Published Works
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • 2003
  • 2002
  • 2001
  • 2000

490. Grigoryev YA, Kurian SM, Nakorchevskiy AA, Burke JP, Campbell D, Head SR, Deng J, Kantor AB, Yates JR 3rd, Salomon DR., Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes. PLoS One. 2009, 4, e7906.

489. Hou H, Wang Y, Kallgren SP, Thompson J, Yates JR, Jia S., Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast. J Biol Chem. 2009 Nov 12.

488. Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT., Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl. 2009, 3, 116-134.

487. Dovey CL, Aslanian A, Sofueva S, Yates JR 3rd, Russell P., Mms1-Mms22 complex protects genome integrity in Schizosaccharomyces pombe., DNA Repair 2009, 8, 1390-9.

484. Joris de Wit1, Emily Sylwestrak1,4, Matthew L. O’Sullivan1,4, Stefanie Otto1, Katie Tiglio1, Jeffrey N. Savas2, John R. Yates III2, Davide Comoletti3, Palmer Taylor3, and Anirvan Ghosh, LRRTM2 interacts with Neurexin1 and Regulates Excitatory Synapse Formation, Neuron 2009, 64, 799-806.

483. Li J, Cai T, Wu P, Cui Z, Chen X, Hou J, Xie Z, Xue P, Shi L, Liu P, Yates JR 3rd, Yang F. Proteomic analysis of mitochondria from Caenorhabditis elegans., Proteomics. 2009, 9, 4539-53.

482. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR 3rd, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell. 2009, 35, 868-80

481. Gu W, Shirayama M, Conte D Jr, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Falgren N, Yates JR 3rd, Mitani S, Carrington JC, Mello CC., Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline. Mol Cell. 2009, 36, 231-44.

480. Kiran S. Ambatipudi#, Bingwen Lu*, Fred K Hagen#, James E. Melvin#, John R. Yates III*§, Quantitative Analysis of Age Specific Variation in the Abundance of Human Female Parotid Salivary Proteins, J. Proteome Research 2009, 8, 5093-102.

479. Kim, Byung-Gyu; Lee, Ji-Hyun; Ahn, Jung-Mo; Park, Sung-Kyu; Cho, Ji-Hoon; Hwang, Daehee; Yoo, Jong Shin; Yates, John; Ryoo, Hyun-Mo; Cho, Je-Yoel, Two-Stage Double-Technique Hybrid (TSDTH) identification strategy for the analysis of BMP2-induced transdifferentiation of premyoblast C2C12 cells to osteoblast, J. Proteome Research 2009, 8, 4441-4454

476. Guang-Hui Liu, Tinglu Guan, Kaustuv Datta, Judith Coppinger, John Yates III, Larry Gerace, Regulation of Myoblast Differentiation by the Nuclear Envelope Protein NET39. Mol Cell Biol. 2009, 29, 5800-12

474. Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR 3rd, Frank J, Manley JL., Molecular architecture of the human pre-mRNA 3' processing complex. Molecular Cell. 2009, 33, 365-76.

473. Shock TR, Thompson J, Yates JR 3rd, Madhani HD., Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity, Eukaryotic Cell. 2009, 8, 606-16.

471. Gonzalez-Begne M, Lu B, Han X, Hagen FK, Hand AR, Melvin JE, Yates JR. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT)., J Proteome Res. 2009, 8, 1304-14.

467. Wang Y, Reddy B, Thompson J, Wang H, Noma K, Yates JR 3rd, Jia S., Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein., Molecular Cell. 2009, 33, 428-37.

466. Cui Z, Chen X, Lu B, Park SK, Xu T, Xie Z, Xue P, Hou J, Hang H, Yates JR 3rd, Yang F., Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture., Proteomics. 2009, 9, 1274-92

465. Chen RQ, Yang QK, Lu BW, Yi W, Cantin G, Chen YL, Fearns C, Yates JR 3rd, Lee JD., CDC25B mediates rapamycin-induced oncogenic responses in cancer cells., Cancer Res. 2009, 69, 2663-8.

464. Chen Y, Lu B, Yang Q, Fearns C, Yates JR 3rd, Lee JD., Combined integrin phosphoproteomic analyses and small interfering RNA--based functional screening identify key regulators for cancer cell adhesion and migration. Cancer Res. 2009, 69, 3713-20.

463. Fonslow BR, Yates JR 3rd., Capillary electrophoresis applied to proteomic analysis., J Separation Science. 2009, 32, 1175-88.

462. Yates JR, Ruse CI, Nakorchevsky A., Proteomics by mass spectrometry: approaches, advances, and applications., Annu Rev Biomed Eng. 2009, 11, 49-79.

461. Curtis CD, Thorngren DL, Ziegler YS, Sarkeshik A, Yates JR, Nardulli AM., Apurinic/Apyrimidinic Endonuclease 1 Alters Estrogen Receptor Activity and Estrogen Responsive Gene Expression., Mol Endocrinol. 2009 May 21. [Epub ahead of print]

460. Choi SH, Péli-Gulli MP, Mcleod I, Sarkeshik A, Yates JR 3rd, Simanis V, McCollum D. Phosphorylation state defines discrete roles for monopolin in chromosome attachment and spindle elongation. Current Biology. 2009, 19, 985-95.

459. Carvalho PC, Fischer JS, Chen EI, Domont GB, Carvalho MG, Degrave WM, Yates JR 3rd, Barbosa VC., GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data, Proteome Sci. 2009, 7, 6.

458. Paulo C Carvalho1,2*, Tao Xu2, Xuemei Han2, Daniel Cociorva2, Valmir C Barbosa1, and John R Yates, III2, YADA: A tool for taking the most out of high-resolution spectra, Bioinformatics 2009 25, 2734-2736

457. CJ, Wolf A, Gromak N, Dreger M, Kramer H, Kessler B, Nielsen ML, Schmitz C, Butler DS, Yates JR 3rd, Delahunty CM, Hahn P, Lengeling A, Mann M, Proudfoot NJ, Schofield CJ, Böttger A.,, Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing.Webby. Science. 2009, 325, 90-3.

456. Daniel B. McClatchy, Lujian Liao, Sung Kyu Park, and John R. Yates III, Global Quantitative Analysis of Discrete Brain Proteomes during Brain Development, Neuron (submitted)

455. Tomohiro Nakamura, Lei Wang, Catherine C. L. Wong, Fiona L. Scott, Brendan P. Eckelman, Xuemei Han, Christos Tzitzilonis, Arjay T. Clemente, Shu-ichi Okamoto, Guy S. Salvesen, Roland Riek, John R. Yates, III, and Stuart A. Lipton, Transnitrosylation of XIAP Regulates Caspase-Dependent Neuronal Cell Death, Molecular Cell (in press)

454. Alexander Dammermann, Hayley Pemble, Brian J. Mitchell, Ian McLeod, John R. Yates III, Chris Kintner, Arshad B. Desai, Karen Oegema, The Hydrolethalus Syndrome Protein HYLS-1 Links Core Centriole Structure To Cilia Formation, Genes and Development 2009, 23, 2046-59

453. Stefano Maffini, Ana R. R. Maia, Amity L. Manning, Zoltan Maliga, Ana L. Pereira, Magno Junqueira, Andrej Shevchenko, Anthony Hyman, John R. Yates III, Niels Galjart, Duane A. Compton, Helder Maiato, Motor-independent targeting of CLASPs to kinetochores by CENP-E promotes microtubule turnover and poleward flux, Current Biology 2009, 19, 1566-72

452. Rodriguez H, Snyder M, Uhle´n M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Ponte´n F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R., Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles., J Proteome Res. 2009, 8, 3689-3692.

451. Liao, Lujian*, McClatchy, Daniel B.*, and Yates, John R., Primer: Shotgun Proteomics in Neuroscience, Neuron 2009, 63, 12-26.

450. Sasa Koncarevic, Petra Rohrbach, Marcel Deponte, Georg Krohne, Judith Prieto, John Yates III, Stefan Rahlfs, Katja Becker, The malarial parasite P. falciparum imports the human protein peroxiredoxin 2 for peroxide detoxification, PNAS 2009, 106, 13323-8.

449. Daniel R. Foltz, Lars E.T. Jansen, Aaron O. Bailey, John R. Yates III, Emily A. Bassett, Stacey Wood, Ben E. Black, and Don W. Cleveland, Centromere-Specific Assembly of CENP-A Nucleosomes Is Mediated by HJURP, Cell 2009, 137, 472-84.

445. Samira Fekairi, Sarah Scaglione, Charly Chahwan, Ewan R. Taylor, Agnès Tissier, Stéphane Coulon, Meng-Qiu Dong, Cristian Ruse, John R. Yates III, Paul Russell, Robert P. Fuchs, Clare H. McGowan, Pierre-Henri L. Gaillard, Human SLX4 is a Holliday Junction Resolvase Subunit that Binds Multiple DNA Repair/Recombination Endonucleases, Cell 2009, 138, 78-89

444. Welburn, J. P. I., E. L. Grishchuk, C. B. Backer, E. M. Wilson- Kubalek, J. R. Yates III, and I. M. Cheeseman (2009). “The human kinetochore Ska1 complex facilitates microtubule depolymerization- coupled motility”. Developmental Cell 16 (3): 374-385.

443. Robin J. Rosenfeld, Joseph Bonaventura, Michael J. MacCoss, Andrew S. Arvai, John R. Yates III, John A. Tainer, Elizabeth D. Getzoff, Inducible nitric oxide synthase mechanism and allosteric regulation modulated by N-NO-pterin and S-NO-Cys, J. Biological Chemistry ( submitted)

442. Qingkai Yang1,6, Xianming Deng4,6, Bingwen Lu2,6, Michael Cameron5, Colleen Fearns3, John R. Yates III2, Nathanael S. Gray4 and Jiing-Dwan Lee, BMK1 promotes tumorigenicity by suppressing PML IV activity (to be submitted)

441. Cornillez-Ty CT, Liao L, Yates JR 3rd, Kuhn P, Buchmeier MJ., SARS Coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling. J Virology. 2009, 83, 10314-8.

440. Wong CCL, Cociorva D, Xu T, Venable J, Yates JR 3rd, Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures, Journal of the American Society for Mass Spectrometry, 2009, 20, 1405-14

438. Li-Chiou Chuang1+, Leonardo K. Teixeira1+, James A. Wohlschlegel1,2,3, Martha Henze1, John Yates2, Juan Méndez4, and Steven I. Reed1*, Phosphorylation of MCM2 by Cdc7 promotes pre-replication complex assembly, Molecular Cell 2009, 35, 206-16.

436. Chang-Young Jang, Judith A. Coppinger, Akiko Seki, John R. Yates III and Guowei Fang, Plk1 and Aurora A Regulate the Depolymerase Activity and the Cellular Localization of Kif2a, Journal of Cell Science 2009, 122, 1334-41

435. Paulo C Carvalho1,2, Daniel Cociorva2, Catherine Wong2, Maria da Gloria da C Carvalho3, Joshua Coon4, Valmir C Barbosa1, John R. Yates, III, Charge Prediction Machine: A tool for inferring precursor charge states of Electron Transfer Dissociation tandem mass spectra Analytical Chemistry 2009 Feb 9. [Epub ahead of print]

432. Jiou Wang, George Farr, Caroline Zeiss, Diego J. Rodriguez-Gil, Jean H. Wilson, Krystyna Furtak, D. Thomas Rutkowski, Randal J. Kaufman, Cristian I. Ruse, John R. Yates, III, Steve Perrin, Mel B. Feany, and Arthur Horwich, Optical and proteomic analyses of a misfolded SOD1-YFP fusion protein in transgenic mice that develop ALS reveal progressive aggregation despite chaperone associations. Proc Natl Acad Sci USA. 2009, 106, 1392-7.

426. Weihong Yan1, Rolf Apweiler10, Brian M. Balgley5, Pinmanee Boontheung1, Jonathan L. Bundy8, Benjamin J. Cargile8, Steve Cole3, Xueping Fang4, Mireya Gonzalez-Begne13, Timothy J. Griffin6, Fred Hagen13, Shen Hu3, Cheng S. Lee4, Daniel Malamud9, James E. Melvin13, Rajasree Menon11, Michael Mueller10, Renli Qiao14, Nelson L. Rhodus7, Joel R. Sevinsky8, David States11, James L. Stephenson, Jr.8, Shawn Than3, John R. Yates, III12,Weixia Yu3, Hongwei Xie6, Yongming Xie1, Gilbert S. Omenn11, Joseph A. Loo1,2, and David T. Wong3, Systematic Comparison of the Human Saliva and Plasma Proteomes Proteomics: Clinical Applications, 2009, 3, 116-134

425. Sougata Saha1#, Catherine C. L. Wong2#, Tao Xu2#, Henry Zebroski3, John R. Yates, III2, and Anna Kashina1*, Arginylation meets methylation: double posttranslational regulation of proteins in vivo, Science (to be submitted)

424. Sunil Kurian, Raymond Heilman, Tony Mondala, Aleksey Nakorchevsky, Johannes Hewel, Daniel Campbell, Elizabeth Robison, Lin Wang, Lillian Gaber, Kim Solez, Hamid Shidban, Robert Mendez, Randall Schaffer, Jonathan Fisher, Stuart Flechner, Steve Head, Steve Horvath, John Yates III, Christopher Marsh and Daniel R. Salomon, Candidate Biomarkers for Early and Late Stage Chronic Allograft Nephropathy by Proteogenomic Profiling of Peripheral Blood, PLoS ONE, 2009, 4, e6212

418. Tao Xu1*, Catherine C.L. Wong1*, Anna Kashina2,3, and John R. Yates, III, Identification of N-terminally arginylated proteins and peptides by mass spectrometry Nature Protocols 2009, 4, 325-32.

