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SPS' DigestIssue 65, 31-Dec-2009 |
Target-decoy search strategy for mass spectrometry-based proteomics
Elias JE, Gygi SP.
Methods Mol Biol (2010) 604: 55-71
Improved prediction of lysine acetylation by support vector machines
Li S, Li H, Li M, Shyr Y, Xie L, Li Y.
Protein Pept Lett (2009) 16(8): 977-83
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
Stefan P. Albaum, Heiko Neuweger, Benjamin Franzel, Sita Lange, Dominik Mertens, Christian Trotschel, Dirk Wolters, Jorn Kalinowski, Tim W. Nattkemper, and Alexander Goesmann
Bioinformatics (2009) 25(23): 3128-3134
Empirical bayes analysis of quantitative proteomics experiments
Margolin AA, Ong SE, Schenone M, Gould R, Schreiber SL, Carr SA, Golub TR.
PLoS One (2009) 4(10): e7454
An introduction to proteome bioinformatics
Jones AR, Hubbard SJ.
Methods Mol Biol (2010) 604: 1-5
Mining gene functional networks to improve mass-spectrometry-based protein identification
Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, and Daniel P. Miranker
Bioinformatics (2009) 25(22): 2955-2961
Exploiting amino Acid composition for predicting protein-protein interactions
Roy S, Martinez D, Platero H, Lane T, Werner-Washburne M.
PLoS One (2009) 4(11): e7813
Understanding and exploiting Peptide fragment ion intensities using experimental and informatic approaches
Gucinski AC, Dodds ED, Li W, Wysocki VH.
Methods Mol Biol (2010) 604: 73-94
Charting the proteome of Cryptosporidium parvum sporozoites using sequence similarity-based BLAST searching
Siddiki AM, Wastling JM.
J Vet Sci (2009) 10(3): 203-10
Identifying related journals through log analysis
Zhiyong Lu, Natalie Xie, and W. John Wilbur
Bioinformatics (2009) 25(22): 3038-3039
Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics
Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP.
PLoS One (2009) 4(10): e7310
Critical role of glycosylation in determining the length and structure of T cell epitopes - As suggested by a combined in silico systems biology approach
Szabo TG, Palotai R, Antal P, Tokatly I, Tothfalusi L, Lund O, Nagy G, Falus A, Buzas EI.
Immunome Res (2009) 5(1): 4
Trans-proteomic pipeline: a pipeline for proteomic analysis
Pedrioli PG.
Methods Mol Biol (2010) 604: 213-38
Eukaryotic protein domains as functional units of cellular evolution
Jin J, Xie X, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao Y, Pawson T.
Sci Signal (2009) 2(98): ra76
Proteomics computational analyses suggest that the bornavirus glycoprotein is a class III viral fusion protein (gamma penetrene)
Garry CE, Garry RF.
Virol J (2009) 6(1): 145
Finding one's way in proteomics: a protein species nomenclature
Schluter H, Apweiler R, Holzhutter HG, Jungblut PR.
Chem Cent J (2009) 3(1): 11
The Modular Organization of Protein Interactions in Escherichia coli
Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J.
PLoS Comput Biol (2009) 5(10): e1000523
An intensity-region driven multi-classifier scheme for improving the classification accuracy of proteomic MS-spectra
Bougioukos P, Glotsos D, Cavouras D, Daskalakis A, Kalatzis I, Kostopoulos S, Nikiforidis G, Bezerianos A.
Comput Methods Programs Biomed Early Edition: published 8-Dec-2009
The PSI semantic validator: A framework to check MIAPE compliance of proteomics data
Luisa Montecchi-Palazzi, Samuel Kerrien, Florian Reisinger, Bruno Aranda, Andrew R. Jones, Lennart Martens, Henning Hermjakob
PROTEOMICS (2009) 9(22): 5112-5119
Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine
Ostrowski J, Wyrwicz LS.
Expert Rev Mol Diagn (2009) 9(6): 623-30
Proteomics Data Collection (ProDaC): Publishing and Collecting Proteomics Data Sets in Public Repositories Using Standard Formats
Stephan C, Eisenacher M, Kohl M, Meyer HE.
Methods Mol Biol (2010) 604: 345-68
digeR: a graphical user interface R package for analyzing 2D-DIGE data
Yue Fan, T. Brendan Murphy, and R. William G. Watson
Bioinformatics (2009) 25(22): 3033-3034
Molecular interactions and data standardisation
Orchard S, Kerrien S.
Methods Mol Biol (2010) 604: 309-18
The PeptideAtlas Project
Deutsch EW.
Methods Mol Biol (2010) 604: 285-96
Mining Proteomic MS/MS Data for MRM Transitions
Chem Mead JA, Bianco L, Bessant C.
Methods Mol Biol (2010) 604: 187-99
Gene model detection using mass spectrometry
Nanduri B, Wang N, Lawrence ML, Bridges SM, Burgess SC.
Methods Mol Biol (2010) 604: 137-44
Proteomics data mining
Marc Wilkins
Expert Review of Proteomics (2009) 6(6): 599-603
Improving peptide identification with single-stage mass spectrum peaks
Zengyou He and Weichuan Yu
Bioinformatics (2009) 25(22): 2969-2974
Metalloproteomes: A Bioinformatic Approach
Andreini C, Bertini I, Rosato A.
Acc Chem Res (2009) 42(10): 1471-9
Computational Approaches to Peptide Identification via Tandem MS
Hubbard SJ.
Methods Mol Biol (2010) 604: 23-42
PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information
Kebing Yu, Arthur R. Salomon
PROTEOMICS (2009) 9(23): 5350-5358
Mixed-model of ANOVA for measurement reproducibility in proteomics
Catherine Mercier, Caroline Truntzer, Delphine Pecqueur, Jean-Pascal Gimeno, Guillaume Belz, Pascal Roy
Journal of Proteomics (2009) 72(6): 974-981
Informatics and statistics for analyzing 2-d gel electrophoresis images
Dowsey AW, Morris JS, Gutstein HB, Yang GZ.
Methods Mol Biol (2010) 604: 239-55
A computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging
Khamir Mehta, Adam D. Hoppe, Raghunandan Kainkaryam, Peter J. Woolf, Jennifer J. Linderman
PROTEOMICS (2009) 9(23): 5371-5383
Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system
Peter Bowden, Ron Beavis, John Marshall
Journal of Proteomics (2009) 73(1): 103-111
Grafta: A 3D environment for biomolecular networks
Najmabadi P, Lee HH, Aung T, Thuya A, Ng J, Clair J, Burkart M.
Int J Bioinform Res Appl (2009) 5(5): 564-9
Disulfide bond formation and cysteine exclusion in Gram-positive bacteria
Daniels R, Mellroth P, Bernsel A, Neiers F, Normark S, von Heijne G, Henriques-Normark B.
J Biol Chem Early Edition: published 24-Nov-2009
The Zinc proteome: a tale of stability and functionality
Sousa SF, Lopes AB, Fernandes PA, Ramos MJ.
Dalton Trans (2009) (38): 7946-56.
A software program for more reliable precursor ion assignation from LC-MS analysis using LTQ ultra zoom scan
Takashi Shinkawa, Kohji Nagano, Noriyuki Inomata, Masayuki Haramura
Journal of Proteomics (2009) 73(2): 357-360
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
Reinert K, Kohlbacher O.
Methods Mol Biol (2010) 604: 201-11
Identification of Bacillus anthracis using MALDI-ToF Mass Spectrometry and Artificial Neural Networks
Lasch P, Beyer W, Nattermann H, Stämmler M, Siegbrecht E, Grunow R, Naumann D.
Appl Environ Microbiol (2009) 75(22): 7229-42
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U.
Nucl Acids Res (2010) 38(Database issue): D508-12
Bioinformatics methods for protein identification using Peptide mass fingerprinting
Song Z, Chen L, Xu D.
Methods Mol Biol (2010) 604: 7-22
Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data
Spencer SJ, Bonnin DA, Deasy JO, Bradley JD, El Naqa I.
J Biomed Biotechnol (2009) 2009: 892863
NCBI Peptidome: a new repository for mass spectrometry proteomics data
Ji L, Barrett T, Ayanbule O, Troup DB, Rudnev D, Muertter RN, Tomashevsky M, Soboleva A, Slotta DJ.
Nucl Acids Res Early Edition: published 26-Nov-2009
Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data
Locasale JW, Wolf-Yadlin A.
PLoS One (2009) 4(8): e6522
Identification of "missing" metabolic proteins of Plasmodium falciparum: a bioinformatics approach
Mohanty S, Srinivasan N.
Protein Pept Lett (2009) 16(8): 961-8
Recurated protein interaction datasets
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.
