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SPS' DigestIssue 37, 22-Dec-2006 |
Finding diagnostic biomarkers in proteomic spectra
Pratapa PN, Patz EF Jr, Hartemink AJ.
Pac Symp Biocomput (2006) 1: 279-90.
A machine learning approach to predicting peptide fragmentation spectra
Arnold RJ, Jayasankar N, Aggarwal D, Tang H, Radivojac P.
Pac Symp Biocomput (2006) 1: 219-30.
Elucidation of a protein signature discriminating six common types of adenocarcinoma
Bloom GC, Eschrich S, Zhou JX, Coppola D, Yeatman TJ.
Int J Cancer Early Edition: published 27-Nov-2006
The accuracy of several multiple sequence alignment programs for proteins
Nuin PA, Wang Z, Tillier ER.
BMC Bioinformatics (2006) 7: 471.
Improvements in the search for potential biomarkers by proteomics: Application of principal component and discriminant analyses for two-dimensional maps evaluation
Rodriguez-Pineiro AM, Rodriguez-Berrocal FJ, Paez de la Cadena M.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 27-Oct-2006
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity
Nagarajan V, Kaushik N, Murali B, Zhang C, Lakhera S, Elasri MO, Deng Y.
BMC Bioinformatics (2006) 7(Suppl 2): S2
PIGOK: Linking Protein Identity to Gene Ontology and Function
Richard J. Jacob and Rainer Cramer
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3429-3432
Neural network prediction of peptide separation in strong anion exchange chromatography
Oh C, Zak SH, Mirzaei H, Buck C, Regnier FE, Zhang X.
Bioinformatics Early Edition: published 8-Nov-2006
Quality Assessment of Tandem Mass Spectra Based on Cumulative Intensity Normalization
Seungjin Na and Eunok Paek
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3241-3248
Statistics for proteomics: Experimental design and 2-DE differential analysis
Chich JF, David O, Villers F, Schaeffer B, Lutomski D, Huet S.
J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 31-Oct-2006
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
Falkner JA, Falkner JW, Andrews PC.
Bioinformatics Early Edition: published 22-Nov-2006
SUBA: the Arabidopsis Subcellular Database
Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH.
Nucleic Acids Res Early Edition: published 28-Oct-2006
Large-Scale Predictions of Gram-Negative Bacterial Protein Subcellular Locations
Kuo-Chen Chou and Hong-Bin Shen
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3420-3428
Integrating Medical and Genomic Data: a Sucessful Example for Rare Diseases
Dias GS, Oliveira JL, Vicente J, Martin-Sanchez F.
Stud Health Technol Inform (2006) 124: 125-130
A predictive model for identifying proteins by a single peptide match
Higdon R, Kolker E.
Bioinformatics Early Edition: published 22-Nov-2006
Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-A Pore Size C18 Sorbents
Krokhin OV.
Anal Chem (2006) 78(22): 7785-7795
High-accuracy peak picking of proteomics data using wavelet techniques
Lange E, Gropl C, Reinert K, Kohlbacher O, Hildebrandt A.
Pac Symp Biocomput (2006) 1: 243-54.
Analytical model of peptide mass cluster centres with applications
Wolski W, Farrow M, Emde A, Lehrach H, Lalowski M, Reinert K
Proteome Science (2006) 4: 18
An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry
Wang H, Fu Y, Sun R, He S, Zeng R, Gao W.
Pac Symp Biocomput (2006) 1: 303-14.
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
Zhang Y, Zhang Y, Adachi J, Olsen JV, Shi R, de Souza G, Pasini E, Foster LJ, Macek B, Zougman A, Kumar C, Wisniewski JR, Jun W, Mann M.
Nucleic Acids Res Early Edition: published 7-Nov-2006
Verification of single-Peptide protein identifications by the application of complementary database search algorithms
Rohrbough JG, Breci L, Merchant N, Miller S, Haynes PA.
J Biomol Tech (2006) 17(5): 327-32
Extracellular proteome of human hepatoma cell, HepG2 analyzed using two-dimensional liquid chromatography coupled with tandem mass spectrometry
Yamashita R, Fujiwara Y, Ikari K, Hamada K, Otomo A, Yasuda K, Noda M, Kaburagi Y.
Mol Cell Biochem Early Edition: published 16-Nov-2006
Roles and origins of leukocyte lipid bodies: proteomic and ultrastructural studies
Wan HC, Melo RC, Jin Z, Dvorak AM, Weller PF.
FASEB J Early Edition: published 29-Nov-2006
Pathway analysis of kidney cancer using proteomics and metabolic profiling
Perroud B, Lee J, Valkova N, Dhirapong A, Lin PY, Fiehn O, Kueltz D, Weiss RH.
