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Daniel B. McClatchy, Ph.D. - Publications

Affiliations: 
Emory University, Atlanta, GA 
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Year Citation  Score
2006 McClatchy DB, Fang G, Levey AI. Elongation factor 1A family regulates the recycling of the M4 muscarinic acetylcholine receptor. Neurochemical Research. 31: 975-88. PMID 16845586 DOI: 10.1007/s11064-006-9103-1  0.447
2002 McClatchy DB, Knudsen CR, Clark BF, Kahn RA, Hall RA, Levey AI. Novel interaction between the M4 muscarinic acetylcholine receptor and elongation factor 1A2. The Journal of Biological Chemistry. 277: 29268-74. PMID 12048193 DOI: 10.1074/Jbc.M203081200  0.387
Low-probability matches (unlikely to be authored by this person)
2008 Chen EI, McClatchy D, Park SK, Yates JR. Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome. Analytical Chemistry. 80: 8694-701. PMID 18937422 DOI: 10.1021/ac800606w  0.293
2007 McClatchy DB, Liao L, Park SK, Venable JD, Yates JR. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Research. 17: 1378-88. PMID 17675365 DOI: 10.1101/Gr.6375007  0.29
2009 Liao L, McClatchy DB, Yates JR. Shotgun proteomics in neuroscience. Neuron. 63: 12-26. PMID 19607789 DOI: 10.1016/j.neuron.2009.06.011  0.268
2023 Son A, Kim H, Diedrich JK, Bamberger C, McClatchy DB, Yates JR. Protein Footprinting Reveals the Dynamic Conformational Changes of Proteome of Multiple Tissues in Progressing Alzheimer's Disease. Biorxiv : the Preprint Server For Biology. PMID 37397995 DOI: 10.1101/2023.05.29.542496  0.267
2021 Yu NK, McClatchy DB, Diedrich JK, Romero S, Choi JH, Martínez-Bartolomé S, Delahunty CM, Muotri AR, Yates JR. Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. Iscience. 24: 103321. PMID 34816099 DOI: 10.1016/j.isci.2021.103321  0.256
2014 Lavallée-Adam M, Rauniyar N, McClatchy DB, Yates JR. PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. Journal of Proteome Research. 13: 5496-509. PMID 25177766 DOI: 10.1021/Pr500473N  0.253
2008 Liao L, McClatchy DB, Park SK, Xu T, Lu B, Yates JR. Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events. Journal of Proteome Research. 7: 4743-55. PMID 18823140 DOI: 10.1021/Pr8003198  0.244
2012 McClatchy DB, Liao L, Lee JH, Park SK, Yates JR. Dynamics of subcellular proteomes during brain development. Journal of Proteome Research. 11: 2467-79. PMID 22397461 DOI: 10.1021/pr201176v  0.239
2018 Ma Y, McClatchy DB, Barkallah S, Wood WW, Yates JR. Quantitative analysis of newly synthesized proteins. Nature Protocols. PMID 30038347 DOI: 10.1038/s41596-018-0012-y  0.234
2022 Schiapparelli LM, Xie Y, Sharma P, McClatchy DB, Ma Y, Yates JR, Maximov A, Cline HT. Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 42: 7900-7920. PMID 36261270 DOI: 10.1523/JNEUROSCI.0707-22.2022  0.233
2019 Schiapparelli LM, Shah SH, Ma Y, McClatchy DB, Sharma P, Li J, Yates JR, Goldberg JL, Cline HT. The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo. Cell Reports. 28: 1935-1947.e5. PMID 31412257 DOI: 10.1016/J.Celrep.2019.07.037  0.231
2017 Ma Y, McClatchy DB, Barkallah S, Wood WW, Yates Iii JR. HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification. Journal of Proteome Research. PMID 28437088 DOI: 10.1021/acs.jproteome.7b00005  0.231
