SPS' Digest

Issue 18, 4-May-2005

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Quick jumps to articles in: Bioinformatics (31) / Biological applications (14) / Biomedical and clinical applications (24) / Eukaryotic Cells And Tissues (15) / Prokaryotes (4) / Pharmacology and Toxicology (2) / Protein Characterization - PTMs (4) / Protein-protein interaction (4) / Quantitation (2) / Review (18) / Methodology (31) / Meeting (1) / Other (6) /

In this issue, 154 articles have been selected from:

Am J Pharmacogenomics, Volume 5, Issue 2, 2005 (1 article)
Am J Physiol Cell Physiol, Volume 288, Issue 5, 2005 (1 article)
Am J Physiol Endocrinol Metab, Early Edition, 12-Apr-2005 (1 article)
Amino Acids, Volume 28, Issue 1, 2005 (2 articles)
Anal Biochem, Volume 340, Issue 2, 2005 (1 article)
Anal Chem, Volume 77, Issues 8+9, 2005 (4 articles)
Appl Environ Microbiol, Volume 71, Issue 4, 2005 (1 article)
Appl Microbiol Biotechnol, Early Edition, 26-Apr-2005 (1 article)
BMC Bioinformatics, Volume 6, Issue 1, 2005 (2 articles)
Biochim Biophys Acta, Volume 1749, Issue 1, 2005 (1 article)
Bioinformatics, Early Edition, 7-Apr-2005 (1 article)
Bioinformatics, Volume 21, Issues 8+9, 2005 (9 articles)
Brain Res Brain Res Rev, Volume 48, Issue 2, 2005 (1 article)
Brief Funct Genomic Proteomic, Volume 3, Issue 4, 2005 (2 articles)
Cancer Res, Volume 65, Issue 8, 2005 (1 article)
Clin Chem, Early Edition, 21-Apr-2005 (1 article)
Clin Colorectal Cancer, Volume 4, Issue 6, 2005 (1 article)
Curr Atheroscler Rep, Volume 7, Issue 3, 2005 (1 article)
Curr Drug Metab, Volume 6, Issue 2, 2005 (1 article)
Curr Genet, Early Edition, 27-Apr-2005 (1 article)
Curr Opin Biotechnol, Volume 16, Issue 2, 2005 (1 article)
Curr Opin Plant Biol, Volume 8, Issue 3, 2005 (1 article)
Curr Opin Urol, Volume 15, Issue 3, 2005 (1 article)
Current Proteomics, Volume 1, Issue 4, 2004 (2 articles)
Current Proteomics, Volume 2, Issue 1, 2005 (2 articles)
Dev Dyn, Early Edition, 27-Apr-2005 (1 article)
Electrophoresis, Volume 26, Issue 7-8, 2005 (4 articles)
Eukaryot Cell, Volume 4, Issue 4, 2005 (1 article)
Eur J Cell Biol, Volume 84, Issue 2-3, 2005 (1 article)
Expert Rev Mol Diagn, Volume 5, Issue 2, 2005 (1 article)
FASEB J, Early Edition, 14-Apr-2005->27-Apr-2005 (2 articles)
Genome Biology, Volume 6, 2005 (1 article)
Infect Immun, Volume 73, Issue 5, 2005 (1 article)
Int J Mol Med, Volume 15, Issue 5, 2005 (1 article)
Int J Radiat Oncol Biol Phys, Volume 61, Issue 5, 2005 (1 article)
J Alzheimers Dis, Volume 7, Issue 2, 2005 (1 article)
J Am Chem Soc, Volume 127, Issue 14, 2005 (1 article)
J Am Soc Mass Spectrom, Volume 16, Issue 1, 2005 (1 article)
J Bioinform Comput Biol, Volume 3, Issue 2, 2005 (1 article)
J Biol Chem, Early Edition, 25-Apr-2005->26-Apr-2005 (2 articles)
J Biol Chem, Volume 280, Issue 15, 2005 (1 article)
J Chromatogr A, Volume 1067, Issue 1-2, 2005 (1 article)
J Immunother, Volume 28, Issue 3, 2005 (1 article)
J Mass Spectrom, Volume 40, Issues 4+5, 2005 (4 articles)
J Orthop Sci, Volume 10, Issue 2, 2005 (1 article)
J Perinat Med, Volume 33, Issue 1, 2005 (1 article)
J Proteome Res, Early Edition, 04/22/2005->04/29/2005 (9 articles)
J Proteome Res, Volume 4, Issue 2, 2005 (42 articles)
Lecture Notes in Computer Science, Volume 3380, 2005 (1 article)
Methods Enzymol, Volume 394, 2005 (1 article)
Nat Biotechnol, Early Edition, 17-Apr-2005 (1 article)
Nat Biotechnol, Volume 23, Issue 4, 2005 (1 article)
Neuroreport, Volume 16, Issue 6, 2005 (1 article)
Nucl Acids Res, Volume 33, Issue 8, 2005 (1 article)
Oncogene, Early Edition, 25-Apr-2005 (1 article)
Pharmacogenomics J, Early Edition, 26-Apr-2005 (1 article)
Proc IEEE Comput Soc Bioinform Conf, Volume 1, 2002 (1 article)
Proc Natl Acad Sci U S A, Volume 102, Issues 15+17, 2005 (2 articles)
Proteins, Early Edition, 22-Apr-2005 (1 article)
Proteomics, Early Edition, 19-Apr-2005 (1 article)
Proteomics, Volume 5, Issue 6, 2005 (16 articles)
Rapid Commun Mass Spectrom, Volume 19, Issues 9+10, 2005 (2 articles)
Sci STKE, Volume 2005, Issue 281, 2005 (1 article)
Trends Pharmacol Sci, Volume 26, Issue 4, 2005 (1 article)