Mol Cancer (2006) 5(1): 64
Proteome-wide Profiling of Isoniazid Targets in Mycobacterium tuberculosis
Argyrou A, Jin L, Siconilfi-Baez L, Angeletti RH, Blanchard JS.
Biochemistry (2006) 45(47): 13947-13953
Stem Cells and Experimental Leukemia Can Be Distinguished by Lipid Raft Protein Composition
Osterhues A, Liebmann S, Schmid M, Buk D, Huss R, Graeve L, Zeindl-Eberhart E.
Stem Cells Dev (2006) 15(5): 677-686
Pharmacogenomics of the Polyamine Analog 3,8,13,18-tetraaza-10,11-[(E)-1,2-cyclopropyl]eicosane Tetrahydrochloride, CGC-11093, in the Colon Adenocarcinoma Cell Line HCT1161
Ignatenko NA, Yerushalmi HF, Watts GS, Futscher BW, Stringer DE, Marton LJ, Gerner EW.
Technol Cancer Res Treat (2006) 5(6): 553-64
Genomic and functional evolution of the Drosophila melanogaster sperm proteome
Dorus S, Busby SA, Gerike U, Shabanowitz J, Hunt DF, Karr TL.
Nat Genet Early Edition: published 12-Nov-2006
Cadmium response and redoxin targets in Chlamydomonas reinhardtii: a proteomic approach
Gillet S, Decottignies P, Chardonnet S, Le Marechal P.
Photosynth Res Early Edition: published 14-Nov-2006
Proteomic analysis of phytopathogenic fungus Botrytis cinerea as a potential tool for identifying pathogenicity factors, therapeutic targets and for basic research
Fernandez-Acero FJ, Jorge I, Calvo E, Vallejo I, Carbu M, Camafeita E, Garrido C, Lopez JA, Jorrin J, Cantoral JM.
Arch Microbiol Early Edition: published 24-Nov-2006
A proteomic analysis of the effect of mapk pathway activation on l-glutamate-induced neuronal cell death
Kang S, Kim EY, Bahn YJ, Chung JW, Lee DH, Park SG, Yoon TS, Park BC, Bae KH.
Cell Mol Biol Lett Early Edition: published 24-Nov-2006
The Application of Proteomics and Genomics to the Study of Age-Related Neurodegeneration and Neuroprotection
Weinreb O, Drigues N, Sagi Y, Reznick AZ, Amit T, Youdim MB.
Antioxid Redox Signal Early Edition: published 1-Jan-2007
Development and implementation of a direct detection, quantitation and validation system for class I MHC self-peptide epitopes
Weidanz JA, Piazza P, Hickman-Miller H, Woodburn D, Nguyen T, Wahl A, Neethling F, Chiriva-Internati M, Rinaldo CR, Hildebrand WH.
J Immunol Methods Early Edition: published 25-Oct-2006
Proteome analysis of bell pepper (Capsicum annum L.) chromoplasts
Siddique MA, Grossmann J, Gruissem W, Baginsky S.
Plant Cell Physiol Early Edition: published 10-Nov-2006
Oxidative stress in the aging murine olfactory bulb: Redox proteomics and cellular localization
Vaishnav RA, Getchell ML, Poon HF, Barnett KR, Hunter SA, Pierce WM, Klein JB, Butterfield DA, Getchell TV.
J Neurosci Res Early Edition: published 27-Nov-2006
Proteomic analyses of male contributions to honey bee sperm storage and mating
Collins AM, Caperna TJ, Williams V, Garrett WM, Evans JD.
Insect Mol Biol (2006) 15(5): 541-9
Site-Specific Arylation of Rat Glutathione S-Transferase A1 and A2 by Bromobenzene Metabolites in Vivo
Koen YM, Yue W, Galeva NA, Williams TD, Hanzlik RP.
Chem Res Toxicol (2006) 19(11): 1426-1434
An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics
Lessner DJ, Li L, Li Q, Rejtar T, Andreev VP, Reichlen M, Hill K, Moran JJ, Karger BL, Ferry JG.
Proc Natl Acad Sci U S A Early Edition: published 13-Nov-2006
Bradykinin-related peptides from Phyllomedusa hypochondrialis azurea: mass spectrometric structural characterisation and cloning of precursor cDNAs
Thompson AH, Bjourson AJ, Shaw C, McClean S.
Rapid Commun Mass Spectrom (2006) 20(24): 3780-3788
Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment
Kim JK, Bamba T, Harada K, Fukusaki E, Kobayashi A.
J Exp Bot Early Edition: published 21-Nov-2006
Transgenic Mouse Proteomics Identifies New 14-3-3-associated Proteins Involved in Cytoskeletal Rearrangements and Cell Signaling
Pierre-Olivier Angrand, Inmaculada Segura, Pamela Volkel, Sonja Ghidelli, Rebecca Terry, Miro Brajenovic, Kristina Vintersten, Rudiger Klein, Giulio Superti-Furga, Gerard Drewes, Bernhard Kuster, Tewis Bouwmeester, and Amparo Acker-Palmer
Mol Cell Proteomics (2006) 5(12): 2211-2227
Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum
Williams TI, Combs JC, Lynn BC, Strobel HJ.
