani. “Primary vs. secondary alkylpyridinium salts: a comparison under electrochemical and chemical reduction conditions.” Faraday Discussions 2023247 (0), 324-332, 10.1039/D3FD00120B. DOI: 10.1039/D3FD00120B

(9) J. Cameron Twitty, Yun Hong, Bria Garcia, Stephanie Tsang, Danielle M. Schultz, Jennifer Hanisak, Susan L. Zultanski, Amelie Dion, Dipannita Kalyani, Mary P. Watson. “Diversifying Amino Acids and Peptides via Deaminative Reductive Cross-Couplings Leveraging High-Throughput Experimentation.” Journal of the American Chemical Society 2023145 (10), 5684-5695. DOI: 10.1021/jacs.2c11451.

(10) Allyssa M. Conner, Sarah B. Pawley, Humair B. Omer, Donald A. Watson. Development of a General Method for the Hiyama–Denmark Cross Coupling of Tetrasubstituted Vinyl Silanes. ACS Catal. 2022, 12, 13108-13115.

(11) Ghosh, S.; Ahearn, C.P.; Isabella, C.R.; Marando, V.M.; Dodge, G.J.; Bartlett, H.; McPherson, R.L.; Dugan, A.; Jain, S.; Neznanova, L.; Tettelin, H.; Putnik, R.; Grimes, C.L.; Ruhl, S.; Kiessling, K.L.; Imperiali, B. Human oral Lectin ZG16B Acts as a Cell Wall Polysaccharide Probe to Decode Host-Microbe Interactions with Oral Commensals. PNAS 2023, 120, e2216304120.

(12) Chen, S.*; Putnik, R.*; and Li, X.*; Liu, S.; Zhou, J.; Guo, L.; Xu, L.; Temme, J. S.; Bersch, K.; Gildersleeve, J. C.; Grimes, C. L.; Reinecker, H.-C. “PGLYRP-1: Intracellular Receptor for GMTP that Controls Innate Immunity and Mucosal Recovery.” Sneak Peek available. (* denotes co-first author).

(13) Grunow A.L., Carroll S.C., Kreiman A.N. and Sutherland M.C. (2023) Structure-function analysis of the heme-binding WWD domain in the bacterial holocytochrome c synthase, CcmFH. mBio 10.1128/mbio.01509-23 


Clupper, Michael, Rachael Gill, Malek Elsayyid, Denis Touroutine, Jeffrey L. Caplan, and Jessica E. Tanis. “Kinesin-2Motors Differentially Impact Biogenesis of Extracellular Vesicle Subpopulations Shed from Sensory Cilia.” IScience 25, no. 11 (November 2022): 105262.

———. “Kinesin-II Motors Differentially Impact Biogenesis of Distinct Extracellular Vesicle Subpopulations Shedfrom C. Elegans Sensory Cilia.” Preprint. Cell Biology, December 19, 2021.

Crump, Geneva Maddison, Sharon Rozovsky, and Catherine L. Grimes. “Purification and Characterization of a Stable,Membrane-Associated Peptidoglycan Responsive Adenylate Cyclase LRR Domain from Human Commensal Candida Albicans.” Biochemistry, July 11, 2022, acs.biochem.2c00305.

Dang, Megan N., Elise C. Hoover, Mackenzie A. Scully, Eric H. Sterin, and Emily S. Day. “Antibody Nanocarriers forCancer Management.” Current Opinion in Biomedical Engineering 19 (September 2021): 100295.

Hunt, Victoria M., and Wilfred Chen. “A MicroRNA-Gated ThgRNA Platform for Multiplexed Activation of GeneExpression in Mammalian Cells.” Chemical Communications 58, no. 42 (2022): 6215–18.

———. “Deciphering the Design Rules of Toehold-Gated SgRNA for Conditional Activation of Gene Expression andProtein Degradation in Mammalian Cells.” ACS Synthetic Biology 11, no. 1 (January 21, 2022): 397–405.

Kraus, Jodi, Ryan W. Russell, Elena Kudryashova, Chaoyi Xu, Nidhi Katyal, Juan R. Perilla, Dmitri S. Kudryashov, and Tatyana Polenova. “Magic Angle Spinning NMR Structure of Human Cofilin-2 Assembled on ActinFilaments Reveals Isoform-Specific Conformation and Binding Mode.” Nature Communications 13, no. 1 (April 19, 2022): 2114.

Lieser, Rachel M., Emily J. Hartzell, Daniel Yur, Millicent O. Sullivan, and Wilfred Chen. “EGFR Ligand Clustering on E2 Bionanoparticles for Targeted Delivery of Chemotherapeutics to Breast Cancer Cells.” Bioconjugate Chemistry 33, no. 3 (March 16, 2022): 452–62.

Lo, Chun-Yuan, Yuhang Wu, Elorm Awuyah, Dilara Meli, Dan My Nguyen, Ruiheng Wu, Bohan Xu, et al. “Influence of the Molecular Weight and Size Distribution of PSS on Mixed Ionic-Electronic Transport in PEDOT:PSS.”Polymer Chemistry 13, no. 19 (2022): 2764–75.

Martin, Shea, Gil Repa, Robert Hamburger, Craig Pointer, Kaytlin Ward, Trong-Nhan Pham, Maxwell Martin, JoelRosenthal, Lisa Fredin, and Elizabeth Young. “Elucidation of Complex Triplet Excited State Dynamics in Pd(II)Biladiene Tetrapyrroles.” Preprint. Chemistry, May 5, 2022.

Mitkas, Alexander A., Mauricio Valverde, and Wilfred Chen. “Dynamic Modulation of Enzyme Activity by Synthetic CRISPR–Cas6 Endonucleases.” Nature Chemical Biology 18, no. 5 (May 2022): 492–500.

Pawley, Sarah B., Allyssa M. Conner, Humair M. Omer, and Donald A. Watson. “Development of a General Methodfor the Hiyama–Denmark Cross-Coupling of Tetrasubstituted Vinyl Silanes.” ACS Catalysis 12, no. 20 (October 21, 2022): 13108–15.

Roh, Esther H, Catherine A Fromen, and Millicent O Sullivan. “Inhalable MRNA Vaccines for Respiratory Diseases: A Roadmap.” Current Opinion in Biotechnology 74 (April 2022): 104–9.

Roh, Esther H., Millicent O. Sullivan, and Thomas H. Epps. “A Kinetic Modeling Platform for Predicting the Efficacy of SiRNA Formulations in Vitro and in Vivo.” Preprint. Bioengineering, June 6, 2022.

Rourke, Christine, and Aimee Jaramillo-Lambert. “TOP-2 Is Differentially Required for the Proper Maintenance of the Cohesin Subunit REC-8 on Meiotic Chromosomes in Caenorhabditis Elegans Spermatogenesis and Oogenesis.”Edited by J Engebrecht. Genetics 222, no. 2 (September 30, 2022): iyac120.

