Choi, Sung Hugh, Péli-Gulli, Marie-Pierre, Mcleod, Iain, Sarkeshik, Ali, Yates, John R., Simanis, Viesturs, ...
Background: it is unknown how oscillations in Cdk1 activity drive the dramatic changes in chromosome and spindle dynamics that occur at the metaphase/anaphase transition. Results: we show that the...
Choi, Sung Hugh, Péli-Gulli, Marie-Pierre, Mcleod, Iain, Sarkeshik, Ali, Yates, John R., Simanis, Viesturs, ...
Background: it is unknown how oscillations in Cdk1 activity drive the dramatic changes in chromosome and spindle dynamics that occur at the metaphase/anaphase transition. Results: we show that the...
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data (2009)
Carvalho, Paulo C, Fischer, Juliana SG, Chen, Emily I, Domont, Gilberto B, Carvalho, Maria GC, Degrave, Wim M, ...
Abstract Background Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy...
The hydrolethalus syndrome protein HYLS-1 links core centriole structure to cilia formation (2009)
Dammermann, Alexander, Pemble, Hayley, Mitchell, Brian J., McLeod, Ian, Yates, John R., Kintner, Chris, ...
Centrioles are subcellular organelles composed of a ninefold symmetric microtubule array that perform two important functions: (1) They build centrosomes that organize the microtubule cytoskeleton,...
Neil D. Ebenezer, Michel Michaelides, Sharon A. Jenkins, Isabelle Audo, Andrew R. Webster, Michael E. Cheetham, ...
PURPOSE. To test the incidence of mutations in RPGR ORF15 in six families with X-linked progressive retinal degeneration (cone-rod dystrophy [XLCORD], macular or cone dystrophy) and to undertake a...
Schultz-Norton, Jennifer R, Ziegler, Yvonne S, Likhite, Varsha S, Yates, John R, Nardulli, Ann M
Abstract Background DNA-bound transcription factors recruit an array of coregulatory proteins that influence gene expression. We previously demonstrated that DNA functions as an allosteric modulator...
Le Roch, Karine G, Johnson, Jeffrey R, Ahiboh, Hugues, Chung, Duk-Won D, Prudhomme, Jacques, Plouffe, David, ...
Abstract Background In recent years, a major increase in the occurrence of drug resistant falciparum malaria has been reported. Choline analogs, such as the bisthiazolium T4, represent a novel class...
PatternLab for proteomics: a tool for differential shotgun proteomics (2008)
Carvalho, Paulo C, Fischer, Juliana SG, Chen, Emily I, Yates, John R, Barbosa, Valmir C
Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al . demonstrated a method to perform...
Xia, Dong, Sanderson, Sanya J, Jones, Andrew R, Prieto, Judith H, Yates, John R, Bromley, Elizabeth, ...
Abstract Background Although the genomes of many of the most important human and animal pathogens have now been sequenced, our understanding of the actual proteins expressed by these genomes and how...
Introduction Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun Proteomics (2008)
Emily I. Chen, Daniel Cociorva, Jeremy L. Norris, John R. Yates
Gassmann, Reto, Essex, Anthony, Hu, Jia-Sheng, Maddox, Paul S., Motegi, Fumio, Sugimoto, Asako, ...
Chromosome segregation requires stable bipolar attachments of spindle microtubules to kinetochores. The dynein/dynactin motor complex localizes transiently to kinetochores and is implicated in...
Interaction of estrogen receptor {alpha} with proliferating cell nuclear antigen (2007)
Schultz-Norton, Jennifer R., Gabisi, Vivian A., Ziegler, Yvonne S., McLeod, Ian X., Yates, John R., Nardulli, Ann M.
The ability of estrogen receptor α (ERα) to modulate gene expression is influenced by the recruitment of a host of co-regulatory proteins to target genes. To further understand how...
Schlaitz, Anne-Lore, Srayko, Martin, Dammermann, Alexander, Quintin, Sophie, Wielsch, Natalie, MacLeod, Ian, ...
Microtubule behavior changes during the cell cycle and during spindle assembly. However, it remains unclear how these changes are regulated and coordinated. We describe a complex that targets the...
PMS2 mutations in childhood cancer (2006)
De Vos, Michel, Hayward, Bruce E., Charlton, Ruth, Taylor, Graham R., Glaser, Adam W., Picton, Susan, ...
Until recently, the PMS2 DNA mismatch repair gene has only rarely been implicated as a cancer susceptibility locus. New studies have shown, however, that earlier analyses of this gene have had...
