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ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.

Park SR, Jung T, Thuy-Boun PS, Wang AY, Yates JR, Wolan DW.

J Proteome Res. 2018 Dec 10. doi: 10.1021/acs.jproteome.8b00722. [Epub ahead of print]


Integrated In Vivo Quantitative Proteomics and Nutrient Tracing Reveals Age-Related Metabolic Rewiring of Pancreatic β Cell Function.

Wortham M, Benthuysen JR, Wallace M, Savas JN, Mulas F, Divakaruni AS, Liu F, Albert V, Taylor BL, Sui Y, Saez E, Murphy AN, Yates JR 3rd, Metallo CM, Sander M.

Cell Rep. 2018 Dec 4;25(10):2904-2918.e8. doi: 10.1016/j.celrep.2018.11.031.


Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways.

Halani SH, Yousefi S, Vega JV, Rossi MR, Zhao Z, Amrollahi F, Holder CA, Baxter-Stoltzfus A, Eschbacher J, Griffith B, Olson JJ, Jiang T, Yates JR, Eberhart CG, Poisson LM, Cooper LAD, Brat DJ.

NPJ Precis Oncol. 2018 Nov 6;2:24. doi: 10.1038/s41698-018-0067-9. eCollection 2018.


Zika Virus Infection of Human Mesenchymal Stem Cells Promotes Differential Expression of Proteins Linked to Several Neurological Diseases.

Beys-da-Silva WO, Rosa RL, Santi L, Berger M, Park SK, Campos AR, Terraciano P, Varela APM, Teixeira TF, Roehe PM, Quincozes-Santos A, Yates JR 3rd, Souza DO, Cirne-Lima EO, Guimarães JA.

Mol Neurobiol. 2018 Oct 30. doi: 10.1007/s12035-018-1417-x. [Epub ahead of print]


Secretomic analysis of Beauveria bassiana related to cattle tick, Rhipicephalus microplus, infection.

Santi L, Coutinho-Rodrigues CJB, Berger M, Klein LAS, De Souza EM, Rosa RL, Guimarães JA, Yates JR 3rd, Perinotto WMS, Bittencourt VREP, Beys-da-Silva WO.

Folia Microbiol (Praha). 2018 Oct 25. doi: 10.1007/s12223-018-0659-3. [Epub ahead of print]


DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity.

Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR 3rd, Ruvkun G, Riedel CG.

Nat Commun. 2018 Oct 23;9(1):4400. doi: 10.1038/s41467-018-06624-0.


Understanding molecular mechanisms of disease through spatial proteomics.

Pankow S, Martínez-Bartolomé S, Bamberger C, Yates JR.

Curr Opin Chem Biol. 2018 Oct 8;48:19-25. doi: 10.1016/j.cbpa.2018.09.016. [Epub ahead of print] Review.


Innovation: Structural Proteomics Goes Global.

Yates JR 3rd.

J Proteome Res. 2018 Nov 2;17(11):3613. doi: 10.1021/acs.jproteome.8b00698. Epub 2018 Oct 10. No abstract available.


Social reinstatement: a rat model of peer-induced relapse.

Weiss VG, Yates JR, Beckmann JS, Hammerslag LR, Bardo MT.

Psychopharmacology (Berl). 2018 Dec;235(12):3391-3400. doi: 10.1007/s00213-018-5048-8. Epub 2018 Oct 6.


Proteomic analysis identifies highly expressed plasma membrane proteins for detection and therapeutic targeting of specific breast cancer subtypes.

Ziegler YS, Moresco JJ, Tu PG, Yates JR 3rd, Nardulli AM.

Clin Proteomics. 2018 Sep 19;15:30. doi: 10.1186/s12014-018-9206-0. eCollection 2018.


Characterization of a novel antioxidant peptide from feather keratin hydrolysates.

Fontoura R, Daroit DJ, Corrêa APF, Moresco KS, Santi L, Beys-da-Silva WO, Yates JR 3rd, Moreira JCF, Brandelli A.

N Biotechnol. 2018 Sep 14. pii: S1871-6784(18)30154-7. doi: 10.1016/j.nbt.2018.09.003. [Epub ahead of print]


Proteins that control the geometry of microtubules at the ends of cilia.

