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タグ: proteomics [856 articles]

Recent papers classified by the tag proteomics.
  • How do shotgun proteomics algorithms identify proteins?
    Nature Biotechnology, Vol. 25, No. 7., pp. 755-757.
    by Edward M Marcotte
    posted to dynamicprogramming ms proteomics reference by Yanno on 2007-07-13 12:21:04 as read along with 2 people and 1 group jyuh Jporci Bioinformatics
  • Identification of post-translational modifications by blind search of mass spectra
    Nature Biotechnology, Vol. 23, No. 12. (27 November 2005), pp. 1562-1567.
    by Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A Pevzner
    posted to dynamicprogramming ms proteomics statistics by Yanno on 2007-12-05 13:38:30 as read along with 1 person nedwards
  • Metaproteomics: studying functional gene expression in microbial ecosystems.
    Trends Microbiol, Vol. 14, No. 2. (February 2006), pp. 92-97.
    by P Wilmes, PL Bond
    posted to metaproteomics microorganism proteomics by Yanno on 2007-11-14 08:19:43 as ** along with 6 people knaseanka jmeppley bluto nitiniitk barberan mcox
  • Proteomic characterization of the human centrosome by protein correlation profiling
    Nature, Vol. 426, No. 6966. (4 December 2003), pp. 570-574.
    by Jens S Andersen, Christopher J Wilkinson, Thibault Mayor, Peter Mortensen, Erich A Nigg, Matthias Mann
    posted to centrosome proteomics by Yanno on 2006-10-23 14:27:04 as read along with 1 person balajis
  • A high-quality catalog of the Drosophila melanogaster proteome
    Nature Biotechnology, Vol. 25, No. 5. (22 April 2007), pp. 576-583.
    by Erich Brunner, Christian H Ahrens, Sonali Mohanty, Hansruedi Baetschmann, Sandra Loevenich, Frank Potthast, Eric W Deutsch, Christian Panse, Ulrik de Lichtenberg, Oliver Rinner, Hookeun Lee, Patrick GA Pedrioli, Johan Malmstrom, Katja Koehler, Sabine Schrimpf, Jeroen Krijgsveld, Floyd Kregenow, Albert JR Heck, Ernst Hafen, Ralph Schlapbach, Ruedi Aebersold
    posted to datamining hcs hts ms proteomics reference ressource by Yanno on 2007-06-08 11:36:48 as read along with 1 person and 1 group dpollard EisenLab
  • Coverage and error models of protein-protein interaction data by directed graph analysis
    Genome Biology, Vol. 8 (10 September 2007), R186.
    by Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber
    posted to proteomics statistics by Yanno on 2007-09-18 09:16:48 as ***** along with 5 people jfr chad_davis grahamc winterschlaefer Pao-Yang
  • Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e43.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to datamining proteomics reference by Yanno on 2007-12-18 12:26:29 as read along with 14 people jyuh aalibes bicko jfr chad_davis cjeans iris_2001 zwang lpfernandes groepl carlk Evangelia higueruelo phoenixzxl
  • The purinome, a complex mix of drug and toxicity targets.
    Curr Top Med Chem, Vol. 6, No. 11. (2006), pp. 1117-1127.
    by TA Haystead
    posted to proteomics purine target by Yanno on 2008-01-02 16:43:45 as read
  • Simple bioseparations using self-cleaving elastin-like polypeptide tags
    Nature Methods, Vol. 2, No. 9. (02 August 2005), pp. 659-662.
    by Mahmoud R Banki, Liang Feng, David W Wood
    posted to method proteomics purification by Yanno on 2006-08-28 15:00:13 as read
  • Identifying protein complexes directly from high-throughput TAP data with Markov random fields
    BMC Bioinformatics, Vol. 8 (19 December 2007), 482.
    by Wasinee Rungsarityotin, Roland Krause, Arno Schodl, Alexander Schliep
    posted to bioinformatics datamining hts proteomics statistics by Yanno on 2008-05-30 15:58:18 as read along with 1 person chad_davis
  • High-resolution functional proteomics by active-site peptide profiling.
    Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4996-5001.
    by ES Okerberg, J Wu, B Zhang, B Samii, K Blackford, DT Winn, KR Shreder, JJ Burbaum, MP Patricelli
    posted to method proteomics targetbeads by Yanno on 2007-11-12 12:20:53 as read
  • Proteins, drug targets and the mechanisms they control: the simple truth about complex networks.