Duchaine, Thomas F., Wohlschlegel, James A., Kennedy, Scott, Bei, Yanxia, Conte, Darryl, Pang, Ka Ming, ...
In plants, animals, and fungi, members of the Dicer family of RNase III-related enzymes process double-stranded RNA (dsRNA) to initiate small-RNA-mediated gene-silencing mechanisms. To learn how C....
Sandall, Sharsti, Severin, Fedor, McLeod, Ian X, Yates, John R, Oegema, Karen, Hyman, Anthony, ...
Proper connections between centromeres and spindle microtubules are of critical importance in ensuring accurate segregation of the genome during cell division. Using an in vitro approach based on the...
falciparum antigens by antigenic analysis of genomic and proteomic (2006)
Z. Bozdech, M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, Z. Bozdech, ...
plasmodium
PMS2 Mutations in Childhood Cancer (2006)
De Vos, Michel, Hayward, Bruce E., Charlton, Ruth, Taylor, Graham R., Glaser, Adam W., Picton, Susan, ...
Until recently, the PMS2 DNA mismatch repair gene has only rarely been implicated as a cancer susceptibility locus. New studies have shown, however, that earlier analyses of this gene have had...
Wilson, Adam C, Wu, Christine C, Yates, John R, Tan, Ming
In the pathogenic bacterium Chlamydia trachomatis, a transcriptional repressor, HrcA, regulates the major heat shock operons, dnaK and groE. Cellular stress causes a transient increase in...
Wilson, Adam C, Wu, Christine C, Yates, John R, Tan, Ming
In the pathogenic bacterium Chlamydia trachomatis, a transcriptional repressor, HrcA, regulates the major heat shock operons, dnaK and groE. Cellular stress causes a transient increase in...
Automatic quality assessment of peptide tandem mass spectra (2004)
Marshall Bern, David Goldberg, W. Hayes Mcdonald, John R. Yates
Motivation: A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up,...
A methylation-mediator complex in hormone signaling (2004)
Xu, Wei, Cho, Helen, Kadam, Shilpa, Banayo, Ester M., Anderson, Scott, Yates, John R., ...
The recruitment of coactivators by nuclear hormone receptors (NRs) promotes transcription by subverting chromatin-mediated repression. Although the histone methylation enzyme CARM1 and an...
CEBS object model for systems biology data, SysBio-OM (2004)
Xirasagar, Sandhya, Gustafson, Scott, Merrick, B. Alex, Tomer, Kenneth B., Stasiewicz, Stanley, Chan, Denny D., ...
Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being...
Cheeseman, Iain M., Niessen, Sherry, Anderson, Scott, Hyndman, Francie, Yates, John R., Oegema, Karen, ...
Kinetochores play an essential role in chromosome segregation by forming dynamic connections with spindle microtubules. Here, we identify a set of 10 copurifying kinetochore proteins from...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
CEBS object model for systems biology data, SysBio-OM (2004)
Xirasagar, Sandhya, Gustafson, Scott, Merrick, B. Alex, Tomer, Kenneth B., Stasiewicz, Stanley, Chan, Denny D., ...
Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledgebase is being...
A methylation-mediator complex in hormone signaling (2004)
Xu, Wei, Cho, Helen, Kadam, Shilpa, Banayo, Ester M., Anderson, Scott, Yates, John R., ...
The recruitment of coactivators by nuclear hormone receptors (NRs) promotes transcription by subverting chromatin-mediated repression. Although the histone methylation enzyme CARM1 and an...
Automatic Quality Assessment of Peptide Tandem Mass Spectra (2004)
Bern, Marshall, Goldberg, David, McDonald, W. Hayes, Yates, John R.
Motivation: A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up,...
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle (2004)
Le Roch, Karine G., Johnson, Jeffrey R., Florens, Laurence, Zhou, Yingyao, Santrosyan, Andrey, Grainger, Munira, ...
To investigate the role of post-transcriptional controls in the regulation of protein expression for the malaria parasite, Plasmodium falciparum, we have compared mRNA transcript and protein...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
A methylation-mediator complex in hormone signaling (2004)
Xu, Wei, Cho, Helen, Kadam, Shilpa, Banayo, Ester M., Anderson, Scott, Yates, John R., ...
The recruitment of coactivators by nuclear hormone receptors (NRs) promotes transcription by subverting chromatin-mediated repression. Although the histone methylation enzyme CARM1 and an...
CEBS object model for systems biology data, SysBio-OM (2004)
Xirasagar, Sandhya, Gustafson, Scott, Merrick, B. Alex, Tomer, Kenneth B., Stasiewicz, Stanley, Chan, Denny D., ...
Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledgebase is being...
Parallel Identification of New Genes in Saccharomyces cerevisiae (2002)
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Honey, Sangeet, Schneider, Brandt L., Schieltz, David M., Yates, John R., Futcher, Bruce
A novel multiple affinity purification (MAFT) or tandem affinity purification (TAP) tag has been constructed. It consists of the calmodulin binding peptide, six histidine residues, and three copies...
Osada, Shigehiro, Sutton, Ann, Muster, Nemone, Brown, Christine E., Yates, John R., Sternglanz, Rolf, ...
Functional specialization of β-arrestin interactions revealed by proteomic analysis
Xiao, Kunhong, McClatchy, Daniel B., Shukla, Arun K., Zhao, Yang, Chen, Minyong, Shenoy, Sudha K., ...
β-arrestins are cytosolic proteins that form complexes with seven-transmembrane receptors after agonist stimulation and phosphorylation by the G protein-coupled receptor kinases. They play an...
Induction of Cullin 7 by DNA damage attenuates p53 function
Jung, Peter, Verdoodt, Berlinda, Bailey, Aaron, Yates, John R., Menssen, Antje, Hermeking, Heiko
The p53 tumor suppressor gene encodes a transcription factor, which is translationally and posttranslationally activated after DNA damage. In a proteomic screen for p53 interactors, we found that the...
Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development
McClatchy, Daniel B., Liao, Lujian, Park, Sung Kyu, Venable, John D., Yates, John R.
Large-scale proteomic analysis of the mammalian brain has been successfully performed with mass spectrometry techniques, such as Multidimensional Protein Identification Technology (MudPIT), to...
ZW10 links mitotic checkpoint signaling to the structural kinetochore
Kim, Yumi, Weaver, Beth A.A., Mao, Yinghui, McLeod, Ian, Yates, John R., ...
The mitotic checkpoint ensures that chromosomes are divided equally between daughter cells and is a primary mechanism preventing the chromosome instability often seen in aneuploid human tumors. ZW10...
Kadrmas, Julie L., Smith, Mark A., Clark, Kathleen A., Pronovost, Stephen M., Muster, Nemone, Yates, John R., ...
Cell adhesion and migration are dynamic processes requiring the coordinated action of multiple signaling pathways, but the mechanisms underlying signal integration have remained elusive. Drosophila...
Audhya, Anjon, Hyndman, Francie, McLeod, Ian X., Maddox, Amy S., Yates, John R., Desai, Arshad, ...
Cytokinesis completes cell division and partitions the contents of one cell to the two daughter cells. Here we characterize CAR-1, a predicted RNA binding protein that is implicated in cytokinesis....
Regulation of cell migration and survival by focal adhesion targeting of Lasp-1
Lin, Yi Hsing, Park, Zee-Yong, Lin, Dayin, Brahmbhatt, Anar A., Rio, Marie-Christine, Yates, John R., ...
Large-scale proteomic and functional analysis of isolated pseudopodia revealed the Lim, actin, and SH3 domain protein (Lasp-1) as a novel protein necessary for cell migration, but not adhesion to,...
New Tetrahymena basal body protein components identify basal body domain structure
Kilburn, Chandra L., Pearson, Chad G., Romijn, Edwin P., Meehl, Janet B., Giddings, Thomas H., Culver, Brady P., ...
Basal bodies organize the nine doublet microtubules found in cilia. Cilia are required for a variety of cellular functions, including motility and sensing stimuli. Understanding this biochemically...
New Tetrahymena basal body protein components identify basal body domain structure
Kilburn, Chandra L., Pearson, Chad G., Romijn, Edwin P., Meehl, Janet B., Giddings, Thomas H., Culver, Brady P., ...
Meeusen, Shelly, Tieu, Quinton, Wong, Edith, Weiss, Eric, Schieltz, David, Yates, John R., ...
Maintenance of mitochondrial DNA (mtDNA) during cell division is required for progeny to be respiratory competent. Maintenance involves the replication, repair, assembly, segregation, and...
Goode, Bruce L., Wong, Jonathan J., Butty, Anne-Christine, Peter, Matthias, McCormack, Ashley L., Yates, John R., ...
Coronin is a highly conserved actin-associated protein that until now has had unknown biochemical activities. Using microtubule affinity chromatography, we coisolated actin and a homologue of...
