Published Works
  • 2010 - present

518. Markus Englert, Kelly Sheppard, Aaron Aslanian, John Yates 3rd, Dieter Söll, Archaeal 3’-phosphate tRNA splicing ligase characterization identifies the missing component in tRNA maturation, PNAS (submitted)

517. Sidonie Wicky John, Hendri Tjandra, David Schieltz, John Yates III, and Douglas R. Kellogg, The Zds proteins control entry into mitosis and target protein phosphatase 2A to the Cdc25 phosphatase (accepted for publication)

516. Daniel B. McClatchy, Lujian Liao,Sung Kyu Park, Tao Xu, Bingwen Lu and John R. Yates III, Differential proteomic analysis of mammalian tissues using SILAM. PloSOne (in press)

515. Samuel L. Hutson, Ernest Mui, Karen Kinsley, William H. Witola, Michael S. Behnke, Kamal El Bissati, Stephen P. Muench, Brittany Rohrman, Susan R. Liu, Robert Wollmann, Yuko Ogata, Ali Sarkeshik, John R. Yates III, and Rima McLeod, T. gondii RP Promoters & Knockdown Reveal Molecular Pathways Associated with Proliferation and Cell-cycle Arrest, PloSOne (in press)

514. Paulo C Carvalho, Juliana S G Fischer, Jonas Perales, John R Yates III, Valmir C Barbosa, Elias Bareinboim, Analyzing marginal cases in differential shotgun proteomics, Bioinformatics (submitted)

513. Alphée Michelot, Michael Costanzo, Ali Sarkeshik, Charles Boone, John R. Yates III and David G. Drubin, Reconstitution and Protein Composition Analysis of Endocytic Actin Patches. Current Biology. (in press).

512. Juliana de Saldanha da Gama Fischer 1,2, Paulo Costa Carvalho 1,3, Clovis Orlando da Fonseca4, Lujian Liao5, Maria da Gloria da Costa Carvalho6, Wim M Degrave2, John R Yates III4, and Gilberto B. Domont 7 A chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol, Journal of Proteome Research (in press)

511. Kristen Witte, Amber L. Schuh, Ali Sarkeshik, Jan Hegermann, Jonathan R. Mayers, Katrin Schwarze, John R. Yates III, Stefan Eimer, and Anjon Audhya, Mechanisms by which TFG functions in protein secretion and oncogenesis, Nature Cell Biology (submitted)

510. Roberts-Galbraith RH, Ohi MD, Ballif BA, Chen JS, McLeod I, McDonald WH, Gygi SP, Yates JR 3rd, Gould KL., Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site., Mol Cell. 2010, 39, 86-99

509. Welburn JP, Vleugel M, Liu D, Yates JR 3rd, Lampson MA, Fukagawa T, Cheeseman IM., Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface., Mol Cell. 2010, 38, 383-92.

508. Nakorchevsky A, Hewel JA, Kurian SM, Mondala TS, Campbell D, Head SR, Marsh CL, Yates JR 3rd, Salomon DR., Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies. J Am Soc Nephrol. 2010, 21, 362-73.

507. Zhenming Xu, Zsolt Fulop1§, Guikai Wu, Egest J. Pone, Jinsong Zhang, Thach Mai, Lisa M. Thomas, Ahmed Al-Qahtani, Clayton A. White, Seok-Rae Park¶, Petra Steinacker, Zenggang Li, John Yates, III, Bruce Herron, Markus Otto, Hong Zan, Haian Fu & Paolo Casali, 14-3-3 adaptor proteins recruit AID to 5''-AGCT-3'-rich switch regions for class switch recombination, Nature Structural and Molecular Biology (in press)

506. Huang, H.*, Jeon, M.*, Liao, L.*, Yang, C.*, Elly, C., Yates, J.R., and Liu YC. Unconventional K33-linked polyubiquitination of TCR? regulates T cell activation by modulating endocytosis-independent TCR phosphorylation. Immunity. (accepted)