Louka P, Vasudevan KK, Guha M, Joachimiak E, Wloga D, Tomasi RF, Baroud CN, Dupuis-Williams P, Galati DF, Pearson CG, Rice LM, Moresco JJ, Yates JR 3rd, Jiang YY, Lechtreck K, Dentler W, Gaertig J.

J Cell Biol. 2018 Dec 3;217(12):4298-4313. doi: 10.1083/jcb.201804141. Epub 2018 Sep 14.


MIEF1 Microprotein Regulates Mitochondrial Translation.

Rathore A, Chu Q, Tan D, Martinez TF, Donaldson CJ, Diedrich JK, Yates JR 3rd, Saghatelian A.

Biochemistry. 2018 Sep 25;57(38):5564-5575. doi: 10.1021/acs.biochem.8b00726. Epub 2018 Sep 14.


Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer.

Cao L, Pauthner M, Andrabi R, Rantalainen K, Berndsen Z, Diedrich JK, Menis S, Sok D, Bastidas R, Park SR, Delahunty CM, He L, Guenaga J, Wyatt RT, Schief WR, Ward AB, Yates JR 3rd, Burton DR, Paulson JC.

Nat Commun. 2018 Sep 12;9(1):3693. doi: 10.1038/s41467-018-06121-4.


Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway.

Wang Z, Wu C, Aslanian A, Yates JR 3rd, Hunter T.

Elife. 2018 Sep 7;7. pii: e35447. doi: 10.7554/eLife.35447.


An NMR crystallography investigation of furosemide.

Zilka M, Yates JR, Brown SP.

Magn Reson Chem. 2018 Aug 23. doi: 10.1002/mrc.4789. [Epub ahead of print]


Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos.

Mutlu B, Chen HM, Moresco JJ, Orelo BD, Yang B, Gaspar JM, Keppler-Ross S, Yates JR 3rd, Hall DH, Maine EM, Mango SE.

Sci Adv. 2018 Aug 22;4(8):eaat6224. doi: 10.1126/sciadv.aat6224. eCollection 2018 Aug.


CBD-1 organizes two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans.

González DP, Lamb HV, Partida D, Wilson ZT, Harrison MC, Prieto JA, Moresco JJ, Diedrich JK, Yates JR 3rd, Olson SK.

Dev Biol. 2018 Oct 15;442(2):288-300. doi: 10.1016/j.ydbio.2018.08.005. Epub 2018 Aug 16.


An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches.

Diniz MRV, Paiva ALB, Guerra-Duarte C, Nishiyama MY Jr, Mudadu MA, Oliveira U, Borges MH, Yates JR, Junqueira-de-Azevedo IL.

PLoS One. 2018 Aug 1;13(8):e0200628. doi: 10.1371/journal.pone.0200628. eCollection 2018.


Structural Analysis of Hippocampal Kinase Signal Transduction.

McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier AR, Lavalle-Adam M, Powell SB, Roberto M, Yates JR.

ACS Chem Neurosci. 2018 Aug 13. doi: 10.1021/acschemneuro.8b00284. [Epub ahead of print]


Quantitative analysis of newly synthesized proteins.

Ma Y, McClatchy DB, Barkallah S, Wood WW, Yates JR 3rd.

Nat Protoc. 2018 Aug;13(8):1744-1762. doi: 10.1038/s41596-018-0012-y.


Effects of GluN2B-selective antagonists on delay and probability discounting in male rats: Modulation by delay/probability presentation order.

Yates JR, Prior NA, Chitwood MR, Day HA, Heidel JR, Hopkins SE, Muncie BT, Paradella-Bradley TA, Sestito AP, Vecchiola AN, Wells EE.

Exp Clin Psychopharmacol. 2018 Dec;26(6):525-540. doi: 10.1037/pha0000216. Epub 2018 Jul 23.


Innovations in Proteomics: The Drive to Single Cells.

Yates JR 3rd.

J Proteome Res. 2018 Aug 3;17(8):2563-2564. doi: 10.1021/acs.jproteome.8b00484. Epub 2018 Jul 19. No abstract available.


Quantitative temporal analysis of protein dynamics in cardiac remodeling.