The Septins Are Required for the Mitosis-specific Activation of the Gin4 Kinase
Carroll, Christopher W., Altman, Roger, Schieltz, David, Yates, John R., Kellogg, Douglas
In budding yeast, a protein kinase called Gin4 is specifically activated during mitosis and functions in a pathway initiated by the Clb2 cyclin to control bud growth. We have used genetics and...
Architecture of the budding yeast kinetochore reveals a conserved molecular core
Westermann, Stefan, Cheeseman, Iain M., Anderson, Scott, Yates, John R., Drubin, David G., Barnes, Georjana
How kinetochore proteins are organized to connect chromosomes to spindle microtubules, and whether any structural and organizational themes are common to kinetochores from distantly related...
Implication of a novel multiprotein Dam1p complex in outer kinetochore function
Cheeseman, Iain M., Brew, Christine, Wolyniak, Michael, Desai, Arshad, Anderson, Scott, Muster, Nemone, ...
Dam1p, Duo1p, and Dad1p can associate with each other physically and are required for both spindle integrity and kinetochore function in budding yeast. Here, we present our purification from yeast...
CTA4 Transcription Factor Mediates Induction of Nitrosative Stress Response in Candida albicans▿ †
Chiranand, Wiriya, McLeod, Ian, Zhou, Huaijin, Lynn, Jed J., Vega, Luis A., Myers, Hadley, ...
This work has identified regulatory elements in the major fungal pathogen Candida albicans that enable response to nitrosative stress. Nitric oxide (NO) is generated by macrophages of the host immune...
Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression
Ravnskjaer, Kim, Kester, Henri, Liu, Yi, Zhang, Xinmin, Lee, Dong, Yates, John R, ...
A number of hormones and growth factors stimulate gene expression by promoting the phosphorylation of CREB (P-CREB), thereby enhancing its association with the histone acetylase paralogs p300 and CBP...
Jelluma, Nannette, Brenkman, Arjan B., McLeod, Ian, Yates, John R., Cleveland, Don W., Medema, René H., ...
PatternLab for proteomics: a tool for differential shotgun proteomics
Carvalho, Paulo C, Fischer, Juliana SG, Chen, Emily I, Yates, John R, Barbosa, Valmir C
Regulation of Microtubule Assembly and Organization in Mitosis by the AAA+ ATPase Pontin
Ducat, Daniel, Kawaguchi, Shin-ichi, Liu, Hongbin, Yates, John R., Zheng, Yixian
To identify novel proteins important for microtubule assembly in mitosis, we have used a centrosome-based complementation assay to enrich for proteins with mitotic functions. An RNA interference...
Xia, Dong, Sanderson, Sanya J, Jones, Andrew R, Prieto, Judith H, Yates, John R, Bromley, Elizabeth, ...
A proteomics analysis identifies one third of the predicted Toxoplasma gondii proteins and integrates proteomics and genomics data to refine genome annotation.
Plk1- and β-TrCP–dependent degradation of Bora controls mitotic progression
Seki, Akiko, Coppinger, Judith A., Du, Haining, Jang, Chang-Young, Yates, John R., Fang, Guowei
Through a convergence of functional genomic and proteomic studies, we identify Bora as a previously unknown cell cycle protein that interacts with the Plk1 kinase and the SCF–β-TrCP ubiquitin...
Clifford, Dawn M., Wolfe, Benjamin A., Roberts-Galbraith, Rachel H., McDonald, W. Hayes, Yates, John R., Gould, Kathleen L.
Cdc14 phosphatases antagonize cyclin-dependent kinase–directed phosphorylation events and are involved in several facets of cell cycle control. We investigate the role of the fission yeast Cdc14...
Proteomics Analysis Unravels the Functional Repertoire of Coronavirus Nonstructural Protein 3▿ †
Neuman, Benjamin W., Joseph, Jeremiah S., Saikatendu, Kumar S., Serrano, Pedro, Chatterjee, Amarnath, Johnson, Margaret A., ...
Severe acute respiratory syndrome (SARS) coronavirus infection and growth are dependent on initiating signaling and enzyme actions upon viral entry into the host cell. Proteins packaged during virus...
Jang, Chang-Young, Wong, Jim, Coppinger, Judith A., Seki, Akiko, Yates, John R., Fang, Guowei
Dynamic turnover of the spindle is a driving force for chromosome congression and segregation in mitosis. Through a functional genomic analysis, we identify DDA3 as a previously unknown regulator of...