Stork, Devon, Michaela Jones, Ethan C Garner, and Aditya Kunjapur. “Incorporation of a Chemically Diverse Set ofNon-Standard Amino Acids into a Gram-Positive Organism.” BIO-PROTOCOL 12, no. 17 (2022).

Wodzanowski, Kimberly A., Jeffrey L. Caplan, April M. Kloxin, and Catherine L. Grimes. “Multiscale Invasion Assay for Probing Macrophage Response to Gram-Negative Bacteria.” Frontiers in Chemistry 10 (February 15, 2022): 842602.

Wodzanowski, Kimberly A., Stephen N. Hyland, Sreedevi Chinthamani, Liam-Michael D. Sandles, Kiyonobu Honma,Ashu Sharma, and Catherine L. Grimes. “Investigating Peptidoglycan Recycling Pathways in Tannerella Forsythia with -Acetylmuramic Acid Bioorthogonal Probes.” ACS Infectious Diseases 8, no. 9 (September 9, 2022): 1831–38.


(1) Berckman, Emily A., and Wilfred Chen. “Self‐assembling Protein Nanocages for Modular Enzyme Assembly by Orthogonal Bioconjugation.” Biotechnology Progress, July 2, 2021. 

(2) Bersch, Klare L., Kristen E. DeMeester, Rachid Zagani, Shuyuan Chen, Kimberly A. Wodzanowski, Shuzhen Liu, Siavash Mashayekh, Hans-Christian Reinecker, and Catherine L. Grimes. “Bacterial Peptidoglycan Fragments Differentially Regulate Innate Immune Signaling.” ACS Central Science 7, no. 4 (April 28, 2021): 688–96. 

(3) Brown, Ashley R., Kimberly A. Wodzanowski, Cintia C. Santiago, Stephen N. Hyland, Julianna L. Follmar, PapaNii Asare-Okai, and Catherine Leimkuhler Grimes. “Protected N-Acetyl Muramic Acid Probes Improve Bacterial Peptidoglycan Incorporation via Metabolic Labeling.” ACS Chemical Biology, September 10, 2021, acschembio.1c00268. 

(4) Green, Erica A, and Kelvin H Lee. “Analytical Methods to Characterize Recombinant Adeno-Associated Virus Vectors and the Benefit of Standardization and Reference Materials.” Current Opinion in Biotechnology 71 (October 2021): 65–76. 

(5) Gregory, Gwendolyn J., Katherine E. Boas, and E. Fidelma Boyd. “The Organosulfur Compound Dimethylsulfoniopropionate (DMSP) Is Utilized as an Osmoprotectant by Vibrio Species.” Edited by Eric V. Stabb. Applied and Environmental Microbiology 87, no. 5 (February 12, 2021). 

(6) Hartzell, Emily J., Justin Terr, and Wilfred Chen. “Engineering a Blue Light Inducible SpyTag System (BLISS).” Journal of the American Chemical Society 143, no. 23 (June 16, 2021): 8572–77. 

(7) Hilderbrand, Amber M., Phillip A. Taylor, Francesca Stanzione, Mark LaRue, Chen Guo, Arthi Jayaraman, and April M. Kloxin. “Combining Simulations and Experiments for the Molecular Engineering of Multifunctional Collagen Mimetic Peptide-Based Materials.” Soft Matter 17, no. 7 (2021): 1985–98. 

(8) Irvin-Choy, N’Dea S., Katherine M. Nelson*, Megan N. Dang, Jason P. Gleghorn, and Emily S. Day. “Gold Nanoparticle Biodistribution in Pregnant Mice Following Intravenous Administration Varies with Gestational Age.” Nanomedicine: Nanotechnology, Biology and Medicine 36 (August 2021): 102412. -indicates co-first author

(9) Jarai, Bader M., Zachary Stillman, Kartik Bomb, April M. Kloxin, and Catherine A. Fromen. “Biomaterials-Based Opportunities to Engineer the Pulmonary Host Immune Response in COVID-19.” ACS Biomaterials Science & Engineering 7, no. 5 (May 10, 2021): 1742–64. 

(10) Jarai, Bader M., Zachary Stillman, and Catherine A. Fromen. “Hydrogel Nanoparticle Degradation Influences the Activation and Survival of Primary Macrophages.” Journal of Materials Chemistry B 9, no. 35 (2021): 7246–57. 

(11) Jemas, Andrew, Yixin Xie, Jessica Pigga, Jeffrey Caplan, Christopher am Ende, and Joseph Fox. “Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally-Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light.” Preprint. Chemistry, October 1, 2021. 

(12) Kunjapur, Aditya M., Michael G. Napolitano, Eriona Hysolli, Karen Noguera, Evan M. Appleton, Max G. Schubert, Michaela A. Jones, Siddharth Iyer, Daniel J. Mandell, and George M. Church. “Synthetic Auxotrophy Remains Stable after Continuous Evolution and in Coculture with Mammalian Cells.” Science Advances 7, no. 27 (July 2, 2021): eabf5851. 

(13) Noll, Rebecca R., Colleen M. Pike, Stephanie S. Lehman, Chad D. Williamson, and M. Ramona Neunuebel. “Legionella Pneumophila Targets Autophagosomes and Promotes Host Autophagy during Late Infection.” Preprint. Microbiology, July 9, 2021. 

(14) Pigga, Jessica E., Julia E. Rosenberger, Andrew Jemas, Samantha J. Boyd, Olga Dmitrenko, Yixin Xie, and Joseph M. Fox. “General, Divergent Platform for Diastereoselective Synthesis of Trans ‐Cyclooctenes with High Reactivity and Favorable Physiochemical Properties**.” Angewandte Chemie International Edition 60, no. 27 (June 25, 2021): 14975–80. 

(15) Roh, Esther H., Thomas H. Epps, and Millicent O. Sullivan. “Kinetic Modeling to Accelerate the Development of Nucleic Acid Formulations.” ACS Nano 15, no. 10 (October 26, 2021): 16055–66. 

(16) Rourke, Christine, Darline Murat, Tyler J. Hansen, and Aimee Jaramillo-Lambert. “Endogenous Localization of TOP-2 in C. Elegans Using a C-Terminal GFP-Tag.” MicroPublication BIOLOGY, Open Access, May 28, 2021. 

(17) Spahn, Philipp N., Xiaolin Zhang, Qing Hu, Nathaniel K. Hamaker, Hooman Hefzi, Shangzhong Li, Chih-Chung Kuo, et al. “Restoration of Deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells.” Preprint. Cell Biology, January 7, 2021. 

(18) Spahn, Philipp, Xiaolin Zhang, Qing Hu, Nathaniel Hamaker, Hooman Hefzi, Shangzhong Li, Chih-Chung Kuo, et al. “Restoration of Deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells.” Preprint. In Review, January 6, 2021. 

