Search Results - "Boutz, Daniel R."

A Census of Human Soluble Protein Complexes by Havugimana, Pierre C., Hart, G. Traver, Nepusz, Tamás, Yang, Haixuan, Turinsky, Andrei L., Li, Zhihua, Wang, Peggy I., Boutz, Daniel R., Fong, Vincent, Phanse, Sadhna, Babu, Mohan, Craig, Stephanie A., Hu, Pingzhao, Wan, Cuihong, Vlasblom, James, Dar, Vaqaar-un-Nisa, Bezginov, Alexandr, Clark, Gregory W., Wu, Gabriel C., Wodak, Shoshana J., Tillier, Elisabeth R.M., Paccanaro, Alberto, Marcotte, Edward M., Emili, Andrew

“…Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein…”
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Persistent Antibody Clonotypes Dominate the Serum Response to Influenza over Multiple Years and Repeated Vaccinations by Lee, Jiwon, Paparoditis, Philipp, Horton, Andrew P., Frühwirth, Alexander, McDaniel, Jonathan R., Jung, Jiwon, Boutz, Daniel R., Hussein, Dania A., Tanno, Yuri, Pappas, Leontios, Ippolito, Gregory C., Corti, Davide, Lanzavecchia, Antonio, Georgiou, George

“…Humans are repeatedly exposed to influenza virus via infections and vaccinations. Understanding how multiple exposures and pre-existing immunity impact…”
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Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination by Lee, Jiwon, Boutz, Daniel R, Chromikova, Veronika, Joyce, M Gordon, Vollmers, Christopher, Leung, Kwanyee, Horton, Andrew P, DeKosky, Brandon J, Lee, Chang-Han, Lavinder, Jason J, Murrin, Ellen M, Chrysostomou, Constantine, Hoi, Kam Hon, Tsybovsky, Yaroslav, Thomas, Paul V, Druz, Aliaksandr, Zhang, Baoshan, Zhang, Yi, Wang, Lingshu, Kong, Wing-Pui, Park, Daechan, Popova, Lyubov I, Dekker, Cornelia L, Davis, Mark M, Carter, Chalise E, Ross, Ted M, Ellington, Andrew D, Wilson, Patrick C, Marcotte, Edward M, Mascola, John R, Ippolito, Gregory C, Krammer, Florian, Quake, Stephen R, Kwong, Peter D, Georgiou, George

“…Antibodies that bind to both H1 and H3 influenza strains exist in the pre-vaccination serum repertoire of healthy adults; most vaccine-elicited clonotypes bind…”
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Identification and characterization of the constituent human serum antibodies elicited by vaccination by Lavinder, Jason J., Wine, Yariv, Giesecke, Claudia, Ippolito, Gregory C., Horton, Andrew P., Lungu, Oana I., Hoi, Kam Hon, DeKosky, Brandon J., Murrin, Ellen M., Wirth, Megan M., Ellington, Andrew D., Dörner, Thomas, Marcotte, Edward M., Boutz, Daniel R., Georgiou, George

“…Most vaccines confer protection via the elicitation of serum antibodies, yet more than 100 y after the discovery of antibodies, the molecular composition of…”
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Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line by Vogel, Christine, Penalva, Luiz O, de Sousa Abreu, Raquel, Ko, Daijin, Le, Shu-Yun, Shapiro, Bruce A, Burns, Suzanne C, Sandhu, Devraj, Boutz, Daniel R, Marcotte, Edward M

“…Transcription, mRNA decay, translation and protein degradation are essential processes during eukaryotic gene expression, but their relative global…”
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Ultrafast Ultraviolet Photodissociation at 193 nm and its Applicability to Proteomic Workflows by Madsen, James A, Boutz, Daniel R, Brodbelt, Jennifer S

“…Ultraviolet photodissociation (UVPD) at 193 nm was implemented on a linear ion trap mass spectrometer for high-throughput proteomic workflows. Upon irradiation…”
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Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response by Wine, Yariv, Boutz, Daniel R., Lavinder, Jason J., Miklos, Aleksandr E., Hughes, Randall A., Hoi, Kam Hon, Jung, Sang Taek, Horton, Andrew P., Murrin, Ellen M., Ellington, Andrew D., Marcotte, Edward M., Georgiou, George

“…We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested…”
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Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols by Bean, Björn D. M., Mulvihill, Colleen J., Garge, Riddhiman K., Boutz, Daniel R., Rousseau, Olivier, Floyd, Brendan M., Cheney, William, Gardner, Elizabeth C., Ellington, Andrew D., Marcotte, Edward M., Gollihar, Jimmy D., Whiteway, Malcolm, Martin, Vincent J. J.