505. Pham, Emiley; Crews, Leslie; Ubhi, Kiren; Hansen, Lawrence; Adame, Anthony; Cartier, Anna; Salmon, David; Galasko, Douglas; Michael, Sarah; Savas, Jeffrey; Yates, John; Glabe, Charles; Masliah, Eliezer, Progressive accumulation of amyloid-ß oligomers in Alzheimer’s disease and APP transgenic mice is accompanied by selective alterations in synaptic scaffold proteins, FEBS (in press)

504. Kops GJ, van der Voet M, Manak MS, van Osch MH, Naini SM, Brear A, McLeod IX, Hentschel DM, Yates JR 3rd, van den Heuvel S, Shah JV., APC16 is a conserved subunit of the anaphase-promoting complex/cyclosome. J Cell Sci. 2010, 123, 1623-33.

503. Bryan R. Fonslow, Seong A. Kang, Daniel R. Gestaut, Beth Graczyk, Trisha N. Davis, David M. Sabatini, and John R. Yates III, Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes, Analytical Chemistry 2010, 82, 6643-51.

502. Louis Alexander Saddic; Lisandra E. West; Aaron Aslanian; John Yates; Seth M. Rubin; Or Gozani, Julien Sage, Methylation of the retinoblastoma tumor suppressor by SMYD2, Journal of Biological Chemistry, M110.137612 First Published on September 24, 2010,

501. Junling Wang, Xuemei Han, Sougata Saha, Tao Xu, Reena Rai, Fangliang Zhang, Yuri. I. Wol3, Alexey Wolfson, John R. Yates, III, and Anna Kashina, Arginyltransferase is an atp-independent self-regulating enzyme that forms distinct functional complexes in vivo, Chemistry and Biology (in press)

500. Lemmuel L. Tayo†§, Bingwen Lu¶, Lourdes J. Cruz§, John R. Yates III, Proteomic Analysis Provides Insights on Venom Processing in Conus textile, Journal of Proteome Research 2010, 9, 2292-301

499. Ophelia Papoulas, Kate Monzo, Greg Cantin, Cristian Ruse, John Yates, III, and John Sisson.dFMRP and Caprin, Translational Regulators of Synaptic Plasticity, Control the Cell Cycle Machinery at the Drosophila Mid-blastula Transition. PLos Biology (submitted)

498. James J. Moresco, Paulo C. Carvalho and John R. Yates, III, Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry, Journal of Proteomics 2010, (in press).

497. Graham M. West,† Chandra L. Tucker,§ Tao Xu,‡ Sung Kyu Park,‡ Xuemei Han,‡ John R. Yates III,‡ and Michael C. Fitzgerald, A Quantitative Proteomics Approach for Identifying Protein-Drug Interactions in Complex Mixtures using Protein Stability Measurements, PNAS 2010, 107, 9078-82.

496. T.N.C. Ramyaa, Eranthie Weerapanaa,b, Lujian Liaoa, Ying Zenga, Hiroaki Tatenoa, Liang Liaoa, Shoufa Hana, John R. Yates IIIa, Benjamin F. Cravatta,b and James C. Paulsona,1 In situ trans ligands of CD22 identified by glycan-protein photo-cross-linking enabled proteomics, Molecular and Cellular Proteomics 2010, 9, 1339-51.

495. Kiran S. Ambatipudi#, Fred K. Hagen?,?, Claire M. Delahunty§, Xuemei Han§, Rubina Shafi*, Jennifer Hryhorenko*, Stacy Gregoire*, Robert E. Marquis¥, James E. Melvin#, Hyun Koo*,¥, John R. Yates, III, Human Common Salivary Protein 1 (CSP-1) Promotes Binding of Streptococcus mutans to Experimental Salivary Pellicle and Glucans Formed on Hydroxyapatite Surface, Molecular and Cellular Proteomics (submitted)

494. Juliana de Saldanha da Gama Fischer1,2, Lujian Liao2, Paulo C. Carvalho2,3, Valmir C Barbosa3, Gilberto B. Domont1, Maria da Gloria da Costa Carvalho4, and John R Yates III2,*, Dynamic Proteomic Overview of Glioblastoma Cells (A172) Exposed to Perillyl Alcohol Journal of Proteomics, Journal of Proteomics (in press)