    Nat Rev Drug Discov (12 October 2007)
    by Robyn P P Araujo, Lance A A Liotta, Emanuel F F Petricoin
    posted to drugdiscovery proteomics reference systemsbiology by Yanno on 2007-11-09 14:40:18 as read along with 7 people and 1 group jyuh dragonrez bicko cjeans Babysitter mingzhi stefanoallesina csb_journal_club_public
  • Functional interrogation of the kinome using nucleotide acyl phosphates.
    Biochemistry, Vol. 46, No. 2. (16 January 2007), pp. 350-358.
    by MP Patricelli, AK Szardenings, M Liyanage, TK Nomanbhoy, M Wu, H Weissig, A Aban, D Chun, S Tanner, JW Kozarich
    posted to kinase method proteomics targetbeads by Yanno on 2007-11-12 12:21:06 as read along with 1 person jyuh
  • Discovery of Novel Targets of Quinoline Drugs in the Human Purine Binding Proteome
    Mol Pharmacol, Vol. 62, No. 6. (1 December 2002), pp. 1364-1372.
    by Paul R Graves, Jesse J Kwiek, Patrick Fadden, Rupa Ray, Klaas Hardeman, Andrew M Coley, Michael Foley, Timothy A Haystead
    posted to disease drugdiscovery hcs proteomics purine by Yanno on 2008-01-03 16:04:44 as read
  • Gini Coefficient: A New Way To Express Selectivity of Kinase Inhibitors against a Family of Kinases
    J. Med. Chem., Vol. 50, No. 23. (15 November 2007), pp. 5773-5779.
    by PP Graczyk
    posted to kinase method proteomics statistics by Yanno on 2008-01-04 17:46:05 as read along with 1 person daevans
  • Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e42.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to datamining proteomics reference by Yanno on 2007-12-18 11:14:15 as read along with 6 people IbnBio zwang Evangelia carlk higueruelo ethkim
  • Quantitative mass spectrometry in proteomics: a critical review.
    Anal Bioanal Chem (1 August 2007)
    by Marcus Bantscheff, Markus Schirle, Gavain Sweetman, Jens Rick, Bernhard Kuster
    posted to ms proteomics quantification review by Yanno on 2007-09-12 17:22:59 as read along with 1 person jyuh
  • Protein production and purification.
    Nat Methods, Vol. 5, No. 2. (February 2008), pp. 135-146.
    by , S Gräslund, P Nordlund, J Weigelt, J Bray, O Gileadi, S Knapp, U Oppermann, C Arrowsmith, R Hui, J Ming, S dhe-Paganon, HW Park, A Savchenko, A Yee, A Edwards, R Vincentelli, C Cambillau, R Kim, SH Kim, Z Rao, Y Shi, TC Terwilliger, CY Kim, LW Hung, GS Waldo, Y Peleg, S Albeck, T Unger, O Dym, J Prilusky, JL Sussman, RC Stevens, SA Lesley, IA Wilson, A Joachimiak, F Collart, I Dementieva, MI Donnelly, WH Eschenfeldt, Y Kim, L Stols, R Wu, M Zhou, SK Burley, JS Emtage, JM Sauder, D Thompson, K Bain, J Luz, T Gheyi, F Zhang, S Atwell, SC Almo, JB Bonanno, A Fiser, S Swaminathan, FW Studier, MR Chance, A Sali, TB Acton, R Xiao, L Zhao, LC Ma, JF Hunt, L Tong, K Cunningham, M Inouye, S Anderson, H Janjua, R Shastry, CK Ho, D Wang, H Wang, M Jiang, GT Montelione, DI Stuart, RJ Owens, S Daenke, A Schütz, U Heinemann, S Yokoyama, K Büssow, KC Gunsalus
    posted to proteomics protocols reference review by Yanno on 2008-05-14 16:19:00 as read along with 4 people dchughes neils hchmani jyuh
  • Quantitative proteomic assessment of very early cellular signaling events
    Nat Biotech, Vol. 25, No. 5. (June 2007), pp. 566-568.