2023 Iii JY, Gomes F, Durbin K, Schauer K, Nwachukwu J, Russo R, Njeri J, Saviola A, McClatchy D, Diedrich J, Garrett P, Papa A, Ciolacu I, Kelleher N, Nettles K. Native top-down proteomics reveals EGFR-ERα signaling crosstalk in breast cancer cells dissociates NUTF2 dimers to modulate ERα signaling and cell growth. Research Square. PMID 37546719 DOI: 10.21203/rs.3.rs-3097806/v1  0.23
2014 Schiapparelli LM, McClatchy DB, Liu HH, Sharma P, Yates JR, Cline HT. Direct detection of biotinylated proteins by mass spectrometry. Journal of Proteome Research. 13: 3966-78. PMID 25117199 DOI: 10.1021/Pr5002862  0.229
2013 Rauniyar N, McClatchy DB, Yates JR. Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis. Methods (San Diego, Calif.). 61: 260-8. PMID 23523555 DOI: 10.1016/J.Ymeth.2013.03.008  0.225
2018 Liu HH, Mcclatchy DB, Schiapparelli L, Shen W, Yates JR, Cline HT. Role of the visual experience-dependent nascent proteome in neuronal plasticity. Elife. 7. PMID 29412139 DOI: 10.7554/Elife.33420  0.222
2007 Xiao K, McClatchy DB, Shukla AK, Zhao Y, Chen M, Shenoy SK, Yates JR, Lefkowitz RJ. Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proceedings of the National Academy of Sciences of the United States of America. 104: 12011-6. PMID 17620599 DOI: 10.1073/Pnas.0704849104  0.22
2013 Rauniyar N, Gao B, McClatchy DB, Yates JR. Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method. Journal of Proteome Research. 12: 1031-9. PMID 23214967 DOI: 10.1021/Pr3008896  0.218
2022 Schiapparelli LM, Sharma P, He HY, Li J, Shah SH, McClatchy DB, Ma Y, Liu HH, Goldberg JL, Yates JR, Cline HT. Proteomic screen reveals diverse protein transport between connected neurons in the visual system. Cell Reports. 38: 110287. PMID 35081342 DOI: 10.1016/j.celrep.2021.110287  0.217
2020 McClatchy DB, Martínez-Bartolomé S, Gao Y, Lavallée-Adam M, Yates JR. Quantitative analysis of global protein stability rates in tissues. Scientific Reports. 10: 15983. PMID 32994440 DOI: 10.1038/s41598-020-72410-y  0.215
2020 Ma Y, McClatchy DB, Martínez-Bartolomé S, Bamberger C, Yates JR. Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation. Journal of Proteome Research. PMID 33147027 DOI: 10.1021/acs.jproteome.0c00645  0.214
2014 Shen W, Liu HH, Schiapparelli L, McClatchy D, He HY, Yates JR, Cline HT. Acute synthesis of CPEB is required for plasticity of visual avoidance behavior in Xenopus. Cell Reports. 6: 737-47. PMID 24529705 DOI: 10.1016/J.Celrep.2014.01.024  0.209
2018 McClatchy DB, Ma Y, Liem DA, Ng DCM, Ping P, Yates JR. Quantitative temporal analysis of protein dynamics in cardiac remodeling. Journal of Molecular and Cellular Cardiology. PMID 30009778 DOI: 10.1016/j.yjmcc.2018.07.126  0.204
2008 Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR. Motif-specific sampling of phosphoproteomes. Journal of Proteome Research. 7: 2140-50. PMID 18452278 DOI: 10.1021/Pr800147U  0.2
2017 Savas JN, Wang YZ, DeNardo LA, Martinez-Bartolome S, McClatchy DB, Hark TJ, Shanks NF, Cozzolino KA, Lavallée-Adam M, Smukowski SN, Park SK, Kelly JW, Koo EH, Nakagawa T, Masliah E, et al. Amyloid Accumulation Drives Proteome-wide Alterations in Mouse Models of Alzheimer's Disease-like Pathology. Cell Reports. 21: 2614-2627. PMID 29186695 DOI: 10.1016/J.Celrep.2017.11.009  0.199