(19) Taylor, Jennifer A., Cintia C. Santiago, Joe Gray, Kimberly A. WodzanowskiKristen E. DeMeester, Jacob Biboy, Waldemar Vollmer, Catherine L. Grimes, and Nina R. Salama. “Localizing Peptidoglycan Synthesis in Helicobacter Pylori Using Clickable Metabolic Probes.” Current Protocols 1, no. 4 (April 2021). 

(20) Taylor, Phillip A., and Arthi Jayaraman. “Molecular Modeling and Simulations of Peptide–Polymer Conjugates.” Annual Review of Chemical and Biomolecular Engineering 11, no. 1 (June 7, 2020): 257–76. 

(21) Tcyrulnikov, Sergei, Qiuqi Cai, J. Cameron Twitty, Jianyu Xu, Abderrahman Atifi, Olivia P. Bercher, Glenn P. A. Yap, Joel Rosenthal, Mary P. Watson, and Marisa C. Kozlowski. “Dissection of Alkylpyridinium Structures to Understand Deamination Reactions.” ACS Catalysis 11, no. 14 (July 16, 2021): 8456–66. 

(22) Wang, Chuanqi, He Zhang, Tao Zhang, Xiaoyu Zou, Hui Wang, Julia E. Rosenberger, Raghu Vannam, et al. “Enabling in Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts.” Journal of the American Chemical Society 143, no. 28 (July 21, 2021): 10793–803. 

(23) Wannier, Timothy M., Peter N. Ciaccia, Andrew D. Ellington, Gabriel T. Filsinger, Farren J. Isaacs, Kamyab Javanmardi, Michaela A. Jones, et al. “Recombineering and MAGE.” Nature Reviews Methods Primers 1, no. 1 (December 2021): 7. 

(24) Xu, Jianyu, J. Cameron Twitty, and Mary P. Watson. “Nickel-Catalyzed Deaminative Cyanation: Nitriles and One-Carbon Homologation from Alkyl Amines.” Organic Letters 23, no. 16 (August 20, 2021): 6242–45. 

(25) Yang, Xinxing, Ryan McQuillen, Zhixin Lyu, Polly Phillips-Mason, Ana De La Cruz, Joshua W. McCausland, Hai Liang, Kristen E. DeMeester, Cintia C. Santiago, Catherine Grimes, et al. “A Two-Track Model for the Spatiotemporal Coordination of Bacterial Septal Cell Wall Synthesis Revealed by Single-Molecule Imaging of FtsW.” Nature Microbiology 6, no. 5 (May 2021): 584–93. 


(1) Berckman, Emily A., and Wilfred Chen. “A Modular Approach for DCas9-Mediated Enzyme Cascading viaOrthogonal Bioconjugation.” Chemical Communications 56, no. 77 (2020): 11426–28.

(2) Berckman, Emily A., Emily J. Hartzell, Alexander A. Mitkas, Qing Sun, and Wilfred Chen. “Biological Assembly of Modular Protein Building Blocks as Sensing, Delivery, and Therapeutic Agents.” Annual Review of Chemical and Biomolecular Engineering 11, no. 1 (June 7, 2020): 35–62.

(3) Bhandari, Nirajan, Christine Rourke, Thomas Wilmoth, Alekya Bheemreddy, David Schulman, Dina Collins, Harold E. Smith, Andy Golden, and Aimee Jaramillo-Lambert. “Identification of Suppressors of Top-2Embryonic Lethality in Caenorhabditis Elegans.” G3: Genes|Genomes|Genetics 10, no. 4 (April 2020): 1183–91.

(4) Brown, Ashley R., Rebecca A. Gordon, Stephen N. Hyland, M. Sloan Siegrist, and Catherine L. Grimes. “Chemical Biology Tools for Examining the Bacterial Cell Wall.” Cell Chemical Biology 27, no. 8 (August 2020): 1052–62.

(5) Chen, Rebecca P, Victoria M Hunt, Alexander A Mitkas, Ka-Hei Siu, and Wilfred Chen. “Controlling Metabolic Flux by Toehold-Mediated Strand Displacement.” Current Opinion in Biotechnology 66 (December 2020): 150–57.

(6) Crump, Geneva Maddison, Junhui Zhou, Siavash Mashayekh, and Catherine L. Grimes. “Revisiting Peptidoglycan Sensing: Interactions with Host Immunity and Beyond.” Chemical Communications 56, no. 87 (2020): 13313–22.

(7) Dang, Megan N., Carolina Gomez Casas, and Emily S. Day. “Photoresponsive MiR-34a/Nanoshell Conjugates Enable Light-Triggered Gene Regulation to Impair the Function of Triple-Negative Breast Cancer Cells.” Nano Letters, December 11, 2020, acs.nanolett.0c03152.

(8) Gaynor, Andrew S., and Wilfred Chen. “Conditional Protein Rescue by Binding-Induced Protective Shielding.” ACS Synthetic Biology 9, no. 10 (October 16, 2020): 2639–47.

(9) Gilbert, Rachel M., Michael J. Donzanti, Daniel J. Minahan, Jasmine Shirazi, Christine L. Hatem, Brielle Hayward-Piatkovskyi, Allyson M. Dang, Katherine M. Nelson, Kimberly L. Bothi, and Jason P. Gleghorn. “Mask Reuse in the COVID-19 Pandemic: Creating an Inexpensive and Scalable Ultraviolet System for Filtering Facepiece Respirator Decontamination.” Global Health: Science and Practice 8, no. 3 (October 1, 2020): 582–95.

(10) Hamaker, Nathaniel K., and Kelvin H. Lee. “A Site‐Specific Integration Reporter System That Enables Rapid Evaluation of CRISPR/Cas9‐Mediated Genome Editing Strategies in CHO Cells.” Biotechnology Journal15, no. 8 (August 2020): 2000057.

(11) Hartzell, Emily J., Rachel M. Lieser, Millicent O. Sullivan, and Wilfred Chen. “Modular Hepatitis B Virus-like Particle Platform for Biosensing and Drug Delivery.” ACS Nano 14, no. 10 (October 27, 2020): 12642–51.

(12) Irvin-Choy, N’Dea S., Katherine M. Nelson, Jason P. Gleghorn, and Emily S. Day. “Design of Nanomaterials for Applications in Maternal/Fetal Medicine.” Journal of Materials Chemistry B, 2020, 10.1039.D0TB00612B.

(13) Jarai, Bader M., Zachary Stillman, Lucas Attia, Gerald E. Decker, Eric D. Bloch, and Catherine A. Fromen. “Evaluating UiO-66 Metal–Organic Framework Nanoparticles as Acid-Sensitive Carriers for Pulmonary Drug Delivery Applications.” ACS Applied Materials & Interfaces 12, no. 35 (September 2, 2020): 38989–4.

(14) Jarai, Bader M., Zachary Stillman, Kartik Bomb, April M. Kloxin, and Catherine A. Fromen. “Biomaterials-Based Opportunities to Engineer the Pulmonary Host Immune Response in COVID-19.” ACS Biomaterials Science & Engineering, December 27, 2020, acsbiomaterials.0c01287.

