|
SPS' DigestIssue 52, 18-Jun-2008 |
Cardiovascular GO Annotation Initiative Year 1 Report: Why Cardiovascular GO?
Ruth C. Lovering, Emily Dimmer, Varsha K. Khodiyar, Daniel G. Barrell, Peter Scambler, Mike Hubank, Rolf Apweiler, Philippa J. Talmud
PROTEOMICS (2008) 8(10): 1950-1953
PATIKAmad: Putting microarray data into pathway context
Ozgun Babur, Recep Colak, Emek Demir, Ugur Dogrusoz
PROTEOMICS (2008) 8(11): 2196-2198
Computational methods for protein identification from mass spectrometry data
McHugh L, Arthur JW.
PLoS Comput Biol (2008) 4(2): e12
Integrating clinical, gene expression, protein expression and preanalytical data for in silico cancer research
Rossille D, Burgun A, Pangault-Lorho C, Fest T.
Stud Health Technol Inform (2008) 136: 455-60
Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications
Xiuxia Du, Feng Yang, Nathan P. Manes, David L. Stenoien, Matthew E. Monroe, Joshua N. Adkins, David J. States, Samuel O. Purvine, David G. Camp, II, and Richard D. Smith
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2195-2203
UniProtJAPI: a remote API for accessing UniProt data
Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, and Rolf Apweiler
Bioinformatics (2008) 24(10): 1321-1322; doi:10.1093/bioinformatics/btn122
PARPST: a PARallel algorithm to find peptide sequence tags
Brunetti S, Lodi E, Mori E, Stella M.
BMC Bioinformatics (2008) 9(Suppl 4): S11
Novel approaches to predict the retention of histidine-containing peptides in immobilized metal-affinity chromatography
Hongying Du, Xiaoyun Zhang, Jie Wang, Xiaojun Yao, Zhide Hu
PROTEOMICS (2008) 8(11): 2185-2195
Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor
Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS.
PLoS ONE (2008) 3(5): e2097
Using spectral moments of spiral networks based on PSA/mass spectra outcomes to derive quantitative proteome-disease relationships (QPDRs) and predicting prostate cancer
Ferino G, González-DÃaz H, Delogu G, Podda G, Uriarte E.
Biochem Biophys Res Commun (2008) 372(2): 320-5
Isoform Analysis of LC−MS/MS Data from Multidimensional Fractionation of the Serum Proteome
Alexei L. Krasnoselsky, Vitor M. Faca, Sharon J. Pitteri, Qing Zhang, and Samir M. Hanash
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2546-2552
A review of algorithmic techniques for disulfide-bond determination
Rahul Singh
Brief Funct Genomic Proteomic (2008) 7(2): 157-172; doi:10.1093/bfgp/eln008
MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins
Janosch Hennig, Klaus D. M. Hennig, and Maria Sunnerhagen
Bioinformatics (2008) 24(10): 1310-1312; doi:10.1093/bioinformatics/btn116
Statistical analysis of image data provided by two-dimensional gel electrophoresis for discovery proteomics
Crossett B, Edwards AV, White MY, Cordwell SJ.
Methods Mol Med (2008) 141: 271-85
Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits
Roland A. Pache, Patrick Aloy
PROTEOMICS (2008) 8(10): 1959-1964
Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery
Isserlin R, Emili A.
Curr Opin Mol Ther (2008) 10(3): 231-42
A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
Brick K, Pizzi E.
BMC Bioinformatics (2008) 9(1): 236
MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications
Ishtiaq Ahmad, Wajahat M. Qazi, Ahmed Khurshid, Munir Ahmad, Daniel C. Hoessli, Iffat Khawaja, M. Iqbal Choudhary, Abdul R. Shakoori, Nasir-ud-Din
PROTEOMICS (2008) 8(10): 1954-1958
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M.
Nucl Acids Res Early Edition: published 7-May-2008
A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes
Hu J, Yan C.
Comput Biol Chem Early Edition: published 1-Apr-2008
Cell interaction knowledgebase: an online database for innate immune cells, cytokines and chemokines
Chen S, Chinnaswamy A, Biswas SK, Goryachev AB, Yap CK, Lam KY, Tay CP, Low HS, Pokhilko A, Da-Jun T, Mishra SK.
In Silico Biol (2007) 7(6): 569-74
Using inferred residue contacts to distinguish between correct and incorrect protein models
Miller CS, Eisenberg D.
Bioinformatics Early Edition: published 29-May-2008
FFPred: an integrated feature-based function prediction server for vertebrate proteomes
Lobley AE, Nugent T, Orengo CA, Jones DT.