Appl Microbiol Biotechnol Early Edition: published 24-Nov-2006
An introduction to mass spectrometry based proteomics-Detection and characterization of gonadotropins and related molecules
Kicman AT, Parkin MC, Iles RK.
Mol Cell Endocrinol Early Edition: published 9-Nov-2006
Human saliva proteome and transcriptome
Hu S, Li Y, Wang J, Xie Y, Tjon K, Wolinsky L, Loo RR, Loo JA, Wong DT.
J Dent Res (2006) 85(12): 1129-33
Proteome changes in Arabidopsis thaliana roots upon exposure to Cd2+
Roth U, von Roepenack-Lahaye E, Clemens S.
J Exp Bot Early Edition: published 30-Oct-2006
BMP Stimulation of Alkaline Phosphatase Activity in Pluripotent Mouse C2C12 Cells is Inhibited by Dermatopontin, One of the Most Abundant Low Molecular Weight Proteins in Demineralized Bone Matrix
Behnam K, Murray SS, Brochmann EJ.
Connect Tissue Res (2006) 47(5): 271-7
Comparison of the proteome profiles of Entamoeba histolytica and its close but non-pathogenic relative Entamoeba dispar
Leitsch D, Wilson IB, Paschinger K, Duchene M.
Wien Klin Wochenschr (2006) 118(Supplement 3): 37-41
Dynamic analysis of GS-NS0 cells producing a recombinant monoclonal antibody during fed-batch culture
Stansfield SH, Allen EE, Dinnis DM, Racher AJ, Birch JR, James DC.
Biotechnol Bioeng Early Edition: published 17-Nov-2006
Proteome mapping of the Trichoderma reesei 20S proteasome
Grinyer J, Kautto L, Traini M, Willows RD, Te'o J, Bergquist P, Nevalainen H.
Curr Genet Early Edition: published 22-Nov-2006
Novel approaches for understanding the mechanisms of wound repair
Nanney LB, Caldwell RL, Pollins AC, Cardwell NL, Opalenik SR, Davidson JM.
J Investig Dermatol Symp Proc (2006) 11(1): 132-9
Calpain is required for the rapid, calcium-dependent repair of wounded plasma membrane
Mellgren RL, Zhang W, Miyake K, McNeil PL.
J Biol Chem Early Edition: published 22-Nov-2006
Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS
Thomas O. Metz, Jon M. Jacobs, Marina A. Gritsenko, Ghislaine Fontès, Wei-Jun Qian, David G. Camp II, Vincent Poitout, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3345-3354
A Subset of p23 Localized on Secretory Granules in Pancreatic {beta}-cells
Hosaka M, Watanabe T, Yamauchi Y, Sakai Y, Suda M, Mizutani S, Takeuchi T, Isobe T, Izumi T.
J Histochem Cytochem Early Edition: published 13-Nov-2006
Proteomic profiling of differentiating osteoblasts
Josip Blonder, Zhen Xiao, Timothy D Veenstra
Expert Review of Proteomics (2006) 3(5): 483-496
Comparative proteomics of clathrin-coated vesicles
Borner GH, Harbour M, Hester S, Lilley KS, Robinson MS.
J Cell Biol (2006) 175(4): 571-8
Time-dependent Translational Response of E. coli to Excess Zn(II)
Easton JA, Thompson P, Crowder MW.
J Biomol Tech (2006) 17(5): 303-7
Dexamethasone Alters Bronchoalveolar Lavage Fluid Proteome in a Mouse Asthma Model
Zhao J, Yeong LH, Wong WS.
Int Arch Allergy Immunol (2006) 142(3): 219-229
Characterization of the outer membrane proteome of Leptospira interrogans expressed during acute lethal infection
Nally JE, Whitelegge JP, Bassilian S, Blanco DR, Lovett MA.
Infect Immun Early Edition: published 13-Nov-2006
Proteomic Profiling of Rat Bone Marrow Mesenchymal Stem Cells Induced by 5-Azacytidine
Ye NS, Chen J, Luo GA, Zhang RL, Zhao YF, Wang YM.
Stem Cells Dev (2006) 15(5): 665-676
Extreme skewing of annexin II and S100A6 expression identified by proteomic analysis of peritoneal B-1 cells
Frances R, Tumang JR, Rothstein TL.
Int Immunol Early Edition: published 29-Nov-2006
Identification of several proteins involved in regulation of sperm motility by proteomic analysis
Zhao C, Huo R, Wang FQ, Lin M, Zhou ZM, Sha JH.