417. Yuko Nakajima*, Randall G. Tyers*, Catherine C. L. Wong†, John R. Yates III†, David G. Drubin* and Georjana Barnes, Nbl1p: A Borealin/Dasra/CSC-1-like Protein Essential for Aurora/Ipl1 Complex Function and Integrity in Saccharomyces cerevisiae, Molecular Biology of the Cell 2009, 6, 1772-84.

416. Jourdain, I., Nathalie Spielewoy1, James Thompson2, Susheela Dhut1, John R. Yates III2, and Takashi Toda, Identification of a conserved F-box protein 6 interactor essential for endocytosis and cytokinesis in fission yeast, Biochem J. 2009, 420, 169-77.

404. Devenport, M., Dinglasan, R.R., Florens, L., Johnson, J.R., McHugh, C., Donnelly-Doman, M., Carucci, D.J., Yates, J.R., III, Jacobs-Lorena, M., The Anopheles gambiae Midgut Peritrophic Matrix 1 Proteome, Insect Biochem Mol Biol. 2009, 39, 125-34.

401. Kalpana Lal1, Elizabeth Bromley2, Helena Prieto3, Sanya J Sanderson4, John R Yates III3, Jonathan M Wastling4, Fiona M Tomley2, Robert E Sinden, Characterisation Of Plasmodium Invasive Organelles; An Ookinete Microneme Proteome, Proteomics 2009, 9, 1142-51.

398. Gyorgyi Csankovszki1, Karishma Collette1*, Karin Spahl2*, James Carey2, Martha Snyder1, Emily Petty1, Uchita Patel1, Tomoko Tabuchi2, Hongbin Liu3, Ian McLeod3, James Thompson3, Ali Sarkeshik3, John Yates3, Barbara Meyer4, and Kirsten Hagstrom2., Three distinct condensin complexes control C. elegans chromosome dynamics, Current Biology 2009, 19, 9-19.

397. Renata Usaite1,2, Michael C. Jewett1, Ana P. Oliveira1, John Yates III2, Lisbeth Olsson1,3*, Jens Nielsen1,3, Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator Molecular Systems Biology 2009;5:319.

396. Holinger EP, Old WM, Giddings TH Jr, Wong C, Yates JR 3rd, Winey M. Budding yeast centrosome duplication requires stabilization of Spc29 via Mps1-mediated phosphorylation. J. Biol Chem. 2009, 284, 12949-55.

388. Nicholas M. Andronicos, Emily I. Chen, Nagyung Baik, Hongdong Bai, Mark P. Kamps*, John R. Yates III, Robert J. Parmer† and Lindsey A. Miles‡, Isolation of a Novel Transmembrane Plasminogen Receptor Using Multidimensional Protein Identification Technology, Blood 2009 Nov 6 Epub ahead of press

385. Bingwen Lu, Tao Xu, Robin Park, John R. Yates III, Shotgun Protein Identification and Quantification by Mass Spectrometry, Methods in Molecular Biology 2009, 564, 261-88

472. Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, Roos DS, Wastling JM., The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation., Genome Biology 2008, 9, R116.

470. Kaeser MD, Aslanian A, Dong MQ, Yates JR 3rd, Emerson BM., BRD7, a novel PBAF-specific SWI/SNF subunit, is required for target gene activation and repression in embryonic stem cells., J Biol Chem. 2008, 283, 32254-63.

469. Gassmann R, Essex A, Hu JS, Maddox PS, Motegi F, Sugimoto A, O'Rourke SM, Bowerman B, McLeod I, Yates JR 3rd, Oegema K, Cheeseman IM, Desai A., A new mechanism controlling kinetochore-microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex., Genes Dev. 2008, 22, 2385-99.

468. Zhao WM, Coppinger JA, Seki A, Cheng XL, Yates JR 3rd, Fang G., RCS1, a substrate of APC/C, controls the metaphase to anaphase transition, Proc Natl Acad Sci USA. 2008, 105, 13415-20.

434. Zhu H, Coppinger JA, Jang CY, Yates JR 3rd, Fang G. FAM29A promotes microtubule amplification via recruitment of the NEDD1-{gamma}-tubulin complex to the mitotic spindle., J Cell Biol. 2008, 183, 835-48.

433. Schultz-Norton JR, Ziegler YS, Likhite VS, Yates JR, Nardulli AM Isolation of novel co-regulatory protein networks associated with DNA-bound estrogen receptor alpha, BMC Mol Biol. 2008, 9, 97

431. Reena Rai, Catherine C. L. Wong, Tao Xu, N. Adrian Leu, Dawei W. Dong, Caying Guo, K. John McLaughlin, John R. Yates, III and Anna Kashina, Arginyltransferase regulates alpha cardiac actin function, myofibril formation and contractility during heart development, Development 2008, 135, 3881-9.

430. Lujian Liao, Sung Kyu Park, Tao Xu, Peter Vanderklish, John Yates III, Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice, Proceedings of the National Academy of Sciences 105, 15281-86 (2008).

429. Xuemei Han, Aaron Aslanian, and John R Yates III, Mass spectrometry for proteomics, Current Opinion in Chemical Biology 2008, 12, 1–8

428. Ting-Wei Mu, Derrick Sek Tong Ong, Ya-Juan Wang, William E. Balch, John R. Yates, Laura Segatori, and Jeffery W. Kelly, Chemical and Biological Approaches Synergize to Ameliorate Protein-Folding Diseases, Cell 134, 769-81, 2008

427. Bingwen Lu, Daniel B. McClatchy, Jin Young Kim and John R. Yates III, Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry, Proteomics 8, 3947-55, 2008

422. Jelluma N, Brenkman AB, McLeod I, Yates JR 3rd, Cleveland DW, Medema RH, Kops GJ., Chromosomal instability by inefficient Mps1 auto-activation due to a weakened mitotic checkpoint and lagging chromosomes. PLoS ONE;3, e2415, 2008

421. Seki A, Coppinger JA, Jang CY, Yates JR, Fang G., Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science 320,1655-8, 2008;

420. Creekmore AL, Walt KA, Schultz-Norton JR, Ziegler YS, McLeod IX, Yates JR, Nardulli AM, The role of retinoblastoma-associated proteins 46 and 48 in estrogen receptor alpha mediated gene expression., Mol Cell Endocrinol. 2008, 291, 79-86

419. James J. Moresco, Meng-Qiu Dong, John R. Yates, III, Quantitative Proteomics as a Tool for Nutritional Proteomics, American Journal of Clinical Nutrition 2008, 88, 597-604

415. DiMaggio PA Jr, Floudas CA, Lu B, Yates JR 3rd., A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry., J Proteome Res. 2008, 7, 1584-93.

414. Zhu, J.H., Chen, R., Yi, W., Cantin, G.T., Fearns, C., Yang, Y., Yates, J.R., 3rd, and Lee, J.D. (2008). Protein tyrosine phosphatase PTPN13 negatively regulates Her2/ErbB2 malignant signaling. Oncogene 27, 2525-2531

413. Lu, B., Motoyama, A., Ruse, C., Venable, J., and Yates, J.R., 3rd (2008). Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data. Analytical Chemistry 80, 2018-2025.

412. Mathivanan, S.; Ahmed, M.; Ahn, N. G.; Alexandre, H.; Amanchy, R.; Andrews, P. C.; Bader, J. S.; Balgley, B. M.; Bantscheff, M.; Bennett, K. L.; Bjorling, E.; Blagoev, B.; Bose, R.; Brahmachari, S. K.; Burlingame, A. S.; Bustelo, X. R.; Cagney, G.; Cantin, G. T.; Cardasis, H. L.; Celis, J. E.; Chaerkady, R.; Chu, F.; Cole, P. A.; Costello, C. E.; Cotter, R. J.; Crockett, D.; DeLany, J. P.; De Marzo, A. M.; DeSouza, L. V.; Deutsch, E. W.; Dransfield, E.; Drewes, G.; Droit, A.; Dunn, M. J.; Elenitoba-Johnson, K.; Ewing, R. M.; Van Eyk, J.; Faca, V.; Falkner, J.; Fang, X.; Fenselau, C.; Figeys, D.; Gagne, P.; Gelfi, C.; Gevaert, K.; Gimble, J. M.; Gnad, F.; Goel, R.; Gromov, P.; Hanash, S. M.; Hancock, W. S.; Harsha, H. C.; Hart, G.; Hays, F.; He, F.; Hebbar, P.; Helsens, K.; Hermeking, H.; Hide, W.; Hjerno, K.; Hochstrasser, D. F.; Hofmann, O.; Horn, D. M.; Hruban, R. H.; Ibarrola, N.; James, P.; Jensen, O. N.; Jensen, P. H.; Jung, P.; Kandasamy, K.; Kheterpal, I.; Kikuno, R. F.; Korf, U.; Korner, R.; Kuster, B.; Kwon, M. S.; Lee, H. J.; Lee, Y. J.; Lefevre, M.; Lehvaslaiho, M.; Lescuyer, P.; Levander, F.; Lim, M. S.; Lobke, C.; Loo, J. A.; Mann, M.; Martens, L.; Martinez-Heredia, J.; McComb, M.; McRedmond, J.; Mehrle, A.; Menon, R.; Miller, C. A.; Mischak, H.; Mohan, S. S.; Mohmood, R.; Molina, H.; Moran, M. F.; Morgan, J. D.; Moritz, R.; Morzel, M.; Muddiman, D. C.; Nalli, A.; Navarro, J. D.; Neubert, T. A.; Ohara, O.; Oliva, R.; Omenn, G. S.; Oyama, M.; Paik, Y. K.; Pennington, K.; Pepperkok, R.; Periaswamy, B.; Petricoin, E. F.; Poirier, G. G.; Prasad, T. S.; Purvine, S. O.; Rahiman, B. A.; Ramachandran, P.; Ramachandra, Y. L.; Rice, R. H.; Rick, J.; Ronnholm, R. H.; Salonen, J.; Sanchez, J. C.; Sayd, T.; Seshi, B.; Shankari, K.; Sheng, S. J.; Shetty, V.; Shivakumar, K.; Simpson, R. J.; Sirdeshmukh, R.; Siu, K. W.; Smith, J. C.; Smith, R. D.; States, D. J.; Sugano, S.; Sullivan, M.; Superti-Furga, G.; Takatalo, M.; Thongboonkerd, V.; Trinidad, J. C.; Uhlen, M.; Vandekerckhove, J.; Vasilescu, J.; Veenstra, T. D.; Vidal-Taboada, J. M.; Vihinen, M.; Wait, R.; Wang, X.; Wiemann, S.; Wu, B.; Xu, T.; Yates, J. R.; Zhong, J.; Zhou, M.; Zhu, Y.; Zurbig, P.; Pandey, A. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology 26, 164-167.

411. Rao, A.K., Ziegler, Y.S., McLeod, I.X., Yates, J.R., and Nardulli, A.M. (2008). Effects of Cu/Zn Superoxide Dismutase (SOD1) on Estrogen Responsiveness and Oxidative Stress in Human Breast Cancer Cells. Molecular Endocrinology, 22, 1113-24, 2008

410. Denny, P.; Hagen, F. K.; Hardt, M.; Liao, L.; Yan, W.; Arellanno, M.; Bassilian, S.; Bedi, G. S.; Boontheung, P.; Cociorva, D.; Delahunty, C. M.; Denny, T.; Dunsmore, J.; Faull, K. F.; Gilligan, J.; Gonzalez-Begne, M.; Halgand, F.; Hall, S. C.; Han, X.; Henson, B.; Hewel, J.; Hu, S.; Jeffrey, S.; Jiang, J.; Loo, J. A.; Ogorzalek Loo, R. R.; Malamud, D.; Melvin, J. E.; Miroshnychenko, O.; Navazesh, M.; Niles, R.; Park, S. K.; Prakobphol, A.; Ramachandran, P.; Richert, M.; Robinson, S.; Sondej, M.; Souda, P.; Sullivan, M. A.; Takashima, J.; Than, S.; Wang, J.; Whitelegge, J. P.; Witkowska, H. E.; Wolinsky, L.; Xie, Y.; Xu, T.; Yu, W.; Ytterberg, J.; Wong, D. T.; Yates, J. R., 3rd; Fisher, S. J. (2008). The Proteomes of Human Parotid and Submandibular/Sublingual Gland Salivas Collected as the Ductal Secretions. Journal of Proteome Research, 7, 1994-2006, 2008

409. Jang, C.Y., Wong, J., Coppinger, J.A., Seki, A., Yates, J.R., 3rd, and Fang, G. (2008). DDA3 recruits microtubule depolymerase Kif2a to spindle poles and controls spindle dynamics and mitotic chromosome movement. Journal of Cell Biology 181, 255-67 (2008)

408. Romijn, E.P., and Yates, J.R., 3rd (2008). Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry. Methods in Molecular Biology (Clifton, NJ) 432, 1-16.

407. Duran, J. M.; Kinseth, M.; Bossard, C.; Rose, D. W.; Polishchuk, R.; Wu, C. C.; Yates, J.; Zimmerman, T.; Malhotra, V. The Role of GRASP55 in Golgi Fragmentation and Entry of Cells into Mitosis., Mol Biol Cell 19, 2579-2587, 2008

406. Diop, S.B., Bertaux, K., Vasanthi, D., Sarkeshik, A., Goirand, B., Aragnol, D., Tolwinski, N.S., Cole, M.D., Pradel, J., Yates, J.R., 3rd, Mishra, R. K.; Graba, Y.; Saurin, A. J. Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control. EMBO reports 9, 260-266 (2008).

405. Dentin, R., Hedrick, S., Xie, J., Yates, J., 3rd, and Montminy, M. (2008). Hepatic glucose sensing via the CREB coactivator CRTC2. Science 319, 1402-1405.