Nat Methods (2009) 6(12): 860-1
A high-performance reconfigurable computing solution for Peptide mass fingerprinting
Coca D, Bogdan I, Beynon RJ.
Methods Mol Biol (2010) 604: 163-85
Precursor Ion Independent Algorithm for Top-Down Shotgun Proteomics
Tsai YS, Scherl A, Shaw JL, Mackay CL, Shaffer SA, Langridge-Smith PR, Goodlett DR.
J Am Soc Mass Spectrom (2009) 20(11): 2154-66
Spectral Library Searching for Peptide Identification via Tandem MS
Lam H, Aebersold R.
Methods Mol Biol (2010) 604: 95-103
Scoring and Validation of Tandem MS Peptide Identification Methods
Brosch M, Choudhary J.
Methods Mol Biol (2010) 604: 43-53
A Bayesian approach to the alignment of mass spectra
Xiaoxiao Kong and Cavan Reilly
Bioinformatics (2009) 25(24): 3213-3220
Managing Experimental Data Using FuGE
Jones AR, Lister AL.
Methods Mol Biol (2010) 604: 333-43
Robust features for 2-DE gel image registration
Birgit Mller, Stefan Posch
ELECTROPHORESIS (2009) 30(23): 4137-4148
The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3-D cell
Yose Y. Widjaja, Chi Nam Ignatius Pang, Simone S. Li, Marc R. Wilkins, Tim D. Lambert
PROTEOMICS (2009) 9(23): 5309-5315
Optimization of the Use of Consensus Methods for the Detection and Putative Identification of Peptides via Mass Spectrometry Using Protein Standard Mixtures
Sultana T, Jordan R, Lyons-Weiler J.
J Proteomics Bioinform (2009) 2(6): 262-273
Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis
Jones P, Martens L.
Methods Mol Biol (2010) 604: 297-307
Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels into in vitro diagnostics?
Xavier Robin, Natacha Turck, Alexandre Hainard, Frederique Lisacek, Jean-Charles Sanchez, and Markus Muller
Expert Review of Proteomics (2009) 6(6): 675-689
Machine learning analysis of proteomics data for early diagnosis
Devetyarov D.
Stud Health Technol Inform (2009) 150: 772
Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring
Noirel J, Ow SY, Sanguinetti G, Wright PC.
Mol Biosyst (2009) 5(10): 1214-23
A general-purpose baseline estimation algorithm for spectroscopic data
Barkauskas DA, Rocke DM.
Anal Chim Acta (2010) 657(2): 191-7
The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome
Uversky VN.
J Biomed Biotechnol (2010) 2010: 568068
UniMaP: finding unique mass and peptide signatures in the human proteome
Anastasia Alexandridou, George Th. Tsangaris, Konstantinos Vougas, Konstantina Nikita, and George Spyrou
Bioinformatics (2009) 25(22): 3035-3037
Visualizing Post Genomics Data-sets on customized Pathway Maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A.
BMC Syst Biol (2009) 3(1): 82
Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring
Geraldine M. Walsh, Shujun Lin, Daniel M. Evans, Arash Khosrovi-Eghbal, Ronald C. Beavis, Juergen Kast
Journal of Proteomics (2009) 72(5): 838-852
Automated generic analysis tools for protein quantitation using stable isotope labeling
Hsu WL, Sung TY.
Methods Mol Biol (2010) 604: 257-72
Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data
Zhao W, Davis CE.
Anal Chim Acta (2009) 651(1): 15-23
Bioinformatic approaches to the identification of novel neuropeptide precursors
Clynen E, Liu F, Husson SJ, Landuyt B, Hayakawa E, Baggerman G, Wets G, Schoofs L.
Methods Mol Biol (2010) 615: 357-74
Multi Label Learning for Prediction of Human Protein Subcellular Localizations
Zhu L, Yang J, Shen HB.
Protein J Early Edition: published 6-Oct-2009
A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography
Vu H, Spicer V, Gotfrid A, Krokhin OV.
J Chromatogr A Early Edition: published 27-Nov-2009
Cross species proteomics
Wright JC, Beynon RJ, Hubbard SJ.
Methods Mol Biol (2010) 604: 123-35
Proteomic tools for the analysis of cytoskeleton proteins
Wywial E, Dongre VN, Singh SM.
Methods Mol Biol (2009) 586: 375-88
lipID - a software tool for automated assignment of lipids in mass spectra
Gran Hbner, Catharina Crone, Buko Lindner
Journal of Mass Spectrometry (2009) 44(12): 1676-1683
Profiling analysis of volatile compounds from fruits using comprehensive two-dimensional gas chromatography and image processing techniques
Schmarr HG, Bernhardt J.
J Chromatogr A Early Edition: published 24-Nov-2009
Comparative analysis and unification of domain-domain interaction networks
Patrik Bjorkholm and Erik L. L. Sonnhammer
Bioinformatics (2009) 25(22): 3020-3025
PubMed-EX: a web browser extension to enhance PubMed search with text mining features
Richard Tzong-Han Tsai, Hong-Jie Dai, Po-Ting Lai, and Chi-Hsin Huang
Bioinformatics (2009) 25(22): 3031-3032
Targeted proteomics using selected reaction monitoring (SRM) reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate treated Norway spruce (Picea abies)
Zulak KG, Lippert DN, Kuzyk MA, Domanski D, Chou T, Borchers CH, Bohlmann J.
Plant J (2009) 60(6): 1015-30
Of proteins and DNA-proteomic role in the field of chromatin research
Lambert JP, Baetz K, Figeys D.
Mol Biosyst (2010) 6(1): 30-7
Proteomics Analysis of Human Skeletal Muscle Reveals Novel Abnormalities in Obesity and Type 2 Diabetes Mellitus
Hwang H, Bowen BP, Lefort N, Flynn CR, De Filippis EA, Roberts C, Smoke CC, Meyer C, Højlund K, Yi Z, Mandarino LJ.
Diabetes (2010) 59(1): 33-42
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria
Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA.
Proc Natl Acad Sci U S A (2009) 106(38): 16428-33
Characterization of the Photosynthetic Apparatus and Proteome of Roseobacter denitrificans
Tang K, Zong R, Zhang F, Xiao N, Jiao N.
Curr Microbiol Early Edition: published 14-Oct-2009
Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions
Forner F, Kumar C, Luber CA, Fromme T, Klingenspor M, Mann M.
Cell Metab (2009) 10(4): 324-35
Negative effects of desiccation on the protein sorting and post-translational modification
Wang X, He Y.
Plant Signal Behav (2009) 4(5): 435-7
Proteomic characterization of a temperature-sensitive conditional lethal in Drosophila melanogaster
Pedersen KS, Codrea MC, Vermeulen CJ, Loeschcke V, Bendixen E.
Heredity Early Edition: published 7-Oct-2009
The diminished exoproteome of Frankia in culture and symbiosis
Mastronunzio JE, Huang Y, Benson DR.
Appl Environ Microbiol (2009) 75(21): 6721-8
Endosomal and secretory markers of the Legionella-containing vacuole
Urwyler S, Brombacher E, Hilbi H.
Commun Integr Biol (2009) 2(2): 107-9
Identification and characterization of novel ERC-55 interacting proteins: Evidence for the existence of several ERC-55 splicing variants; including the cytosolic ERC-55-C
Maja Ludvigsen, Christian Jacobsen, Arvid B. Maunsbach, Bent Honor
PROTEOMICS (2009) 9(23): 5267-5287
A proteomics approach to discovering natural products and their biosynthetic pathways
Bumpus SB, Evans BS, Thomas PM, Ntai I, Kelleher NL.
Nat Biotechnol (2009) 27(10): 951-6
The type IV secretion system affects the expression of Omp25/Omp31 and the outer membrane properties of Brucella melitensis
Wang Y, Chen Z, Qiao F, Zhong Z, Xu J, Wang Z, Du X, Qu Q, Yuan J, Jia L, Song H, Sun Y, Huang L.
FEMS Microbiol Lett Early Edition: published 23-Nov-2009
Profiling of host cell proteins by two Dimensional difference Gel Electrophoresis (2D-DIGE): Implications for downstream process development
Jin M, Szapiel N, Zhang J, Hickey J, Ghose S.
Biotechnol Bioeng (2010) 105(2): 306-16
The neuropeptidomics of Ixodes scapularis synganglion
Susanne Neupert, William K. Russell, Reinhard Predel, David H. Russell, Otto F. Strey, Pete D. Teel, Ronald J. Nachman
Journal of Proteomics (2009) 72(6): 1040-1045
Proteomic identification of toxic volatile organic compound-responsive proteins in Arabidopsis thaliana
Park MA, Seo JH, Park JS, Kwon M.