Disclaimer: The selection and categorisation reflect the views and understandings of contributors (i.e. SPS members).

Quick jumps to articles in: Bioinformatics (31) / Biological applications (14) / Biomedical and clinical applications (24) / Eukaryotic Cells And Tissues (15) / Prokaryotes (4) / Pharmacology and Toxicology (2) / Protein Characterization - PTMs (4) / Protein-protein interaction (4) / Quantitation (2) / Review (18) / Methodology (31) / Meeting (1) / Other (6) /

Bioinformatics

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry
Li D, Fu Y, Sun R, Ling CX, Wei Y, Zhou H, Zeng R, Yang Q, He S, Gao W
Bioinformatics Early Edition: published 7-Apr-2005

DBDigger: Reorganized Proteomic Database Identification That Improves Flexibility and Speed
Tabb DL, Narasimhan C, Strader MB, Hettich RL
Anal Chem (2005) 77(8): 2464-2474

Accelerating approximate subsequence search on large protein sequence databases
Yang J, Wang W, Xia Y, Yu PS
Proc IEEE Comput Soc Bioinform Conf (2002) 1: 207-16

Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis
Meunier B, Bouley J, Piec I, Bernard C, Picard B, Hocquette JF
Anal Biochem (2005) 340(2): 226-30

Online Predicted Human Interaction Database
Kevin R. Brown and Igor Jurisica
Bioinformatics (2005) 21(9): 2076-2082

MPSS: an integrated database system for surveying a set of proteins
Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Bo-Shu Liu, Jin-Miao Wang, Yi-Xue Li, and Yang Zhong
Bioinformatics (2005) 21(9): 2142-2143

AGML Central: web based gel proteomic infrastructure
Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, and Jonas S. Almeida
Bioinformatics (2005) 21(9): 1754-1757

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
Garrow AG, Agnew A, Westhead DR
BMC Bioinformatics (2005) 6(1): 56

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, and Ryuji Kobayashi
Bioinformatics (2005) 21(9): 1764-1775

PROTEIOS: an open source proteomics initiative
Per Garden, Rikard Alm, and Jari Hakkinen
Bioinformatics (2005) 21(9): 2085-2087

SpecAlign--processing and alignment of mass spectra datasets
Jason W.H. Wong, Gerard Cagney, and Hugh M. Cartwright
Bioinformatics (2005) 21(9): 2088-2090

Identification of GPI anchor attachment signals by a Kohonen self-organizing map
Niklaus Fankhauser and Pascal Maser
Bioinformatics (2005) 21(9): 1846-1852

An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
Robel Y. Kahsay, Guang Gao, and Li Liao
Bioinformatics (2005) 21(9): 1853-1858

Assessing Data Quality of Peptide Mass Spectra Obtained by Quadrupole Ion Trap Mass Spectrometry
Ming Xu , Lewis Y. Geer , Stephen H. Bryant , Jeri S. Roth , Jeffrey A. Kowalak , Dawn M. Maynard , and Sanford P. Markey
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 300-305

P-Mod: An Algorithm and Software To Map Modifications To Peptide Sequences Using Tandem MS Data
Beau T. Hansen, Sean W. Davey, Amy-Joan L. Ham, and Daniel C. Liebler
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 358-368

Protein Identification in Complex Mixtures
Jan Eriksson and David Fenyö
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 387-393

Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm
Brian C. Searle, Surendra Dasari, Phillip A. Wilmarth, Mark Turner, Ashok P. Reddy, Larry L. David, and Srinivasa R. Nagalla
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 546-554

Prediction of Peptide Retention at Different HPLC Conditions from Multiple Linear Regression Models
Tomasz B czek, Pawe Wiczling, Micha Marsza , Yvan Vander Heyden, and Roman Kaliszan
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 555-563