    by Joern Dengjel, Vyacheslav Akimov, Jesper V Olsen, Jakob Bunkenborg, Matthias Mann, Blagoy Blagoev, Jens S Andersen
    posted to ms proteomics quantification ressource by Yanno on 2007-06-08 11:15:58 as read along with 2 people and 1 group julius rastrol7 SysbioMPI-TCells
  • Proteome survey reveals modularity of the yeast cell machinery
    Nature (22 January 2006)
    by Anne-Claude Gavin, Patrick Aloy, Paola Grandi, Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars J Jensen, Sonja Bastuck, Birgit Dümpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M Rick, Bernhard Kuster, Peer Bork, Robert B Russell, Giulio Superti-Furga
    posted to bio-informatics cell complexes high-throughput large-scale machinery modularity protein proteome proteomics yeast by xico on 2006-01-30 19:41:37 as **** along with 23 people and 10 groups Yanno ana Borelli lfriedl ccots jmeppley chad_davis balajis shantanu nirfriedman balabu dgront noano koller ruvido nicoleq lpfernandes phoenixzxl larsjuhljensen ellakat frohike carlk ethkim structural_bioinformatics kdl MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology WetBiology
  • Combining chemical genetics and proteomics to identify protein kinase substrates
    PNAS, Vol. 102, No. 50. (13 December 2005), pp. 17940-17945.
    by Noah Dephoure, Russell W Howson, Justin D Blethrow, Kevan M Shokat, Erin K O'Shea
    posted to chemical genetics kinases phosphorylation proteomics substrates by wvalleng on 2006-04-26 14:48:46 as *** along with 2 people and 1 group brant anwazo EisenLab
  • Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery
    Brief Funct Genomic Proteomic, Vol. 4, No. 1. (1 January 2005), pp. 16-26.
    by Volker Seibert, Matthias P Ebert, Thomas Buschmann
    posted to proteomics by wolf5052 on 2008-06-04 05:26:02 as **
  • Proteomics in the study of hippocampal plasticity
    Expert Review of Proteomics, Vol. 5, No. 3. (June 2008), pp. 393-404.
    by Cobb, R Stuart, Pitt, Andrew
    posted to proteomics maldi-ms imaging by wilbur on 2008-09-16 13:12:56 as **
  • Tissue imaging using MALDI-MS: a new frontier of histopathology proteomics
    Expert Review of Proteomics, Vol. 5, No. 3. (June 2008), pp. 413-424.
    by Fournier, Isabelle, Wisztorski, Maxence, Salzet, Michel
    posted to proteomics maldi-ms imaging histopathology by wilbur on 2008-09-16 13:15:59 as **
  • Optimized protein extraction for quantitative proteomics of yeasts.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by T von der Haar
    posted to proteomics by westoll on 2007-11-26 09:27:21 as **
  • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.
    Mol Cell Proteomics, Vol. 4, No. 4. (April 2005), pp. 419-434.
    by J Listgarten, A Emili
    posted to lc ms proteomics by waszak on 2008-02-15 08:52:50 as ** along with 2 people ml_and_apps olberd
  • Organelle Proteomics: Implications for Subcellular Fractionation in Proteomics
    Circ Res, Vol. 92, No. 9. (16 May 2003), pp. 962-968.
    by Lukas A Huber, Kristian Pfaller, Ilja Vietor
    posted to organelle organelle_proteomics proteomics subcellular_fractionation by uz_labu_laimi on 2007-06-21 18:14:59 as **
  • A Functional Proteomics Approach to Signal Transduction
    Recent Prog Horm Res, Vol. 58, No. 1. (1 January 2003), pp. 1-24.
    by Paul R Graves, Timothy A Haystead
    posted to functional_proteomics proteomics signal_transduction by uz_labu_laimi on 2007-05-31 05:01:58 as **
  • Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics
    Science (24 April 2008), 1157956.
    by Katja Baerenfaller, Jonas Grossmann, Monica A Grobei, Roger Hull, Matthias Hirsch-Hoffmann, Shaul Yalovsky, Philip Zimmermann, Ueli Grossniklaus, Wilhelm Gruissem, Sacha Baginsky
    posted to athaliana genomics plants proteomics by timflutre on 2008-05-21 09:12:36 as *** along with 6 people druvus renatomilani xwbcn megraw caseybrown jmjimenez
  • Exon level integration of proteomics and microarray data
    BMC Bioinformatics, Vol. 9 (25 February 2008), 118.