McClatchy DB, Ma Y, Liem DA, Ng DCM, Ping P, Yates JR 3rd.

J Mol Cell Cardiol. 2018 Aug;121:163-172. doi: 10.1016/j.yjmcc.2018.07.126. Epub 2018 Jul 19.


Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?

Ma Y, Yates JR 3rd.

Expert Rev Proteomics. 2018 Jul;15(7):545-554. doi: 10.1080/14789450.2018.1500902. Epub 2018 Jul 23.


The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.

Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S.

Sci Transl Med. 2018 Jul 4;10(448). pii: eaat0381. doi: 10.1126/scitranslmed.aat0381.


Nanoscale momentum-resolved vibrational spectroscopy.

Hage FS, Nicholls RJ, Yates JR, McCulloch DG, Lovejoy TC, Dellby N, Krivanek OL, Refson K, Ramasse QM.

Sci Adv. 2018 Jun 15;4(6):eaar7495. doi: 10.1126/sciadv.aar7495. eCollection 2018 Jun.


Publisher Correction: ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase.

Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR 3rd, Fredrick K, Schimmel P, Ackerman SL.

Nature. 2018 Aug;560(7720):E35. doi: 10.1038/s41586-018-0271-3.


NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells.

Richard P, Ogami K, Chen Y, Feng S, Moresco JJ, Yates JR 3rd, Manley JL.

RNA Biol. 2018;15(7):868-876. doi: 10.1080/15476286.2018.1467180. Epub 2018 Aug 2.


Deducing the presence of proteins and proteoforms in quantitative proteomics.

Bamberger C, Martínez-Bartolomé S, Montgomery M, Pankow S, Hulleman JD, Kelly JW, Yates JR 3rd.

Nat Commun. 2018 Jun 13;9(1):2320. doi: 10.1038/s41467-018-04411-5.


Secular changes in severity of intellectual disability in tuberous sclerosis complex: A reflection of improved identification and treatment of epileptic spasms?

Tye C, Thomas LE, Sampson JR, Lewis J, O'Callaghan F, Yates JRW, Bolton PF.

Epilepsia Open. 2018 Apr 6;3(2):276-280. doi: 10.1002/epi4.12111. eCollection 2018 Jun.


Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme.

Nishimura N, Tsuchiya W, Moresco JJ, Hayashi Y, Satoh K, Kaiwa N, Irisa T, Kinoshita T, Schroeder JI, Yates JR 3rd, Hirayama T, Yamazaki T.

Nat Commun. 2018 Jun 6;9(1):2132. doi: 10.1038/s41467-018-04437-9.


Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer.

Zhu Q, Hoong N, Aslanian A, Hara T, Benner C, Heinz S, Miga KH, Ke E, Verma S, Soroczynski J, Yates JR 3rd, Hunter T, Verma IM.

Mol Cell. 2018 Jun 7;70(5):842-853.e7. doi: 10.1016/j.molcel.2018.04.023. Epub 2018 May 31.


SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy.

Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR 3rd, Jones KA.

PLoS Pathog. 2018 May 23;14(5):e1007071. doi: 10.1371/journal.ppat.1007071. eCollection 2018 May.


ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase.

Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR 3rd, Fredrick K, Schimmel P, Ackerman SL.

Nature. 2018 May;557(7706):510-515. doi: 10.1038/s41586-018-0137-8. Epub 2018 May 16. Erratum in: Nature. 2018 Aug;560(7720):E35.


PML Recruits TET2 to Regulate DNA Modification and Cell Proliferation in Response to Chemotherapeutic Agent.

Song C, Wang L, Wu X, Wang K, Xie D, Xiao Q, Li S, Jiang K, Liao L, Yates JR 3rd, Lee JD, Yang Q.

Cancer Res. 2018 May 15;78(10):2475-2489. doi: 10.1158/0008-5472.CAN-17-3091. Epub 2018 May 7.


Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.

Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR 3rd, Li JJ, Madhani HD.

Cell. 2018 May 3;173(4):1014-1030.e17. doi: 10.1016/j.cell.2018.03.020.


Global site-specific analysis of glycoprotein N-glycan processing.