Fertil Steril Early Edition: published 27-Oct-2006
Actin deficiency induces cofilin phosphorylation: Proteome analysis of HeLa cells after beta-actin gene silencing
Liu N, Academia K, Rubio T, Wehr T, Yeck T, Jordan L, Hamby K, Paulus A.
Cell Motil Cytoskeleton Early Edition: published 22-Nov-2006
Proteomic analysis identifies candidate proteins associated with distant recurrences in breast cancer after adjuvant chemotherapy
Nimeus E, Malmstrom J, Johnsson A, Marko-Varga G, Ferno M.
J Pharm Biomed Anal Early Edition: published 3-Nov-2006
Proteomic analysis of early left ventricular hypertrophy secondary to hypertension: modulation by antihypertensive therapies
Gallego-Delgado J, Lazaro A, Osende JI, Esteban V, Barderas MG, Gomez-Guerrero C, Vega R, Vivanco F, Egido J.
J Am Soc Nephrol (2006) 17(12 Suppl 3): S159-64
Molecular markers of prostate cancer
Bradford TJ, Tomlins SA, Wang X, Chinnaiyan AM.
Urol Oncol (2006) 24(6): 538-51
Proteins are specifically altered in disease - really?
Claus Zabel
Expert Review of Proteomics (2006) 3(5): 469-470
Proteomic Analysis of Secreted Proteins of Non-small Cell Lung Cancer
Huang LJ, Chen SX, Luo WJ, Jiang HH, Zhang PF, Yi H.
Ai Zheng (2006) 25(11): 1361-1367
Mass Spectrometry-Based Metabolic Profiling Reveals Different Metabolite Patterns in Invasive Ovarian Carcinomas and Ovarian Borderline Tumors
Denkert C, Budczies J, Kind T, Weichert W, Tablack P, Sehouli J, Niesporek S, Konsgen D, Dietel M, Fiehn O.
Cancer Res (2006) 66(22): 10795-10804
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis
Shi Y, Chen L, Liotta LA, Wan HH, Rodgers GP.
Genomics Proteomics Bioinformatics (2006) 4(3): 145-55
BMP Stimulation of Alkaline Phosphatase Activity in Pluripotent Mouse C2C12 Cells is Inhibited by Dermatopontin, One of the Most Abundant Low Molecular Weight Proteins in Demineralized Bone Matrix
Behnam K, Murray SS, Brochmann EJ.
Connect Tissue Res (2006) 47(5): 271-7
Elevated Levels of Phosphorylated Fibrinogen--Isoforms and Differential Expression of Other Post-Translationally Modified Proteins in the Plasma of Ovarian Cancer Patients
Yuko Ogata, Carrie J. Hepplmann, M. Cristine Charlesworth, Benjamin J. Madden, Melinda N. Miller, Kimberly R. Kalli, William A. Cilby, H. Robert Bergen III, Diana A. Saggese, and David C. Muddiman
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3318-3325
Pathway analysis of kidney cancer using proteomics and metabolic profiling
Perroud B, Lee J, Valkova N, Dhirapong A, Lin PY, Fiehn O, Kueltz D, Weiss RH.
Mol Cancer (2006) 5(1): 64
Characterization of the outer membrane proteome of Leptospira interrogans expressed during acute lethal infection
Nally JE, Whitelegge JP, Bassilian S, Blanco DR, Lovett MA.
Infect Immun Early Edition: published 13-Nov-2006
Changes in the serum proteome of patients with sepsis and septic shock
Kalenka A, Feldmann RE Jr, Otero K, Maurer MH, Waschke KF, Fiedler F.
Anesth Analg (2006) 103(6): 1522-6
Proteomic Signatures in Laryngeal Squamous Cell Carcinoma
Sewell DA, Yuan CX, Robertson E.
ORL J Otorhinolaryngol Relat Spec (2006) 69(2): 77-84
Functional genome and proteome analyses of cutaneous autoimmune diseases
Trcka J, Kunz M.
Curr Pharm Des (2006) 12(29): 3787-98
Protein pattern difference in the colon cancer cell lines examined by two-dimensional differential in-gel electrophoresis and mass spectrometry
Katayama M, Nakano H, Ishiuchi A, Wu W, Oshima R, Sakurai J, Nishikawa H, Yamaguchi S, Otsubo T.
Surg Today (2006) 36(12): 1085-93
Perspectives of proteomics in acute myeloid leukemia
Czibere A, Grall F, Aivado M.
Expert Rev Anticancer Ther (2006) 6(11): 1663-75
Proteomics in the diagnosis of hepatocellular carcinoma: focus on high risk hepatitis B and C patients
El-Aneed A, Banoub J.