493. Yingchun Wang, Hop Tran Cao, Greg Cantin, Rui Lin, Wei Wang, Sharmeela Kaushal, Jonathan Kelber, Thomas Edgington, Robert Hoffman, Michael Bouvet, John Yates III, Richard Klemke, PEAK1, a new kinase that regulates cytoskeleton, Proc Natl Acad Sci USA 2010, 107, 10920-5

492. Casimir Bamberger, Sandra Pankow, Tao Xu, Sung Kyu Park and John R. Yates III, p63 surveys the Mobilome to enable Germ Cell Immortality, (to be submitted)

491. Paulo C Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria da Gloria da Costa Carvalho, Valmir C Barbosa, and John R Yates, III, XDIA: Improving on the label-free data-independent analysis, Bioinformatics 2010, 26, 847-8.

486. Hutt DM, Herman D, Rodrigues AP, Noel S, Pilewski JM, Matteson J, Hoch B, Kellner W, Kelly JW, Schmidt A, Thomas PJ, Matsumura Y, Skach WR, Gentzsch M, Riordan JR, Sorscher EJ, Okiyoneda T, Yates JR 3rd, Lukacs GL, Frizzell RA, Manning G, Gottesfeld JM, Balch WE, Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nature Chemical Biology. 2010; 6, 25-33.

485. Miller*, Timothy M.1,2, Vande Velde*, Christine1,3, Li, Quan2, Xie, Jing5 , Bailey, Aaron, O4., Dong, Meng-Qui4, Chun, Seung-Joo2, Roy, Tamal1, Yates, John R4, Capaldi, Rod A5 and Cleveland, Don W.1 ALS-linked mutant SOD1 alters mitochondrial protein composition and decreases protein import and complex I activity. PNAS (to be submitted)

478. Koulov AV, Lapointe P, Lu B, Razvi A, Coppinger J, Dong MQ, Matteson J, Laister R, Arrowsmith C, Yates JR 3rd, Balch WE., Biological and Structural Basis for Aha1 Regulation of Hsp90 ATPase Activity in Maintaining Proteostasis in the Human Disease Cystic Fibrosis. Mol Biol Cell. 2010, 21, 871-84.

477. Chang-Young Jang, Judith A. Coppinger, John R. Yates III and Guowei Fang, Phospho-Regulation of DDA3 Function in Mitosis. Biochem Biophys Res Commun. 2010 Feb 1. [Epub ahead of print]

475. Nishimura, Noriyuki; Sarkeshik, Ali; Nito, Kazumasa; Park, Sang-Youl; Wang, Angela; Carvalho, Paulo; Lee, Stephen; Cutler, Sean; Chory, Joanne; Yates, John; Schroeder, Julian Corresponding Author: Julian Schroeder, PYR/PYL/RACR family members are major in vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant Journal 2010, 61, 290-299.

446. Kristina Herzberg1,#, Michael Rolfsmeier1,#, Ryan Janke1, Jordan Mar1, Vladimir I. Bashkirov1,#, Edwin Haghnazari1,# Greg Cantin3, John R. Yates 3rd3, and Wolf-Dietrich Heyer, A truncated DNA damage signaling response is activated after DSB formation in the G1 phase of Saccharomyces cerevisiae Nucleic Acid Research 2010, 38, 2302-13.

439. Stephen P. Baker, Jennifer Phillips, Scott Anderson, John R. Yates 3rd, Jeffrey Shabanowitz, Donald F. Hunt, Patrick A. Grant; Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae, Nature Cell Biology 2010, 12, 294-8

437. Laurie S. Minamide, Sankar Maiti, Judith A. Boyle, Richard C. Davis, Judith A. Coppinger, Yunhe Bao, Timothy Huang, John Yates, Gary Bokoch and James R. Bamburg, Isolation and Characterization of Cofilin-Actin Rods, J. Biological Chemistry 2010, 285, 5450-60.

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