    by Danny A Bitton, Michal J Okoniewski, Yvonne Connolly, Crispin J Miller
    posted to microarray proteomics transcriptomics by thomaskelder on 2008-02-26 10:15:18 as ** along with 5 people jo_davies jyuh phoenixzxl huali jfr
  • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    Nature (28 September 2008)
    by Lyris MF de Godoy, Jesper V Olsen, Jürgen Cox, Michael L Nielsen, Nina C Hubner, Florian Fröhlich, Tobias C Walther, Matthias Mann
    posted to proteomics by thomaskelder on 2008-10-01 08:31:31 as ** along with 2 people and 1 group dullhunk brianb microbiology_nijmegen
  • Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations.
    Genome research (24 July 2008)
    by Gennifer E E Merrihew, Colleen Davis, Brent Ewing, Gary Williams, Lukas Kall, Barbara E E Frewen, William Stafford S Noble, Phil Green, James H H Thomas, Michael J J Maccoss
    posted to confirmation elegans genemodels proteomics by tharris on 2008-07-31 00:53:11 as *** along with 1 person mdperry
  • Mass spectrometry-based proteomics
    Nature, Vol. 422, No. 6928. (13 March 2003), pp. 198-207.
    by Ruedi Aebersold, Matthias Mann
    posted to proteins proteomics spectrometry by sverzijl on 2007-08-19 17:26:51 as read along with 7 people emmackinnon jmeppley dgront frohike olberd carlk taenneken
  • Application of Mass Spectrometry in Proteomics
    Bioscience Reports, Vol. 25, No. 1-2. (February 2005), pp. 71-93.
    by Ida Guerrera, Oliver Kleiner
    posted to mass proteins proteomics spectrometry by sverzijl on 2007-08-19 17:24:21 as read along with 1 person taenneken
  • The Application of Proteomics in Neurology
    Current Proteomics, Vol. 2, No. 1. (April 2005), pp. 41-53.
    by Tsuji Teruyuki, Shiozaki Aiko, Shimohama Shun
    posted to alzheimer neurodegeneration neurology proteomics by suizan on 2008-04-23 20:23:46 as ** along with 1 person manoes1
  • Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
    Genome Res., Vol. 18, No. 7. (1 July 2008), pp. 1133-1142.
    by Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S Lipton, Margaret Romine, Vineet Bafna, Richard D Smith, Pavel A Pevzner
    posted to proteomics undergraduate_research by stajich on 2008-07-08 18:20:05 as ** along with 3 people and 1 group druvus biehl Neeperando Berkeley Mycology
  • Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: Assessing experimental effects in a melanoma cell study.
    Bioinformatics (Oxford, England) (25 September 2008)
    by Elmer A A Fernández, María R R Girotti, Del Olmo Juan A O López, Andrea S S Llera, Osvaldo L L Podhajcer, Rodolfo J C J Cantet, Mónica Balzarini
    posted to proteomics dige 2d-gels by sjcockell on 2008-09-29 19:53:30 as **
  • A Toolkit for Capturing and Sharing FuGE Experiments.
    Bioinformatics (Oxford, England) (17 September 2008)
    by Khalid Belhajjame, Andrew R R Jones, Norman W W Paton
    posted to proteomics gelml fuge data-standards by sjcockell on 2008-09-24 09:46:24 as **
  • Proteomics in animal models of Alzheimer's and Parkinson's diseases.
    Ageing research reviews (18 July 2008)
    by Renã A A Sowell, Joshua B B Owen, D Allan Butterfield
    posted to alzheimers parkinsons proteomics by sjcockell on 2008-08-18 09:55:07 as ***
  • Mass spectrometry for proteomics.
    Current opinion in chemical biology (18 August 2008)
    by Xuemei Han, Aaron Aslanian, John R R Yates
    posted to mass-spectrometry proteomics by sjcockell on 2008-08-26 14:18:33 as **
  • Higher criticism thresholding: Optimal feature selection when useful features are rare and weak
    Proceedings of the National Academy of Sciences, Vol. 105, No. 39. (2008), pp. 14790-14795.
    by David Donoho, Jiashun Jin
    posted to thresholding selection proteomics higher genomics feature criticism classification by sg45653 on 2008-10-01 03:53:27 as ** along with 4 people sschurer phoenixzxl rdiaz briordan
  • Proteomics, networks and connectivity indices.