(15) Kolewe, Emily L., Zachary Stillman, Ian R. Woodward, and Catherine A. Fromen. “Check the Gap: Facemask Performance and Exhaled Aerosol Distributions around the Wearer.” Edited by Amitava Mukherjee. PLOS ONE 15, no. 12 (December 16, 2020): e0243885.

(16) Kraus, Jodi, Rupal Gupta, Manman Lu, Angela M. Gronenborn, Mikael Akke, and Tatyana Polenova. “Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin‐3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.” ChemPhysChem 21, no. 13 (July 2, 2020): 1436–43.

(17) Kunjapur, Aditya M., Michael G. Napolitano, Eriona Hysolli, Karen Noguera, Evan M. Appleton, Max G. Schubert, Michaela A. Jones, Siddharth Iyer, Daniel J. Mandell, and George M. Church. “Synthetic Auxotrophy Remains Stable after Continuous Evolution and in Co-Culture with Mammalian Cells.” Preprint. Synthetic Biology, September 28, 2020.

(18) Nelson, Katherine M., N’Dea Irvin-Choy, Matthew K. Hoffman, Jason P. Gleghorn, and Emily S. Day. “Diseases and Conditions That Impact Maternal and Fetal Health and the Potential for Nanomedicine Therapies.” Advanced Drug Delivery Reviews, September 2020, S0169409X2030137X.

(19) Shirazi, Jasmine, Michael J. Donzanti, Katherine M. Nelson, Ryan Zurakowski, Catherine A. Fromen, and Jason P. Gleghorn. “Significant Unresolved Questions and Opportunities for Bioengineering in Understanding and Treating COVID-19 Disease Progression.” Cellular and Molecular Bioengineering, July 27, 2020.

(20) Stillman, Zachary, Bader M. Jarai, Nisha Raman, Premal Patel, and Catherine A. Fromen. “Degradation Profiles of Poly(Ethylene Glycol)Diacrylate (PEGDA)-Based Hydrogel Nanoparticles.” Polymer Chemistry 11, no. 2 (2020): 568–80.

(21) Taylor, Phillip A., Haofu Huang, Kristi L. Kiick, and Arthi Jayaraman. “Placement of Tyrosine Residues as a Design Element for Tuning the Phase Transition of Elastin-Peptide-Containing Conjugates: Experiments and Simulations.” Molecular Systems Design & Engineering 5, no. 7 (2020): 1239–54.

(22) Ukaegbu, Ophelia I., Kristen E. DeMeester, Hai Liang, Ashley R. Brown, Zachary S. Jones, and Catherine Leimkuhler Grimes. “Utility of Bacterial Peptidoglycan Recycling Enzymes in the Chemoenzymatic Synthesis of Valuable UDP Sugar Substrates.” In Methods in Enzymology, 638:1–26. Elsevier, 2020.

(23) Valcourt, Danielle M., Megan N. Dang, Mackenzie A. Scully, and Emily S. Day. “Nanoparticle-Mediated Co-Delivery of Notch-1 Antibodies and ABT-737 as a Potent Treatment Strategy for Triple-Negative Breast Cancer.” ACS Nano 14, no. 3 (March 24, 2020): 3378–88.

(24) Valcourt, Danielle M., Chintan H. Kapadia, Mackenzie A. Scully, Megan N. Dang, and Emily S. Day. “Best Practices for Preclinical In Vivo Testing of Cancer Nanomedicines.” Advanced Healthcare Materials 9, no. 12 (June 2020): 2000110.

(25) Wang, Jianxin, Megan N. Dang, and Emily S. Day. “Inhibition of Wnt Signaling by Frizzled7 Antibody-Coated Nanoshells Sensitizes Triple-Negative Breast Cancer Cells to the Autophagy Regulator Chloroquine.” Nano Research 13, no. 6 (June 2020): 1693–1703.

(26) Wodzanowski, Kimberly A., Samantha E. Cassel, Catherine L. Grimes, and April M. Kloxin. “Tools for Probing Host-Bacteria Interactions in the Gut Microenvironment: From Molecular to Cellular Levels.” Bioorganic & Medicinal Chemistry Letters 30, no. 10 (May 2020): 127116.


(1)  D’Ambrosio, Elizabeth A., Walter R. Drake, Siavash Mashayekh, Ophelia I. Ukaegbu, Ashley R.  Brown, and Catherine L. Grimes. “Modulation of the NOD-like Receptors NOD1 and NOD2: A Chemist’s Perspective.” Bioorganic & Medicinal Chemistry Letters 29, no. 10 (May 15, 2019): 1153–61.

(2)  DeMeester, Kristen E., Hai Liang, Junhui Zhou, Kimberly A. Wodzanowski, Benjamin L. Prather, Cintia C. Santiago, and Catherine L. Grimes. “Metabolic Incorporation of N ‐Acetyl Muramic Acid Probes into Bacterial Peptidoglycan.” Current Protocols in Chemical Biology 11, no. 4 (December 2019).

(3)  Fritz, Matthew, Jodi Kraus, Caitlin M. Quinn, Glenn P. A. Yap, Jochem Struppe, Ivan V. Sergeyev, Angela M. Gronenborn, and Tatyana Polenova. “Measurement of Accurate Interfluorine Distances in Crystalline Organic Solids: A High-Frequency Magic Angle Spinning NMR Approach.” The Journal of Physical Chemistry B, December 10, 2019, acs.jpcb.9b08919.

(4)  Lazor, Klare M., Junhui Zhou, Kristen E. DeMeester, Elizabeth A. D’Ambrosio, and Catherine L. Grimes. “Synthesis and Application of Methyl N,O-Hydroxylamine Muramyl Peptides.” Chembiochem: A European Journal of Chemical Biology, January 22, 2019.

(5)  M. Pike, Colleen, Rebecca R. Noll, and M. Ramona Neunuebel. “Exploitation of Phosphoinositides by the Intracellular Pathogen, Legionella Pneumophila.” In Pathogenic Bacteria [Working Title]. IntechOpen, 2019.

(6)  McDonald, Nathan D., Abish Regmi, Daniel P. Morreale, Joseph D. Borowski, and E. Fidelma Boyd. “CRISPR-Cas Systems Are Present Predominantly on Mobile Genetic Elements in Vibrio Species.” BMC Genomics 20, no. 1 (December 2019).

(7)  Millar-Haskell, Catherine S., Allyson M. Dang, and Jason P. Gleghorn. “Coupling Synthetic Biology and Programmable Materials to Construct Complex Tissue Ecosystems.” MRS Communications 9, no. 02 (June 2019): 421–32.

(8)  Munsell, Erik V., Bing Fang, and Millicent O. Sullivan. “Histone-Mimetic Gold Nanoparticles as Versatile Scaffolds for Gene Transfer and Chromatin Analysis.” Bioconjugate Chemistry 29, no. 11 (November 21, 2018): 3691–3704.