Plant Cell Rep (2009) 28(10): 1603-14
Proteome analysis of Citrus sinensis L. (Osbeck) flesh at ripening time
Vera Muccilli, Concetta Licciardello, Debora Fontanini, Maria Patrizia Russo, Vincenzo Cunsolo, Rosaria Saletti, Giuseppe Reforgiato Recupero, Salvatore Foti
Journal of Proteomics (2009) 73(1): 134-152
Regulation of dauer formation by O-GlcNAcylation in caenorhabditis elegans
Lee J, Kim KY, Lee J, Paik YK.
J Biol Chem Early Edition: published 23-Nov-2009
Comparative proteomics analysis of cardiac muscle samples from pufferfish Takifugu rubripes exposed to excessive fluoride: initial molecular response to fluorosis
Lu J, Xu Q, Zheng J, Liu H, Li J, Chen K.
Toxicol Mech Methods (2009) 19(6-7): 468-75
Quantitative Proteomic Analysis of CMS-Related Changes in Honglian CMS Rice Anther
Sun Q, Hu C, Hu J, Li S, Zhu Y.
Protein J Early Edition: published 16-Sep-2009
A proteomic analysis of secretory proteins of a pre-vacuolar mutant of Candida albicans
Derek P. Thomas, Jose Luis Lopez-Ribot, Samuel A. Lee
Journal of Proteomics (2009) 73(2): 342-351
Snake venomics and antivenomics of Bothrops atrox venoms from Colombia and the Amazon regions of Brazil, Peru and Ecuador suggest the occurrence of geographic variation of venom phenotype by a trend towards paedomorphism
Vitelbina Nunez, Pedro Cid, Libia Sanz, Pilar De La Torre, Yamileth Angulo, Bruno Lomonte, Jose Maria Gutierrez, Juan J. Calvete
Journal of Proteomics (2009) 73(1): 57-78
Estrogen regulates cytoskeletal flexibility, cellular metabolism and synaptic proteins: A proteomic study
Szegő EM, Kékesi KA, Szabó Z, Janáky T, Juhász GD.
Psychoneuroendocrinology Early Edition: published 10-Dec-2009
Proteomics of proteins associated with astaxanthin accumulation in the green algae Haematococcus lacustris under the influence of sodium orthovanadate
Tran NP, Park JK, Hong SJ, Lee CG.
Biotechnol Lett (2009) 31(12): 1917-22
The natural history of Anaplasma marginale
Kocan KM, de la Fuente J, Blouin EF, Coetzee JF, Ewing SA.
Vet Parasitol Early Edition: published 19-Sep-2009
Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress
Maaty WS, Wiedenheft B, Tarlykov P, Schaff N, Heinemann J, Robison-Cox J, Valenzuela J, Dougherty A, Blum P, Lawrence CM, Douglas T, Young MJ, Bothner B.
PLoS One (2009) 4(9): e6964
Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) using a Proteomic Platform
Ramalingam R, Prakash S, Archunan G, Sowdhamini R.
Protein Pept Lett Early Edition: published 16-Dec-2009
Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae
Pinto PM, Klein CS, Zaha A, Ferreira HB.
Proteome Science (2009) 7(1): 45
Is oxidative stress a cause or consequence of disuse muscle atrophy in mice? A proteomic approach in hindlimb unloaded mice
Brocca L, Pellegrino MA, Desaphy JF, Pierno S, Conte Camerino D, Bottinelli R.
Exp Physiol Early Edition: published 9-Oct-2009
Altered protein-expressing profile in hPNAS4-induced apoptosis in A549 human lung adenocarcinoma cells
Gou LT, Tong AP, Yan F, Yuan Z, He F, Wang W, Zhou Y, Chen LJ, Tang MH, Yang JL.
J Cell Biochem (2009) 108(5): 1211-9
Engineering of Bacillus subtilis 168 for increased Nisin Resistance
Hansen ME, Wangari R, Hansen EB, Mijakovic I, Jensen PR.
Appl Environ Microbiol (2009) 75(21): 6688-95
The cAMP Capture Compound Mass Spectrometry as a Novel Tool for Targeting
cAMP-binding Proteins: FROM PROTEIN KINASE A TO POTASSIUM/SODIUM
Mol Cell Proteomics (2009) 8(12): 2843-2856
"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus
Zaparty M, Esser D, Gertig S, Haferkamp P, Kouril T, Manica A, Pham TK, Reimann J, Schreiber K, Sierocinski P, Teichmann D, van Wolferen M, von Jan M, Wieloch P, Albers SV, Driessen AJ, Klenk HP, Schleper C, Schomburg D, van der Oost J, Wright PC, Siebers B.
Extremophiles Early Edition: published 4-Oct-2009
Synaptic Proteins Linked to HIV-1 Infection and Immunoproteasome Induction: Proteomic Analysis of Human Synaptosomes
Gelman BB, Nguyen TP.
J Neuroimmune Pharmacol Early Edition: published 20-Aug-2009
Proteomic analysis of cold stress-responsive proteins in Thellungiella rosette leaves
Gao F, Zhou Y, Zhu W, Li X, Fan L, Zhang G.
Planta (2009) 230(5): 1033-46
Deciphering diatom biochemical pathways via whole-cell proteomics
Nunn BL, Aker JR, Shaffer SA, Tsai S, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmström L, Goodlett DR.
Aquat Microb Ecol (2009) 55(3): 241-253
Biochemical and PMF MALDI-TOF analyses of two novel papain-like plant proteinases
Obregón WD, Liggieri CS, Morcelle SR, Trejo SA, Avilés FX, Priolo NS.
Protein Pept Lett (2009) 16(11): 1323-33
Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships
Albenne C, Canut H, Boudart G, Zhang Y, San Clemente H, Pont-Lezica R, Jamet E.
Mol Plant (2009) 2(5): 977-89
Deciphering the proteomic profile of rice (Oryza sativa) bran: A pilot study
Fabio Ferrari, Marco Fumagalli, Antonella Profumo, Simona Viglio, Alberto Sala, Lorenzo Dolcini, Caterina Temporini, Stefania Nicolis, Daniele Merli, Federica Corana, Begona Casado, Paolo Iadarola
ELECTROPHORESIS (2009) 30(23): 4083-4094
S-Nitrosylation in plants: Pattern and function
Christian Lindermayr, Jorg Durner
Journal of Proteomics (2009) 73(1): 1-9
Specification of cortical parenchyma and stele of maize (Zea mays L.) primary roots by asymmetric levels of auxin, cytokinin and cytokinin-regulated proteins
Saleem M, Lamkemeyer T, Schutzenmeister A, Madlung J, Sakai H, Piepho HP, Nordheim A, Hochholdinger F.
Plant Physiol (2010) 152(1): 4-18
Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex
Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L, Washburn MP, Conaway JW, Conaway RC.
J Biol Chem Early Edition: published 14-Dec-2009
Proteomic analysis reveals a major role for contact inhibition in the terminal differentiation of hepatocytes
Mancone C, Conti B, Amicone L, Bordoni V, Cicchini C, Calvo L, Perdomo AB, Fimia GM, Tripodi M, Alonzi T.
J Hepatol Early Edition: published 25-Nov-2009
A novel S3S-TAP-tag for the isolation of T-cell interaction partners of adhesion and degranulation promoting adaptor protein
Roland Lehmann, Johann Meyer, Michael Schuemann, Eberhard Krause, Christian Freund
PROTEOMICS (2009) 9(23): 5288-5295
Echinococcus multilocularis: Two-Dimensional Western Blotting Method for the Identification and Expression Analysis of Immunogenic Proteins in Infected Dogs
Kouguchi H, Matsumoto J, Katoh Y, Suzuki T, Oku Y, Yagi K.
Exp Parasitol Early Edition: published 18-Sep-2009
Gene identification and proteomic analysis of the esterases of the cotton bollworm, Helicoverpa armigera
Teese MG, Campbell PM, Scott C, Gordon KH, Southon A, Hovan D, Robin C, Russell RJ, Oakeshott JG.
Insect Biochem Mol Biol Early Edition: published 10-Dec-2009
Proteome analysis of round-headed and normal spermatozoa by 2-D fluorescence difference gel electrophoresis and mass spectrometry
Liao TT, Xiang Z, Zhu WB, Fan LQ.
Asian J Androl (2009) 11(6): 683-93
The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins
Rembert Pieper, Quanshun Zhang, Prashanth P. Parmar, Shih-Ting Huang, David J. Clark, Hamid Alami, Arthur Donohue-Rolfe, Robert D. Fleischmann, Scott N. Peterson, Saul Tzipori
PROTEOMICS (2009) 9(22): 5029-5045
Leaf proteome responses of Arabidopsis thaliana exposed to mild cadmium stress
Semane B, Dupae J, Cuypers A, Noben JP, Tuomainen M, Tervahauta A, Kärenlampi S, Van Belleghem F, Smeets K, Vangronsveld J.