    Proteomics, Vol. 8, No. 4. (February 2008), pp. 750-778.
    by H González-Díaz, Y González-Díaz, L Santana, FM Ubeira, E Uriarte
    posted to proteomics by Scis0000002 on 2008-09-02 10:05:22 as ** along with 2 people jyuh ptrobajo
  • Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets
    Nature (17 February 2008)
    by May H Han, Sun-Il Hwang, Dolly B Roy, Deborah H Lundgren, Jordan V Price, Shalina S Ousman, Guy H Fernald, Bruce Gerlitz, William H Robinson, Sergio E Baranzini, Brian W Grinnell, Cedric S Raine, Raymond A Sobel, David K Han, Lawrence Steinman
    posted to multiple proteomics sclerosis by SciNika on 2008-02-29 14:31:45 as ** along with 1 person brianb
  • The impact of microRNAs on protein output
    Nature (30 July 2008)
    by Daehyun Baek, Judit Villã©n, Chanseok Shin, Fernando D Camargo, Steven P Gygi, David P Bartel
    posted to proteomics mirna by samgj on 2008-09-29 19:20:37 as ** along with 16 people and 1 group heliopais askrajiv natsdorf jfr frohike giovenko mtagaya megraw djkt brianb emptyhb erel10 maralena ajaymalik caizhiqiang gdb microRNA
  • Analysis of Nanoarchaeum equitansgenome and proteome composition: indications for hyperthermophilic and parasitic adaptation
    BMC Genomics, Vol. 7 (25 July 2006), 186.
    by Sabyasachi Das, Sandip Paul, Sumit Bag, Chitra Dutta
    posted to amino-acidusage codon-usage genomics nanoarchaeum proteomics thermophiles by Saby2000 on 2008-04-13 03:14:03 as *****
  • Molecular Signature of Hypersaline Adaptation: Insights from Genome and Proteome Composition of Halophilic Prokaryotes
    Genome Biology, Vol. 9, No. 4. (2008)
    by Sandip Paul, Sumit Bag, Sabyasachi Das, Eric Harvill, Chitra Dutta
    posted to aminoacid-usage codon-usage genomics halophiles proteomics by Saby2000 on 2008-04-13 03:09:43 as ***** along with 2 people neils rowenabrennavart
  • Codon and amino Acid usage in two major human pathogens of genus bartonella -- optimization between replicational-transcriptional selection, translational control and cost minimization.
    DNA Res, Vol. 12, No. 2. (2005), pp. 91-102.
    by S Das, S Paul, S Chatterjee, C Dutta
    posted to aminoacid-usage codon-usage genomics proteomics by Saby2000 on 2008-04-13 18:28:28 as ** along with 2 people bjorns michaelbarton
  • THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION
    Evolution, Vol. 61, No. 5. (2007), pp. 995-1016.
    by Hopi E Hoekstra, Jerry A Coyne
    posted to adaptation clock-like evolution genome protein proteins proteomics speciation by rvosa on 2008-08-18 04:27:53 as ** along with 12 people and 2 groups gjuggler stevanspringer mcphee dpollard balicea bpcusack TaqSys epigenetics jayster4 mimulus_99 mjoach kndiaye EisenLab FAB-lab
  • How to distinguish healthy from diseased? Classification strategy for mass spectrometry-based clinical proteomics
    PROTEOMICS, Vol. 7, No. 20. (2007), pp. 3672-3680.
    by Margriet MWB Hendriks, Suzanne Smit, Wies LMW Akkermans, Theo H Reijmers, Paul HC Eilers, Huub CJ Hoefsloot, Carina M Rubingh, Chris G de Koster, Johannes M Aerts, Age K Smilde
    posted to algorithms data-mining proteomics statistics by rvosa on 2007-11-19 21:27:26 as **
  • Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup
    Genomics, Vol. 88, No. 6. (December 2006), pp. 745-751.
    by Xiao-Jing Yu, Hong-Kun Zheng, Jun Wang, Wen Wang, Bing Su
    posted to adaptation alignment amino-acid animals anthropology clock-like comparative data-mining divergence dna encephalization evolution genetics genome hominidae humans mammals models phylogenomics primates protein proteins proteomics rates ratio-test selection sequence-evolution by rvosa on 2008-08-12 08:00:47 as ** along with 1 group FAB-lab
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