(9)  Prhashanna, Ammu, Phillip A. Taylor, Jingya Qin, Kristi L. Kiick, and Arthi Jayaraman. “Effect of Peptide Sequence on the LCST-Like Transition of Elastin-Like Peptides and Elastin-Like Peptide–Collagen-Like Peptide Conjugates: Simulations and Experiments.” Biomacromolecules 20, no. 3 (March 11, 2019): 1178–89.

(10) Russell, Ryan W., Matthew P. Fritz, Jodi Kraus, Caitlin M. Quinn, Tatyana Polenova, and Angela M. Gronenborn. “Accuracy and Precision of Protein Structures Determined by Magic Angle Spinning NMR Spectroscopy: For Some ‘with a Little Help from a Friend.’” Journal of Biomolecular NMR 73, no. 6–7 (July 2019): 333–46.

(11) Zhang, Yuhao, Cristian Coarfa, Xiaoyu Dong, Weiwu Jiang, Brielle Hayward-Piatkovskyi, Jason P. Gleghorn, and Krithika Lingappan. “MicroRNA-30a as a Candidate Underlying Sex-Specific Differences in Neonatal Hyperoxic Lung Injury: Implications for BPD.” American Journal of Physiology-Lung Cellular and Molecular Physiology 316, no. 1 (January 2019): L144–56.


(1)DeMeester, K. E.; Liang, H.; Jensen, M. R.; Jones, Z. S.; D’Ambrosio, E. A.; Scinto, S. L.; Zhou, J.; Grimes, C. L. Synthesis of Functionalized N-Acetyl Muramic Acids To Probe Bacterial Cell Wall Recycling and Biosynthesis. J. Am. Chem. Soc. 2018140 (30), 9458–9465.

(2)DeWaal, D.; Nogueira, V.; Terry, A. R.; Patra, K. C.; Jeon, S.-M.; Guzman, G.; Au, J.; Long, C. P.; Antoniewicz, M. R.; Hay, N. Hexokinase-2 Depletion Inhibits Glycolysis and Induces Oxidative Phosphorylation in Hepatocellular Carcinoma and Sensitizes to Metformin. Nat Commun 20189 (1), 446.

(3)DeWaal, D.; Nogueira, V.; Terry, A. R.; Patra, K. C.; Jeon, S.-M.; Guzman, G.; Au, J.; Long, C. P.; Antoniewicz, M. R.; Hay, N. Author Correction: Hexokinase-2 Depletion Inhibits Glycolysis and Induces Oxidative Phosphorylation in Hepatocellular Carcinoma and Sensitizes to Metformin. Nat Commun 20189 (1), 2539.

(4)Drake, W. R.; Hou, C.-W.; Zachara, N. E.; Grimes, C. L. New Use for CETSA: Monitoring Innate Immune Receptor Stability via Post-Translational Modification by OGT. J. Bioenerg. Biomembr. 201850 (3), 231–240.

(5)Fritz, M.; Quinn, C. M.; Wang, M.; Hou, G.; Lu, X.; Koharudin, L. M. I.; Struppe, J.; Case, D. A.; Polenova, T.; Gronenborn, A. M. Determination of Accurate Backbone Chemical Shift Tensors in Microcrystalline Proteins by Integrating MAS NMR and QM/MM. Phys Chem Chem Phys 201820 (14), 9543–9553.

(6)Hamaker, N. K.; Lee, K. H. Site-Specific Integration Ushers in a New Era of Precise CHO Cell Line Engineering. Current Opinion in Chemical Engineering 201822, 152–160.

(7)Hudson, D. A.; Caplan, J. L.; Thorpe, C. Designing Flavoprotein-GFP Fusion Probes for Analyte-Specific Ratiometric Fluorescence Imaging. Biochemistry 201857 (7), 1178–1189.

(8)Jones, A. J.; Fast, A. G.; Clupper, M.; Papoutsakis, E. T. Small and Low but Potent: The Complex Regulatory Role of the Small RNA SolB in Solventogenesis in Clostridium Acetobutylicum. Appl. Environ. Microbiol. 201884 (14).

(9)Kraus, J.; Gupta, R.; Yehl, J.; Lu, M.; Case, D. A.; Gronenborn, A. M.; Akke, M.; Polenova, T. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations. J Phys Chem B 2018122 (11), 2931–2939.

(10)Liu, J.; Chen, Q.; Rozovsky, S. Selenocysteine-Mediated Expressed Protein Ligation of SELENOM. Methods Mol. Biol. 20181661, 265–283.

(11)Long, C. P.; Antoniewicz, M. R. How Adaptive Evolution Reshapes Metabolism to Improve Fitness: Recent Advances and Future Outlook. Current Opinion in Chemical Engineering 201822, 209–215.

(12)Long, C. P.; Gonzalez, J. E.; Feist, A. M.; Palsson, B. O.; Antoniewicz, M. R. Dissecting the Genetic and Metabolic Mechanisms of Adaptation to the Knockout of a Major Metabolic Enzyme in Escherichia Coli. Proc. Natl. Acad. Sci. U.S.A. 2018115 (1), 222–227.

(13)Lu, M.; Sarkar, S.; Wang, M.; Kraus, J.; Fritz, M.; Quinn, C. M.; Bai, S.; Holmes, S. T.; Dybowski, C.; Yap, G. P. A.; et al. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B 2018122 (23), 6148–6155.

(14)MacDonald, M. L.; Hamaker, N. K.; Lee, K. H. Bioinformatic Analysis of Chinese Hamster Ovary Host Cell Protein Lipases. AIChE Journal 201864 (12), 4247–4254.

(15)McDonald, N. D.; DeMeester, K. E.; Lewis, A. L.; Grimes, C. L.; Boyd, E. F. Structural and Functional Characterization of a Modified Legionaminic Acid Involved in Glycosylation of a Bacterial Lipopolysaccharide. J. Biol. Chem. 2018293 (49), 19113–19126.

(16)Munsell, E. V.; Fang, B.; Sullivan, M. O. Histone-Mimetic Gold Nanoparticles as Versatile Scaffolds for Gene Transfer and Chromatin Analysis. Bioconjug. Chem. 201829 (11), 3691–3704.

(17)Munsell, E. V.; Kurpad, D. S.; Freeman, T. A.; Sullivan, M. O. Histone-Targeted Gene Transfer of Bone Morphogenetic Protein-2 Enhances Mesenchymal Stem Cell Chondrogenic Differentiation. Acta Biomater 201871, 156–167.

(18)O’Brien, J. G. K.; Chintala, S. R.; Fox, J. M. Stereoselective Synthesis of Bicyclo[6.1.0]Nonene Precursors of the Bioorthogonal Reagents s-TCO and BCN. J. Org. Chem. 201883 (14), 7500–7503.