J Plant Physiol Early Edition: published 9-Dec-2009
ZP Domain Proteins in the Abalone Egg Coat include a Paralog of VERL Under Positive Selection that Binds Lysin and 18-kDa Sperm Proteins
Aagaard JE, Vacquier VD, Maccoss MJ, Swanson WJ.
Mol Biol Evol (2010) 27(1): 193-203
Biomechanical and proteomic analysis of INF- beta-treated astrocytes
Vergara D, Martignago R, Leporatti S, Bonsegna S, Maruccio G, Nuccio FD, Santino A, Cingolani R, Nicolardi G, Maffia M, Rinaldi R.
Nanotechnology (2009) 20(45): 455106
Upregulation of Hic-5 in glomerulosclerosis and its regulation of mesangial cell apoptosis
Hornigold N, Craven RA, Keen JN, Johnson T, Banks RE, Mooney AF.
Kidney Int Early Edition: published 9-Dec-2009
Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring
Noirel J, Ow SY, Sanguinetti G, Wright PC.
Mol Biosyst (2009) 5(10): 1214-23
Shotgun redox proteomics in sub-proteomes trapped on functionalised beads: Identification of proteins targeted by oxidative stress
Hu W, Tedesco S, McDonagh B, Sheehan D.
Mar Environ Res Early Edition: published 14-Nov-2009
Plant lipid rafts: fluctuat nec mergitur
Furt F, Lefebvre B, Cullimore J, Bessoule JJ, Mongrand S.
Plant Signal Behav (2007) 2(6): 508-11
Identification of proteins from tuberculin purified protein derivative (PPD) by LC-MS/MS
Borsuk S, Newcombe J, Mendum TA, Dellagostin OA, McFadden J.
Tuberculosis (Edinb) (2009) 89(6): 423-30
The oxido-redox potential of albuminMethodological approach and relevance to human diseases
Giovanni Candiano, Andrea Petretto, Maurizio Bruschi, Laura Santucci, Veronica Dimuccio, Marco Prunotto, Rosanna Gusmano, Andrea Urbani, Gian Marco Ghiggeri
Journal of Proteomics (2009) 73(2): 188-195
Proteomic and functional characterisation of platelet microparticle size classes
Dean WL, Lee MJ, Cummins TD, Schultz DJ, Powell DW.
Thromb Haemost (2009) 102(4): 711-8
Protein and metabolite analysis reveals permanent induction of stress defense and cell regeneration processes in a tobacco cell suspension culture
Lippmann R, Kaspar S, Rutten T, Melzer M, Kumlehn J, Matros A, Mock HP.
Int J Mol Sci (2009) 10(7): 3012-32
Livers overexpressing BRE transgene are under heightened state of stress-response, as revealed by comparative proteomics
Mei-Kuen Tang, Guanjun Liu, Zhibo Hou, Yiu-Loon Chui, John Y. H. Chan, Kenneth Ka Ho Lee
PROTEOMICS - CLINICAL APPLICATIONS (2009) 3(12): 1362-1370
From proteomics to structural studies of cytosolic/mitochondrial-type thioredoxin systems in barley seeds
Shahpiri A, Svensson B, Finnie C.
Mol Plant (2009) 2(3): 378-89
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U.
Nucl Acids Res (2010) 38(Database issue): D508-12
The effect of electroaucpuncture for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced proteomic changes in the mouse striatum
Kim ST, Moon W, Chae Y, Kim YJ, Lee H, Park HJ.
J Physiol Sci Early Edition: published 18-Sep-2009
Membrane proteomes of Pseudomonas aeruginosa and Acinetobacter baumannii
Dé E, Cosette P, Coquet L, Siroy A, Alexandre S, Duncan A, Naudin B, Rihouey C, Schaumann A, Junter GA, Jouenne T.
Pathol Biol (Paris) Early Edition: published 24-Nov-2009
Human myelin proteome and comparative analysis with mouse myelin
Ishii A, Dutta R, Wark GM, Hwang SI, Han DK, Trapp BD, Pfeiffer SE, Bansal R.
Proc Natl Acad Sci U S A (2009) 106(34): 14605-10
Proteome analysis of Aspergillus niger: Lactate added in starch-containing medium can increase production of the mycotoxin fumonisin B2 by modifying acetyl-CoA metabolism
Sorensen LM, Lametsch R, Andersen MR, Nielsen PV, Frisvad JC.
BMC Microbiol (2009) 9(1): 255
Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS
Gao C, Zhang F, Zhang J, Guo S, Shao H.
Int J Biol Sci (2009) 5(7): 727-35
Association of nuclear-intermediate filament lamin B1 with necrotic- and apoptotic-morphologies in cell death induced by 5-fluoro-2'-deoxyuridine
Sato A, Satake A, Hiramoto A, Okamatsu A, Nakama K, Kim HS, Wataya Y.
Nucleic Acids Symp Ser (Oxf) (2009) (53): 293-4
Gene expression analysis, proteomics, and network discovery
Baginsky S, Hennig L, Zimmermann P, Gruissem W.
Plant Physiol Early Edition: published 11-Dec-2009
From the Cover: Identification of functional marker proteins in the mammalian growth cone
Nozumi M, Togano T, Takahashi-Niki K, Lu J, Honda A, Taoka M, Shinkawa T, Koga H, Takeuchi K, Isobe T, Igarashi M.
Proc Natl Acad Sci U S A (2009) 106(40): 17211-6
A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16
Edward Schwartz, Birgit Voigt, Daniela Zhlke, Anne Pohlmann, Oliver Lenz, Dirk Albrecht, Alexander Schwarze, Yvonne Kohlmann, Cornelia Krause, Michael Hecker, Brbel Friedrich
PROTEOMICS (2009) 9(22): 5132-5142
Induction of glioma apoptosis by microglia-secreted molecules: The role of nitric oxide and cathepsin B
Hwang SY, Yoo BC, Jung JW, Oh ES, Hwang JS, Shin JA, Kim SY, Cha SH, Han IO.
Biochim Biophys Acta (2009) 1793(11): 1656-68
Urine Proteome Analysis in Murine Nephrotoxic Serum Nephritis
Wenderfer SE, Dubinsky WP, Hernandez-Sanabria M, Braun MC.
Am J Nephrol (2009) 30(5): 450-458
Proteomic analysis of integrin alphaIIbbeta3 outside-in signalling reveals Src-kinase-independent phosphorylation of Dok-1 and Dok-3 leading to SHIP-1 interactions
Senis YA, Antrobus R, Severin S, Parguiña AF, Rosa I, Zitzmann N, Watson SP, García A.
J Thromb Haemost (2009) 7(10): 1718-26
Proteomic analysis to identify the cellular responses induced by hydroquinone in human embryonic lung fibroblasts
Li X, Zhuang Z, Liu J, Huang H, Wei Q, Yang X.
Toxicol Mech Methods (2006) 16(1): 1-6
Characterization of two different acyl carrier proteins in complex I from Yarrowia lipolytica
Dobrynin K, Abdrakhmanova A, Richers S, Hunte C, Kerscher S, Brandt U.
Biochim Biophys Acta Early Edition: published 16-Sep-2009
Prolactin Exerts a Prosurvival Effect on Human Spermatozoa via Mechanisms that Involve the Stimulation of Akt Phosphorylation and Suppression of Caspase Activation and Capacitation
Pujianto DA, Curry BJ, Aitken RJ.
Endocrinology Early Edition: published 23-Dec-2009
Global analysis of the yeast osmotic stress response by quantitative proteomics
Soufi B, Kelstrup CD, Stoehr G, Fröhlich F, Walther TC, Olsen JV.
Mol Biosyst (2009) 5(11): 1337-46
Protein composition of Trypanosoma brucei mitochondrial membranes
Nathalie Acestor, Aswini K. Panigrahi, Yuko Ogata, Atashi Anupama, Kenneth D. Stuart
PROTEOMICS (2009) 9(24): 5497-5508
Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies
Zhao H, Xing D, Li QQ.
Plant Physiol (2009) 151(3): 1546-56
A two-dimensional electrophoretic profile of the proteins secreted by Herbaspirillum seropedicae strain Z78
Daniela Fojo Seixas Chaves, Emanuel Maltempi de Souza, Rose Adele Monteiro, Fabio de Oliveira Pedrosa
Journal of Proteomics (2009) 73(1): 50-56
Brown recluse spider venom: proteomic analysis and proposal of a putative mechanism of action
dos Santos LD, Dias NB, Roberto J, Pinto AS, Palma MS.