Cao L, Diedrich JK, Ma Y, Wang N, Pauthner M, Park SR, Delahunty CM, McLellan JS, Burton DR, Yates JR, Paulson JC.

Nat Protoc. 2018 Jun;13(6):1196-1212. doi: 10.1038/nprot.2018.024. Epub 2018 May 3.


Content Is King: Databases Preserve the Collective Information of Science.

Yates JR 3rd.

J Biomol Tech. 2018 Apr;29(1):1-3. doi: 10.7171/jbt.18-2901-002. Epub 2018 Mar 22.


Effects of N-methyl-d-aspartate receptor (NMDAr) uncompetitive antagonists in a delay discounting paradigm using a concurrent-chains procedure.

Yates JR, Gunkel BT, Rogers KK, Breitenstein KA, Hughes MN, Johnson AB, Sharpe SM.

Behav Brain Res. 2018 Sep 3;349:125-129. doi: 10.1016/j.bbr.2018.03.039. Epub 2018 Mar 28.


PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

Martínez-Bartolomé S, Medina-Aunon JA, López-García MÁ, González-Tejedo C, Prieto G, Navajas R, Salazar-Donate E, Fernández-Costa C, Yates JR 3rd, Albar JP.

J Proteome Res. 2018 Apr 6;17(4):1547-1558. doi: 10.1021/acs.jproteome.7b00858. Epub 2018 Mar 28.


A proteomic insight into vitellogenesis during tick ovary maturation.

Xavier MA, Tirloni L, Pinto AFM, Diedrich JK, Yates JR 3rd, Mulenga A, Logullo C, da Silva Vaz I Jr, Seixas A, Termignoni C.

Sci Rep. 2018 Mar 16;8(1):4698. doi: 10.1038/s41598-018-23090-2.


Publisher Correction: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, Vargas-Rodriguez O, Diedrich JK, Yates JR 3rd, Kishi S, Musier-Forsyth K, Schimmel P.

Nat Commun. 2018 Mar 13;9(1):1113. doi: 10.1038/s41467-018-03594-1.


Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na+/K+ transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses.

Iwasaki M, Minder P, Caì Y, Kuhn JH, Yates JR 3rd, Torbett BE, de la Torre JC.

PLoS Pathog. 2018 Feb 20;14(2):e1006892. doi: 10.1371/journal.ppat.1006892. eCollection 2018 Feb.


Increased proteomic complexity in Drosophila hybrids during development.

Bamberger C, Martínez-Bartolomé S, Montgomery M, Lavallée-Adam M, Yates JR 3rd.

Sci Adv. 2018 Feb 7;4(2):eaao3424. doi: 10.1126/sciadv.aao3424. eCollection 2018 Feb.


The Speed of Publication.

Yates JR 3rd.

J Proteome Res. 2018 Mar 2;17(3):935. doi: 10.1021/acs.jproteome.8b00044. Epub 2018 Feb 8. No abstract available.


Role of the visual experience-dependent nascent proteome in neuronal plasticity.

Liu HH, McClatchy DB, Schiapparelli L, Shen W, Yates JR 3rd, Cline HT.

Elife. 2018 Feb 7;7. pii: e33420. doi: 10.7554/eLife.33420.


Tick-Host Range Adaptation: Changes in Protein Profiles in Unfed Adult Ixodes scapularis and Amblyomma americanum Saliva Stimulated to Feed on Different Hosts.

Tirloni L, Kim TK, Pinto AFM, Yates JR 3rd, da Silva Vaz I Jr, Mulenga A.

Front Cell Infect Microbiol. 2017 Dec 19;7:517. doi: 10.3389/fcimb.2017.00517. eCollection 2017.


Dissecting drug effects in preclinical models of impulsive choice: emphasis on glutamatergic compounds.

Yates JR.

Psychopharmacology (Berl). 2018 Mar;235(3):607-626. doi: 10.1007/s00213-017-4825-0. Epub 2018 Jan 6. Review.


Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, Vargas-Rodriguez O, Diedrich JK, Yates JR, Kishi S, Musier-Forsyth K, Schimmel P.

Nat Commun. 2017 Dec 22;8(1):2281. doi: 10.1038/s41467-017-02201-z. Erratum in: Nat Commun. 2018 Mar 13;9(1):1113.

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