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Tag proteomics [827 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
  • 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 review reference protocols proteomics by Yanno on 2008-05-14 16:19:00 as read along with 4 people hchmani jyuh dchughes neils
  • 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 13 people higueruelo carlk jyuh aalibes bicko jfr chad_davis cjeans iris_2001 zwang lpfernandes groepl Evangelia
  • 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
  • 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
  • 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
  • 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
  • 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 5 people higueruelo carlk IbnBio zwang Evangelia
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 statistics proteomics hts datamining bioinformatics by Yanno on 2008-05-30 15:58:18 as read along with 1 person chad_davis
  • 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
  • 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 mcox knaseanka jmeppley bluto nitiniitk barberan
  • 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
  • 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
  • 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 22 people and 10 groups ellakat frohike carlk Yanno ana Borelli lfriedl ccots jmeppley chad_davis balajis shantanu nirfriedman balabu dgront noano koller ruvido nicoleq lpfernandes phoenixzxl larsjuhljensen 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 **
  • 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 olberd ml_and_apps
  • 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 **
  • 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 **
  • 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 proteomics plants genomics athaliana by timflutre on 2008-05-21 09:12:36 as *** along with 4 people megraw renatomilani caseybrown xwbcn
  • 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 4 people jfr jyuh phoenixzxl huali
  • 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 5 people carlk olberd jmeppley dgront frohike
  • 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
  • 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 proteomics neurology neurodegeneration alzheimer 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 undergraduate_research proteomics by stajich on 2008-07-08 18:20:05 as ** along with 1 person and 1 group biehl Berkeley Mycology
  • 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
  • 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
  • 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
  • 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 **
  • ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3043-3048.
    by Age K Smilde, Jeroen J Jansen, Huub C Hoefsloot, Robert-Jan A Lamers, Jan van der Greef, Marieke E Timmerman
    posted to algorithms metabolomics proteomics statistics by rvosa on 2007-11-19 20:58:07 as ** along with 1 person drubtsov
  • An idea whose time has gone
    Genome Biology, Vol. 8 (02 July 2007), 107.
    by Gregory A Petsko
    posted to proteomics review by rph on 2008-03-27 16:55:38 as read along with 1 person dullhunk
  • Role for NMR in structural genomics
    Journal of Structural and Functional Genomics, Vol. 2, No. 3. (2002), pp. 155-169.
    by Michael A Kennedy, Gaetano T Montelione, Cheryl H Arrowsmith, John L Markley
    posted to review proteomics nmr by rph on 2008-06-17 21:32:54 as **
  • Protein identification by spectral networks analysis
    PNAS, Vol. 104, No. 15. (10 April 2007), pp. 6140-6145.
    by Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A Pevzner
    posted to bioinformatics proteomics by rph on 2008-04-07 18:32:30 as ** along with 2 people jyuh nedwards
  • A global analysis of NMR distance constraints from the PDB
    Journal of Biomolecular NMR, Vol. 39, No. 4. (2 December 2007), pp. 303-314.
    by Wim Vranken
    posted to structure-determination proteomics noesy bioinformatics by rph on 2008-06-17 21:27:27 as **
  • Application of NMR in Structural Proteomics: Screening for Proteins Amenable to Structural Analysis
    Structure, Vol. 10, No. 12. (December 2002), pp. 1613-1618.
    by Till Rehm, Robert Huber, Tad A Holak
    posted to screening review proteomics by rph on 2008-06-26 17:16:59 as ** along with 1 person EvaKaltenborn
  • NMR and X-ray Crystallography, Complementary Tools in Structural Proteomics of Small Proteins
    J. Am. Chem. Soc., Vol. 127, No. 47. (30 November 2005), pp. 16512-16517.
    by AA Yee, A Savchenko, A Ignachenko, J Lukin, X Xu, T Skarina, E Evdokimova, CS Liu, A Semesi, V Guido, AM Edwards, CH Arrowsmith
    posted to review proteomics nmr by rph on 2008-06-26 17:13:42 as ** along with 1 person viktor21614
  • An idea whose time has come
    Genome Biology, Vol. 8 (09 November 2007), 408.
    by Lucia Banci, Wolfgang Baumeister, Udo Heinemann, Gunter Schneider, Israel Silman, David I Stuart, Joel L Sussman
    posted to proteomics by rph on 2008-03-26 16:54:55 as read along with 1 person dullhunk
  • Structural proteomics: toward high-throughput structural biology as a tool in functional genomics.
    Acc Chem Res, Vol. 36, No. 3. (March 2003), pp. 183-189.
    by A Yee, K Pardee, D Christendat, A Savchenko, AM Edwards, CH Arrowsmith
    posted to proteomics review by rph on 2008-03-26 16:53:12 as ** along with 1 person blackbart
  • Structural proteomics of an archaeon.
    Nat Struct Biol, Vol. 7, No. 10. (October 2000), pp. 903-909.
    by D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, JR Cort, V Booth, CD Mackereth, V Saridakis, I Ekiel, G Kozlov, KL Maxwell, N Wu, LP McIntosh, K Gehring, MA Kennedy, AR Davidson, EF Pai, M Gerstein, AM Edwards, CH Arrowsmith
    posted to proteomics review by rph on 2008-03-26 16:51:34 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Cell-free complements in vivo expression of the E. coli membrane proteome
    Protein Sci, Vol. 16, No. 5. (1 May 2007), pp. 966-976.
    by David F Savage, Corey L Anderson, Yaneth Robles-Colmenares, Zachary E Newby, Robert M Stroud
    posted to cell-free imp proteomics by rph on 2008-03-20 21:11:56 as **
  • Measuring Protein Concentrations by NMR Spectroscopy
    J. Am. Chem. Soc., Vol. 128, No. 8. (1 March 2006), pp. 2571-2576.
    by G Wider, L Dreier
    posted to proteomics nmr-methods by rph on 2008-06-24 21:32:29 as **** along with 1 person viktor21614
  • Non-globular domains in protein sequences: automated segmentation using complexity measures.
    Comput Chem, Vol. 18, No. 3. (September 1994), pp. 269-285.
    by JC Wootton
    posted to bioinformatics proteomics by rph on 2008-03-18 23:45:51 as **
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