Nucl Acids Res Early Edition: published 7-May-2008
A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images
Justin Newberg and Robert F. Murphy
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2300-2308
Identification and characterization of microbial proteins using peptide mass fingerprinting strategies
Arthur JW.
Methods Mol Med (2008) 141: 257-70
IMGT((R)), the International ImMunoGeneTics Information System((R) )for Immunoinformatics : Methods for Querying IMGT((R)) Databases, Tools, and Web Resources in the Context of Immunoinformatics
Lefranc MP.
Mol Biotechnol Early Edition: published 8-May-2008
Computational Approaches to Protein-Protein Docking
Lee, Kyoungrim; Lee, Joo-Woon
Current Proteomics (2008) 5(1): 10-19
Proteomic and phosphoproteomic analysis of cellular responses in medaka fish (Oryzias latipes) following oral gavage with microcystin-LR
Mezhoud K, Bauchet AL, Château-Joubert S, Praseuth D, Marie A, François JC, Fontaine JJ, Jaeg JP, Cravedi JP, Puiseux-Dao S, Edery M.
Toxicon Early Edition: published 25-Mar-2008
Proteomic Identification of the Cus System as a Major Determinant of Constitutive Escherichia coli Silver Resistance of Chromosomal Origin
Chun-Nam Lok, Chi-Ming Ho, Rong Chen, Paul Kwong-Hang Tam, Jen-Fu Chiu, and Chi-Ming Che
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2351-2356
Bacillus anthracis Spores Influence ATP Synthase Activity in Murine Macrophages
Seo GM, Jung KH, Kim SJ, Kim JC, Yoon JW, Oh KK, Lee JH, Chai YG.
J Microbiol Biotechnol (2008) 18(4): 778-83
MicroRNA and proteome expression profiling in early-symptomatic ?-synuclein(A30P)-transgenic mice
Frank Gillardon, Matthias Mack, Wolfgang Rist, Cathrin Schnack, Martin Lenter, Tobias Hildebrandt, Bastian Hengerer
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(5): 697-705
Metabolic Action of Thyroid Hormones: Insights from Functional and Proteomic Studies
Silvestri, Elena; Lombardi, Assunta; Lange, Pieter d.; Lanni, Antonia; Goglia, Fernando; Moreno, Maria
Current Proteomics (2008) 5(1): 45-61
Searching for candidate speciation genes using a proteomic approach: seminal proteins in field crickets
Andrés JA, Maroja LS, Harrison RG.
Proc Biol Sci Early Edition: published 21-May-2008
Cysteine proteinases regulate chloroplast protein content and composition in tobacco leaves: a model for dynamic interactions with ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) vesicular bodies
Prins A, van Heerden PD, Olmos E, Kunert KJ, Foyer CH.
J Exp Bot (2008) 59(7): 1935-50
Integrative proteomic analysis of the nucleus accumbens in rhesus monkeys following cocaine self-administration
Tannu NS, Howell LL, Hemby SE.
Mol Psychiatry Early Edition: published 27-May-2008
Proteomic and Metabolomic Analyses of the White-Rot Fungus Phanerochaete chrysosporium Exposed to Exogenous Benzoic Acid
Fumiko Matsuzaki, Motoyuki Shimizu, and Hiroyuki Wariishi
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2342-2350
Chaperone proteins identified from synthetic proteasome inhibitor-induced inclusions in PC12 cells by proteomic analysis
Li X, Zhang Y, Hu Y, Chang M, Liu T, Wang D, Zhang Y, Zhang L, Hu L.
Acta Biochim Biophys Sin (Shanghai) (2008) 40(5): 406-18
Proteome of monocyte priming by lipopolysaccharide, including changes in interleukin 1 beta and leukocyte elastase inhibitor
Pabst MJ, Pabst KM, Handsman DB, Beranova-Giorgianni S, Giorgianni F.
Proteome Science (2008) 6(1): 13
Plastoglobule proteome
Grennan AK.
Plant Physiol (2008) 147(2): 443-5
An evaluation of the basis and consequences of a stay-green mutation in the navel negra (nan) citrus mutant using transcriptomic and proteomic profiling and metabolite analysis
Alos E, Roca M, Iglesias DJ, Minguez-Mosquera MI, Damasceno CM, Thannhauser TW, Rose JK, Talon M, Cercos M.