2015 McClatchy DB, Ma Y, Liu C, Stein BD, Martínez-Bartolomé S, Vasquez D, Hellberg K, Shaw RJ, Yates JR. Pulsed Azidohomoalanine Labeling in Mammals (PALM) detects changes in Liver-specific LKB1 knockout mice. Journal of Proteome Research. PMID 26445171 DOI: 10.1021/Acs.Jproteome.5B00653  0.198
2008 McClatchy DB, Yates JR. Stable Isotope Labeling of Mammals (SILAM). Csh Protocols. 2008: pdb.prot4940. PMID 21356771  0.197
2018 Natividad LA, Buczynski MW, McClatchy DB, Yates JR. From Synapse to Function: A Perspective on the Role of Neuroproteomics in Elucidating Mechanisms of Drug Addiction. Proteomes. 6. PMID 30544849 DOI: 10.3390/Proteomes6040050  0.18
2018 McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier A, Lavalle-Adam M, Powell S, Roberto M, Yates JR. Structural Analysis of Hippocampal Kinase Signal Transduction. Acs Chemical Neuroscience. PMID 30053369 DOI: 10.1021/Acschemneuro.8B00284  0.18
2023 McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. Biorxiv : the Preprint Server For Biology. PMID 38168169 DOI: 10.1101/2023.12.12.571320  0.173
2014 McClatchy DB, Yates JR. Stable isotope labeling in mammals (SILAM). Methods in Molecular Biology (Clifton, N.J.). 1156: 133-46. PMID 24791985 DOI: 10.1007/978-1-4939-0685-7_8  0.17
2011 McClatchy DB, Liao L, Park SK, Xu T, Lu B, Yates Iii JR. Differential proteomic analysis of mammalian tissues using SILAM. Plos One. 6: e16039. PMID 21283754 DOI: 10.1371/Journal.Pone.0016039  0.169
2015 McClatchy DB, Savas JN, Martínez-Bartolomé S, Park SK, Maher P, Powell SB, Yates JR. Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex. Molecular Psychiatry. PMID 25869802 DOI: 10.1038/Mp.2015.41  0.165
2007 Venable JD, Wohlschlegel J, McClatchy DB, Park SK, Yates JR. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Analytical Chemistry. 79: 3056-64. PMID 17367114 DOI: 10.1021/Ac062054I  0.165
2023 Kawata M, McClatchy DB, Diedrich JK, Olmer M, Johnson KA, Yates JR, Lotz MK. Mocetinostat activates Krüppel-like factor 4 and protects against tissue destruction and inflammation in osteoarthritis. Jci Insight. 8. PMID 37681413 DOI: 10.1172/jci.insight.170513  0.163
2020 Huang L, McClatchy DB, Maher P, Liang Z, Diedrich JK, Soriano-Castell D, Goldberg J, Shokhirev M, Yates JR, Schubert D, Currais A. Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death. Cell Death & Disease. 11: 828. PMID 33024077 DOI: 10.1038/s41419-020-03020-9  0.155
2005 Chen X, McClatchy DB, Geller EB, Tallarida RJ, Adler MW. The dynamic relationship between mu and kappa opioid receptors in body temperature regulation. Life Sciences. 78: 329-33. PMID 16257420 DOI: 10.1016/J.Lfs.2005.04.084  0.152
2021 Negraes PD, Trujillo CA, Yu NK, Wu W, Yao H, Liang N, Lautz JD, Kwok E, McClatchy D, Diedrich J, de Bartolome SM, Truong J, Szeto R, Tran T, Herai RH, et al. Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy. Molecular Psychiatry. PMID 33888873 DOI: 10.1038/s41380-021-01104-2  0.151
2024 Yang D, Wang Y, Qi T, Zhang X, Shen L, Ma J, Pang Z, Lal NK, McClatchy DB, Seradj SH, Leung VH, Wang K, Xie Y, Polli FS, Maximov A, et al. Phosphorylation of pyruvate dehydrogenase inversely associates with neuronal activity. Neuron. PMID 38266644 DOI: 10.1016/j.neuron.2023.12.015  0.146
2009 Lu B, Xu T, Park SK, McClatchy DB, Liao L, Yates JR. Shotgun protein identification and quantification by mass spectrometry in neuroproteomics. Methods in Molecular Biology (Clifton, N.J.). 566: 229-59. PMID 20058176 DOI: 10.1007/978-1-59745-562-6_16  0.145