(19)Quinn, C. M.; Wang, M.; Fritz, M. P.; Runge, B.; Ahn, J.; Xu, C.; Perilla, J. R.; Gronenborn, A. M.; Polenova, T. Dynamic Regulation of HIV-1 Capsid Interaction with the Restriction Factor TRIM5α Identified by Magic-Angle Spinning NMR and Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U.S.A. 2018115 (45), 11519–11524.

(20)Wang, M.; Lu, M.; Fritz, M. P.; Quinn, C. M.; Byeon, I.-J. L.; Byeon, C.-H.; Struppe, J.; Maas, W.; Gronenborn, A. M.; Polenova, T. Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies. Angew. Chem. Int. Ed. Engl. 201857 (50), 16375–16379.

(21)Wolfsberg, E.; Long, C. P.; Antoniewicz, M. R. Metabolism in Dense Microbial Colonies: 13C Metabolic Flux Analysis of E. Coli Grown on Agar Identifies Two Distinct Cell Populations with Acetate Cross-Feeding. Metabolic Engineering 201849, 242–247.

(22)Yu, X.; Noll, R. R.; Romero Dueñas, B. P.; Allgood, S. C.; Barker, K.; Caplan, J. L.; Machner, M. P.; LaBaer, J.; Qiu, J.; Neunuebel, M. R. Legionella Effector AnkX Interacts with Host Nuclear Protein PLEKHN1. BMC Microbiol. 201818 (1), 5.


(1)Allgood, S. C.; Romero Dueñas, B. P.; Noll, R. R.; Pike, C.; Lein, S.; Neunuebel, M. R. Legionella Effector AnkX Disrupts Host Cell Endocytic Recycling in a Phosphocholination-Dependent Manner. Front Cell Infect Microbiol 20177, 397.

(2)Chiu, J.; Valente, K. N.; Levy, N. E.; Min, L.; Lenhoff, A. M.; Lee, K. H. Knockout of a Difficult-to-Remove CHO Host Cell Protein, Lipoprotein Lipase, for Improved Polysorbate Stability in Monoclonal Antibody Formulations. Biotechnol. Bioeng. 2017114 (5), 1006–1015.

(3)Cordova, L. T.; Cipolla, R. M.; Swarup, A.; Long, C. P.; Antoniewicz, M. R. 13C Metabolic Flux Analysis of Three Divergent Extremely Thermophilic Bacteria: Geobacillus Sp. LC300, Thermus Thermophilus HB8, and Rhodothermus Marinus DSM 4252. Metab. Eng. 201744, 182–190.

(4)Fritz, M.; Quinn, C. M.; Wang, M.; Hou, G.; Lu, X.; Koharudin, L. M. I.; Polenova, T.; Gronenborn, A. M. Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin. J Phys Chem B 2017121 (15), 3574–3585.

(5)Gaynor, A. S.; Chen, W. Induced Prodrug Activation by Conditional Protein Degradation. J. Biotechnol. 2017260, 62–66.

(6)Gonzalez, J. E.; Long, C. P.; Antoniewicz, M. R. Comprehensive Analysis of Glucose and Xylose Metabolism in Escherichia Coli under Aerobic and Anaerobic Conditions by 13C Metabolic Flux Analysis. Metab. Eng. 201739, 9–18.

(7)Lauro, M. L.; D’Ambrosio, E. A.; Bahnson, B. J.; Grimes, C. L. Molecular Recognition of Muramyl Dipeptide Occurs in the Leucine-Rich Repeat Domain of Nod2. ACS Infect Dis 20173 (4), 264–270.

(8)Liang, H.; DeMeester, K. E.; Hou, C.-W.; Parent, M. A.; Caplan, J. L.; Grimes, C. L. Metabolic Labelling of the Carbohydrate Core in Bacterial Peptidoglycan and Its Applications. Nat Commun 20178, 15015.

(9)Liu, J.; Chen, Q.; Rozovsky, S. Utilizing Selenocysteine for Expressed Protein Ligation and Bioconjugations. J. Am. Chem. Soc. 2017139 (9), 3430–3437.

(10)Long, C. P.; Au, J.; Sandoval, N. R.; Gebreselassie, N. A.; Antoniewicz, M. R. Enzyme I Facilitates Reverse Flux from Pyruvate to Phosphoenolpyruvate in Escherichia Coli. Nat Commun 20178, 14316.

(11)Long, C. P.; Gonzalez, J. E.; Cipolla, R. M.; Antoniewicz, M. R. Metabolism of the Fast-Growing Bacterium Vibrio Natriegens Elucidated by 13C Metabolic Flux Analysis. Metab. Eng. 201744, 191–197.

(12)Long, C. P.; Gonzalez, J. E.; Feist, A. M.; Palsson, B. O.; Antoniewicz, M. R. Fast Growth Phenotype of E. Coli K-12 from Adaptive Laboratory Evolution Does Not Require Intracellular Flux Rewiring. Metab. Eng. 201744, 100–107.

(13)Luo, T.; David, M. A.; Dunshee, L. C.; Scott, R. A.; Urello, M. A.; Price, C.; Kiick, K. L. Thermoresponsive Elastin-b-Collagen-Like Peptide Bioconjugate Nanovesicles for Targeted Drug Delivery to Collagen-Containing Matrices. Biomacromolecules 201718 (8), 2539–2551.

(14)McNeely, P. M.; Naranjo, A. N.; Forsten-Williams, K.; Robinson, A. S. A2AR Binding Kinetics in the Ligand Depletion Regime. SLAS Discov 201722 (2), 166–175.

(15)Ott, C. A.; Baljinnyam, B.; Zakharov, A. V.; Jadhav, A.; Simeonov, A.; Zhuang, Z. Cell Lysate-Based AlphaLISA Deubiquitinase Assay Platform for Identification of Small Molecule Inhibitors. ACS Chem. Biol. 201712 (9), 2399–2407.

(16)Rohlhill, J.; Sandoval, N. R.; Papoutsakis, E. T. Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia Coli Growth on Methanol. ACS Synth Biol 20176 (8), 1584–1595.

(17)Schaefer, A. K.; Melnyk, J. E.; Baksh, M. M.; Lazor, K. M.; Finn, M. G.; Grimes, C. L. Membrane Association Dictates Ligand Specificity for the Innate Immune Receptor NOD2. ACS Chem. Biol. 201712 (8), 2216–2224.

(18)Schaefer, A. K.; Wastyk, H. C.; Mohanan, V.; Hou, C.-W.; Lauro, M. L.; Melnyk, J. E.; Burch, J. M.; Grimes, C. L. Crohn’s Disease Variants of Nod2 Are Stabilized by the Critical Contact Region of Hsp70. Biochemistry 201756 (34), 4445–4448.

(19)Struppe, J.; Quinn, C. M.; Lu, M.; Wang, M.; Hou, G.; Lu, X.; Kraus, J.; Andreas, L. B.; Stanek, J.; Lalli, D.; et al. Expanding the Horizons for Structural Analysis of Fully Protonated Protein Assemblies by NMR Spectroscopy at MAS Frequencies above 100 KHz. Solid State Nucl Magn Reson 201787, 117–125.