Plant Physiol Early Edition: published 8-May-2008
Redox proteomics: understanding oxidative stress in the progression of age-related neurodegenerative disorders
Butterfield DA, Sultana R
Expert Rev Proteomics (2008) 5(2): 157-60
Proteomic analyses of Fusarium graminearum grown under mycotoxin-inducing conditions
Rebecca D. Taylor, Audrey Saparno, Barbara Blackwell, Valar Anoop, Steve Gleddie, Nicholas A. Tinker, Linda J. Harris
PROTEOMICS (2008) 8(11): 2256-2265
Global and comparative protein profiles of the pronotum of the southern pine beetle, Dendroctonus frontalis
Pechanova O, Stone WD, Monroe W, Nebeker TE, Klepzig KD, Yuceer C.
Insect Mol Biol (2008) 17(3): 261-77
Different Signaling Pathways Expressed by Chicken Naïve CD4+ T Cells, CD4+ Lymphocytes Activated with Staphylococcal Enterotoxin B, and Those Malignantly Transformed by Marek’s Disease Virus
Joram J. Buza and Shane C. Burgess
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2380-2387
The rat sperm proteome characterized via IPG strip prefractionation and LC-MS/MS identification
Mark A. Baker, Louise Hetherington, Gabi Reeves, Jörg Müller, R. John Aitken
PROTEOMICS (2008) 8(11): 2312-2321
Identification of Genes Associated with Fumonisin Biosynthesis in Fusarium verticillioides via Proteomics and Quantitative Real-Time PCR
Choi YE, Shim WB.
J Microbiol Biotechnol (2008) 18(4): 648-57
Comparative proteomic analysis of brains of naturally aging mice
Yang S, Liu T, Li S, Zhang X, Ding Q, Que H, Yan X, Wei K, Liu S.
Neuroscience Early Edition: published 12-Apr-2008
Analysis of organelles within the nervous system: impact on brain and organelle functions
Tribl F, Meyer HE, Marcus K
Expert Rev Proteomics (2008) 5(2): 333-51
Proteomics in the study of hippocampal plasticity
Cobb SR, Pitt A
Expert Rev Proteomics (2008) 5(3): 393-404
Heat-shock protein-27, -70 and peroxiredoxin-II show molecular chaperone function in sickle red cells: Evidence from transgenic sickle cell mouse model
Andrea Biondani, Franco Turrini, Franco Carta, Alessandro Matté, Alida Filippini, Angela Siciliano, Yves Beuzard, Lucia De Franceschi
PROTEOMICS - CLINICAL APPLICATIONS (2008) 2(5): 706-719
Acid adaptation of Lactobacillus delbrueckii subsp. bulgaricus induces physiological responses at membrane and cytosolic levels that improves cryotolerance
Streit F, Delettre J, Corrieu G, Béal C.
J Appl Microbiol Early Edition: published 21-May-2008
Proteomic response to iron deficiency in tomato root
Jie Li, Xu-Dong Wu, Shan-Ting Hao, Xiu-Jie Wang, Hong-Qing Ling
PROTEOMICS (2008) 8(11): 2299-2311
Identification of Pasteurella multocida CHAPS-soluble outer membrane proteins
Tabatabai LB.
Avian Dis (2008) 52(1): 147-9
HDGF is dephosphorylated during the early steps of endothelial cell apoptosis in a caspase-dependent way
Clermont F, Gonzalez NS, Communi D, Franken S, Dumont JE, Robaye B.
J Cell Biochem Early Edition: published 8-May-2008
Proteomic analysis of miltefosine-resistant Leishmania reveals the possible involvement of eukaryotic initiation factor 4A (eIF4A)
Singh G, Chavan HD, Dey CS.
Int J Antimicrob Agents (2008) 31(6): 584-6
Proteomic analysis in the lichen Physcia adscendens exposed to cadmium stress
Rustichelli C, Visioli G, Kostecka D, Vurro E, Sanità di Toppi L, Marmiroli N.
Environ Pollut Early Edition: published 29-May-2008
Proteomic evolution of a wine yeast during the first hours of fermentation
Salvadó Z, Chiva R, RodrÃguez-Vargas S, Rández-Gil F, Mas A, Guillamón JM.
FEMS Yeast Res Early Edition: published 22-May-2008
Proteomic Analysis of Trypanosoma cruzi Resistance to Benznidazole
Hélida M. Andrade, Silvane M. F. Murta, Alex Chapeaurouge, Jonas Perales, Phillipe Nirdé, and Alvaro J. Romanha
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2357-2367
Proteomic analysis of HuH-7 cells harboring in vitro-transcribed full-length hepatitis C virus 1b RNA
Xun M, Zhao SH, Cao CX, Song J, Shao MM, Chu YL.