403. Benjamin W. Neuman, Jeremiah S. Joseph, Kumar S. Saikatendu, Pedro Serrano, Amarnath Chatterjee, Margaret A. Johnson, Lujian Liao, Joseph P. Klaus, John R. Yates III, Kurt Wu¨thrich, Raymond C. Stevens, Michael J. Buchmeier, and Peter Kuhn, Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3, Journal of Virology 2008, 82, 5279-94.

402. Sebastian C.J. Steiniger1§, Judith A. Coppinger3§, Jörg A. Krüger3, Ralph A. Reisfeld3, John R. Yates III3, Kim D. Janda, Quantitative Mass Spectrometry Identifies Drug Target In Stem-Like Breast Cancer Cells, Stem Cells. 2008, 12, 3037-46.

400. Paulo C. Carvalho, Johannes Hewel, Valmir C. Barbosa, John R. Yates, III, Identifying differences in protein expression levels by spectral counting and feature selection, Genetics and Molecular Research 15;7, 342-56, 2008

399. Yi Liu, Renaud Dentin, Danica Chen, Susan Hedrick, Kim Ravnskjaer1, Simon Schenk, Jill Milne, David J. Meyers, Phil Cole, John Yates III, Jerrold Olefsky, Leonard Guarente & Marc Montminy, A fasting inducible switch modulates gluconeogenesis via activator/coactivator exchange, Nature 2008, 456, 269-73.

395. S.X.Xu, Catherine C.L.Wong, Edith H.Y. Tong, Stephen S.M. Chung, John R. Yates, III, Y.B.Yin, and Ben C.B. Ko, Phosphorylation by Casein Kinase 1 Regulates Tonicity-induced OREBP/TonEBP Nucleocytoplasmic Trafficking, Journal of Biological Chemistry 2008, 283, 17624-34.

394. Bingwen Lu, Cristian Ruse, and John R. Yates, III, Colander: a probability based support vector machine learning algorithm for automatic screening of CID-phosphopeptide spectra prior to database search. Journal of Proteome Research 2008, 7, 3628-34..

393. Emily I. Chen1&, Daniel McClatchy1, Sung Kyu Park1, and John R. Yates 3rd1, Optimizing Mass-Spectrometry Based Approach for Global Analysis of the Mammalian Brain Proteome, Analytical Chemistry 2008, 80, 8694-701.

392. Rujun Kang1*, Junmei Wan2*, Pamela Arstikaitis1, Hideto Takahashi1, Kun Huang1, Amy F. Roth2, Renaldo C. Drsidel3, Ryna Mastro3, William N. Green3, Aaron Bailey, James Thomson, John R. Yates 3rd4, Nicholas G. Davis2, Alaa El-Husseini1, Palmitoyl-proteomics reveals the dynamic neuronal palmitoyl-proteome of the synapse, Nature 2008, 456, 904-9

391. Daniel Ducat, Shin-ichi Kawaguchi, Hongbin Liu, John R. Yates III, and Yixian Zheng, Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase Pontin, Mol Biol Cell., 19, 3097-110, 2008.

390. Akira Motoyama and John R. Yates, III, Multidimensional LC Separations in Shotgun Proteomics, Analytical Chemistry 2008, 80, 7187-93.

387. Mabelle Ashe, Robertus A.M. de Bruin, Tatyana Kalashnikova, W. Hayes MacDonald, John R. Yates III, Curt Wittenberg, The Sbf And Mbf-Associated Protein Msa1 Is Required For Proper Timing Of G1-Specific Transcription In Saccharomyces Cerevisiae, J. Biological Chemistry 283, 6040-6049 (2008)

386. Judith A. Coppinger1, Darren M. Hutt1, Atanas V. Koulov1, Sandra Pankow1, Bingwen, William E Balch1,2,3,4 and John R Yates An Hsp90 Dependent Folding Defect in CFTR NBD1 Is Responsible for Cystic Fibrosis, (to be submitted).

382. Renata Usaite1,2, James Wohlschlegel2, John D. Venable2, Sung K. Park2, Jens Nielsen1, Lisbeth Olsson1, John R. Yates III2, Characterization of global yeast quantitative proteome data generated from the wild type and glucose repression Saccharomyces cerevisiae strains: the comparison of two quantitative methods, Journal of Proteome Research, 2008, 7, 266–275

381. Greg T. Cantin134, Wei Yi23, Bingwen Lu1, Sung Kyu Park1, Tao Xu1, Jiing-Dwan Lee2*, and John R. Yates III1*, Combining protein-based IMAC, peptide-based IMAC, and MudPIT in the quantitative phosphoproteomic analysis of the EGF pathway Journal of Proteome Research 7, 1346-1351 (2008)

380. Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC., PatternLab for proteomics: a tool for differential shotgun proteomics, BMC Bioinformatics. 2008, 9, 316.

379. Sanya J. Sanderson1, Dong Xia1, Helena Prieto2, John Yates2, Mark Heiges3, Jessica Kissinger3, Fiona Tomley, Elizabeth Bromley, Robert Sinden, Lal Kalpana & Jonathan M. Wastling1*, Determining the protein repertoire of Cryptosporidium parvum sporozoites: a multi-directional approach Proteomics 8, 1398-1414 (2008)

372. Wiriya Chiranand1, Ian McLeod2, Melissa Ramirez3, Luis A. Vega1, Hadley Myers1, Michael C. Lorenz3, John R. Yates, III2, Michael C. Gustin, The CTA4 Transcription Factor Mediates Induction of Nitrosative Stress Response in Candida albicans, Eukaryotic Biology 7, 268-278 (2008)

371. Helena Prieto, Sasa Koncarevic2#, Robin Park1, John Yates III1* and Katja Becker, Differential proteome analysis in Plasmodium falciparum under drug pressure using stable isotope labelling, fractionation and multidimensional protein identification technology PLOS One (in press)

370. Park, S.K., Venable, J.D., Xu, T., and Yates, J.R., 3rd (2008). A quantitative analysis software tool for mass spectrometry-based proteomics. Nature Methods 5, 319-322.

368. Kailash P. Patra KP, Johnson JR, Cantin GT, Yates JR 3rd, Vinetz JM., Proteomic analysis of zygote and ookinete stages of the avian malaria parasite Plasmodium gallinaceum delineates the homologous proteomes of the lethal human malaria parasite Plasmodium falciparum. Proteomics, 8, 2492-9, 2008

364. Seki, A., Coppinger, J.A., Du, H., Jang, C.Y., Yates, J.R., 3rd, and Fang, G. (2008). Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression. The Journal of Cell Biology 181, 65-78.

363. de Bruin, R. A. M., Kalashnikova, T., Wohlschlegel, J., Chahwan, C., Yates, J., Russell, P., and Wittenberg, C. DNA replication checkpoint promotes G1-S transcription by inactivating the MBF repressor Nrm1, Proc. Natl. Acad. Sci USA. 2008, 105, 11230-5

320. Le Roch KG, Johnson JR, Ahiboh H, Chung DW, Prudhomme J, Plouffe D, Henson K, Zhou Y, Witola W, Yates JR, Mamoun CB, Winzeler EA, Vial H., A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum., BMC Genomics. 2008, 9, 513.

314. Dawn M. Clifford1, Benjamin A. Wolfe1, Rachel H. Roberts-Galbraith1, W. Hayes McDonald2, John R. Yates III2, and Kathleen L. Gould, The Clp1/Cdc14 phosphatase contributes to the robustness of cytokinesis by association with anillin-related Mid1, J. Cell Biology 181, 79-88 (2008)

423. Delahunty CM, Yates JR 3rd., MudPIT: multidimensional protein identification technology., Biotechniques. 2007, 43, 563-67.

389. Angela J. Ahrendt, Sandra L. Tollaksen, Carl Lindberg, Wenhong Zhu, John R. Yates III, Kelly P. Nevin, Gyorgy Babnigg, Derek R. Lovley and Carol S. Giometti, Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor, Proteomics 2007, 7, 4148–4157

384. Benjamin F. Cravatt, Gabriel M. Simon, & John R. Yates, III, The biological impact of mass spectrometry-based proteomics, Nature 450, 991-1000, 2007

383. Carol D Curtis, Varsha S Likhite, Ian X McLeod, John R Yates and Ann M Nardulli, Interaction of Nonmetastatic Protein 23 Homolog H1 and Estrogen Receptor a Alters Estrogen-Responsive Gene Expression, Cancer Research 2007, 67, 10600-7.

377. Toshima J, Toshima JY, Duncan MC, Cope MJ, Sun Y, Martin AC, Anderson S, Yates JR 3rd, Mizuno K, Drubin DG., Negative regulation of yeast Eps15-like Arp2/3 complex activator, Pan1p, by the Hip1R-related protein, Sla2p, during endocytosis., Mol Biol Cell. (2007) 658-68.

376. Jung P, Verdoodt B, Bailey A, Yates JR 3rd, Menssen A, Hermeking H., Induction of Cullin 7 by DNA damage attenuates p53 function., Proc Natl Acad Sci U S A. (2007) 104, 11388-93

375. Kiselev AO, Stamm WE, Yates JR, Lampe MF., Expression, Processing, and Localization of PmpD of Chlamydia trachomatis Serovar L2 during the Chlamydial Developmental Cycle., PLoS ONE. 2007, 2, e568.

374. Jennifer R. Schultz-Norton, Kjirsten A. Walt, Yvonne S. Ziegler, Ian X. McLeod, John R. Yates, Lori T. Raetzman, and Ann M. Nardulli, The Deoxyribonucleic Acid Repair Protein Flap Endonuclease-1 Modulates Estrogen-Responsive Gene Expression, Molecular Endocrinology 21, 1569–1580 (2007).

373. Catherine C. L. Wong2#, Tao Xu2#, Reena Rai1, Aaron Bailey2,5, John R. Yates, III2, Yuri I. Wolf3, Henry Zebroski4, and Anna Kashina1*, Global analysis of posttranslational protein arginylation, PLoS Biology (2007), 5, e258

369. Emily I. Chen,1 and John R. III Yates1*, Cancer Proteomics by Quantitative Shotgun Proteomics, Molecular Oncology (2007), 1, 144-159.

367. Dentin R, Liu Y, Koo SH, Hedrick S, Vargas T, Heredia J, Yates J 3rd, Montminy M., Insulin modulates gluconeogenesis by inhibition of the coactivator TORC2., Nature (2007) 449, 366-9.

366. Kunhong Xiao, Daniel B. McClatchy, Arun Shukla, Xue Li, Sudha K. Shenoy, Yang Zhao, Minyong Chen, John R. Yates, III, and Robert J. Lefkowitz, Functional Specialization of the ß-arrestin Proteome, Proc. Natl. Acad. Sci. USA (2007) 104, 12011-6.

365. Sofia Aronova, Karen Wedaman, John Yates III, and Ted Powers, Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in S. cerevisae, Molecular Biology of Cell (2007), 18, 2779-94

362. Cynthia L. Cass1, Jeffrey Johnson2, Lindsay L. Califf1, Tao Xu2, Hector Hernandez3, Miguel J. Stadecker3, John R.Yates, III2, David L. Williams1* Proteomic Analysis Of Schistosoma Mansoni Egg Secretions, Molecular and Biochemical Parasitology (2007) 155, 84-93.

361. Chandra L. Kilburn*, Chad G. Pearson*, Edwin P. Romijn§?, Janet B. Meehl*, Thomas H. Giddings, Jr.*, Brady P. Culver*, John R. Yates III§, and Mark Winey*, Tetrahymena basal body proteome: Identification of basal body domain structure, Journal of Cell Biology (2007)178, 905-12

360. Lei Ding1,4, Liang Zhang1,4, Tom Cheung3 Meng-Qiu Dong2, Jun Chen1, Aileen K. Sewell1, Xuedong Liu3, John Yates 3rd2 and Min Han1*, Analysis of the redundant functions of AIN-1 and AIN-2 leads to systematic identification of miRNAs and their mRNA targets in C. elegans, Molecular Cell , 28, 598-613, 2007

359. Schultz-Norton, Jennifer R; Gabisi, Vivian A; Ziegler, Yvonne S; McLeod, Ian X; Yates, John R; Nardulli, Ann M., Interaction of estrogen receptor alpha with proliferating cell nuclear antigen, Nucleic Acids Res. (2007) 35, 5028-38

358. McClatchy, DB, Liao, L, Park, R., Venable J., and Yates, J.R.*, Quantification of the synaptic proteome of the rat cerebellum during postnatal development, Genome Research (2007), 17, 1378-88.

357. Meng-Qiu Dong, John Venable, Nora Au, Tao Xu, Sung Kyu Park, Daniel Cociorva, Jeffrey Johnson, Andrew Dillin, John R Yates, III, Quantitative Mass Spectrometry Identifies New Insulin/IGF-1 Signaling Targets, Science 2007;317, 660-3

356. Emily I. Chen,1 Daniel Cociorva1, Jeremy L. Norris2, and John R. III Yates1*, Optimization of Mass Spectrometry Compatible Surfactants for Shotgun Proteomics, J. Proteome Research (2007) 6, 2529-38

354. Akira Motoyama, Tao Xu, Cristian I. Ruse, James A. Wohlschlegel and John R. Yates, III*, Anion and Cation Mixed-Bed Ion Exchange for Enhanced Multidimensional Separations of Peptides and Phosphopeptides, Analytical Chemistry 79, 3623-3634, 2007,

353. Alexey Kharitonov1,8, Nadia Efimova2,8, Andrey Efimov2,8, Jadranka Loncarek3, Paul M. Miller2, Natalia Andreeva1, Paul Gleeson4, Niels Galjart5, Ana R. R. Maia6, Ian X. McLeod7, John R. Yates 3rd7, Alexey Khodjakov3, Helder Maiato6, Anna Akhmanova5 and Irina Kaverina2, 9, Non-centrosomal microtubules are asymmetrically nucleated at the trans-Golgi network in CLASP-dependent manner, Dev Cell 2007, 12, 917-30

352. Gyorgy Babnigg1, Wenhong Zhu2, Carl Lindberg1, Sandra L. Tollaksen1, John R. Yates III2, and Carol S. Giometti1, Protein Phosphorylation in Shewanella oneidensis MR-1 grown aerobically and anaerobically with fumarate. Journal of Proteome Research (to be submitted)

351. Kim Ravnskjaer*, Yi Liu*, Xinmin Zhang, Henri Kester, Dong Lee, Lawryn H. Kasper?, Marek Cebrat?, Philip A. Cole?, Paul Brindle?, John R.Yates III+, and Marc Montminy?, Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression. EMBO J. 2007, 26, 2880-9.

