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Daniel R. Boutz, Ph.D. - Publications

Affiliations: 
2006 University of California, Los Angeles, Los Angeles, CA 
Area:
structural and computational biology
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ. Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching. G3 (Bethesda, Md.). PMID 38135291 DOI: 10.1093/g3journal/jkad293  0.774
2023 Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, ... ... Boutz DR, et al. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Communications Biology. 6: 1250. PMID 38082099 DOI: 10.1038/s42003-023-05649-6  0.629
2023 Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ. Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching. Biorxiv : the Preprint Server For Biology. PMID 37790497 DOI: 10.1101/2023.09.21.558736  0.774
2023 June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ. Protein nonadditive expression and solubility contribute to heterosis in hybrids and allotetraploids. Frontiers in Plant Science. 14: 1252564. PMID 37780492 DOI: 10.3389/fpls.2023.1252564  0.679
2023 Abdullah M, Greco BM, Laurent JM, Garge RK, Boutz DR, Vandeloo M, Marcotte EM, Kachroo AH. Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast. Cell Reports Methods. 3: 100464. PMID 37323580 DOI: 10.1016/j.crmeth.2023.100464  0.743
2022 Bean BDM, Mulvihill CJ, Garge RK, Boutz DR, Rousseau O, Floyd BM, Cheney W, Gardner EC, Ellington AD, Marcotte EM, Gollihar JD, Whiteway M, Martin VJJ. Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. Nature Communications. 13: 2882. PMID 35610225 DOI: 10.1038/s41467-022-30570-7  0.727
2021 Goike J, Hsieh CL, Horton A, Gardner EC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, ... ... Boutz DR, et al. Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. Biorxiv : the Preprint Server For Biology. PMID 33851158 DOI: 10.1101/2021.04.07.438849  0.636
2019 Jack BR, Boutz DR, Paff ML, Smith BL, Wilke CO. Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus Evolution. 5: vez055. PMID 31908847 DOI: 10.1093/Ve/Vez055  0.314
2019 Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Genes & Development. PMID 31753913 DOI: 10.1101/Gad.331231.119  0.694
2019 Lindesmith LC, McDaniel JR, Changela A, Verardi R, Kerr SA, Costantini V, Brewer-Jensen PD, Mallory ML, Voss WN, Boutz DR, Blazeck JJ, Ippolito GC, Vinje J, Kwong PD, Georgiou G, et al. Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination. Immunity. 50: 1530-1541.e8. PMID 31216462 DOI: 10.1016/J.Immuni.2019.05.007  0.317
2017 Jack BR, Boutz DR, Paff ML, Smith BL, Bull JJ, Wilke CO. Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization. G3 (Bethesda, Md.). PMID 28698233 DOI: 10.1534/G3.117.041020  0.4
2017 Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO. The E. coli molecular phenotype under different growth conditions. Scientific Reports. 7: 45303. PMID 28417974 DOI: 10.1038/Srep45303  0.663
2017 Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. Bmc Genomics. 18: 301. PMID 28412930 DOI: 10.1186/S12864-017-3676-8  0.685
2017 Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW. Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis. Mbio. 8. PMID 28096485 DOI: 10.1128/Mbio.01864-16  0.617
2016 Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, et al. Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination. Nature Medicine. PMID 27820605 DOI: 10.1038/Nm.4224  0.628
2016 Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, ... Boutz DR, et al. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data in Brief. 6: 715-21. PMID 26870755 DOI: 10.1016/J.Dib.2015.11.062  0.663
2015 Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, ... Boutz DR, et al. Panorama of ancient metazoan macromolecular complexes. Nature. 525: 339-44. PMID 26344197 DOI: 10.1038/Nature14877  0.664
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. Plos Computational Biology. 11: e1004400. PMID 26275208 DOI: 10.1371/Journal.Pcbi.1004400  0.711
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004400  0.597
2014 Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM. Proteomic identification of monoclonal antibodies from serum. Analytical Chemistry. 86: 4758-66. PMID 24684310 DOI: 10.1021/Ac4037679  0.65
2014 O'Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM. A proteomic survey of widespread protein aggregation in yeast. Molecular Biosystems. 10: 851-61. PMID 24488121 DOI: 10.1039/C3Mb70508K  0.684
2014 Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature Chemical Biology. 10: 178-80. PMID 24487692 DOI: 10.1038/Nchembio.1450  0.63
2014 Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, DeKosky BJ, Murrin EM, Wirth MM, Ellington AD, Dörner T, Marcotte EM, Boutz DR, Georgiou G. Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proceedings of the National Academy of Sciences of the United States of America. 111: 2259-64. PMID 24469811 DOI: 10.1073/Pnas.1317793111  0.632
2013 Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G. Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proceedings of the National Academy of Sciences of the United States of America. 110: 2993-8. PMID 23382245 DOI: 10.1073/Pnas.1213737110  0.641
2012 Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, et al. A census of human soluble protein complexes. Cell. 150: 1068-81. PMID 22939629 DOI: 10.1016/J.Cell.2012.08.011  0.796
2012 Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NS. Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Molecular Systems Biology. 8: 573. PMID 22415777 DOI: 10.1038/Msb.2012.5  0.672
2011 Boutz DR, Collins PJ, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein ND, Marcotte EM, et al. Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. The Journal of Biological Chemistry. 286: 18066-78. PMID 21402708 DOI: 10.1074/Jbc.M110.196451  0.635
2010 Laurent JM, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM. Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics. 10: 4209-12. PMID 21089048 DOI: 10.1002/Pmic.201000327  0.702
2010 Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Molecular Systems Biology. 6: 400. PMID 20739923 DOI: 10.1038/Msb.2010.59  0.7
2008 Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM. A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Molecular Systems Biology. 4: 180. PMID 18414481 DOI: 10.1038/Msb.2008.19  0.75
2007 Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. Journal of Molecular Biology. 368: 1332-44. PMID 17395198 DOI: 10.1016/J.Jmb.2007.02.078  0.618
2005 Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO. The genomics of disulfide bonding and protein stabilization in thermophiles. Plos Biology. 3: e309. PMID 16111437 DOI: 10.1371/Journal.Pbio.0030309  0.775
2002 Mallick P, Boutz DR, Eisenberg D, Yeates TO. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proceedings of the National Academy of Sciences of the United States of America. 99: 9679-84. PMID 12107280 DOI: 10.1073/Pnas.142310499  0.666
2001 Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO. Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. Journal of Molecular Biology. 313: 1103-16. PMID 11700066 DOI: 10.1006/Jmbi.2001.5095  0.65
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