(20)Urello, M. A.; Kiick, K. L.; Sullivan, M. O. ECM Turnover-Stimulated Gene Delivery through Collagen-Mimetic Peptide-Plasmid Integration in Collagen. Acta Biomater 201762, 167–178.

(21)Wang, Y.; Lazor, K. M.; DeMeester, K. E.; Liang, H.; Heiss, T. K.; Grimes, C. L. Postsynthetic Modification of Bacterial Peptidoglycan Using Bioorthogonal N-Acetylcysteamine Analogs and Peptidoglycan O-Acetyltransferase B. J. Am. Chem. Soc. 2017139 (39), 13596–13599.


(1)Ahn, W. S.; Crown, S. B.; Antoniewicz, M. R. Evidence for Transketolase-like TKTL1 Flux in CHO Cells Based on Parallel Labeling Experiments and (13)C-Metabolic Flux Analysis. Metab. Eng. 201637, 72–78.

(2)Baeyens, N.; Larrivée, B.; Ola, R.; Hayward-Piatkowskyi, B.; Dubrac, A.; Huang, B.; Ross, T. D.; Coon, B. G.; Min, E.; Tsarfati, M.; et al. Defective Fluid Shear Stress Mechanotransduction Mediates Hereditary Hemorrhagic Telangiectasia. J. Cell Biol. 2016214 (7), 807–816.

(3)Bascom, C. S.; Wu, S.-Z.; Nelson, K.; Oakey, J.; Bezanilla, M. Long-Term Growth of Moss in Microfluidic Devices Enables Subcellular Studies in Development. Plant Physiol. 2016172 (1), 28–37.

(4)Cordova, L. T.; Lu, J.; Cipolla, R. M.; Sandoval, N. R.; Long, C. P.; Antoniewicz, M. R. Co-Utilization of Glucose and Xylose by Evolved Thermus Thermophilus LC113 Strain Elucidated by (13)C Metabolic Flux Analysis and Whole Genome Sequencing. Metab. Eng. 201637, 63–71.

(5)Crown, S. B.; Kelleher, J. K.; Rouf, R.; Muoio, D. M.; Antoniewicz, M. R. Comprehensive Metabolic Modeling of Multiple 13C-Isotopomer Data Sets to Study Metabolism in Perfused Working Hearts. Am. J. Physiol. Heart Circ. Physiol. 2016311 (4), H881–H891.

(6)Crown, S. B.; Long, C. P.; Antoniewicz, M. R. Optimal Tracers for Parallel Labeling Experiments and 13C Metabolic Flux Analysis: A New Precision and Synergy Scoring System. Metab. Eng. 201638, 10–18.

(7)DeAngelis, A.; Panish, R.; Fox, J. M. Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration. Acc. Chem. Res. 201649 (1), 115–127.

(8)Fu, J.; Sun, F.; Liu, W.; Liu, Y.; Gedam, M.; Hu, Q.; Fridley, C.; Quigley, H. A.; Hanes, J.; Pitha, I. Subconjunctival Delivery of Dorzolamide-Loaded Poly(Ether-Anhydride) Microparticles Produces Sustained Lowering of Intraocular Pressure in Rabbits. Mol. Pharm. 201613 (9), 2987–2995.

(9)Hilderbrand, A. M.; Ovadia, E. M.; Rehmann, M. S.; Kharkar, P. M.; Guo, C.; Kloxin, A. M. Biomaterials for 4D Stem Cell Culture. Curr Opin Solid State Mater Sci 201620 (4), 212–224.

(10)Hou, C.-W.; Lauro, M. L.; Leimkuhler Grimes, C. Redefining the Defensive Line: Critical Components of the Innate Immune System. ACS Infect Dis 20162 (11), 746–748.

(11)Kharkar, P. M.; Rehmann, M. S.; Skeens, K. M.; Maverakis, E.; Kloxin, A. M. Thiol-Ene Click Hydrogels for Therapeutic Delivery. ACS Biomater Sci Eng 20162 (2), 165–179.

(12)Lauro, M. L.; Burch, J. M.; Grimes, C. L. The Effect of NOD2 on the Microbiota in Crohn’s Disease. Curr. Opin. Biotechnol. 201640, 97–102.

(13)Long, C. P.; Au, J.; Gonzalez, J. E.; Antoniewicz, M. R. 13C Metabolic Flux Analysis of Microbial and Mammalian Systems Is Enhanced with GC-MS Measurements of Glycogen and RNA Labeling. Metab. Eng. 201638, 65–72.

(14)Long, C. P.; Gonzalez, J. E.; Sandoval, N. R.; Antoniewicz, M. R. Characterization of Physiological Responses to 22 Gene Knockouts in Escherichia Coli Central Carbon Metabolism. Metab. Eng. 201637, 102–113.

(15)McDonald, N. D.; Lubin, J.-B.; Chowdhury, N.; Boyd, E. F. Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo. MBio 20167 (2), e02237-02215.

(16)Munsell, E. V.; Ross, N. L.; Sullivan, M. O. Journey to the Center of the Cell: Current Nanocarrier Design Strategies Targeting Biopharmaceuticals to the Cytoplasm and Nucleus. Curr. Pharm. Des. 201622 (9), 1227–1244.

(17)Panish, R. A.; Chintala, S. R.; Fox, J. M. A Mixed-Ligand Chiral Rhodium(II) Catalyst Enables the Enantioselective Total Synthesis of Piperarborenine B. Angew. Chem. Int. Ed. Engl. 201655 (16), 4983–4987.

(18)Raeeszadeh-Sarmazdeh, M.; Hartzell, E.; Price, J. V.; Chen, W. Protein Nanoparticles as Multifunctional Biocatalysts and Health Assessment Sensors. Current Opinion in Chemical Engineering 201613, 109–118.

(19)Rehmann, M. S.; Luna, J. I.; Maverakis, E.; Kloxin, A. M. Tuning Microenvironment Modulus and Biochemical Composition Promotes Human Mesenchymal Stem Cell Tenogenic Differentiation. J Biomed Mater Res A 2016104 (5), 1162–1174.

(20)Sandberg, T. E.; Long, C. P.; Gonzalez, J. E.; Feist, A. M.; Antoniewicz, M. R.; Palsson, B. O. Evolution of E. Coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS ONE 201611 (3), e0151130.

(21)Urello, M. A.; Kiick, K. L.; Sullivan, M. O. Integration of Growth Factor Gene Delivery with Collagen-Triggered Wound Repair Cascades Using Collagen-Mimetic Peptides. Bioeng Transl Med 20161 (2), 207–219.

(22)Yao, M.; Elling, F. J.; Jones, C.; Nomosatryo, S.; Long, C. P.; Crowe, S. A.; Antoniewicz, M. R.; Hinrichs, K.-U.; Maresca, J. A. Heterotrophic Bacteria from an Extremely Phosphate-Poor Lake Have Conditionally Reduced Phosphorus Demand and Utilize Diverse Sources of Phosphorus. Environ. Microbiol. 201618 (2), 656–667.