348. Paul R. Sanders1,2,3, Greg T. Cantin4, Doron C. Greenbaum1, Thomas Nebl1, Robert L. Moritz5, John R. Yates 3rd4, Anthony N. Hodder1, and Brendan S. Crabb1., Identification of protein complexes in detergent-resistant membranes of Plasmodium falciparum schizonts, Mol Biochem Parasitol. 154, 148-57, 2007

340. Emily I. Chen, Johannes Hewel, Joseph S. Krueger, Martin R. Weber, Claire Tiraby, Anastasia Kralli, Katja Becker, John .R. III Yates, and Brunhilde Felding-Habermann, Adaptation of Energy Metabolism in Breast Cancer Brain Metastases, Cancer Research 2007;67, 1472-86

339. John D. Venable1, James Wohlschlegel1, Dan McClatchy, Sung Kyu Park and John R. Yates III*, Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer, Analytical Chemistry (2007) 79, 3056-3064.

337. Aaron O. Bailey 1, Timothy M. Miller 2, Don W. Cleveland 2, John R. Yates 1*, RCADIA: Simple Automation Platform For Comparative Multidimensional Protein Identification (Mudpit), Analytical Chemistry 79, 6410-8, 2007

336. Greg T. Cantin1, Teresa R. Shock2, Sung Kyu Park1, Hiten D. Madhani2, and John R. Yates III1*, Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry, Analytical Chemistry (2007) 79, 4666-4673

335. McClatchy DB#, Dong MQ#, Wu CC#, Venable JD, Yates, III JR*, 15N Metabolic Labeling of Mammalian Tissue with Slow Protein Turnover, Journal of Proteome research (2007) 6, 2005-2010.

333. Derek McCusker1, Carilee Denison2, Scott Anderson3, Thea Egelhofer1, John Yates 3rd3, Steve Gygi2 and Douglas Kellogg1, Cdk1 coordinates cell surface growth with the cell cycle, Nature Cell Biology (2007), 506-15.

332. Zee-Yong Park1, Rovshan Sadygov2, Judy M. Clark3, John I. Clark3, and John R. Yates, III4, Assigning In vivo Carbamylation and Acetylation In Human Lens Proteins using Tandem Mass Spectrometry and Database Searching, International Journal of Mass Spectrometry 2007, 259, 161-173.

331. Bingwen Lu1, Cristian Ruse1, Tao Xu, Sung Kyu Park, John Yates III*, Automatic Validation of Phosphopeptide Identifications from Tandem Mass Spectra, Analytical Chemistry (2007) 79, 1301-1310

328. Anne-Lore Schlaitz, Martin Srayko, Alexander Dammermann, Sophie Quintin, Natalie Schmalz, Ian MacLeod, Andrea Zinke, John R. Yates III, Andrei Shevchenko, Karen Oegema, Anthony A. Hyman, The C. elegans RSA protein complex targets Protein Phosphatase 2A to centrosomes and regulates mitotic spindle assembly in Caenorhabditis elegans embryos, Cell 2007, 128, 115-27.

324. Marie-Louise Lunn, Rounak Nassirpour, Christine Arrabit, Josh Tan, Ian Mcleod, Carlos M. Arias, Paul Sawchenko, John R. Yates, III, and Paul A. Slesinger, A unique PDZ-containing protein, sorting nexin 27, regulates Kir3 channels, Nature Neuroscience 10, 1249-59, 2007.

323. Bryan M. O’Neill, Shawn J. Szyjka, Ewa T. Lis, Aaron O. Bailey, John R. Yates III, Oscar M. Aparicio & Floyd E. Romesberg, Psy2 and Pph3 form a Rad53 phosphatase complex that promotes restart of arrested replication forks, PNAS 2007, 104, 9290-5

322. Peiqing Sun, Liguo New, Bettina Moser, Yilei Li, Rong Liao, Natoto Yoshizuka, Qingdong Deng, Maria Yamout, Meng-Qiu Dong, John R. Yates III, Peter Wright, and Jiahuai Han, PRAK Mediates Oncogenic Ras-induced Senescence and Tumor Suppression by Regulating p53 Activity Cell 2007, 128, 295-308

315. Lujian Liao*, Tao Xu*, Julie Pilotte†, Gerald M. Edelman†, Peter Vanderklish†, and John R. Yates III*, BDNF increases protein synthesis in a large scale via increasing translation capacity at synapse J. Proteome Research (2007) 6, 1059-71

306. Jaeki Min, Yun Kyung Kim, Patricia G Cipriani, Mira Kang, Sonya M Khersonsky, Daniel P Walsh, Ji-Young Lee, Sherry Niessen, John R Yates III, Kristin Gunsalus, Fabio Piano & Young-Tae Chang, Forward chemical genetic approach identifies new role for GAPDH in insulin signaling, Nature Chemical Biology 2007, 3, 55-9.

297. Heike B. Koch1, Nemone Muster2, John R. Yates III2 and Heiko Hermeking1* Large-Scale Identification of c-MYC-Associated Proteins using a Combined TAP/MudPIT Approach. Cell Cycle. (2007), 6, 205-17.

350. Eli Chapman, George W. Farr, Renata Usaite, Krystyna Furtak, Wayne A. Fenton, Tapan K. Chaudhuri, Elise R. Hondorp, Rowena G. Matthews, Sharon G. Wolf, John R. Yates, Marc Pypaert, and Arthur L. Horwich, Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL, PNAS 2006, 103, 15800-5

349. Daniel Cociorva, David Tabb, and John R. Yates, III, Validation of Tandem Mass Spectrometry Database Search Results using DTASelect, Current Protocols in Bioinformatics 13.4.1-13.4.14, supplement 16, (2006), John Wiley and Sons,

347. Chen EI, Yates JR., Maspin and tumor metastasis., IUBMB Life. 2006, 58, 25-9.

346. De Craene JO, Coleman J, Estrada de Martin P, Pypaert M, Anderson S, Yates JR 3rd, Ferro-Novick S, Novick P., Rtn1p is involved in structuring the cortical endoplasmic reticulum., Mol Biol Cell. 2006, 17, 3009-20.

345. Martin V, Chahwan C, Gao H, Blais V, Wohlschlegel J, Yates JR 3rd, McGowan CH, Russell P. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells., EMBO J. 2006, 25, 2564-74.

344. Krishnamurthy T, Hewel J, Bonzagni NJ, Dabbs J, Bull RL, Yates JR 3rd., Simultaneous identification and verification of Bacillus anthracis., Rapid Commun Mass Spectrom. 2006, 20, 2053-6.

343. Raffa GD, Wohlschlegel J, Yates JR 3rd, Boddy MN., SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association., J Biol Chem. 2006, 281, 27973-81.

342. Varsano T, Dong MQ, Niesman I, Gacula H, Lou X, Ma T, Testa JR, Yates JR 3rd, Farquhar MG., GIPC is recruited by APPL to Peripheral TrkA Endosomes and Regulates TrkA Trafficking and Signaling., Mol Cell Biol. 2006, 26, 8942-52.

341. Roth AF, Wan J, Green WN, Yates JR, Davis NG., Proteomic identification of palmitoylated proteins., Methods. 2006, 40, 135-42.

338. Kate Monzo, Ophelia Papoulas, Greg T. Cantin, John R. Yates, III, John C. Sisson, Fragile X mental retardation protein controls trailer hitch expression and cleavage furrow formation in Drosophila embryos, Proc. Natl. Acad. Sci. USA 2006, 103, 18160-5

334. Sharsti Sandall; Fedor Severin, Ian X McLeod, John R Yates 3rd, Karen Oegema, Anthony A Hyman, Arshad Desai, A Complex of Sli15-Bir1 (INCENP-Survivin) Connects Centromeres to Microtubules and is the Likely Tension Sensor Controlling Aurora B Activation, Cell 2006, 127, 1179-91

330. Khare T, Esteve-Nunez A, Nevin KP, Zhu W, Yates JR 3rd, Lovley D, Giometti CS., Differential protein expression in the metal-reducing bacterium Geobacter sulfurreducens strain PCA grown with fumarate or ferric citrate., Proteomics. 2006, 6, 632-40.

327. Azarian SM, McLeod I, Lillo C, Gibbs D, Yates JR, Williams DS. Related Articles, Links Proteomic analysis of mature melanosomes from the retinal pigmented epithelium. J Proteome Res. 2006, 5, 521-9.

326. Daniel R. Foltz, Lars E.T. Jansen, Ben E. Black, Aaron O Bailey, John R. Yates III and Don W. Cleveland, The human CENP-A centromeric nucleosome associated Complex, Nature Cell Biology 2006, 8, 458-69

325. Chantelle Sedgwick, James DeCesare, Matthew Rawluk, Sheetal Raithatha, James Wohlschlegel, Paul Semchuck, Michael Ellison, John Yates III, and David Stuart, Saccharomyces cerevisiae Ime2 phosphorylates Sic1 at multiple PXS/T sites but is insufficient to trigger Sic1 degradation, Biochemical Journal (2006), 399, 151-60

321. Akira Motoyama, John D. Venable, Cristian I. Ruse, and John R. Yates, III, Automated Ultra-high Pressure Multidimensional Protein Identification Technology (MudPIT) for Improved Peptide Identification of Proteomic Samples, Analytical Chemistry 2006, 78, 5109-18

319. Yates JR, Cociorva D, Liao L, Zabrouskov V., Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Analytical Chemistry 78, 493-500 (2006)

318. Pebernard S, Wohlschlegel J, McDonald WH, Yates JR 3rd, Boddy MN. The nse5-nse6 dimer mediates DNA repair roles of the smc5-smc6 complex. Mol Cell Biol. 26, 1617-30 (2006).

317. Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Anderson S, Yates JR 3rd, Washburn MP, Abmayr SM, Workman JL., Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila., Mol Cell Biol. 26, 871-82, 2006.

313. Schneider DA, French S, Bailey AO, Vu L, Dodd J, Yates J, Beyer A, and Nomura M , The RNA Polymerase II elongation complex Spt4p/Spt5p affects transcription elongation by RNA polymerase I. Proc. Natl. Acad. Sci. USA 2006, 103, 12707-12.

308. James A. Wohlschlegel1,3, Erica S. Johnson2, Steven I. Reed3, and John R. Yates, III1*, Improved Identification of SUMO Attachment Sites Using C-terminal SUMO Mutants and Tailored Protease Digestion Strategies, J. Proteome Research 2006, 5, 761-770.

307. Ling Qi*, Jose Heredia*, Robert Screaton, Judith Y. Altarejos, Sherry Neissen?, Ian McLeod?, ChongWee Liew?, Rohit Kulkarni?, James Bain?, Christopher Newgard?, Ronald M. Evans, John Yates?, and Marc Montminy?, TRB3 Links the E3 Ubiquitin Ligase COP1 to Lipid Metabolism Science 2006, 312, 1763-6.

302. Joshua A. Rosenberg, Gregory C. Tomlin, W. Hayes McDonald, Brian E. Snydsman, Eric G. Muller, John R. Yates, III, and Kathleen L. Gould, Ppc89p, a novel fission yeast spindle pole body protein required for spindle formation. Mol Biol Cell. 2006, 17, 3793-805

301. Marina Karakozova1, Marina Kozak1, Catherine C. L. Wong2, Aaron Bailey2, John R. Yates, III2, and Anna Kashina1*., Arginylation of beta actin regulates actin cytoskeleton and cell motility, Science 2006, 313, 192-6.

299. Greg T. Cantin, John D. Venable, Daniel Cociorva, and John R. Yates III, Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway, J. Proteome Research 5, 127-34 (2006)

298. Bianka L. Grosshans1, Anna Andreeva2, Akanksha Gangar2, Sherry Niessen3, John R Yates III3, Patrick Brennwald2 and Peter Novick, The yeast lgl family member Sro7p is an effector of the secretory Rab GTPase Sec4p, J. Cell Biology 172, 55-66 (2006).

296. Wolfe BA, McDonald WH, Yates JR 3rd, Gould KL., Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe., Developmental Cell. 2006, 11, 423-30.

295. Robertus A. M. de Bruin, Tatyana I. Kalashnikova, Charly Chahwan, W. Hayes McDonald, James Wohlschlegel, John Yates, 3rd, Paul Russell and Curt Wittenberg, Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Molecular Cell. 2006, 23, 483-96.

293. Jennifer R. Schultz-Norton, Hayes McDonald, John R. Yates, and Ann M. Nardulli, Protein disulfide isomerase serves as a molecular chaperone to maintain estrogen receptor alpha structure and function. Mol Endocrinol. 2006, 20, 1982-95.

292. Sébastien Léon, James M. Cregg, John Yates III, and Suresh Subramani, Peroxisomal protein import by the PTS1 and PTS2 pathways:similarities revealed by study of Pichia pastoris Pex20p, J. Cell Biology 172, 67-78 (2006)

291. Masahiro Okada, Iain M. Cheeseman, Tetsuya Hori, Katsuya Okawa, Ian X. McLeod, John R. Yates III, Arshad Desai, and Tatsuo Fukagawa, The CHIP complex is required for the incorporation of newly synthesized CENP-A into centromeres, Nature Cell Biology 8, 446-57 (2006).