Protein Pept Lett (2009) 16(8): 933-43
Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies
Hemm MR, Paul BJ, Miranda-Rios J, Zhang A, Soltanzad N, Storz G.
J Bacteriol (2010) 192(1): 46-58
Chlamydia vaccine candidates and tools for chlamydial antigen discovery
Rockey DD, Wang J, Lei L, Zhong G.
Expert Rev Vaccines (2009) 8(10): 1365-77
Mapping the lipolytic proteome of adipose tissue using fluorescent suicide inhibitors
Schicher M, Kollroser M, Hermetter A.
Methods Mol Biol (2009) 579: 497-511
Proteomic analysis of livers from a transgenic mouse line with activated polyamine catabolism
Cerrada-Gimenez M, Häyrinen J, Juutinen S, Reponen T, Jänne J, Alhonen L.
Amino Acids Early Edition: published 10-Dec-2009
Inter-individual variability of protein patterns in saliva of healthy adults
Mercedes Quintana, Olivier Palicki, Geraldine Lucchi, Patrick Ducoroy, Christophe Chambon, Christian Salles, Martine Morzel
Journal of Proteomics (2009) 72(5): 822-830
Proteomic profiling of the insoluble fractions in the rat hippocampus post-propofol anesthesia
Zhang X, Liu Y, Feng C, Yang S, Wang Y, Wu AS, Yue Y.
Neurosci Lett (2009) 465(2): 165-70
Comparative proteomics of a lycopene-accumulating mutant reveals the important role of oxidative stress on carotenogenesis in sweet orange (Citrus sinensis [L.] osbeck)
Zhiyong Pan, Qing Liu, Ze Yun, Rui Guan, Wenfang Zeng, Qiang Xu, Xiuxin Deng
PROTEOMICS (2009) 9(24): 5455-5470
2D Proteome Analysis initiates new Insights on the Salmonella Typhimurium LuxS Protein
Kint G, Sonck KA, Schoofs G, De Coster D, Vanderleyden J, De Keersmaecker SC.
BMC Microbiol (2009) 9(1): 198
Preliminary biochemical characterization of the venoms of five Colubridae species from Brazil
Zelanis A, Teixeira da Rocha MM, de Fátima Domingues Furtado M.
Toxicon Early Edition: published 29-Sep-2009
Wheat quality related differential expressions of albumins and globulins revealed by two-dimensional difference gel electrophoresis (2-D DIGE)
Liyan Gao, Aili Wang, Xiaohui Li, Kun Dong, Ke Wang, Rudi Appels, Wujun Ma, Yueming Yan
Journal of Proteomics (2009) 73(2): 279-296
HLA Class I Molecules Reflect an Altered Host Proteome Following Influenza Virus Infection
Wahl A, Schafer F, Bardet W, Hildebrand WH.
Hum Immunol (2010) 71(1): 14-22
Proteomic studies of Bacillus anthracis
Chitlaru T, Shafferman A.
Future Microbiol (2009) 4: 983-98.
Schweinfurthins I and J from Macaranga schweinfurthii ( perpendicular)
Klausmeyer P, Van QN, Jato J, McCloud TG, Beutler JA.
J Nat Prod Early Edition: published 10-Dec-2009
Evidence for the existence in Arabidopsis thaliana of the proteasome proteolytic pathway: Activation in response to cadmium
Polge C, Jaquinod M, Holzer F, Bourguignon J, Walling L, Brouquisse R.
J Biol Chem (2009) 284(51): 35412-24
Transduction of redox signaling by electrophile-protein reactions
Rudolph TK, Freeman BA.
Sci Signal (2009) 2(90): re7
Comparative proteomic analysis of mouse melanoma cell line B16, a metastatic descendant B16F10, and B16 overexpressing the metastasis-associated tyrosine phosphatase PRL-3
Kim SH, Kim Y, Kim M, Kim DS, Lee SC, Chi SW, Lee do H, Park SG, Park BC, Bae KH, Kang S.
Oncol Res (2009) 17(11-12): 601-12
Dynamic Proteomic and Metabonomic Analysis Reveal Dysfunction and Subclinical Injury in Rat Liver during Restraint Stress
Chen M, Wang Y, Zhao Y, Wang L, Gong J, Wu L, Gao X, Yang Z, Qian L.
Biochim Biophys Acta (2009) 1794(12): 1751-65
Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid
Le Trionnaire G, Francis F, Jaubert-Possamai S, Bonhomme J, De Pauw E, Gauthier JP, Haubruge E, Legeai F, Prunier-Leterme N, Simon JC, Tanguy S, Tagu D.
BMC Genomics (2009) 10(1): 456
A comprehensive proteome map of bovine cerebrospinal fluid
Anja Brenn, Axel Karger, Martin Skiba, Ute Ziegler, Martin H. Groschup
PROTEOMICS (2009) 9(22): 5199-5205
Global Survey of Protein Expression during Gonadal Sex Determination in
Mice
Mol Cell Proteomics (2009) 8(12): 2624-2641
Comparative proteomic analysis of Rhodosporidium toruloides during lipid accumulation
Liu H, Zhao X, Wang F, Li Y, Jiang X, Ye M, Zhao ZK, Zou H.
Yeast (2009) 26(10): 553-66
Proteomic analysis reveals differentially expressed proteins in the rat frontal cortex after methamphetamine treatment
Faure JJ, Hattingh SM, Stein DJ, Daniels WM.
Metab Brain Dis Early Edition: published 14-Oct-2009
Evidence for Co-purification of Micronuclei in Sucrose Density Gradient Enriched Plasma Membranes from Cell Lines
Damaraju S, Zhang N, Li N, Tao L, Damaraju VL, Dufour J, Santos C, Sun XJ, Mackey J, Wishart DS, Cass CE, Li L.
Anal Biochem (2010) 396(1): 69-75
Proteomic characterization of the released/secreted proteins of Leishmania (Viannia) braziliensis promastigotes
Patricia Cuervo, Jose B. De Jesus, Leonardo Saboia-Vahia, Leila Mendonca-Lima, Gilberto B. Domont, Elisa Cupolillo
Journal of Proteomics (2009) 73(1): 79-92
Proteomic Analysis of Phosphorylated Nuclear Proteins Underscores Novel Roles for Rapid Actions of Retinoic Acid in the Regulation of mRNA Splicing and Translation
Laserna EJ, Valero ML, Sanz L, Sánchez Del Pino MM, Calvete JJ, Barettino D.
Mol Endocrinol (2009) 23(11): 1799-814
Proteomic analyses of the effects of drugs of abuse on monocyte-derived mature dendritic cells
Reynolds JL, Mahajan SD, Aalinkeel R, Nair B, Sykes DE, Schwartz SA.
Immunol Invest (2009) 38(6): 526-50
Proteomic analyses of recombinant human follicle-stimulating hormone and urinary-derived gonadotropin preparations
Kuwabara Y, Mine K, Katayama A, Inagawa T, Akira S, Takeshita T.
J Reprod Med (2009) 54(8): 459-66
Characterization of the endocannabinoid system in human neuronal cells, and proteomic analysis of anandamide-induced apoptosis
Pasquariello N, Catanzaro G, Marzano V, Amadio D, Barcaroli D, Oddi S, Federici G, Urbani A, Finazzi Agro A, Maccarrone M.
J Biol Chem (2009) 284(43): 29413-26
Proteome analysis of the Escherichia coli heat shock response under steady-state conditions
Luders S, Fallet C, Franco-Lara E.
Proteome Science (2009) 7(1): 36
Immunoproteomic analysis of the development of natural immunity in subjects colonised by Neisseria meningitidis reveals potential vaccine candidates
Williams JN, Skipp PJ, O'Connor CD, Christodoulides M, Heckels JE.
Infect Immun (2009) 77(11): 5080-9
Yeast prion [PSI(+)] lowers the levels of mitochondrial prohibitins
Sikora J, Towpik J, Graczyk D, Kistowski M, Rubel T, Poznanski J, Langridge J, Hughes C, Dadlez M, Boguta M.
Biochim Biophys Acta (2009) 1793(11): 1703-9
Proteome-wide Substrate Analysis Indicates Substrate Exclusion as a
Mechanism to Generate Caspase-7 Versus Caspase-3 Specificity
Mol Cell Proteomics (2009) 8(12): 2700-2714
Discovery of naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass spectrometry for vaccine development
Johnson KL, Ovsyannikova IG, Mason CJ, Bergen HR 3rd, Poland GA.