Anticancer Res (2006) 26(5A): 3293-300
A Comparative Study of Protein Profiling by Proteomic Analysis in Camptothecin-Resistant PC3 and Camptothecin-Sensitive LNCaP Human Prostate Cancer Cells
Hasegawa N, Mizutani K, Suzuki T, Deguchi T, Nozawa Y.
Urol Int (2006) 77(4): 347-54
Differential proteomic analysis of the anti-proliferative effect of glucocorticoid hormones in ST1 rat glioma cells
Demasi MA, Montor WR, Ferreira GB, Pimenta DC, Labriola L, Sogayar MC.
J Steroid Biochem Mol Biol Early Edition: published 24-Nov-2006
Site-Specific Arylation of Rat Glutathione S-Transferase A1 and A2 by Bromobenzene Metabolites in Vivo
Koen YM, Yue W, Galeva NA, Williams TD, Hanzlik RP.
Chem Res Toxicol (2006) 19(11): 1426-1434
Differential serum proteomic analysis in a model of metabolic disease
Matsumura T, Suzuki T, Kada N, Aizawa K, Munemasa Y, Nagai R.
Biochem Biophys Res Commun (2006) 351(4): 965-971
Proteomic analysis of isolated membrane fractions from superinvasive cancer cells
Dowling P, Meleady P, Dowd A, Henry M, Glynn S, Clynes M.
Biochim Biophys Acta Early Edition: published 30-Sep-2006
Identification of Novel Citrullinated Autoantigens of Synovium in Rheumatoid Arthritis Using a Proteomic Approach
Matsuo K, Xiang Y, Nakamura H, Masuko K, Yudoh K, Noyori K, Nishioka K, Saito T, Kato T.
Arthritis Res Ther (2006) 8(6): R175
Synergistic effects of retinoic acid and tamoxifen on human breast cancer cells: Proteomic characterization
Wang Y, He QY, Chen H, Chiu JF.
Exp Cell Res Early Edition: published 25-Oct-2006
Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human
Deng SS, Xing TY, Zhou HY, Xiong RH, Lu YG, Wen B, Liu SQ, Yang HJ.
Genomics Proteomics Bioinformatics (2006) 4(3): 165-72
Spots, blots, peaks and chips: proteomic approaches in autoimmune diseases
Dotzlaw H, Eggert M, Neeck G, Schulz M.
Curr Pharm Des (2006) 12(29): 3699-706
Toxicogenomics--A New Systems Toxicology Approach to Understanding of Gene-Environment Interactions
Olden K.
Ann N Y Acad Sci (2006) 1076: 703-706.
Developing a tool for noninvasive monitoring of renal allografts
Stefan Schaub, John A Wilkins, David Rush, Peter Nickerson
Expert Review of Proteomics (2006) 3(5): 497-509
Proteome-based plasma biomarkers for Alzheimer's disease
Hye A, Lynham S, Thambisetty M, Causevic M, Campbell J, Byers HL, Hooper C, Rijsdijk F, Tabrizi SJ, Banner S, Shaw CE, Foy C, Poppe M, Archer N, Hamilton G, Powell J, Brown RG, Sham P, Ward M, Lovestone S.
Brain (2006) 129(Pt 11): 3042-50
Identification of squamous cell carcinoma associated proteins by proteomics and loss of beta tropomyosin expression in esophageal cancer
Jazii FR, Najafi Z, Malekzadeh R, Conrads TP, Ziaee AA, Abnet C, Yazdznbod M, Karkhane AA, Salekdeh GH.
World J Gastroenterol (2006) 12(44): 7104-12
Gastrokine 1 expression in patients with and without Helicobacter pylori infection
Nardone G, Rippa E, Martin G, Rocco A, Siciliano RA, Fiengo A, Cacace G, Malorni A, Budillon G, Arcari P.
Dig Liver Dis Early Edition: published 6-Nov-2006
Dexamethasone Alters Bronchoalveolar Lavage Fluid Proteome in a Mouse Asthma Model
Zhao J, Yeong LH, Wong WS.
Int Arch Allergy Immunol (2006) 142(3): 219-229
Proteomics-Based Approach Identifying Autoantibody against Peroxiredoxin VI as a Novel Serum Marker in Esophageal Squamous Cell Carcinoma
Fujita Y, Nakanishi T, Hiramatsu M, Mabuchi H, Miyamoto Y, Miyamoto A, Shimizu A, Tanigawa N.
Clin Cancer Res (2006) 12(21): 6415-20
Applying proteomic methodologies to analyze the effect of methionine restriction on proliferation of human gastric cancer SGC7901 cells
Xin L, Cao WX, Fei XF, Wang Y, Liu WT, Liu BY, Zhu ZG.
Clin Chim Acta Early Edition: published 7-Oct-2006
Attractin Is Elevated in the Cerebrospinal Fluid of Patients with Malignant Astrocytoma and Mediates Glioma Cell Migration
Khwaja FW, Duke-Cohan JS, Brat DJ, Van Meir EG.