290. Ke Hu, Laurence Florens, Jeff Johnson, Martin Fraunholz, Sapna Suravajjala, Camille DiLullo, John Yates, David S Roos, and John M. Murray, Cytoskeletal components of an invasion machine - the apical complex of Toxoplasma gondii, PLoS Pathogens 2, e13, (2006)

287. Widlund, P. O., J. S. Lyssand, S. Anderson, S. Niessen, J. R. Yates, III, and T. N. Davis (2006) Phosphorylation of the chromosomal passenger protein, Bir1, is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation. Mol. Biol. Cell, 2006, 17, 1065-74

286. Toshiaki Harashima, Scott Anderson, John R. Yates III, and Joseph Heitman, The kelch proteins Gpb1 and Gpb2 inhibit Ras activity by stabilizing the Saccharomyces cerevisiae RasGAP neurofibromin homologs Ira1 and Ira2, Molecular Cell 2006, 22, 819-30

284. Thomas F. Duchaine, James Wohlshlegel, Scott Kennedy, Yanxia Bei, Darryl Conte, KaMing Pang, Dan Brownell, Shohei Mitani, Gary Ruvkun John Yates III, and Craig C. Mello, Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways, Cell 124, 343-54 (2006)

282. Stephanie Cherqui, Sunil M. Kurian, Olivier Schussler, Johannes A. Hewel, John R.Yates III and Daniel R. Salomon, Isolation and angiogenesis by endothelial progenitors in the fetal liver, Stem Cell 2006, 24, 44-54.

275. Susan E. Francis1, Michelle M. Shimogawa1,2, Beth Graczyk1, Melissa K. Gardner3, Michael Ess1, Cristian Ruse4, Sherry Niessen4, Tennessee J. Yoder1,2, Jeff N. Molk5, Kerry Bloom5, John R. Yates, III4, David J. Odde3, and Trisha N. Davis1,2,*, Mps1 phosphorylation of the kinetochore component Dam1 alters the metaphase kinetochore arrangement by decreasing the affinity of Dam1 for microtubules Current Biology 2006, 16, 1489-501

274. Diana S. Chu1, Hongbin Liu2, 3, John R. Yates III2, Barbara J. Meyer, Sperm Chromatin Proteomics Identifies Evolutionarily Conserved Fertility Factors, Nature 2006, 443, 101-5.

269. Tripti Khare1, Carol S. Giometti1, Abraham Nunez2, Kelly Nevin2, Wenhong Zhu3, John R. Yates III3, and Derek Lovley2 Differential Protein Expression in the Metal-Reducing Bacterium Geobacter sulfurreducens PCA Grown with Fumarate or Ferric Citrate Proteomics 2006, 6, 632-40.

268. Rovshan Sadygov, James Wohlschlegel, and John R. Yates, III., Central limit theorem as an approximation for intensity-based scoring function. Analytical Chemistry 78, 89-95, (2006)

264. Herzberg K, Bashkirov VI, Rolfsmeier M, Haghnazari E, McDonald WH, Anderson S, Bashkirova EV, Yates JR 3rd, Heyer WD., Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks., Mol Cell Biol. 2006, 26, 8396-409

252. Heping Cao, Leesa J. Deterding, John D. Venable, Elizabeth A. Kennington, John R. Yates, 3rd, Kenneth B. Tomer And Perry J. Blackshear, Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis, Biochemical Journal 394(Pt 1), 285-97, (2006).

249. J. Venable and J. Yates, Cross correlation algorithm for calculation of peptide molecular weight from tandem mass spectra, Analytical Chemistry 2006, 78, 1921-9

241. Wang X, Venable J, Lapointe P, Hutt DM, Koulov AV, Coppinger J, Gurkan C, Kellner W, Matteson J, Plutner H, Riordan JR, Kelly JW, Yates JR 3rd, Balch WE., Hsp90 Co-chaperone Aha1 Downregulation Rescues Misfolding of CFTR in Cystic Fibrosis, Cell, 127, 803-81, (2006)

210. Varsano T, Dong MQ, Niesman I, Gacula H, Lou X, Ma T, Testa JR, Yates JR 3rd, Farquhar MG. GIPC is recruited by APPL to peripheral TrkA endosomes and regulates TrkA trafficking and signaling. Mol Cell Biol. 2006, 26, 8942-52.

378. McMahon SJ, Pray-Grant MG, Schieltz D, Yates JR 3rd, Grant PA., Polyglutamine-expanded spinocerebellar ataxia-7 protein disrupts normal SAGA and SLIK histone acetyltransferase activity., Proc Natl Acad Sci U S A. (2005)102, 8478-82

355. John R. Yates, Proteomics Power to the People, The Scientist 2005, 19, 30

316. Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex., Biochim Biophys Acta. 1731, 77-87; 2005

312. Liu J, Rivas FV, Wohlschlegel J, Yates JR 3rd, Parker R, Hannon GJ., A role for the P-body component GW182 in microRNA function., Nat Cell Biol. 2005, 7, 1161-6.

311. Chen EI, Hewel J, Brunhilde Felding-Habermann B, Yates JR 3rd., Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)., Mol Cell Proteomics. 5, 53-56 (2005)

310. Page LJ, Suk JY, Huff ME, Lim HJ, Venable J, Yates J, Kelly JW, Balch WE., Metalloendoprotease cleavage triggers gelsolin amyloidogenesis., EMBO J. 2005, 24, 4124-32.

309. Zhu W, Venable J, Giometti CS, Khare T, Tollaksen S, Ahrendt AJ, Yates JR 3rd.Large-scale muLC-MS/MS for silver- and Coomassie blue-stained polyacrylamide gels.. Electrophoresis. 2005, 26, 4495-507.

304. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell, 123, 581-92 (2005)

303. Sherry Niessen, Ian Mcleod, and John R. Yates III, Identification of Novel Protein Complexes and Protein:Protein Interactions by Mass Spectrometry, Protein-protein Interactions: A Molecular Cloning Manual, eds. Erica Golemis and Peter D. Adams, Cold Spring Harbor Press, Cold Spring Harbor, 2nd Edition, pp 329-354, 2005

300. Adam C. Wilson1, Christine C. Wu3, John R. Yates, III4, and Ming Tan, Chlamydial GroEL auto-regulates its own expression through direct interactions with the HrcA repressor protein., J. Bacteriology 187, 7535-7542, 2005

294. Anjon Audhya, Francie Hyndman, Ian X. McLeod, Amy S. Maddox, John R. Yates III, Arshad Desai, and Karen Oegema, A complex containing the Sm-protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in C. elegans, Journal of Cell Biology 2005, 171, 267-79.

289. Jeffrey K. Huang, Greg R. Phillips, Alejandro D. Roth, Liliana Pedraza, Weisong Shan, Wiam Belkaid, Sha Mi, Asa Fex-Svenningsen, Laurence Florens, John R. Yates III, and David R. Colman, Glial membranes at the CNS node of Ranvier prevent neurite outgrowth, Science 2005, 310, 1813-7.

288. Nadim Jessani, Sherry Niessen, BinQing Q Wei1, Monica Nicolau, Mark Humphrey, Youngran Ji, Wonshik Han, Dong-Young Noh, John R Yates III, Stefanie S Jeffrey & Benjamin F Cravatt, A streamlined platform for high-content functional proteomics of primary human specimens, Nature Methods 2, 691-7 (2005)

285. Greg R. Phillips, Laurence Florens, Hidekazu Tanaka, Zin Z. Khaing, Lazar Fidler, John R. Yates III, and David R. Colman, Proteomic Comparison of Two Fractions Derived From the Transsynaptic Scaffold, Journal of Neuroscience 81, 762-775 (2005)

283. Michael J. MacCoss1*, Christine C. Wu2*, Dwight E. Matthews3, and John R. Yates III, Measurement of the Atomic Enrichment of Stable Isotope Labeled Proteins Using High Resolution Mass Spectra of Peptides, Analytical Chemistry 2005, 77, 7646-7653

281. Paul R. Sanders, Paul R. Gilson, Greg T. Cantin, Thomas Nebl, Doron C. Greenbaum, Daniel J. Carucci, Malcolm J. McConville, Louis Schofield, Anthony N. Hodder, John R. Yates III and Brendan S. Crabb, Antigen discovery in Plasmodium falciparum blood-stages by membrane proteomics J. Biological Chemistry 2005, 280, 40169-76.

280. Erin M. Green1, Andrew J. Antczak1, Aaron O. Bailey2, Alexa A. Franco1, Kevin Wu1, John R. Yates 3rd,2, and Paul D. Kaufman3, Replication-Independent Histone Deposition by the HIR Complex and Asf1, Curr Biol. 2005, 15, 2044-9.

279. Alexander Gottschalk, Ruta B. Almedom, Thorsten Schedletzky, Scott D. Anderson, John R. Yates, III, and William R. Schafer, Identification and characterization of novel nicotinic receptor associated proteins in C. elegans, EMBO 24, 2566-78 (2005)

278. Liu H, Du X, Wang M, Huang Q, Ding L, McDonald HW, Yates JR 3rd, Beutler B, Horwitz J, Gong X , Crystallin gamma B-I4F mutant protein binds to alpha -crystallin and affects lens transparency., J Biol Chem. 280, 25071-8 (2005)

277. Martin SG, McDonald WH, Yates JR 3rd, Chang F. Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity., Dev Cell., 8, 479-91. (2005)

276. John R. Yates III1, Annalyn Gilchrist2, Kathryn E. Howell3 and John J. M. Bergeron,, Proteomics of organelles and large cellular structures, Nature Reviews Molecular and Cellular Biology 2005, 6, 702-14.

273. Susan Lee1, Frank Comer2, Atsuo Sasaki1, Ian McLeod3, Duong, Yung1, Koichi Okumura4, John R. Yates, III3, Carole Parent2, and Richard A. Firtel1,5, TOR Complex 2 Integrates Chemotaxis and Signal Relay in Dictyostelium Mol Biol Cell. 2005, 16, 4572-83.

272. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM, Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A.102, 2099-104, 2005

271. Lani Keller, Edwin Romijn, Ivan Zamora, John R. Yates 3rd, and Wallace F. Marshall, The Centriole Proteome: Protein Composition Analysis of Isolated Chlamydomonas Basal Bodies Reveals Orthologs of Ciliary Disease Genes, Current Biology 15, 1090-8, (2005)

270. Schirmer EC, Florens L, Guan T, Yates JR, Gerace L., Identification of novel integral membrane proteins of the nuclear envelope with potential disease links using subtractive proteomics., Novartis Found Symp 2005; 264, 63-76.

267. Anselm Sauerwald, Wenhong Zhu, Tiffany A. Major, Hervé Roy, Sotiria Palioura, Dieter Jahn, William Whitman, John R. Yates, 3rd, Michael Ibba and Dieter Söll, RNA-dependent cysteine biosynthesis in archaea, Science 307, 1969-1972 (2005)

266. Iain M. Cheeseman, Ian MacLeod, John R. Yates III, Karen Oegema, and Arshad Desai, The CENP-F-like proteins HCP-1 and HCP-2 Target CLASP to Kinetochores to Regulate Microtubule Dynamics, Current Biology, 15, :771-7 (2005)

265. Carnahan, R. H., Feoktistova, A.S., Ren, L., Niessen, S., Yates, Jr., J. R., and Gould, K.L. (2005) Dim1p is required for efficient splicing and export of mRNA for lid1+, a component of the fission yeast Anaphase Promoting Complex. Eukaryot. Cell 4, 577-87 (2005).

261. C. Delahunty and J. R. Yates, Protein Identification using 2-D LC-MS/MS, Methods 35, 248-55 (2005)

260. Geert J.P.L. Kops, Yumi Kim1, Beth A.A. Weaver1, Yinghui Mao1, Ian McLeod, John R. Yates III, Mitsuo Tagaya, Don W. Cleveland, ZW10 Links Mitotic Checkpoint Signaling to the Structural Kinetochore, J. Cell Biology 169, 49-60 (2005).

259. Cristian Ruse and John R. Yates, Mass Spectrometry in Systems Biology, Systems Biology, Springer-Verlag (in press)

251. Marilyn G. Pray-Grant, Jeremy A. Daniel, David Schieltz, Grant A. Hartzog, C. David Allis, John R. Yates III, and Patrick A. Grant, Chd1 mediates SAGA and SLIK dependent acetylation via chromodomain recognition of methylated histone H3., Nature 433, 434-8, 2005.

245. Anne Benzinger1, Nemone Muster2, John Yates III2 and Heiko Hermeking1Targets for tumor suppression by the p53-14-3-3?-pathwayidentified using a combined TAP-MudPIT approach Mol. Cell Proteomics 2005, 4, 785-95.244.

234. Chen E.I.,1* Florens L,2$ Axelrod F.T.,3 Monosov E,3 Barbas CF 3rd,2 Yates J.R. III,2 Felding-Habermann B,1 Smith J.W4 , Molecular analysis of Maspin, a tumor suppressor in breast cancer FASEB J. 2005, 19, 1123-4.

229. Neil Hall,1* Marianna Karras,2 J. Dale Raine,3 Jane M. Carlton,4,5,6 Taco W. A. Kooij,2 Matthew Berriman,1 Laurence Florens,7 Christoph S. Janssen,8 Arnab Pain,1 Georges K. Christophides,9 Keith James,1 Kim Rutherford,1 Barbara Harris,1 David Harris,1 Carol Churcher,1 Michael A. Quail,1 Doug Ormond,1 Jon Doggett,1 Holly E. Trueman,3 Jacqui Mendoza,3 Shelby L. Bidwell,4 Marie-Adele Rajandream,1 Daniel J. Carucci,10 John R. Yates, III,7 Fotis C. Kafatos,9 Chris J. Janse,2 Bart Barrell,1 C. Michael R. Turner,8 Andrew P. Waters,2* Robert E. Sinden3*, A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses, Science 307, 82-86 2005.