Vaccine (2009) 28(1): 38-47
Proteomic approach for identification of protein S-nitrosation in mouse gastric mucosa treated with S-nitrosoglutathione
Kazuo Ohtake, Norihisa Shimada, Hiroyuki Uchida, Jun Kobayashi
Journal of Proteomics (2009) 72(5): 750-760
Matrix Metalloproteinases: What don't they do? New substrates and biological roles identified by murine models and proteomics
Rodríguez D, Morrison CJ, Overall CM.
Biochim Biophys Acta Early Edition: published 30-Sep-2009
Peptidomics: identification of pathogenic and marker peptides
Xiang Y, Kurokawa MS, Kanke M, Takakuwa Y, Kato T.
Methods Mol Biol (2010) 615: 259-71
Mitochondrial-targeted antioxidants and oxidative stress: a proteomic prospective study
Rocha M, Esplugues JV, Hernández-Mijares A, Víctor VM.
Curr Pharm Des (2009) 15(26): 3052-62
Quantitative neuroproteomics of the synapse
Ramos-Ortolaza DL, Bushlin I, Abul-Husn N, Annangudi SP, Sweedler J, Devi LA.
Methods Mol Biol (2010) 615: 227-46
Comparative proteomic profiling of two muscles from five different pure pig breeds using SELDI-TOF proteomics technology
Mach N, Keuning E, Kruijt L, Hortós M, Arnau J, Te Pas MF.
J Anim Sci Early Edition: published 18-Dec-2009
Mare's colostrum globules stimulate fibroblast growth in vitro: a biochemical study
Zava S, Barello C, Pessione A, Garoffo LP, Fattori P, Montorfano G, Conti A, Giunta C, Pessione E, Berra B, Giuffrida MG.
J Med Food (2009) 12(4): 836-45
In situ chemical cross-linking on living cells reveals CD9P-1 cis-oligomer at cell surface
Magali Andre, Celia Chambrion, Stephanie Charrin, Sabrina Soave, Joelle Chaker, Claude Boucheix, Eric Rubinstein, Francois Le Naour
Journal of Proteomics (2009) 73(1): 93-102
Transcriptome and proteome analysis of chinese hamster ovary cells under low temperature and butyrate treatment
Kantardjieff A, Jacob NM, Yee JC, Epstein E, Kok YJ, Philp R, Betenbaugh M, Hu WS.
J Biotechnol Early Edition: published 18-Sep-2009
Evaluation of protein pattern changes in roots and leaves of Zea mays plants in response to nitrate availability by two-dimensional gel electrophoresis analysis
Prinsi B, Negri AS, Pesaresi P, Cocucci M, Espen L.
BMC Plant Biol (2009) 9(1): 113
Roles of TOM70 in import of presequence-containing mitochondrial proteins
Yamamoto H, Fukui K, Takahashi H, Kitamura S, Shiota T, Terao K, Uchida M, Esaki M, Nishikawa SI, Yoshihisa T, Yamano K, Endo T.
J Biol Chem (2009) 284(46): 31635-46
Compensatory role of inducible annexin A2 for impaired biliary epithelial anion-exchange activity of inflammatory cholangiopathy
Kido O, Fukushima K, Ueno Y, Inoue J, Jefferson DM, Shimosegawa T.
Lab Invest (2009) 89(12): 1374-86
A DIGE approach for the assessment of differential expression of the CHO proteome under sodium butyrate addition: Effect of Bcl-x(L) overexpression
Baik JY, Lee GM.
Biotechnol Bioeng (2010) 105(2): 358-67
Proteomic analysis of the triglyceride-rich lipoprotein-laden foam cells
Lu Y, Guo J, Di Y, Zong Y, Qu S, Tian J.
Mol Cells Early Edition: published 7-Sep-2009
Proteomic approaches to study plant-pathogen interactions
Quirino BF, Candido ES, Campos PF, Franco OL, Krüger RH.
Phytochemistry Early Edition: published 10-Dec-2009
Changes of defense proteins in the extracellular proteome of grapevine (Vitis vinifera cv. Gamay) cell cultures in response to elicitors
M.J. Martinez-Esteso, S. Selles-Marchart, J.C. Vera-Urbina, M.A. Pedreno, R. Bru-Martinez
Journal of Proteomics (2009) 73(2): 331-341
First proteomic assay of Pakistani Pisum sativum L. germplasm relation to geographic pattern
Nisar M, Ghafoor A, Khan MR, Asmatullah.
Genetika (2009) 45(7): 920-5
Proteomic profiling of the rat cerebral cortex in sleep and waking
Cirelli C, Pfister-Genskow M, McCarthy D, Woodbury R, Tononi G.
Arch Ital Biol (2009) 147(3): 59-68
Changes induced by the Pepper mild mottle tobamovirus on the chloroplast proteome of Nicotiana benthamiana
Pineda M, Sajnani C, Barón M.
Photosynth Res Early Edition: published 10-Oct-2009
Hypothyroidism Induced by Polychlorinated Biphenyls and Up-Regulation of Transthyretin
Han DY, Kang SR, Park OS, Cho JH, Won CK, Park HS, Park KI, Kim EH, Kim GS.
Bull Environ Contam Toxicol Early Edition: published 6-Oct-2009
Environmental monitoring of Domingo Rubio stream (Huelva Estuary, SW Spain) by combining conventional biomarkers and proteomic analysis in Carcinus maenas
Montes Nieto R, García-Barrera T, Gómez-Ariza JL, López-Barea J.
Environ Pollut Early Edition: published 6-Oct-2009
The relationship between increased growth and resistance induced in plants by root colonizing microbes
Shoresh M, Harman GE.
Plant Signal Behav (2008) 3(9): 737-9
Proteome of acidic phospholipid-binding proteins: Spatial and temporal regulation of coronin 1A by phosphoinositides
Tsujita K, Itoh T, Kondo A, Oyama M, Kozuka-Hata H, Irino Y, Hasegawa J, Takenawa T.
J Biol Chem Early Edition: published 22-Dec-2009
Peptide-binding specificity of the prosurfactant protein C Brichos domain analyzed by electrospray ionization mass spectrometry
Michael Fitzen, Gunvor Alvelius, Kerstin Nordling, Hans Jrnvall, Tomas Bergman, Jan Johansson
Rapid Communications in Mass Spectrometry (2009) 23(22): 3591-3598
Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6
Humphries JD, Byron A, Bass MD, Craig SE, Pinney JW, Knight D, Humphries MJ.
Sci Signal (2009) 2(87): ra51
Proteomics of Arabidopsis redox proteins in response to methyl jasmonate
Sophie Alvarez, Mengmeng Zhu, Sixue Chen
Journal of Proteomics (2009) 73(1): 30-40
A novel fractionation method prior to MS-based proteomics analysis using cascade biomimetic affinity chromatography
Tan Q, Dong D, Li R.
J Chromatogr B (2009) 877(30): 3799-805
Proteomic and Phosphoproteomic Analyses of the Soluble Fraction Following Acute Spinal Cord Contusion in Rats
Chen A, McEwen ML, Sun S, Ravikumar R, Springer JE.
J Neurotrauma Early Edition: published 19-Aug-2009
Natural modifiers of seed longevity in the Arabidopsis mutants abscisic acid insensitive3-5 (abi3-5) and leafy cotyledon1-3 (lec1-3)
Sugliani M, Rajjou L, Clerkx EJ, Koornneef M, Soppe WJ.
New Phytol (2009) 184(4): 898-908
Zinc and DHA have opposing effects on the expression levels of histones H3 and H4 in human neuronal cells
Suphioglu C, Sadli N, Coonan D, Kumar L, De Mel D, Lesheim J, Sinclair AJ, Ackland L.
Br J Nutr Early Edition: published 14-Sep-2009
Protein turnover in mycobacterial proteomics
Rao PK, Li Q.
Molecules (2009) 14(9): 3237-58
Relationship Between Expression of Voltage-Dependent Anion Channel (VDAC) Isoforms and Type of Hexokinase Binding Sites on Brain Mitochondria
Poleti MD, Tesch AC, Crepaldi CR, Souza GH, Eberlin MN, de Cerqueira César M.
J Mol Neurosci Early Edition: published 18-Aug-2009
Structural and kinetic determinants of protease substrates
Timmer JC, Zhu W, Pop C, Regan T, Snipas SJ, Eroshkin AM, Riedl SJ, Salvesen GS.
Nat Struct Mol Biol (2009) 16(10): 1101-8
Comparative 2-DE proteomic analysis of date palm (Phoenix dactylifera L.) somatic and zygotic embryos
Besma Sghaier-Hammami, Noureddine Drira, Jesus V. Jorrin-Novo
Journal of Proteomics (2009) 73(1): 161-177
Isolation and characterization of cytoplasmic cofilin-actin rods
Minamide LS, Maiti S, Boyle JA, Davis RC, Coppinger JA, Bao Y, Huang TY, Yates J, Bokoch GM, Bamburg JR.