Acta Pharmacol Sin (2008) 29(6): 720-7
Cellular proteins in influenza virus particles
Shaw ML, Stone KL, Colangelo CM, Gulcicek EE, Palese P.
PLoS Pathog (2008) 4(6): e1000085
Effects of Coffee Bean Aroma on the Rat Brain Stressed by Sleep Deprivation: A Selected Transcript- and 2D Gel-Based Proteome Analysis
Seo HS, Hirano M, Shibato J, Rakwal R, Hwang IK, Masuo Y.
J Agric Food Chem Early Edition: published 3-Jun-2008
Proteomic Analysis of Neonatal Mouse Brain: Evidence for Hypoxia- and Ischemia-Induced Dephosphorylation of Collapsin Response Mediator Proteins
Yuan Zhou, Inderjeet Bhatia, Zhen Cai, Qing-Yu He, Pik-To Cheung, and Jen-Fu Chiu
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2507-2515
Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris
Sidhu VK, Vorhoelter FJ, Niehaus K, Watt SA.
BMC Microbiol (2008) 8(1): 87
Retroviral proteomics and interactomes: intricate balances of cell survival and viral replication
Van Duyne R, Kehn-Hall K, Klase Z, Easley R, Heydarian M, Saifuddin M, Wu W, Kashanchi F
Expert Rev Proteomics (2008) 5(3): 507-28
A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2
Clokie MR, Thalassinos K, Boulanger P, Slade SE, Stoilova-McPhie S, Cane M, Scrivens JH, Mann NH.
Microbiology (2008) 154(Pt 6): 1775-82
Toponomics and neurotoponomics: a new way to medical systems biology
Schubert W, Bode M, Hillert R, Krusche A, Friedenberger M
Expert Rev Proteomics (2008) 5(2): 361-9
Changes in the proteome of Escherichia coli during growth at 15 degrees C after incubation at 2, 6 or 8 degrees C for 4 days
Jones TH, Johns MW, Gill CO.
Int J Food Microbiol (2008) 124(3): 299-302
Pathogenesis-related proteins in somatic hybrid rice induced by bacterial blight
Yu CL, Yan SP, Wang CC, Hu HT, Sun WN, Yan CQ, Chen JP, Yang L.
Phytochemistry Early Edition: published 3-Jun-2008
Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC - tandem mass spectrometry
Zhao Y, Denner L, Haidacher SJ, Lejeune WS, Tilton RG.
Proteome Science (2008) 6(1): 15
Proteomic Analysis of Mouse Hypothalamus under Simulated Microgravity
Sarkar P, Sarkar S, Ramesh V, Kim H, Barnes S, Kulkarni A, Hall JC, Wilson BL, Thomas RL, Pellis NR, Ramesh GT.
Neurochem Res Early Edition: published 13-May-2008
The up-regulation of 14-3-3 proteins in Smad4 deficient epidermis and hair follicles at catagen
Cunzhong Yuan, Liyan Jiao, Leilei Yang, Wantao Ying, Zhishang Hu, Jinfeng Liu, Fang Cui, Lei Li, Linyi Qian, Yan Teng, Haiying Hang, Xiaohong Qian, Xiao Yang
PROTEOMICS (2008) 8(11): 2230-2243
Altered protein expression in neutrophils of calves treated with dexamethasone
Beveridge JD, Mitchell GB, Brewer D, Clark ME, Caswell JL.
Can J Vet Res (2008) 72(3): 249-52
Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and low-P tolerant mutant reveal root characteristics associated with P-efficiency
Li K, Xu C, Li Z, Zhang K, Yang A, Zhang J.
Plant J Early Edition: published 19-May-2008
Biochemical characterization of membrane-associated septin from rat brain
Maimaitiyiming M, Kumanogoh H, Nakamura S, Nagata KI, Suzaki T, Maekawa S.
J Neurochem Early Edition: published 3-May-2008
Tissue imaging using MALDI-MS: a new frontier of histopathology proteomics
Fournier I, Wisztorski M, Salzet M
Expert Rev Proteomics (2008) 5(3): 413-24
Synapse proteomics: current status and quantitative applications
Li KW, Jimenez CR
Expert Rev Proteomics (2008) 5(2): 353-60
Dachshund inhibits oncogene-induced breast cancer cellular migration and invasion through suppression of interleukin-8
Wu K, Katiyar S, Li A, Liu M, Ju X, Popov VM, Jiao X, Lisanti MP, Casola A, Pestell RG.