219. C. Xu and J. Yates, Mass Spectrometry-based Proteomics for Cancer Biology, The Oncogenomics Handbook: Understanding and Treating Cancer in the 21st Century. Humana Press, Totowa, NJ (2005) pages 91-108.

329. Bern, M., Goldberg, D., McDonald, W. H., Yates, J. R., III, Automatic quality assessment of Peptide tandem mass spectra, Bioinformatics, 20 Suppl 1, I49-I54 (2004)

305. Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR 3rd, Howell KE., Organellar proteomics reveals Golgi arginine dimethylation., Mol Biol Cell., 15, 2907-19, (2004)

263. M. Z. Bao, M.A. Schwartz, G. T. Cantin, J. R. Yates, H. Madhani, Phermone dependent destruction of the Tec1 Transcription factor is required for MAP kinase Signaling Specificity in Yeast, Cell, 119, 1-20, (2004)

262. C. Delahunty and J. R. Yates, Making Nano Columns and Tips, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley Interscience.

258. Flick K, Ouni I, Wohlschlegel JA, Capati C, McDonald WH, Yates JR, Kaiser P., Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain., Nat Cell Biol. 6, 634-41, 2004

257. Loven MA, Davis RE, Curtis CD, Muster N, Yates JR, Nardulli AM., A novel estrogen receptor alpha-associated protein alters receptor-deoxyribonucleic acid interactions and represses receptor-mediated transcription., Mol Endocrinol. 2004, 18, 2649-59.

256. Phillips GR, Anderson TR, Florens L, Gudas C, Magda G, Yates JR 3rd, Colman DR., Actin-binding proteins in a postsynaptic preparation: lasp-1 is a component of central nervous system synapses and dendritic spines., J Neurosci Res. 2004, 78, 38-48

255. Screaton RA, Conkright MD, Katoh Y, Best JL, Canettieri G, Jeffries S, Guzman E, Niessen S, Yates JR 3rd, Takemori H, Okamoto M, Montminy M., The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell 2004, 119, 61-74.

254. Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR 3rd, Winzeler EA, Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004, 14, 2308-18.

253. Thomas Kusch, Laurence Florens, W. Hayes MacDonald, Selene K. Swanson, Robert L. Glaser, John R. Yates III, Susan M. Abmayr, Michael P. Washburn, and Jerry L. Workman, Acetylation by Tip60 Is Required for Selective Histone Variant Exchange at DNA Lesions, Science 2004, 306, 2084-7.

250. Florens, L., Liu, X., Wang, Y., Yang, S., Schwartz, O, Peglar, M., Carrucci, D. J., Yates, J. R., Wub, Y., Proteomics reveals novel proteins on the surface of malaria infected erthrocytes, Mol. Biochem., Parasitology 135, 1-11 (2004)

248. Jessani et al, .Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo, Proc. Natl. Acad. Sci. USA 2004, 101, 13756-61

247. Iain M. Cheeseman1,3, Sherry Niessen2, Scott Anderson2, Francie Hyndman1, John R. Yates III2, Karen Oegema1, and Arshad Desai1,3, A Conserved Protein Network Controls Assembly Of The Outer Kinetochore And Its Ability To Sustain Tension, Genes and Development 2004, 18, 2255-68.

246. Julie L. Kadrmas1, Mark A. Smith1,2, Kathleen A. Clark1,2, Stephen M. Pronovost1, Nemone Muster4, John R. Yates, III4 and Mary C. Beckerle1,2,3,5, Integrin effector PINCH modulates JNK activation during morphogenesis with Ras suppressor RSU-1, Journal of Cell Biology 167, 1019-24, 2004

244. W. Hayes McDonald, David L. Tabb, Rovshan G. Sadygov, Michael J. MacCoss, John Venable, Johannes Graumann, Jeff R. Johnson, Daniel Cociorva, John R. Yates III, MS1, MS2, and SQT - three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications, Rapid Communications in Mass Spectrometry 2004, 18, 2162-8.

243. Durr E, Yu J, Krasinska KM, Carver LA, Yates JR, Testa JE, Oh P, Schnitzer JE., Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture, Nature Biotechnology, 22, 985-92, 2004

242. John Yates, Mass Spectrometry in Systems Biology, Biotechniques 36, 917-9 (2004)

240. Greg T. Cantin and J. R. Yates, III, Strategies for shotgun identification of posttranslational modification by mass spectrometry, J. Chromatography A 1053, 7-14 (2004).

239. Kesti T, McDonald WH, Yates JR 3rd, Wittenberg C., Cell cycle-dependent phosphorylation of the DNA polymerase epsilon subunit, Dpb2, by the Cdc28 cyclin-dependent protein kinase., J Biol Chem. 2004, 279, 14245-55.

238. Robertus A.M. de Bruin, W. Hayes McDonald, Tatyana I. Kalashnikova, John Yates, and Curt Wittenberg, Cln3 Activates G1-Specific Transcription via Phosphorylation of the SBF Bound Repressor Whi5, Cell 117, 887-98 (2004)

237. Rovshan Sadygov, Daniel Cociorva and Yates, J., Database Searching using Tandem Mass Spectra: looking up the answer in the back of the book, Nature Methods, 1, 195-202 (2004)

236. John D. Venable, Mengqui Dong, James Wohlschlegel, Andrew Dillin and John R. Yates III, A novel approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nature Methods 1, 39-45, 2004.

235. James A. Wohlschlegel1, Erica S. Johnson2, Steven I. Reed3, and John R. Yates, III1, Global Analysis of Protein Sumoylation in Saccharomyces cerevisiae Journal of Biological Chemistry 2004, 279, 45662-8.

232. Reinke A, Anderson S, McCaffery JM, Yates J 3rd, Aronova S, Chu S, Fairclough S, Iverson C, Wedaman KP, Powers T. TOR complex 1 (TORC1) includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in S. cerevisiae., J Biol Chem. 2004, 279, 14752-62.

231. Tobili Y. Sam-Yellowe*, Laurence Florens†#, Tongmin Wang*, J. Dale Raine‡, Daniel J. Carucci§, Robert Sinden‡, and John R. Yates, III, Proteome analysis of rhoptry organelles isolated from Plasmodium merozoites, J. Proteome Research 2004, 3, 995-1001.

230. Sandhya Xirasagar1*, Scott Gustafson1*, Alex B. Merrick2, Kenneth B. Tomer2, Stanley Stasiewicz2, Denny D. Chan1, Kenneth J. Yost III1, John R. Yates III3, Susan Sumner4 Nianqing Xiao1, Michael D. Waters2, CEBS OBJECT MODEL FOR SYSTEMS BIOLOGY DATA, CEBS MAGE SysBio-OM, Bioinformatics 20, 2004-15, 2004

225. Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR 3rd, Russell P.Slx1-Slx4 Are Subunits of a Structure-specific Endonuclease That Maintains Ribosomal DNA in Fission Yeast., Mol Biol Cell. 2004, 15, 71-80.

223. Jeffrey R. Johnson, Laurence Florens†, Daniel J. Carucci‡, and John R. Yates III Proteomics in Malaria, J. Proteome Research 3, 296-306 (2004)

222. Wenhong Zhu†, Claudia I. Reich‡, Gary J. Olsen‡, Carol S. Giometti§, John R. Yates III, Shotgun Proteomics of Methanococcus jannaschii and insights into methanogenesis, J. Proteome Research 3, 538-48 (2004).

221. H. Liu, R. G. Sadygov, J. R. Yates, A model for random sampling and estimation of relative protein abundance in Shotgun Proteomics Analytical Chemistry 76, 4193-201 (2004).

220. J. Yates, Mass Spectral Analysis in Proteomics, Annual Reviews in Biophysics and Biomolecular Structure, Annual Reviews, Palo Alto 2004, 33:297-316.

218. Y. H Lin, Z. Y. Park, D. Lin, A. A. Brahmbhatt, Maire-Christine, Rio, J. R. Yates, R. L. Klemke, Requirement of Lasp-1 for Cell Migration Through Regulation of Focal Adhesion Dynamics, J. Cell Biology 165. 421-32 (2004).

217. Jeremy A. Daniel*, Michael S. Torok*, Zu-Wen Sun*, David Schieltz†, C. David Allis*, John R. Yates III§, and Patrick A. Grant, Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription, J. Biol. Chem. 2004, 279, 1867-71

216. Hongbin Liu, Nicholas Bergman, Brendan Thomason, Shamira Shallom, Alyson Hazen4, Joseph Crossno, Scott Peterson, John Yates, III. & Philip Hanna, Formation and Composition of the Anthrax Endospore, J. Bacteriology 186, 164-78 (2004).

215. Dmitri Leonoudakis*, Lisa R. Conti*, Scott Anderson‡, Carolyn M. Radeke*, Leah McGuire*, Marvin E. Adams#, Stanley C. Froehner#, John R. Yates III‡, and Carol A. Vandenberg, Protein Trafficking and Anchoring Complexes Revealed by Proteomic Analysis of Inward Rectifier Potassium Channel (Kir2.x) Associated Protein, J. Biological Chemistry 2004, 279, 22331-46.

213. Lorraine B. Anderson, Anthony J. A. Ouellette‡, Julian Eaton-Rye, Melissa, Michael J. MacCoss, John R. Yates III, and Bridgette A. Barry, Evidence for a post-translational modification in the CP47 subunit of Photosystem II, J. American Chemical Society 2004, 126, 8399-405.

211. Rovshan Sadygov, Hongbin Liu, and John R. Yates, Novel Statistical Models for Protein Validation using Tandem Mass Spectral Data and Protein Amino acid sequence databases, Analytical Chemistry 76, 1664-71 (2004)

209. Johannes Graumann, Jae Hong Seol, Leslie Dunipace, W. Hayes McDonald, John R. Yates III, Barbara J. Wold and Raymond J. Deshaies, Applicability of TAP-MudPIT to pathway proteomics in yeast, Molecular and Cellular Proteomics 3, 227-237 (2004).

207. Varsha S. Likhite, Emily I. Cass, Scott D. Anderson, John R. Yates, and Ann M. Nardulli,, Interaction of Estrogen Receptor with 3-Methyladenine DNA Glycosylase Modulates Transcription and DNA Repair, J. Biol. Chem., 2004; 279: 16875 - 16882

206. Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Drazba JA, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, Yates JR 3rd, A Plasmodium Gene Family Encoding Maurer's Cleft Membrane Proteins: Structural Properties and Expression Profiling, Genome Res. 2004, 14, 1052-9.

204. Holly E. Trueman, J. Dale Raine, Laurence Florens, Johannes T. Dessens, Jacqui Mendoza, Cecilia C. Waller, Anthony A. Holder, Jean Langhorne, Daniel J. Carucci, John R. Yates III and Robert E. Sinden, Functional characterisation of an LCCL/lectin-domain containing protein family in Plasmodium berghei. J. Parasitology 90, 1062-71 (2004)

203. John D. Venable, and John R. Yates III, The Impact of Ion Trap Tandem Mass Spectra Variability on the Identification of Peptides Analytical Chemistry 76, 2928-37 (2004)

201. Christine C. Wu1†, Michael J. MacCoss1†, Kathryn E. Howell2, Dwight E. Matthews3, and John R. Yates, III, Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis, Analytical Chemistry2004, 76, 4951-9.

199. Irene T. Ling, Laurence Florens, Anton R. Dluzewski, Osamu Kaneko, Munira Grainger, Brian Yim Lim, Tsuboi Takafumi, John M. Hopkins, Jeffrey R. Johnson, Motomi Torii5, Lawrence H. Bannister, John R. Yates, III, Anthony A. Holder and Denise Mattei, The Plasmodium falciparum clag 9 gene encodes a rhoptry protein Molecular Microbiology 52, 107-18 (2004).

196. David L. Tabb, Yingying Huang † Vicki H. Wysocki †John R. Yates, III, Basic residue content influences fragment ion peak intensities in low-energy CID spectra of peptides, Analytical Chemistry 76, 1243-8 (2004)

186. Wei Xu, Shilpa Kadam, Helen Cho, Ester M. Banayo, Scott Anderson, John R. Yates III, Beverly M. Emerson & Ronald M. Evans A Methylation-mediator complex in hormone signalling; Genes and Development,18, 144-56 (2004)

180. Skop, A. R., Liu, H., Yates, J. R., Meyer, B. J., Heald, R., Functional proteomic analysis of the mammalian midbody reveals conserved cell division components, Science 305, 61-6 (2004)

166. Claire Delahunty and John R. Yates, III, Identification of Proteins in Complex Mixtures Using Liquid Chromatography and Mass Spectrometry, Current Protocols in Cell Biology 2004

233. Doolan DL, Aguiar JC, Weiss WR, Sette A, Felgner PL, Regis DP, Quinones-Casas P, Yates JR 3rd, Blair PL, Richie TL, Hoffman SL, Carucci DJ. Utilization of genomic sequence information to develop malaria vaccines, J Exp Biol. 2003, 206,:3789-802

227. McDonald WH, Yates JR 3rd. Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther. 2003, 5, 302-9.

226. McDonald WH, Pavlova Y, Yates JR 3rd, Boddy MN. Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex., J Biol Chem. 2003, 278, 45460-7.

224. Rodriguez-Gabriel MA, Burns G, McDonald WH, Martin V, Yates JR 3rd, Bahler J, Russell P.RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress., EMBO J. 2003, 22, 6256-66.