Clin Cancer Res (2006) 12(21): 6331-6336
Proteomics-based identification of biomarkers for predicting sensitivity to a PI3-kinase inhibitor in cancer
Akashi T, Nishimura Y, Wakatabe R, Shiwa M, Yamori T.
Biochem Biophys Res Commun Early Edition: published 20-Nov-2006
SELDI-TOF plasma profiles distinguish individuals in a protein C-deficient family with thrombotic episodes occuring before age 40
Svensson AM, Whiteley GR, Callas PW, Bovill EG.
Thromb Haemost (2006) 96(6): 725-30
The Application of Proteomics and Genomics to the Study of Age-Related Neurodegeneration and Neuroprotection
Weinreb O, Drigues N, Sagi Y, Reznick AZ, Amit T, Youdim MB.
Antioxid Redox Signal Early Edition: published 1-Jan-2007
Urinary markers for prostate cancer
Downes MR, Byrne JC, Pennington SR, Dunn MJ, Fitzpatrick JM, Watson RW.
BJU Int Early Edition: published 1-Dec-2006
Clinical proteomics: an insight into the urinary proteome
Hassan Dihazi
Expert Review of Proteomics (2006) 3(5): 481-482
Differential proteomic profiling to study the mechanism of cardiac pharmacological preconditioning by resveratrol
Bezstarosti K, Das S, Lamers JM, Das DK.
J Cell Mol Med (2006) 10(4): 896-907
Disease Biomarkers in Cerebrospinal Fluid of Patients with First-Onset Psychosis
Huang JT, Leweke FM, Oxley D, Wang L, Harris N, Koethe D, Gerth CW, Nolden BM, Gross S, Schreiber D, Reed B, Bahn S.
PLoS Med Early Edition: published 7-Nov-2006
Urinary bladder tumor markers
Lokeshwar VB, Selzer MG.
Urol Oncol (2006) 24(6): 528-537
Toward the application of proteomics to human thyroid tissue
Krause K, Schierhorn A, Sinz A, Wissmann JD, Beck-Sickinger AG, Paschke R, Fuhrer D.
Thyroid (2006) 16(11): 1131-43
Toxicoproteomics in liver injury and inflammation
Alex Merrick B.
Ann N Y Acad Sci (2006) 1076: 707-17.
Elucidation of a protein signature discriminating six common types of adenocarcinoma
Bloom GC, Eschrich S, Zhou JX, Coppola D, Yeatman TJ.
Int J Cancer Early Edition: published 27-Nov-2006
Discovery and validation of new protein biomarkers for urothelial cancer: A prospective analysis Theodorescu D, Wittke S, Ross MM, Walden M, Conaway M, Just I, Mischak H, Frierson HF, Department of Molecular Physiology, Mellon Prostate Cancer Institute, University of Virginia, Charlottesville, VA
Lotan Y.
Urol Oncol (2006) 24(6): 561-2
Proteomic Analysis of Hypoxia-Induced Responses in the Syncytialization of Human Placental Cell Line BeWo
Hu R, Jin H, Zhou S, Yang P, Li X.
Placenta Early Edition: published 9-Nov-2006
Proteomic Identification of Altered Proteins in Skeletal Muscle During Chronic Potassium Depletion: Implications for Hypokalemic Myopathy
Visith Thongboonkerd, Rattiyaporn Kanlaya, Supachok Sinchaikul, Paisal Parichatikanond, Shui-Tein Chen, and Prida Malasit
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3326-3335
Differential liver protein expression during schistosomiasis
Harvie M, Jordan TW, La Flamme AC.
Infect Immun Early Edition: published 13-Nov-2006
Amniocentesis results and novel proteomic analysis in a case of occult candidal chorioamnionitis
Crawford JT, Pereira L, Buckmaster J, Gravett MG, Tolosa JE.
J Matern Fetal Neonatal Med (2006) 19(10): 667-70
Current status and prospects of clinical proteomics studies on detection of colorectal cancer: Hopes and fears
de Noo ME, Tollenaar RA, Deelder AM, Bouwman LH.
World J Gastroenterol (2006) 12(41): 6594-601
Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs
Aagaard JE, Yi X, Maccoss MJ, Swanson WJ.
Proc Natl Acad Sci U S A Early Edition: published 3-Nov-2006
Rat Neuropeptidomics by LC-MS/MS and MALDI-FTMS: Enhanced Dissection and Extraction Techniques Coupled with 2D RP-RP HPLC
James A. Dowell, William Vander Heyden, and Lingjun Li
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3368-3375
Analysis of the Soluble ATP-Binding Proteome of Plant Mitochondria Identifies New Proteins and Nucleotide Triphosphate Interactions within the Matrix
Jun Ito, Joshua L. Heazlewood, and A. Harvey Millar
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3459-3469
Proteomic and micro-array analyses of the Dictyostelium Zak1-GSK-3 signalling pathway reveals a role in early development
Strmecki L, Bloomfield G, Araki T, Dalton E, Skelton J, Schilde C, Harwood A, Williams JG, Ivens A, Pears C.