J Biol Chem Early Edition: published 17-Dec-2009
Proteomics reveal rat hippocampal lateral asymmetry
Samara A, Vougas K, Papadopoulou A, Anastasiadou E, Baloyanni N, Paronis E, Chrousos GP, Tsangaris GT.
Hippocampus Early Edition: published 17-Dec-2009
Acinetobacter baumannii increases tolerance to antibiotics in response to monovalent cations
Hood MI, Jacobs AC, Sayood K, Dunman PM, Skaar EP.
Antimicrob Agents Chemother Early Edition: published 22-Dec-2009
Proteomic analysis of astroglial connexin43 silencing uncovers a cytoskeletal platform involved in process formation and migration
Olk S, Turchinovich A, Grzendowski M, Stühler K, Meyer HE, Zoidl G, Dermietzel R.
Glia (2009) 58(4): 494-505
A proteomic study reveals unspecific apoptosis induction and reduction of glycolytic enzymes by the phosphorothioate antisense oligonucleotide oblimersen in human melanoma cells
Martina Stessl, Martina Marchetti-Deschmann, Johannes Winkler, Bodo Lachmann, Gunter Allmaier, Christian R. Noe
Journal of Proteomics (2009) 72(6): 1019-1030
Comparative proteomic analysis provides new insights into mulberry dwarf responses in mulberry (Morus alba L.)
Xianling Ji, Yingping Gai, Chengchao Zheng, Zhimei Mu
PROTEOMICS (2009) 9(23): 5328-5339
Proteolysis activation and proteome alterations in murine skeletal muscle submitted to 1 week of hindlimb suspension
Ferreira R, Vitorino R, Neuparth MJ, Appell HJ, Duarte JA, Amado F.
Eur J Appl Physiol (2009) 107(5): 553-63
Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry
Wayengera M.
PLoS One (2009) 4(10): e7420
Lipidomic analysis of prostanoids by liquid chromatography-electrospray tandem mass spectrometry
Nicolaou A, Masoodi M, Mir A.
Methods Mol Biol (2009) 579: 271-86
A jumbo phage infecting the phytopathogen Ralstonia solanacearum defines a new lineage of the Myoviridae family
Yamada T, Satoh S, Ishikawa H, Fujiwara A, Kawasaki T, Fujie M, Ogata H.
Virology Early Edition: published 23-Dec-2009
Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways
Rasheed S, Yan JS, Hussain A, Lai B.
J Transl Med (2009) 7(1): 75
B16 melanoma secretomes and in vitro invasiveness: syntenin as an invasion modulator
Rondepierre F, Bouchon B, Bonnet M, Moins N, Chezal JM, Dʼincan M, Degoul F.
Melanoma Res Early Edition: published 15-Dec-2009
Proteomic analysis of microdissected facial nuclei of the rat following facial nerve injury
Melle C, Ernst G, Grosheva M, Angelov DN, Irintchev A, Guntinas-Lichius O, von Eggeling F.
J Neurosci Methods (2009) 185(1): 23-8
Immunomodulatory effects of holothurian triterpene glycosides on mammalian splenocytes determined by mass spectrometric proteome analysis
Dmitri L. Aminin, Conelia Koy, Pavel S. Dmitrenok, Brigitte Muller-Hilke, Dirk Koczan, Brian Arbogast, Aleksandra A. Silchenko, Vladimir I. Kalinin, Sergey A. Avilov, Valentin A. Stonik, Peter D. Collin, Hans-Juergen Thiesen, Max L. Deinzer, Michael O. Glocker
Journal of Proteomics (2009) 72(5): 886-906
Proteomic analysis during larval development and metamorphosis of the spionid polychaete Pseudopolydora vexillosa
Mok FS, Thiyagarajan V, Qian PY.
Proteome Science (2009) 7(1): 44
A Proteomics Approach Highlights a Myriad of Transporters in the Arabidopsis thaliana Vacuolar Membrane
Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J.
Plant Signal Behav (2007) 2(5): 413-5
A mouse model of anxiety molecularly characterized by altered protein networks in the brain proteome
Szegő EM, Janáky T, Szabó Z, Csorba A, Kompagne H, Müller G, Lévay G, Simor A, Juhász G, Kékesi KA.
Eur Neuropsychopharmacol Early Edition: published 14-Dec-2009
Proteomic evaluation of coffee zygotic embryos in two different stages of seed development
Franco OL, Pelegrini PB, Gomes CP, Souza A, Costa FT, Domont G, Quirino BF, Eira MT, Mehta A.
Plant Physiol Biochem (2009) 47(11-12): 1046-50
Molecular mechanisms of apoptosis induced by 3'-ethynylcytidine
Wataya Y, Naito T, Sato A, Hiramoto A, Kitade Y, Sasaki T, Matsuda A, Fukushima M, Kim HS.
Nucleic Acids Symp Ser (Oxf) (2009) (53): 291-2
Helicobacter pylori proteins response to nitric oxide stress
Qu W, Zhou Y, Shao C, Sun Y, Zhang Q, Chen C, Jia J.
J Microbiol (2009) 47(4): 486-93
Global effects of inactivation of the pyruvate kinase gene in the Mycobacterium tuberculosis complex
Sivagami Sundaram CA, Wooff E, Coldham NG, Sritharan M, Hewinson RG, Gordon SV, Wheeler PR.
J Bacteriol (2009) 191(24): 7545-53
Proteomics reveals a physical and functional link between hepatocyte nuclear factor 4{alpha} and TFIID
Takahashi H, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC.
J Biol Chem (2009) 284(47): 32405-12
Peroxisomal proteomics: Biomonitoring in mussels after the Prestige's oil spill
Apraiz I, Cajaraville MP, Cristobal S.
Mar Pollut Bull (2009) 58(12): 1815-26
Identification of potential DREB2C targets in Arabidopsis thaliana plants overexpressing DREB2C using proteomic analysis
Lee K, Han KS, Kwon YS, Lee JH, Kim SH, Chung WS, Kim Y, Chun SS, Kim HK, Bae DW.
Mol Cells Early Edition: published 13-Oct-2009
Proteomic-based analytical approach for the characterization of glutenin subunits in durum wheat
Mamone G, Caro SD, Luccia AD, Addeo F, Ferranti P.
J Mass Spectrom (2009) 44(12): 1709-23
Synthesis and biological evaluation of phosphatidylinositol phosphate affinity probes
Conway SJ, Gardiner J, Grove SJ, Johns MK, Lim ZY, Painter GF, Robinson DE, Schieber C, Thuring JW, Wong LS, Yin MX, Burgess AW, Catimel B, Hawkins PT, Ktistakis NT, Stephens LR, Holmes AB.
Org Biomol Chem (2010) 8(1): 66-76
Differential Expression of Proteins in Listeria monocytogenes Under Thermotolerance-Inducing, Heat Shock, and Prolonged Heat Shock Conditions
Agoston R, Soni K, Jesudhasan PR, Russell WK, Mohácsi-Farkas C, Pillai SD.
Foodborne Pathog Dis (2009) 6(9): 1133-40
The Effect of Oxytocin and an Oxytocin Antagonist on the Human Myometrial Proteome
de Wit NC, Heck AJ, Thornton S.
Reprod Sci (2010) 17(1): 40-6
Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis
Dressaire C, Gitton C, Loubière P, Monnet V, Queinnec I, Cocaign-Bousquet M.
PLoS Comput Biol (2009) 5(12): e1000606
Methylmercury disrupts the balance between phosphorylated and non-phosphorylated cofilin in primary cultures of mice cerebellar granule cells. A proteomic study
Vendrell I, Carrascal M, Campos F, Abián J, Suñol C.
Toxicol Appl Pharmacol (2010) 242(1): 109-18
The Cytotoxic Pathway Triggered by Palytoxin Involves a Change in the Cellular Pool of Stress Response Proteins
Sala GL, Bellocci M, Rossini GP.
Chem Res Toxicol (2009) 22(12): 2009-16
Understanding the blood-brain barrier using gene and protein expression profiling technologies
Pottiez G, Flahaut C, Cecchelli R, Karamanos Y.
Brain Res Rev (2009) 62(1): 83-98
O-Linked N-Acetylglucosamine Modification of Insulin Receptor Substrate-1
Occurs in Close Proximity to Multiple SH2 Domain Binding Motifs
Mol Cell Proteomics (2009) 8(12): 2733-2745
Regulation of Myoblast Differentiation by the Nuclear Envelope Protein NET39
Liu GH, Guan T, Datta K, Coppinger J, Yates J 3rd, Gerace L.