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(24)Zuñiga, C.; Li, C.-T.; Huelsman, T.; Levering, J.; Zielinski, D. C.; McConnell, B. O.; Long, C. P.; Knoshaug, E. P.; Guarnieri, M. T.; Antoniewicz, M. R.; et al. Genome-Scale Metabolic Model for the Green Alga Chlorella Vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiol. 2016172 (1), 589–602.


(1)Boyd, E. F.; Carpenter, M. R.; Chowdhury, N.; Cohen, A. L.; Haines-Menges, B. L.; Kalburge, S. S.; Kingston, J. J.; Lubin, J. B.; Ongagna-Yhombi, S. Y.; Whitaker, W. B. Post-Genomic Analysis of Members of the Family Vibrionaceae. Microbiol Spectr 20153 (5).

(2)Cordova, L. T.; Long, C. P.; Venkataramanan, K. P.; Antoniewicz, M. R. Complete Genome Sequence, Metabolic Model Construction and Phenotypic Characterization of Geobacillus LC300, an Extremely Thermophilic, Fast Growing, Xylose-Utilizing Bacterium. Metab. Eng. 201532, 74–81.

(3)Crown, S. B.; Long, C. P.; Antoniewicz, M. R. Integrated 13C-Metabolic Flux Analysis of 14 Parallel Labeling Experiments in Escherichia Coli. Metab. Eng. 201528, 151–158.

(4)Crown, S. B.; Marze, N.; Antoniewicz, M. R. Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes. PLoS ONE 201510 (12), e0145850.

(5)Doolan, K. M.; Colby, D. W. Conformation-Dependent Epitopes Recognized by Prion Protein Antibodies Probed Using Mutational Scanning and Deep Sequencing. J. Mol. Biol. 2015427 (2), 328–340.

(6)Gebreselassie, N. A.; Antoniewicz, M. R. 13 C-Metabolic Flux Analysis of Co-Cultures: A Novel Approach. Metabolic Engineering 201531, 132–139.

(7)Haines-Menges, B. L.; Whitaker, W. B.; Lubin, J. B.; Boyd, E. F. Host Sialic Acids: A Delicacy for the Pathogen with Discerning Taste. Microbiol Spectr 20153 (4).

(8)Hudson, D. A.; Gannon, S. A.; Thorpe, C. Oxidative Protein Folding: From Thiol–Disulfide Exchange Reactions to the Redox Poise of the Endoplasmic Reticulum. Free Radical Biology and Medicine 201580, 171–182.

(9)Hudson, D. A.; Thorpe, C. Mia40 Is a Facile Oxidant of Unfolded Reduced Proteins but Shows Minimal Isomerase Activity. Archives of Biochemistry and Biophysics 2015579, 1–7.

(10)Lewis, K. M.; Bharadwaj, U.; Eckols, T. K.; Kolosov, M.; Kasembeli, M. M.; Fridley, C.; Siller, R.; Tweardy, D. J. Small-Molecule Targeting of Signal Transducer and Activator of Transcription (STAT) 3 to Treat Non-Small Cell Lung Cancer. Lung Cancer 201590 (2), 182–190.

(11)Lewus, R. A.; Levy, N. E.; Lenhoff, A. M.; Sandler, S. I. A Comparative Study of Monoclonal Antibodies. 1. Phase Behavior and Protein-Protein Interactions. Biotechnol. Prog. 201531 (1), 268–276.

(12)Lubin, J.-B.; Lewis, W. G.; Gilbert, N. M.; Weimer, C. M.; Almagro-Moreno, S.; Boyd, E. F.; Lewis, A. L. Host-like Carbohydrates Promote Bloodstream Survival of Vibrio Vulnificus in Vivo. Infect. Immun. 201583 (8), 3126–3136.

(13)Melnyk, J. E.; Mohanan, V.; Schaefer, A. K.; Hou, C.-W.; Grimes, C. L. Peptidoglycan Modifications Tune the Stability and Function of the Innate Immune Receptor Nod2. J. Am. Chem. Soc. 2015137 (22), 6987–6990.

(14)Monillas, E. S.; Caplan, J. L.; Thévenin, A. F.; Bahnson, B. J. Oligomeric State Regulated Trafficking of Human Platelet-Activating Factor Acetylhydrolase Type-II. Biochim. Biophys. Acta 20151854 (5), 469–475.

(15)Ongagna-Yhombi, S. Y.; McDonald, N. D.; Boyd, E. F. Deciphering the Role of Multiple Betaine-Carnitine-Choline Transporters in the Halophile Vibrio Parahaemolyticus. Appl. Environ. Microbiol. 201581 (1), 351–363.

(16)Panish, R.; Selvaraj, R.; Fox, J. M. Rh(II)-Catalyzed Reactions of Diazoesters with Organozinc Reagents. Org. Lett. 201517 (16), 3978–3981.

(17)Ross, N. L.; Munsell, E. V.; Sabanayagam, C.; Sullivan, M. O. Histone-Targeted Polyplexes Avoid Endosomal Escape and Enter the Nucleus During Postmitotic Redistribution of ER Membranes. Mol Ther Nucleic Acids 20154, e226.


(1)Haines-Menges, B.; Whitaker, W. B.; Boyd, E. F. Alternative Sigma Factor RpoE Is Important for Vibrio Parahaemolyticus Cell Envelope Stress Response and Intestinal Colonization. Infect. Immun. 201482 (9), 3667–3677.

(2)He, L.; Xiao, Y.; Gebreselassie, N.; Zhang, F.; Antoniewiez, M. R.; Tang, Y. J.; Peng, L. Central Metabolic Responses to the Overproduction of Fatty Acids in Escherichia Coli Based on 13C-Metabolic Flux Analysis. Biotechnol. Bioeng. 2014111 (3), 575–585.

(3)Levy, N. E.; Valente, K. N.; Choe, L. H.; Lee, K. H.; Lenhoff, A. M. Identification and Characterization of Host Cell Protein Product-Associated Impurities in Monoclonal Antibody Bioprocessing. Biotechnol. Bioeng. 2014111 (5), 904–912.

(4)Liang, Q.; Dexheimer, T. S.; Zhang, P.; Rosenthal, A. S.; Villamil, M. A.; You, C.; Zhang, Q.; Chen, J.; Ott, C. A.; Sun, H.; et al. A Selective USP1-UAF1 Inhibitor Links Deubiquitination to DNA Damage Responses. Nat. Chem. Biol. 201410 (4), 298–304.

(5)Long, C. P.; Antoniewicz, M. R. Metabolic Flux Analysis of Escherichia Coli Knockouts: Lessons from the Keio Collection and Future Outlook. Curr. Opin. Biotechnol. 201428, 127–133.

(6)Long, C. P.; Antoniewicz, M. R. Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry. Anal. Chem. 201486 (19), 9423–9427.

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