Eukaryot Cell Early Edition: published 3-Nov-2006
Proteomic analysis of ovine muscle hypertrophy
Hamelin M, Sayd T, Chambon C, Bouix J, Bibe B, Milenkovic D, Leveziel H, Georges M, Clop A, Marinova P, Laville E.
J Anim Sci (2006) 84(12): 3266-76
The Nuclear Proteome of Chickpea (Cicer arietinum L.) Reveals Predicted and Unexpected Proteins
Aarti Pandey, Mani Kant Choudhary, Deepti Bhushan, Arnab Chattopadhyay, Subhra Chakraborty, Asis Datta, and Niranjan Chakraborty
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3301-3311
Protein-RNA Cross-Linking in the Ribosomes of Yeast under Oxidative Stress
Hamid Mirzaei and Fred Regnier
JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3249-3259
Generation of plant protein microarrays and investigation of antigen-antibody interactions
Kersten B, Feilner T.
Methods Mol Biol (2006) 355: 365-78
Identification of several proteins involved in regulation of sperm motility by proteomic analysis
Zhao C, Huo R, Wang FQ, Lin M, Zhou ZM, Sha JH.
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Proteomic Analysis of Saccharomyces cerevisiae under High Gravity Fermentation Conditions
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The Medicago truncatula Small Protein Proteome and Peptidome
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Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS
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Analysis of the extracellular matrix vesicle proteome in mineralizing osteoblasts
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Isolation and Identification of a Paenibacillus polymyxa Strain That Co-produces a Novel Lantibiotic and Polymyxin
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Systematic Identification of the Subproteome of Escherichia coli Cell Envelope Reveals the Interaction Network of Membrane Proteins and Membrane-Associated Peripheral Proteins
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Quantitative Analysis of Representative Proteome Components and Clustering of Helicobacter pylori Clinical Strains
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Helicobacter (2006) 11(6): 533-43
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BMC Genomics (2006) 7(1): 296
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Global Comparison of the Membrane Subproteomes between a Multidrug-Resistant Acinetobacter baumannii Strain and a Reference Strain
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Proteome and Antigen Profiling of Coxiella burnetii Developmental Forms
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Infect Immun Early Edition: published 6-Nov-2006
Complete and Integrated Pyrene Degradation Pathway in Mycobacterium vanbaalenii PYR-1 Based on Systems Biology
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Regulation of female fertility and identification of future contraceptive targets
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Pharmacoproteomics Study of Cetuximab in Nasopharyngeal Carcinoma
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The use of proteomics in identifying differentially expressed serum proteins in humans with type 2 diabetes
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Glycoproteomics of Trypanosoma cruzi Trypomastigotes Using Subcellular Fractionation, Lectin Affinity, and Stable Isotope Labeling
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Actin deficiency induces cofilin phosphorylation: Proteome analysis of HeLa cells after beta-actin gene silencing
Liu N, Academia K, Rubio T, Wehr T, Yeck T, Jordan L, Hamby K, Paulus A.
Cell Motil Cytoskeleton Early Edition: published 22-Nov-2006
Proteome-wide Profiling of Isoniazid Targets in Mycobacterium tuberculosis
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Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
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J Cell Biol (2006) 175(4): 571-8
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Biochemistry (Mosc) (2006) 71(10): 1060-72
Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors
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Proteomics in Renal Research
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Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors
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Spots, blots, peaks and chips: proteomic approaches in autoimmune diseases
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Phenol extraction of proteins for proteomic studies of recalcitrant plant tissues
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Isolation and subfractionation of plant mitochondria for proteomic analysis
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The blood peptidome: a higher dimesion of information content for cancer biomarker discovery
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Peptide mass fingerprinting: identification of proteins by maldi-tof
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Methods Mol Biol (2006) 355: 219-34
Proteins are specifically altered in disease - really?
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Expert Review of Proteomics (2006) 3(5): 469-470
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Protein microarrays for the diagnosis of allergic diseases: state-of-the-art and future development
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Isolation of Chloroplast Proteins from Arabidopsis thaliana for Proteome Analysis
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Mol Cancer (2006) 5(1): 59
Molecular markers of prostate cancer
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Urol Oncol (2006) 24(6): 538-51
Developing a tool for noninvasive monitoring of renal allografts
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Expert Review of Proteomics (2006) 3(5): 497-509
Developing and evaluating genomics- or proteomics-based diagnostic tests: statistical perspectives
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Current status and prospects of clinical proteomics studies on detection of colorectal cancer: Hopes and fears
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World J Gastroenterol (2006) 12(41): 6594-601
Functional genome and proteome analyses of cutaneous autoimmune diseases
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Quantitative Analysis of 2D Gels
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J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 16-Nov-2006
Proteomic profiling of differentiating osteoblasts
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Protein extraction from xylem and Phloem sap
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Functional proteomic profiling of glycan-processing enzymes
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Proteomics with two-dimensional gel electrophoresis and mass spectrometry analysis in cardiovascular research
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OMICS and brain tumour biomarkers
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Br J Neurosurg (2006) 20(5): 275-80
Proteomic analysis of cytochromes P450: a mass spectrometry approach
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Biochem Soc Trans (2006) 34(Pt 6): 1246-51
Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view?