Proc Natl Acad Sci U S A (2008) 105(19): 6924-9
Proteomic analysis of proteins associated with body mass and length in yellow perch, Perca flavescens
John Mark Reddish, Normand St-Pierre, Andy Nichols, Kari Green-Church, Macdonald Wick
PROTEOMICS (2008) 8(11): 2333-2343
Temporal Profiling of the Chromatin Proteome Reveals System-wide Responses to Replication Inhibition
Khoudoli GA, Gillespie PJ, Stewart G, Andersen JS, Swedlow JR, Blow JJ.
Curr Biol (2008) 18(11): 838-43
A proteomic approach for evaluating the cell response to a novel histone deacetylase inhibitor in colon cancer cells
Milli A, Cecconi D, Campostrini N, Timperio AM, Zolla L, Righetti SC, Zunino F, Perego P, Benedetti V, Gatti L, Odreman F, Vindigni A, Righetti PG.
Biochim Biophys Acta Early Edition: published 4-May-2008
Developmental changes in the milk fat globule membrane proteome during the transition from colostrum to milk
Reinhardt TA, Lippolis JD.
J Dairy Sci (2008) 91(6): 2307-18
Multidimensional advancement of neuroproteomics
Veenstra TD, Marcus K
Expert Rev Proteomics (2008) 5(2): 149-51
A Metabonomic and Proteomic Analysis of Changes in IMCD3 Cells Chronically Adapted to Hypertonicity
Klawitter J, Rivard CJ, Brown LM, Capasso JM, Almeida NE, Maunsbach AB, Pihakaski-Maunsbach K, Berl T, Leibfritz D, Christians U, Chan L.
Nephron Physiol (2008) 109(1): p1-p10
Proteomic analysis of phosphoproteins regulated by abscisic acid in rice leaves
He H, Li J.
Biochem Biophys Res Commun (2008) 371(4): 883-8
Critical dependence of blood-borne biomarker concentrations on the half-lives of their carrier proteins
Araujo RP, Petricoin EF, Liotta LA.
J Theor Biol Early Edition: published 18-Apr-2008
Snake Venomics and Antivenomics of the Arboreal Neotropical Pitvipers Bothriechis lateralis and Bothriechis schlegelii
Bruno Lomonte, José Escolano, Julián Fernández, Libia Sanz, Yamileth Angulo, José María Gutiérrez, and Juan J. Calvete
JOURNAL OF PROTEOME RESEARCH (2008) 7(06): 2445-2457
A Proteomic Comparison of Immature and Mature Gonadotrophs in Mice Reveals Novel Differentially Expressed Nuclear Proteins That Regulate Gonadotropin Gene Transcription and RNA Splicing
Feng J, Lawson MA, Melamed P.
Biol Reprod Early Edition: published 14-May-2008
Structure and Dynamics of Photosystem II Light-Harvesting Complex Revealed by High-Resolution FTICR Mass Spectrometric Proteome Analysis
Galetskiy D, Susnea I, Reiser V, Adamska I, Przybylski M.
J Am Soc Mass Spectrom Early Edition: published 4-Apr-2008
Proteomic identification of novel proteins associated with Lewy bodies
Xia Q, Liao L, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J.
Front Biosci (2008) 13: 3850-6.
Proteomic changes in rat hippocampus and adrenals following short-term sleep deprivation
Poirrier JE, Guillonneau F, Renaut J, Sergeant K, Luxen A, Maquet P, Leprince P.
Proteome Science (2008) 6(1): 14
NK Cell Protease Granzyme M Targets {alpha}-Tubulin and Disorganizes the Microtubule Network
Bovenschen N, de Koning PJ, Quadir R, Broekhuizen R, Damen JM, Froelich CJ, Slijper M, Kummer JA.
J Immunol (2008) 180(12): 8184-91
Clozapine causes oxidation of proteins involved in energy metabolism: a possible mechanism for antipsychotic-induced metabolic alterations
Walss-Bass C, Weintraub ST, Hatch J, Mintz J, Chaudhuri AR.
Int J Neuropsychopharmacol Early Edition: published 9-May-2008
Identification and distribution of thioredoxin-like 2 as the antigen for the monoclonal antibody MC3 specific to colorectal cancer
Yuanyuan Lu, Xin Wang, Zhenxiong Liu, Bin Jin, Dake Chu, Huihong Zhai, Faming Zhang, Kai Li, Gui Ren, Antonio Miranda-Vizuete, Xuegang Guo, Daiming Fan
PROTEOMICS (2008) 8(11): 2220-2229