Isolation of novel coregulatory protein networks associated with DNA-bound estrogen receptor alpha
Schultz-Norton, Jennifer R, Ziegler, Yvonne S, Likhite, Varsha S, Yates, John R, Nardulli, Ann M
Le Roch, Karine G, Johnson, Jeffrey R, Ahiboh, Hugues, Chung, Duk-Won D, Prudhomme, Jacques, Plouffe, David, ...
Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control
Diop, Soda Balla, Bertaux, Karine, Vasanthi, Dasari, Sarkeshik, Ali, Goirand, Benjamin, Aragnol, Denise, ...
Pontin (Pont) and Reptin (Rept) are paralogous ATPases that are evolutionarily conserved from yeast to human. They are recruited in multiprotein complexes that function in various aspects of DNA...
Gassmann, Reto, Essex, Anthony, Hu, Jia-Sheng, Maddox, Paul S., Motegi, Fumio, Sugimoto, Asako, ...
Chromosome segregation requires stable bipolar attachments of spindle microtubules to kinetochores. The dynein/dynactin motor complex localizes transiently to kinetochores and is implicated in...
RCS1, a substrate of APC/C, controls the metaphase to anaphase transition
Zhao, Wei-meng, Coppinger, Judith A., Seki, Akiko, Cheng, Xiao-li, Yates, John R., Fang, Guowei
The anaphase-promoting complex/cyclosome (APC/C) controls the onset of anaphase by targeting securin for destruction. We report here the identification and characterization of a substrate of APC/C,...
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data
Carvalho, Paulo C, Fischer, Juliana SG, Chen, Emily I, Domont, Gilberto B, Carvalho, Maria GC, Degrave, Wim M, ...
Liao, Lujian, Park, Sung Kyu, Xu, Tao, Vanderklish, Peter, Yates, John R.
Fragile X syndrome (FXS) is a common inherited form of mental retardation that is caused, in the vast majority of cases, by the transcriptional silencing of a single gene, fmr1. The encoded protein,...
Rao, Abhi K., Ziegler, Yvonne S., McLeod, Ian X., Yates, John R., Nardulli, Ann M.
The effects of estrogen on gene expression in mammary cells are mediated by interaction of the estrogen receptor (ER) with estrogen response elements in target DNA. Whereas the ER is the primary...
Nakajima, Yuko, Tyers, Randall G., Wong, Catherine C.L., Yates, John R., Drubin, David G., Barnes, Georjana
The Aurora kinase complex, also called the chromosomal passenger complex (CPC), is essential for faithful chromosome segregation and completion of cell division. In Fungi and Animalia, this complex...
Zhu, Hui, Coppinger, Judith A., Jang, Chang-Young, Yates, John R., Fang, Guowei
Microtubules (MTs) are nucleated from centrosomes and chromatin. In addition, MTs can be generated from preexiting MTs in a γ-tubulin–dependent manner in yeast, plant, and Drosophila cells,...
Wang, Jiou, Farr, George W., Zeiss, Caroline J., Rodriguez-Gil, Diego J., Wilson, Jean H., Furtak, Krystyna, ...
Recent studies suggest that superoxide dismutase 1 (SOD1)-linked amyotrophic lateral sclerosis results from destabilization and misfolding of mutant forms of this abundant cytosolic enzyme. Here, we...
Scorah, Jennifer, Dong, Meng-Qiu, Yates, John R., Scott, Mary, Gillespie, David, McGowan, Clare H.
Human checkpoint kinase 1 (Chk1) is an essential kinase required for cell cycle checkpoints and for coordination of DNA synthesis. To gain insight into the mechanisms by which Chk1 carries out these...
Xu, SongXiao, Wong, Catherine C. L., Tong, Edith H. Y., Chung, Stephen S. M., Yates, John R., Yin, YiBing, ...
The osmotic response element-binding protein (OREBP), also known as tonicity enhancer-binding protein (TonEBP) or NFAT5, is the only known osmo-sensitive transcription factor that mediates cellular...
Kurian, Sunil M., Heilman, Raymond, Mondala, Tony S., Nakorchevsky, Aleksey, Hewel, Johannes A., Campbell, Daniel, ...
Shock, Teresa R., Thompson, James, Yates, John R., Madhani, Hiten D.
In Saccharomyces cerevisiae, the mating, filamentous growth (FG), and high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) signaling pathways share components and yet mediate...
Kaeser, Matthias D., Aslanian, Aaron, Dong, Meng-Qiu, Yates, John R., Emerson, Beverly M.
The composition of chromatin-remodeling complexes dictates how these enzymes control transcriptional programs and cellular identity. In the present study we investigated the composition of SWI/SNF...