2008 Lu B, McClatchy DB, Kim JY, Yates JR. Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry. Proteomics. 8: 3947-55. PMID 18780349 DOI: 10.1002/pmic.200800120  0.145
2019 Martínez-Bartolomé S, Bamberger TC, Lavallée-Adam M, McClatchy DB, Yates JR. Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. Journal of Proteome Research. PMID 31260318 DOI: 10.1021/acs.jproteome.8b00711  0.142
2023 Yang D, Wang Y, Qi T, Zhang X, Shen L, Ma J, Pang Z, Lal NK, McClatchy DB, Wang K, Xie Y, Polli F, Maximov A, Augustine V, Cline HT, et al. Phosphorylation of pyruvate dehydrogenase marks the inhibition of neuronal activity. Biorxiv : the Preprint Server For Biology. PMID 36993270 DOI: 10.1101/2023.03.13.532494  0.14
2020 Fernandez-Costa C, Martínez-Bartolomé S, McClatchy DB, Saviola AJ, Yu NK, Yates JR. Impact of the identification strategy on the reproducibility of DDA and DIA results. Journal of Proteome Research. PMID 32510229 DOI: 10.1021/acs.jproteome.0c00153  0.136
2012 Raso C, Cosentino C, Gaspari M, Malara N, Han X, McClatchy D, Park SK, Renne M, Vadalà N, Prati U, Cuda G, Mollace V, Amato F, Yates JR. Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap Velos mass spectrometry, and pathway analysis. Journal of Proteome Research. 11: 3199-210. PMID 22563702 DOI: 10.1021/Pr2012347  0.134
2007 McClatchy DB, Dong MQ, Wu CC, Venable JD, Yates JR. 15N metabolic labeling of mammalian tissue with slow protein turnover. Journal of Proteome Research. 6: 2005-10. PMID 17375949 DOI: 10.1021/Pr060599N  0.132
2001 Chen X, McClatchy DB, Geller EB, Liu-Chen L, Tallarida RJ, Adler MW. Possible mechanism of hypothermia induced by intracerebroventricular injection of orphanin FQ/nociceptin. Brain Research. 904: 252-8. PMID 11406123 DOI: 10.1016/S0006-8993(01)02467-2  0.122
2024 McClatchy DB. Quantitative analysis of proteostasis networks: are there applications for dementia? Expert Review of Proteomics. 21: 1-3. PMID 38366325 DOI: 10.1080/14789450.2024.2320807  0.119
2014 Park SK, Aslanian A, McClatchy DB, Han X, Shah H, Singh M, Rauniyar N, Moresco JJ, Pinto AF, Diedrich JK, Delahunty C, Yates JR. Census 2: isobaric labeling data analysis. Bioinformatics (Oxford, England). 30: 2208-9. PMID 24681903 DOI: 10.1093/Bioinformatics/Btu151  0.119
2017 Oh CK, Sultan A, Platzer J, Dolatabadi N, Soldner F, McClatchy DB, Diedrich JK, Yates JR, Ambasudhan R, Nakamura T, Jaenisch R, Lipton SA. S-Nitrosylation of PINK1 Attenuates PINK1/Parkin-Dependent Mitophagy in hiPSC-Based Parkinson's Disease Models. Cell Reports. 21: 2171-2182. PMID 29166608 DOI: 10.1016/J.Celrep.2017.10.068  0.115
2020 Fernández-Costa C, Martínez-Bartolomé S, McClatchy D, Yates JR. Improving Proteomics Data Reproducibility with a Dual-Search Strategy. Analytical Chemistry. 92: 1697-1701. PMID 31880919 DOI: 10.1021/acs.analchem.9b04955  0.11
2023 Lev-Ram V, Lemieux SP, Deerinck TJ, Bushong EA, Toyama BH, Perez A, Pritchard DR, Park SKR, McClatchy DB, Savas JN, Taylor SS, Ellisman MH, Yates J, Tsien RY. Do perineuronal nets stabilize the engram of a synaptic circuit? Biorxiv : the Preprint Server For Biology. PMID 37066274 DOI: 10.1101/2023.04.09.536164  0.088
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