“…The yeast Saccharomyces cerevisiae is powerful for studying human G protein-coupled receptors as they can be coupled to its mating pathway. However, some…”
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Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions by Brown, Colin W, Sridhara, Viswanadham, Boutz, Daniel R, Person, Maria D, Marcotte, Edward M, Barrick, Jeffrey E, Wilke, Claus O

“…Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth…”
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Proteomic Identification of Monoclonal Antibodies from Serum by Boutz, Daniel R, Horton, Andrew P, Wine, Yariv, Lavinder, Jason J, Georgiou, George, Marcotte, Edward M

“…Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen,…”
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The E. coli molecular phenotype under different growth conditions by Caglar, Mehmet U., Houser, John R., Barnhart, Craig S., Boutz, Daniel R., Carroll, Sean M., Dasgupta, Aurko, Lenoir, Walter F., Smith, Bartram L., Sridhara, Viswanadham, Sydykova, Dariya K., Vander Wood, Drew, Marx, Christopher J., Marcotte, Edward M., Barrick, Jeffrey E., Wilke, Claus O.

“…Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While…”
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Protein abundances are more conserved than mRNA abundances across diverse taxa by Laurent, Jon M, Vogel, Christine, Kwon, Taejoon, Craig, Stephanie A, Boutz, Daniel R, Huse, Holly K, Nozue, Kazunari, Walia, Harkamal, Whiteley, Marvin, Ronald, Pamela C, Marcotte, Edward M

“…Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post‐transcriptional,…”
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Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation by Houser, John R, Barnhart, Craig, Boutz, Daniel R, Carroll, Sean M, Dasgupta, Aurko, Michener, Joshua K, Needham, Brittany D, Papoulas, Ophelia, Sridhara, Viswanadham, Sydykova, Dariya K, Marx, Christopher J, Trent, M Stephen, Barrick, Jeffrey E, Marcotte, Edward M, Wilke, Claus O

“…How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and…”
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Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis by Hilterbrand, Adam T, Boutz, Daniel R, Marcotte, Edward M, Upton, Jason W

“…Maintaining control over inflammatory processes represents a paradox for viral pathogens. Although many viruses induce host inflammatory responses to…”
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A proteomic survey of widespread protein aggregation in yeast by O'Connell, Jeremy D, Tsechansky, Mark, Royal, Ariel, Boutz, Daniel R, Ellington, Andrew D, Marcotte, Edward M

“…Many normally cytosolic yeast proteins form insoluble intracellular bodies in response to nutrient depletion, suggesting the potential for widespread protein…”
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The genomics of disulfide bonding and protein stabilization in thermophiles by Beeby, Morgan, O'Connor, Brian D, Ryttersgaard, Carsten, Boutz, Daniel R, Perry, L Jeanne, Yeates, Todd O

“…Thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. Recently, genomic evidence has implicated a…”
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Discovery of a Thermophilic Protein Complex Stabilized by Topologically Interlinked Chains by Boutz, Daniel R., Cascio, Duilio, Whitelegge, Julian, Perry, L. Jeanne, Yeates, Todd O.

“…A growing number of organisms have been discovered inhabiting extreme environments, including temperatures in excess of 100 °C. How cellular proteins from such…”
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Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization by Jack, Benjamin R, Boutz, Daniel R, Paff, Matthew L, Smith, Bartram L, Bull, James J, Wilke, Claus O

“…A general means of viral attenuation involves the extensive recoding of synonymous codons in the viral genome. The mechanistic underpinnings of this approach…”
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SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode by Goike, Jule, Hsieh, Ching-Lin, Horton, Andrew P., Gardner, Elizabeth C., Zhou, Ling, Bartzoka, Foteini, Wang, Nianshuang, Javanmardi, Kamyab, Herbert, Andrew, Abbassi, Shawn, Xie, Xuping, Xia, Hongjie, Shi, Pei-Yong, Renberg, Rebecca, Segall-Shapiro, Thomas H., Terrace, Cynthia I., Wu, Wesley, Shroff, Raghav, Byrom, Michelle, Ellington, Andrew D., Marcotte, Edward M., Musser, James M., Kuchipudi, Suresh V., Kapur, Vivek, Georgiou, George, Weaver, Scott C., Dye, John M., Boutz, Daniel R., McLellan, Jason S., Gollihar, Jimmy D.

“…The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune…”
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Genomic Evidence That the Intracellular Proteins of Archaeal Microbes Contain Disulfide Bonds by Mallick, Parag, Boutz, Daniel R., Eisenberg, David, Yeates, Todd O.

“…Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent with the chemically reducing environment inside the cells of…”
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