Mol Cell Biol (2009) 29(21): 5800-12
Biomarker candidate discovery in Atlantic cod (Gadus morhua) continuously exposed to North Sea produced water from egg to fry
Bohne-Kjersem A, Bache N, Meier S, Nyhammer G, Roepstorff P, Sæle O, Goksøyr A, Grøsvik BE.
Aquat Toxicol Early Edition: published 13-Nov-2009
Determination of enzymatic source of alanine aminotransferase activity in serum from dogs with liver injury
Miyazaki M, Rosenblum J, Kasahara Y, Nakagawa I, Patricelli M.
J Pharmacol Toxicol Methods (2009) 60(3): 307-15
Identification of differentially expressed proteins in adipose tissue of divergently selected broilers
Wang D, Wang N, Li N, Li H.
Poult Sci (2009) 88(11): 2285-92
Biochemical and proteomic analysis of 'Dixiland' peach fruit (Prunus persica) upon heat treatment
Lara MV, Borsani J, Budde CO, Lauxmann MA, Lombardo VA, Murray R, Andreo CS, Drincovich MF.
J Exp Bot (2009) 60(15): 4315-33
Proteomic analysis of enriched lysosomes at early phase of camptothecin-induced apoptosis in human U-937 cells
Nicolas Parent, Eric Winstall, Myriam Beauchemin, Claudie Paquet, Guy G. Poirier, Richard Bertrand
Journal of Proteomics (2009) 72(6): 960-973
Proteome analysis of human nuclear insoluble fractions
Takata H, Nishijima H, Ogura S, Sakaguchi T, Bubulya PA, Mochizuki T, Shibahara K.
Genes Cells (2009) 14(8): 975-90
The innate immune and systemic response in honey bees to a bacterial pathogen, Paenibacillus larvae
Chan QW, Melathopoulos AP, Pernal SF, Foster LJ.
BMC Genomics (2009) 10(1): 387
Identification of novel protein targets regulated by maternal dietary fatty acid composition in neonatal rat liver
Elizabeth M. Novak, Erin K. Lee, Sheila M. Innis, Bernd O. Keller
Journal of Proteomics (2009) 73(1): 41-49
Comparative proteomic analysis on Salmonella Gallinarum and Salmonella Enteritidis exploring proteins that may incorporate host adaptation in poultry
Kamelia M. Osman, Mona M. Ali, Moustafa I. Radwan, Hyoung Kyu Kim, Jin Han
Journal of Proteomics (2009) 72(5): 815-821
Proteomic DIGE analysis of the mitochondria-enriched fraction from aged rat skeletal muscle
Kathleen O'Connell, Kay Ohlendieck
PROTEOMICS (2009) 9(24): 5509-5524
Azaspiracid Poisoning (AZP) Toxins in Shellfish: Toxicological and Health Considerations
Furey A, O'Doherty S, O'Callaghan K, Lehane M, James KJ.
Toxicon Early Edition: published 16-Dec-2009
In vivo residue-specific histone methylation dynamics
Zee BM, Levin RS, Xu B, Leroy G, Wingreen NS, Garcia BA.
J Biol Chem Early Edition: published 23-Nov-2009
Intra-specific variation in venom of the African Puff Adder (Bitis arietans): differential expression and activity of snake venom metalloproteinases (SVMPs)
Currier RB, Harrison RA, Rowley PD, Laing GD, Wagstaff SC.
Toxicon Early Edition: published 17-Dec-2009
Distinct changes in soybean xylem sap proteome in response to pathogenic and symbiotic microbe interactions
Subramanian S, Cho UH, Keyes C, Yu O.
BMC Plant Biol (2009) 9(1): 119
A biotinylated analog of the anti-proliferative prostaglandin A(1) allows assessment of PPAR-independent effects and identification of novel cellular targets for covalent modification
Garzón B, Gayarre J, Gharbi S, Díez-Dacal B, Sánchez-Gómez FJ, Timms JF, Pérez-Sala D.
Chem Biol Interact (2010) 183(1): 212-21
A rapid method for depletion of Rubisco from soybean (Glycine max) leaf for proteomic analysis of lower abundance proteins
Krishnan HB, Natarajan SS.
Phytochemistry (2009) 70(17-18): 1958-64
Proteomic clues to the identification of QX disease-resistance biomarkers in selectively bred Sydney rock oysters, Saccostrea glomerata
Margaret Simonian, Sham V. Nair, John A. Nell, David A. Raftos
Journal of Proteomics (2009) 73(2): 209-217
Identification of cleistogamy-associated proteins in flower buds of near-isogenic lines of soybean by differential proteomic analysis
Khan NA, Takahashi R, Abe J, Komatsu S.
Peptides (2009) 30(12): 2095-102
Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium
Charles RC, Harris JB, Chase MR, Lebrun LM, Sheikh A, LaRocque RC, Logvinenko T, Rollins SM, Tarique A, Hohmann EL, Rosenberg I, Krastins B, Sarracino DA, Qadri F, Calderwood SB, Ryan ET.
PLoS One (2009) 4(9): e6994
Proteomic analysis of stromal cells derived from the dental pulp of human exfoliated deciduous teeth
Pivoriūnas A, Surovas A, Borutinskaitė V, Matuzevičius D, Treigytė G, Savickienė J, Tunaitis V, Aldonytė R, Jarmalavičiūtė A, Suriakaitė K, Liutkevičius E, Venalis A, Navakauskas D, Navakauskienė R, Magnusson KE.
Stem Cells Dev Early Edition: published 13-Oct-2009
Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle
Cornman RS, Willis JH.
Insect Mol Biol (2009) 18(5): 607-22
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
Tian C, Beeson WT, Iavarone AT, Sun J, Marletta MA, Cate JH, Glass NL.
Proc Natl Acad Sci U S A Early Edition: published 15-Dec-2009
NDRG1 and CRK-I/II are regulators of endothelial cell migration under intermittent hypoxia
Toffoli S, Delaive E, Dieu M, Feron O, Raes M, Michiels C.
Angiogenesis Early Edition: published 17-Sep-2009
Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS
Natalie Lefort, Zhengping Yi, Benjamin Bowen, Brian Glancy, Eleanna A. De Filippis, Rebekka Mapes, Hyonson Hwang, Charles R. Flynn, Wayne T. Willis, Anthony Civitarese, Kurt Højlund, Lawrence J. Mandarino
Journal of Proteomics (2009) 72(6): 1046-1060
Differential protein expression in Spirometra erinacei according to its development in its final host
Kim JH, Kim YJ, Sohn WM, Bae YM, Hong ST, Choi MH.
Parasitol Res (2009) 105(6): 1549-56
Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches
Kong FJ, Oyanagi A, Komatsu S.
Biochim Biophys Acta (2010) 1804(1): 124-36
Quantitative cell wall protein profiling of invasive and non-invasive Saccharomyces cerevisiae strains
Zupan J, Mavri J, Raspor P.
J Microbiol Methods (2009) 79(3): 260-5
An update on the mouse liver proteome
Gazzana G, Borlak J.
Proteome Science (2009) 7(1): 35
Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations
Tartaglia GG, Vendruscolo M.
Mol Biosyst (2009) 5(12): 1873-6
Proteomics approach for identifying osmotic-stress-related proteins in soybean roots
Toorchi M, Yukawa K, Nouri MZ, Komatsu S.
Peptides (2009) 30(12): 2108-17
Arachidonic acid and calcium signals in human breast tumor-derived endothelial cells: a proteomic study
Antoniotti S, Fattori P, Tomatis C, Pessione E, Munaron L.
J Recept Signal Transduct Res (2009) 29(5): 257-65
Of mice and men: comparative proteomics of bronchoalveolar fluid
Gharib SA, Nguyen E, Altemeier WA, Shaffer SA, Doneanu CE, Goodlett DR, Schnapp LM.
Eur Respir J Early Edition: published 23-Dec-2009
Comparative systems biology across an evolutionary gradient within the Shewanella genus
Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM.
Proc Natl Acad Sci U S A (2009) 106(37): 15909-14
Adaptation to ?-myrcene catabolism in Pseudomonas sp. M1: An expression proteomics analysis
Pedro M. Santos, Isabel S-Correia
PROTEOMICS (2009) 9(22): 5101-5111
Isolation of an oxalate-resistant Ashbya gossypii strain and its improved riboflavin production
Sugimoto T, Morimoto A, Nariyama M, Kato T, Park EY.
J Ind Microbiol Biotechnol Early Edition: published 14-Oct-2009
Proteomic identification of membrane proteins regulating antimicrobial peptide resistance in Vibrio parahaemolyticus
Shen CJ, Kuo TY, Lin CC, Chow LP, Chen WJ.
J Appl Microbiol Early Edition: published 28-Aug-2009