Kraljevic S, Sedic M, Scott M, Gehrig P, Schlapbach R, Pavelic K.
Cancer Treat Rev Early Edition: published 24-Oct-2006
Clinical proteomics: an insight into the urinary proteome
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Protein kinase inhibition: different approaches to selective inhibitor design
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Plant proteomics and glycosylation
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Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis
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Quantitative Analysis of Complex Peptide Mixtures Using FTMS and Differential Mass Spectrometry
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Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK)
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Nat Methods Early Edition: published 29-Oct-2006
Challenges Related to Analysis of Protein Spot Volumes from Two-Dimensional Gel Electrophoresis As Revealed by Replicate Gels
Harald Grove, Kristin Hollung, Anne Kjersti Uhlen, Harald Martens, and Ellen Mosleth Færgestad
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Separation of acidic and basic proteins by nanoparticle-filled capillary electrophoresis
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Anal Chem (2006) 78(23): 8004-10
Atmospheric molding of ionic copolymer MALDI-TOF/MS arrays: A new tool for protein identification/profiling
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Electrophoresis Early Edition: published 15-Nov-2006
MALDI TOF/TOF Tandem Mass Spectrometry as a New Tool for Amino Acid Analysis
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Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis
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Application of phenylboronic acid modified hydrogel affinity chips for high-throughput mass spectrometric analysis of glycated proteins
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Rapid Commun Mass Spectrom (2006) 21(1): 1-6
Mass spectrometric characterization of low-molecular-mass color pI markers and their use for direct determination of pI value of proteins
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J Mass Spectrom (2006) 41(12): 1570-1577
Prediction of Liquid Chromatographic Retention Times of Peptides Generated by Protease Digestion of the Escherichia coli Proteome Using Artificial Neural Networks
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JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3312-3317
RP-HPLC prefractionation and its application in expressional proteomics analysis of an in vitro viral infection model
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Neural network prediction of peptide separation in strong anion exchange chromatography
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A Clean, More Efficient Method for In-Solution Digestion of Protein Mixtures without Detergent or Urea
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JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3446-3452
High-throughput protein digestion by trypsin-immobilized monolithic silica with pipette-tip formula
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Optimization of microfabricated nanoliter-scale solid-phase extraction device for detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization mass spectrometry
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Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-A Pore Size C18 Sorbents
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Anal Chem (2006) 78(22): 7785-7795
Hexadecanedionic Acid-Sepharose 4B: A New Tool for Preparation of Albumin-Depleted Plasma
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JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3453-3458
Rapid Expression of Functional Genomic Libraries
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JOURNAL OF PROTEOME RESEARCH (2006) 5(12): 3288-3300
Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry
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Protein folding liquid chromatography and its recent developments
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The use of proteomics in identifying differentially expressed serum proteins in humans with type 2 diabetes
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Proteome Science (2006) 4: 22
A New Functional, Chemical Proteomics Technology To Identify Purine Nucleotide Binding Sites in Complex Proteomes
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A Standard Operating Procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis
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SELDI-TOF-MS of saliva: Methodology and pre-treatment effects
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J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 25-Oct-2006
Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics
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J Chromatogr B Analyt Technol Biomed Life Sci Early Edition: published 15-Nov-2006
Mild Protease Treatment as a Small-Scale Biochemical Method for Mitochondria Purification and Proteomic Mapping of Cytoplasm-Exposed Mitochondrial Proteins
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Differential serum proteomic analysis in a model of metabolic disease
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Evaluation of Low Energy CID and ECD Fragmentation Behavior of Mono-Oxidized Thio-Ether Bonds in Peptides
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Homogeneous Silver-Coated Nanoparticle Substrates for Enhanced Fluorescence Detection
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J Phys Chem B Condens Matter Mater Surf Interfaces Biophys (2006) 110(46): 23085-23091
Considerations for proteolytic labeling-optimization of (18)O incorporation and prohibition of back-exchange
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Evaluation of an on-target sample preparation system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in conjunction with normal-flow peptide high-performance liquid chromatography for peptide mass fingerprint analyses
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A Capital Workshop for the HUPO Proteomics Standards Initiative
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Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
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