214. J. Wohlschlegel and J. Yates, Proteomics: Where’s Waldo in Yeast, Nature, 425, 671, 2003.

212. Eric C. Schirmer, J. R. Yates III, and Larry Gerace, MudPIT: A powerful proteomics tool for discovery, limited primarily by our imagination, Discovery Medicine 3, 38-39 (2003)

208. M. P. Washburn, R. R. Ulaszek, and J. R. Yates, Reproducibility of Quantitative Proteomic Analyses of Complex Biological Mixtures by Multi-dimensional Protein identification technology, Analytical Chemistry 75, 5054-5061 (2003).

205. Tony R. Hazbun, Lars Malmström, Scott Anderson, Beth J. Graczyk, Bethany Fox, Michael Riffle, Bryan A. Sundin, J. Derringer Aranda, W. Hayes McDonald, Chun-Hwei Chiu, Brian E. Snydsman, Phillip Bradley, Eric G. D. Muller, Stanley Fields, David Baker, John R. Yates III and Trisha N. Davis, Assigning Function to Yeast Proteins by Integration of Technologies, Molecular Cell 12, 1243-52 (2003)

202. Stefan Westermann1, Iain M. Cheeseman1, Scott Anderson2, John R. Yates III2, David G. Drubin1, and Georjana Barnes, Molecular Architecture of the Budding Yeast Inner Kinetochore Reveals a Conserved Core of Structural Components J. Cell Biology 163, 215-22 (2003)

200. Rory Geyer, Susan Wee, Scott Anderson, John R. Yates, III, Dieter Wolf, BTB/POZ domain proteins are putative substrate adaptors for cullin 3 ubiquitin ligases, Molecular Cell 12, 783-90 (2003)

198. Eric C. Schrimer, Laurence Florens, Tinglu Guan, John R. Yates III, and Larry Gerace, Novel Membrane Proteins With Potential Disease Links Found By Subtractive Proteomics, Science 301, 1380-1382 (2003)

197. Michael J. MacCoss, Christine C. Wu, Hongbin Liu, Rovshan Sadygov, and John R. Yates III, A Correlation Algorithm for the Automated Analysis of Quantitative Proteomics Data, Analytical Chemistry 75, 6912-6921 (2003)

195. Tabb, D., Saraf, A., Yates, J. R., GutenTag: high throughput sequence tagging via an empirically derived fragmentation model, Analytical Chemistry 75, 6415-6421 (2003).

194. Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG., A systematic approach to modeling, capturing, and disseminating proteomics experimental data., Nature Biotechnol 21, 247-54 (2003)

193. Tabb, D. L.; Smith, L. L.; Breci, L. A.; Wysocki, V. H.; Lin, D.; Yates, J. R., III; Statistical Characterization of Ion Trap Tandem Mass Spectra from Doubly Charged Tryptic Peptides, Anal. Chem. 75; 1155-1163, (2003)

192. Breci, L. A.; Tabb, D. L.; Yates, J. R., III; Wysocki, V. H., Cleavage N-Terminal to Proline: Analysis of a Database of Peptide Tandem Mass Spectra; Anal. Chem.75, 1963-1971, 2003.

191. W. Hayes McDonald and John R. Yates III, Shotgun Proteomics: Integrating Technologies to Answer Biological Question, Current Opinion in Molecular Therapeutics 5, 302-309 (2003)

190. Karl Willert, Jeff Brown, Esther Danenberg, Andrew Duncan, Irving L. Weissman, Tannishtha Reya, John R. Yates III, and Roel Nusse, Properties of purified biologically active Wnt protein; a lipid modified stem cell growth factor, Nature 423, 448-451 (2003)

189. Rovshan Sadygov and John R. Yates, A hypergeometric probability model for protein identification using tandem mass spectral data and protein sequence databases, Analytical Chemistry 75, 3792-3798 (2003).

188. Bret Cooper, Donna Eckert, Nancy L. Andon, John R. Yates III and Paul A. Haynes, Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry JASMS 14, 736-741 (2003).

187. Christine Wu and Yates, J. R. The application of mass spectrometry to membrane proteomics, Nature Biotechnology 21, 262-7 (2003).

185. Gianluca Canettieri, Ianessa Morantte, Ernesto Guzman, Hiroshi Asahara, Stephan Herzig, Scott D. Anderson, John R. Yates III, Marc Montminy Attenuation of a Phosphorylation Dependent Activator by an HDAC:PP1 Complex; Nat Struct Biol. 10, 175-81, (2003)

184. Direct database searching using tandem mass spectra of peptides, J. R. Yates, III, and Hayes McDonald, Cell Biology: A laboratory Handbook, 3rd Edition, Ed. J. E. Celis, Academic Press.

183. Peptide sequencing by tandem mass spectrometry, J. R. Yates, III, Antonius Koller and David Schieltz, Cell Biology: A laboratory Handbook, Second Edition, Ed. J. E. Celis, Academic Press.

181. B. Li, H. L. J., Anderson, S., Yates, J., Stitzer, L., Workman, J. L., The Set2 histone methyltransferase functions through the phosphorylated CTD of RNA polymerase II, J Biol Chem. (2003) 278, 8897-903

179. Andon, N. L., Eckert, D., Koller, A., Yates, J. R., Haynes, P. A., High Throughput Functional Affinity Purification of Mannose Binding Proteins from Oryza sativa Proteomics 3, 1270-8 (2003)

178. Hanjo Lim1@, Lara G. Hays1*, Jimmy Eng1^, Sandra L. Tollaksen2, Carol S. Giometti2, James F. Holden3, Michael W. W. Adams3, Claudia I. Reich4, Gary J. Olsen4, and John R. Yates III1* , Identification of 2D-gel Proteins: A Comparison of MALDI/TOF Peptide Mass Mapping to ? LC-ESI Tandem Mass Spectrometry, J. Am. Soc. Mass Spectrom.14, 957-70 (2003)

177. Kenichi Yamaguchi a, María Verónica Beligni a, Susana Prieto a, 1, Paul A. Haynes b, W. Hayes McDonald c, John R. Yates III c, and Stephen P. Mayfield a, 2, Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome identifying proteins unique to the 70S ribosome,.J. Biological Chemistry 278, 33774-85 (2003)

175. Christine C. Wu, Michael J. MacCoss, Kathryn E. Howell, John R. Yates, III, A novel method for the comprehensive proteomic analysis of membrane proteins: Identification, Modifications, and Topology, Nature Biotechnology 21, 262-7 (2003)

174. Jingping Zhong, Paul A. Haynes, Shiping Zhang, Xinping Yang, Nancy Andon, Antonius Koller, Donna Eckert, John Yates III, Xun Wang, and Paul Budworth, An in vivo system for protein-protein interaction study and its use in characterization of TBP complex in rice, J. Proteome Research 2, 514-22 (2003(

167. Doolan DL, Southwood S, Freilich DA, Sidney J, Graber NL, Shatney L, Bebris L, Florens L, Dobano C, Witney AA, Appella E, Hoffman SL, Yates JR 3rd, Carucci DJ, Sette A., Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A, 100, 9952-7 (2003).

164. Dayin Lin, David Tabb, and John R. Yates, Large-scale protein identification using mass spectrometry, Biochim Biophys Acta. 1646, 1-10(2003).

163. Thomas Sellers and John R. Yates, Applications of Proteomics to Genetic Epidemiology, Genetic Epidemiology 24, 83-89 (2003)

161. Michael P. Washburn, Antonius Koller, Guy Oshiro, Ryan R. Ulaszek, David Plouffe, Cosmin Deciu, Elizabeth Winzeler¶, and John R. Yates, III,¶ Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae., Proc Natl Acad Sci U S A. (2003) 100, 3107-12.

154. Margaret A. Loven, Nemone Muster, John R. Yates and Ann M. Nardulli, A novel estrogen receptor alpha associated protein, template activating factor I beta, inhibits acetylation and transactivation, Molecular Endocrinology 17, 67-78 (2003).

150. Carol S. Giometti, Tripti Khare, Sandra L. Tollaksen, Alexandre Tsapin, Wenhong Zhu, John R. Yates III, and Kenneth H. Nealson, Analysis of the Shewanella oneidensis Proteome by Two-dimensional Gel Electrophoresis Under Nondenaturing Conditions, Proteomics. 2003, 3, 777-85.

135. Lindstrom DL, Squazzo SL, Muster N, Burckin TA, Wachter KC, Emigh CA, McCleery, JA, Yates JR 3rd, Hartzog GA. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins., Mol Cell Biol (2003) 23, 1368-78

228. McDonald WH, Yates JR 3rd.Shotgun proteomics and biomarker discovery., Disease Markers. 2002, 18, 99-105

176. David l. Tabb, Michael J. MacCoss, Christine C. Wu, Scott D. Anderson, John R. Yates, III, Similarity among tandem mass spectra of proteomic experiments: detection, significance, and utility, Analytical Chemistry 75, 2470-7 (2002)

173. Andon NL, Hollingworth S, Koller A, Greenland AJ, Yates JR 3rd, Haynes PA. Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry, Proteomics. 2, 1156-68, (2002).

172. Wenhong Zhu and John R. Yates, Proteome Analysis of Microbes: to gel or not to gel, Applied Genomics and Proteomics 1, 3-12 (2002)

171. Iain Cheeseman, Scott Anderson, Miri Jwa, Erin Green, Jung-seong Kang, John R. Yates, Clarence Chan, David Drubin, Georjana Barnes, Phospho-regulation of Kinetochore-Microtubule attachments by the Aurora kinase Ipl1p, Cell 111, 163-172 (2002).

170. R. Verma, L. Aravind, R. Oania, W. H. McDonald, J. R. Yates III, E.V. Koonin, R. J. Deshaies, Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome, Science 298, 611-5 (2002)

169. Jane M. Carlton*, Samuel V. Angiuoli*, Bernard B. Suh*, Taco Kooij†, Mihaela Pertea*, Maria D. Ermolaeva*, Jonathan E. Allen*, Joana C. Silva*, Jeremy D. Selengut*, Hean L. Koo*, Jeremy D. Peterson*, Mihai Pop*, Daniel S. Kosack*, Martin F. Shumway*, Shelby L. Bidwell*, Shamira J. Shallom*, Azadeh Shoaibi*, Leda M. Cummings*, Jennifer K. Cho*, John Quackenbush*, Susan E. van Aken*, Steven B. Riedmuller*, Tamara V. Feldbylum*, Laurence Florens‡, John R. Yates III‡, Dale J. Raine§, Robert E. Sinden§, Michael A. Harris||, Deirdre A. Cunningham¶, Peter R. Preiser¶, Lawrence W. Bergman#, Akhil Vaidya#, Leo H. van Lin†, Chris J. Janse†, Andrew P. Waters†, Hamilton O. Smith||, Owen R. White*, Steven L. Salzberg*, J. Craig Venter*, Claire M. Fraser*, Stephen L. Hoffman**, Malcolm J. Gardner*, Daniel J. Carucci**, Whole genome shotgun sequencing of a model rodent malaria parasite and comparative analysis with Plasmodium falciparum, Nature 419, 512-519 (2002)

168. Laurence Florens*, Michael P. Washburn†, J. Dale Raine‡, Robert M. Anthony§, Munira Grainger||, J. David Haynes§,**, J. Kathleen Moch§, Nemone Muster*, John B. Sacci§,††, David L. Tabb*, Adam A. Witney§,‡‡, Dirk Wolters†,§§, Yimin Wu¶, Malcolm J. Gardner#, Anthony A. Holder||, Robert E. Sinden‡, John R. Yates III*, † and Daniel J. Carucci§, A Proteomic View of the Plasmodium falciparum Life Cycle, Nature 419, 520-526 (2002)

165. Claire Delahunty and John R,. Yates, Proteomics: a shotgun approach without 2-DE gels, Encyclopedia of the Human Genome 2002.

162. Howe L, Kusch T, Muster N, Chaterji R, Yates JR 3rd, Workman JL, Yng1p Modulates the Activity of Sas3p as a Component of the Yeast NuA3 Histone Acetyltransferase Complex, Mol Cell Biol. 14, 5047-53, 2002

160. Shigeaki Saitoh, Andrei Chabes, W. Hayes McDonald, Lars Thelander, John R. Yates, III, Paul Russell, Cid13 is a cytoplasmic poly (A) polymerase that regulates ribonucleotide reductase mRNA, Cell 109, 563-573 (2002).

159. Michael MacCoss, Christine Wu, and John R. Yates, III, Probability Based Validation of Protein Identifications Using a Modified SEQUEST Algorithm, Analytical Chemistry 74, 5593-5599 (2002).

158. Thomas C. Hunter, Nancy L. Andon, Antonius Koller, John R. Yates III and Paul A. Haynes, The functional proteomics toolbox: methods and applications, J Chromatogr B Analyt Technol Biomed Life Sci. 782, 165-81 (2002)

157. Daniel J. Carucci1, John R. Yates, III2 and Laurence Florens, Exploring the Proteome of Plasmodium, Int J Parasitol. 32, 1539-42, (2002).

156. Toshifumi Inada, Eric Winstall, Salvador Z. Tarun Jr, John R. Yates, III, Dave Schieltz, and Alan B. Sachs, One step affinity purification of the yeast ribosome and its associated proteins and mRNAs, RNA 8, 948-58 (2002)

155. Kenichi Yamaguchi , Susana Prieto, María Verónica Beligni, Paul A. Haynes, Hayes McDonald, John Yates III, and Stephen P. Mayfield, Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: Identification of a novel S1 domain-containing protein and unusually large orthologues of bacterial S2, S3 and S5, Plant Cell. 14, 2957-74, (2002).

153. Jaekyung Shim, Hanjo Lim, John R.Yates III, Michael Karin, Nuclear export of NF90 is required for interleukin-2 mRNA stabilization, Molecular Cell 10, 1331-1344 (2002).

151. Carol S. Giometti, Claudia Reich., Sandra Tollaksen, Gyorgy Babnigg, Hanjo Lim, Wenhong Zhu, John Yates III, and Gary Olsen, Global Analysis of a “Simple” Proteome: Methanococcus jannaschii, J Chromatogr B Analyt Technol Biomed Life Sci. (2002) 782, 227-43.

149. Marilyn G. Pray-Grant, David Schieltz, Stacey J. McMahon, Jennifer M. Wood, Erin L. Kennedy, Richard G. Cook, Jerry L. Workman, John R. Yates III and Patrick A. Grant, The novel SLIK (SAGA-Like) histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol Cell Biol. (2002), 22, 8774-86

146. Michael J. MacCoss1†, W. Hayes McDonald1†, Anita Saraf1†, Rovshan Sadygov1, Judy M. Clark2, Joseph J. Tasto3, Kathleen L. Gould3, Dirk Wolters4, Michael Washburn5, Avery Weiss6, John I. Clark3 and John R. Yates, III1,5, Shotgun Identification of Protein Modifications from Protein Complexes and Lens Tissue, PNAS 99, 7900-7905 (2002).

144. Yingying Huang, Vicki H. Wysocki, David L. Tabb, John R. Yates, III, The Influence of Histidine on Cleavage C-terminal to Acidic Residues in Doubly Protonated Tryptic Peptides, Int. J. Mass Spectrom. 219, 233-244 (2002).

143. Lorraine B. Anderson, Melissa Maderia, Anthony J. A. Ouellette, LeeAnn Higgins, Thomas Krick, Hayes McDonald, Mike MacCoss, Hanjo Lim, John R. Yates, III, and Bridgette A. Barry, Post-translational Modifications of Proline and Tryptophanin CP43 of the Photosynthetic Water Oxidizing Complex, Proc Natl Acad Sci U S A. (2002) 99, 14676-81

142. Raymond J. Deshaies, Greg Cope, Svetlana Lyapina, Hayes McDonald, Jae Hong Seol, Andrej Shevchenko, Anna Shevchenko, Rati Verma, and John Yates, Charting the protein 'complexome' in yeast, Molecular and Cellular Proteomics 1, 3-10, (2002)

140. Eric Mortensen, Hayes McDonald, John R. Yates, III, Douglas R. Kellogg, Cell cycle-dependent assembly of a Gin4-septin complex, Mol Biol Cell. (2002) 13, 2091-105.

139. Rovshan G. Sadygov, Jimmy Eng, Eberhard Durr, Anita Saraf, Hayes McDonald, Michael J. MacCoss, and John R. Yates, III, Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation, Journal of Proteome Research 2, 211-15 (2002)

138. Guy Oshiro, Lisa M. Wodicka, Michael P. Washburn, John R. Yates III, David J. Lockhart, and Elizabeth A. Winzeler, Highly parallel identification of new open reading frames in S. cerevisiae, Genome Research 12, 1210-1220 (2002)

137. A. Koller, M. P. Washburn, B. Markus Lange, N. Andon, C. Deciu,. P. Haynes, L. Hays, D. Schieltz, R. Ulaszek, J. Wei, D. Wolters, J. R. Yates, III; Proteomic survey of metabolic pathways in rice, Proc Natl Acad Sci U S A. (2002) 99, 11969-74

136. M. Washburn, R. Ulaszek, C. Deciu, D. M. Schieltz, J. R. Yates, III, Analysis of quantitative proteomic data generated by multi-dimensional protein identification technology, Anal. Chem. 74, 1650-1657 (2002).

134. W. Hayes McDonald, Ryoma Ohi, David T. Miyamoto, Timothy J. Mitchison, and John R. Yates III; Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT, Int. J. Mass Spectrom. 219, 245-251 (2002).

133. D. Tabb, W. H. McDonald, J. R. Yates, DTASelect and Contrast: Proteomic Tools for Filtering, Summarizing, and Comparing Tandem Mass Spectrometry Results, J. Proteome Research 1, 21-26 (2002)

132. Jizhong Zhou, Carol Giometti, Hanjo Lim, John R. Yates Gene and Protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors, Omics, 6, 39-60 (2002).

131. Hongbin Liu, Dayin Lin, J. R. Yates, Biotechniques 32, 898-911 (2002).

125. Hayes McDonald and John R. Yates, Functional Genomics: Proteomics, 2002 Yearbook of Science and Technology, McGraw-Hill.

121. Dorothea K. Thompson, Alexander S. Beliaev, Carol S. Giometti, Douglas Lies, Kenneth H. Nealson, Hanjo Lim, John Yates III, Craig C. Brandt, James M. Tiedje, and Jizhong Zhou, Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis Using DNA Microarrays and Proteomic Tools, Applied and Environmental Microbiology, 68, 881-92 (2002).

182. MacCoss, M. and Yates, J. R., Proteomics: analytical tools and techniques, Current Opinion in Clinical Nutrition and Metabolic Care 4, 369-375, (2001).

152. Dongre AR, Kovats S, deRoos P, McCormack AL, Nakagawa T, Paharkova-Vatchkova V, Eng J, Caldwell H, Yates JR 3rd, Rudensky AY. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur J Immunol. (2001) 31(5):1485-94.

148. Lim, Hanjo and Yates, John R III (October 2001) Mass Spectrometry: Analysis of Two–dimensional Protein Gels. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester [doi:10.1038/npg.els.0003110]

147. Cheeseman, I. M., M. Enquist-Newman, et al. (2001). Mitotic spindle integrity and kinetochore function linked by the Duo1p/Dam1p complex. J Cell Biol 152(1): 197-212.

145. Boddy, M.N., Gaillard, P.-H.L., McDonald, W.H., Shanahan, P., Yates, J.R., 3rd, and Russell, P. (2001). Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell. 107, 537-548 (2001)

141. James F. Holden, Farris L. Poole II, Sandra L. Tollaksen, Carol S. Giometti, Hanjo Lim, John R. Yates III, Michael W. W. Adams Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs, Comparative and Functional Genomics 2, 275-288 (2001)

130. D. Lin, A. Alpert, J. R. Yates, American Genomic/Proteomics Technology 1, 38, 2001.

129. R. Verma, H. McDonald, J. Yates III, and R. J. Deshaies, Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields fully active S phase cyclin-Cdk, Molecular Cell 8, 439-448, 2001.

128. S. Honey, B. L. Schneider, D. M. Schieltz, J. R. Yates, B. Futcher, A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-Cdk complex, Nucleic Acid Research 29, E24, 2001.

127. Shigehiro Osada Ann Sutton Nemone Muster Christine E. Brown John R. Yates III, Rolf Sternglanz, and Jerry L. Workman, The yeast SAS (something about silencing) protein complex contains a MYST-type acetyltransferase and functions with chromatin assembly factor ASF1, Genes and Development 15, 3155-3168 (2001).

126. D. Wolters, M. P. Washburn, J. R. Yates, III, An automated Multidimensional Protein Identification Technology for Shotgun Proteomics, Analytical Chemistry 73, 5683-5690 (2001)

122. Carol S. Giometti, Claudia Reich, Sandra Tollaksen, Gyorgy Babnigg, Hanjo Lim, John Yates III, and Gary Olsen, Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis, Proteomics 1, 1033-42 (2001)

118. S. Bark, N. Muster, J. Yates, G. Siuzdak, High temperature mass mapping using a thermophilic protease. J. American Chemical Society 123, 1774-1775 (2001).

117. K. E. Laidig, W. Chen, Y. Park, K. Park, J. R. Yates, III, R. J. Lamont, M. Hackett, Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra in absence of annotations or known open reading frames, The Analyst, 126, 52-7 (2001).

116. M. P. Washburn, D. Wolters, J. R. Yates, III, Large Scale analysis of the yeast proteome via multidimensional protein identification technology Nature Biotechnology 19, 242-247 (2001)

111. A. Emili, D. M. Schieltz, J. R. Yates, III, L. H. Hartwell, Dynamic interaction of DNA damage checkpoint Rad53 with chromatin assembly factor Asf1, Molecular Cell 7, 13-20 (2001).

107. Patricia R. Segarini, James E. Nesbitt, Dongxia Li, Lara G. Hayes, John R. Yates III and David E. Carmichael, The Low Density Lipoprotein Receptor-Related Protein/alpha 2-Macroglobulin Receptor is a Receptor for Connective Tissue Growth Factor (CTGF) J. Biological Chemistry 276, 40659-40667 (2001).

106. Tong, W. and Yates, J. R., Sensitive and High Resolution CE/MS/MS for Protein identification in Complex Mixtures, Chromatographia 53, S-90 (2001).

104. Friedman, D. B., Vinh, D., Kern, J., Crawford, D., Steiner, E., Schieltz, D., Yates, III, J., Resing, K., Ahn, N. G., Winey, M., Davis, T. N., Phosphorylation at Spc110p at Msp1p and CDK sites is required for proper interaction with the Tub4p-complex at the centrosome in S. cerevisiae. J. Biological Chemistry 276, 17958-67 (2001).

95. Molecular properties of matrilin-3 isolated from human growth cartilage, D. Kleemann-Fischer, G. R. Kleemann, D. Engel, J. R. Yates, III, J.-J. Wu, and D. R. Eyre, Archives of Biochemistry and Biophysics 387, 216-222 (2001).

82. The Arp2/3 complex is required for actin dependent mitochondrial motility and inheritance in budding yeast, I. Boldogh, S. L. Karmon, W. D. Nowakowski, L. G. Hays, J. R. Yates, J.and L. A. Pon, PNAS 98, 3162-3167 (2001).

124. Hefner Y, Borsch-Haubold AG, Murakami M, Wilde JI, Pasquet S, Schieltz D, Ghomashchi F, Yates JR, Armstrong CG, Paterson A, Cohen P, Fukunaga R, Hunter T, Kudo I, Watson SP, Gelb MH. Serine 727 phosphorylation and activation of cytosolic phospholipase A2 by MNK1-related protein kinases. J Biol Chem. 275, 37542-51 (2000).

123. Todorow, Z., Spang, A., Carmack, E., Yates, J., and Schekman, R. (2000). Active recycling of yeast golgi mannosyltransferase complexes through the endoplasmic reticulum. Proc Natl Acad Sci U S A 97, 13643-13648.

120. M. T. Krahmer, J. J. Waltersm, K. F. Fox, A. Fox, K. E. Creek, L. Pirisi, D. Wunschel, R. D. Smith, D. L. Tabb, J. R. Yates, III, MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR products, Anal. Chem. 72, 4033-4040 (2000).

119. L. Tabb. J. K. Eng, J. R. Yates, Protein Identification by SEQUEST, Proteome Research: Mass Spectrometry, Ed. Peter James, Springer, Berlin, pp125-142 (2000).

115. H. McDonald and J. R. Yates, III, Proteomic Tools for Cell Biology, Traffic 1, 1-8, 2000.

114. P. Haynes and J. R. Yates, III, Protein Profiling, Comparative and Functional Genomics 17, 81-87 (2000)

113. M. Washburn and J. R. Yates, III, Novel methods of proteome analysis: multidimensional chromatography and mass spectrometry, Proteomics A Current Trends Supplement 27-36, (2000).

112. Proteomic Analysis of Two Functional States of the Golgi Complex in Mammary Epithelial Cells, Christine C. Wu, John R. Yates, III, Margaret C. Neville, and Kathryn E. Howell, Traffic 1, 747-754 (2000).

110. C.C. Wu, K. E. Howell, M. C. Neville, J. R. Yates, III, J. L. McManaman, Proteomics reveals contribution of endoplasmic reticulum membranes to the lipid secretion process in mammary epithelial cells, Electrophoresis 21, 3470-3482 (2000).

109. R. Verma, S. Chen, R. Feldman, D. Schieltz1, J. Yates2, and R. J. Deshaies Characterization of 26S Proteasomes isolated by a novel one-step method of purification: effect of nucleotides on assembly and composition, Molecular Cellular Biology 11, 3425 (2000).

108. Randall S. Taylor, Christine C. Wu, Lara G. Hays, Jimmy K. Eng, John R. Yates, III, Kathryn E. Howell, Proteomics of rat liver Golgi complex: Minor proteins are identified through sequential fractionation, Electrophoresis 21, 3441-3459 (2000).

105. Washburne, M. and Yates, J., Analysis of the Microbial Proteome, Current Opinion in Microbiology 3, 292-297 (2000).

102. Michael Sacher, Jemima Barrowman, David Schieltz, John R. Yates III and Susan Ferro-Novick, Identification and characterization of five new subunits of TRAPP, Eur. J. Cell. Biol. 79, 71-80 (2000)

101. Identifying SNPS expressed in Proteins: rapid identification of amino acid sequence variations by LC/MS/MS with SEQUEST data analysis, C. L. Gatlin, J. K. Eng, S. T. Terashita, J. C. Detter, J. R. Yates, III, Analytical Chemistry 72, 757-763 (2000).

99. Mass Spectrometry: From Genome and Proteome, J. R. Yates, Trends in Genetics 16, 5-8, 2000.

97. Improved methods for structural analysis of protein prenyl groups and associated C-terminal modifications, M. E. Whitten, K. Yokoyama, D. Schieltz F. Ghomashchi, D. Lam, J. R. Yates, K. Palczewski, M. H. Gelb, Methods in Enzymology, 316, 436-51, (2000).

93. Direct analysis of proteins in mixtures: application to protein complexes, J. R. Yates, III, A. J. Link, and D. Schieltz, Protein and Peptide Analysis: Advances in the Use of Mass Spectrometry, Ed. J. R. Chapman, Humana Press, London, England, pp. (2000)

89. Yates, John R (August 2000) Mass Spectrometry in Biology. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester [doi:10.1038/npg.els.0000999]


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