GPSDB: a new database for synonyms expansion of gene and protein names
Violaine Pillet, Marc Zehnder, Alexander K. Seewald, Anne-Lise Veuthey, and Johann Petrak
Bioinformatics (2005) 21(8): 1743-1744

SVM-based method for subcellular localization of human proteins using amino acid compositions, their order and similarity search
Garg A, Bhasin M, Raghava GP
J Biol Chem (2005) 280(15): 14427-14432

Algorithm for accurate similarity measurements of peptide mass fingerprints and its application
Monigatti F, Berndt P
J Am Soc Mass Spectrom (2005) 16(1): 13-21

Ontological visualization of protein-protein interactions
Harold J Drabkin, Christopher Hollenbeck, David P Hill and Judith A Blake
BMC Bioinformatics (2005) 6: 29

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories
Manuel Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David Juan and Alfonso Valencia
Lecture Notes in Computer Science (2005) 3380: 1-13

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
Arun K Ramani , Razvan C Bunescu , Raymond J Mooney and Edward M Marcotte
Genome Biology (2005) 6: R40

Domain Graph of Arabidopsis Proteome by Comparative Analysis
Song Liu, Chi Zhang, and Yaoqi Zhou
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 435-444

Clinical and Pharmacogenomic Data Mining: 3. Zeta Theory As a General Tactic for Clinical Bioinformatics
Barry Robson
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 445-455

MultiProtIdent: Identifying Proteins Using Database Search and Protein-Protein Interactions
Hsien-Da Huang, Tzong-Yi Lee, Li-Cheng Wu, Feng-Mao Lin, Hsueh-Fen Juan, Jorng-Tzong Horng, and Ann-Ping Tsou
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/08/2005

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals
Nakao M, Barrero RA, Mukai Y, Motono C, Suwa M, Nakai K
Nucl Acids Res (2005) 33(8): 2355-63

Bayesian network analysis of signaling networks: a primer
Pe'er D
Sci STKE (2005) 2005(281): pl4

The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry
Fridman T, Razumovskaya J, Verberkmoes N, Hurst G, Protopopescu V, Xu Y
J Bioinform Comput Biol (2005) 3(2): 455-76

CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data
Giuseppe Raucci, Meri Gabrielli, Sabrina Novelli, Gianluca Picariello, Stephen H. Collins
Journal of Mass Spectrometry (2005) 40(4): 475-488

Biological applications

Differential display of proteins involved in the neural differentiation of mouse embryonic carcinoma P19 cells by comparative proteomic analysis
Jie An, Quan Yuan, Chen Wang, Li Liu, Ke Tang, Hong-yu Tian, Nai-he Jing, Fu-kun Zhao
PROTEOMICS (2005) 5(6): 1656-1668

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform
Mark E. Weeks, John Sinclair, Richard J. Jacob, Malcolm J. Saxton, Susan Kirby, James Jones, Michael D. Waterfield, Rainer Cramer, John F. Timms
PROTEOMICS (2005) 5(6): 1669-1685

Proteomic analysis on insulin signaling in human hematopoietic cells: identification of CLIC1 and SRp20 as novel downstream effectors of insulin
Saeki K, Yasugi E, Okuma E, Breit SN, Nakamura M, Toda T, Kaburagi Y, Yuo A
Am J Physiol Endocrinol Metab Early Edition: published 12-Apr-2005

Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry
Shen Hu, Yongming Xie, Prasanna Ramachandran, Rachel R. Ogorzalek Loo, Yang Li, Joseph A. Loo, David T. Wong
PROTEOMICS (2005) 5(6): 1714-1728

A Proteomic Approach To Analyze Auxin- and Zinc-Responsive Protein in Rice
Guangxiao Yang, Akihiko Inoue, Hironori Takasaki, Hisatoshi Kaku, Shoichiro Akao, and Setsuko Komatsu
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 456-463

Predicted Roles for Hypothetical Proteins in the Low-Temperature Expressed Proteome of the Antarctic Archaeon Methanococcoides burtonii
Neil F. W. Saunders, Amber Goodchild, Mark Raftery, Michael Guilhaus, Paul M. G. Curmi, and Ricardo Cavicchioli
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 464-472

Cold Adaptation of the Antarctic Archaeon, Methanococcoides burtonii Assessed by Proteomics Using ICAT
Amber Goodchild, Mark Raftery, Neil F. W. Saunders, Michael Guilhaus, and Ricardo Cavicchioli
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 473-480

Human Plasma Proteome Analysis by Multidimensional Chromatography Prefractionation and Linear Ion Trap Mass Spectrometry Identification
Wen-Hai Jin, Jie Dai, Su-Jun Li, Qi-Chang Xia, Han-Fa Zou, and Rong Zeng
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 613-619

Use of two-dimensional gel electrophoresis to differentiate morphospecies of Alexandrium minutum, a paralytic shellfish poisoning toxin-producing dinoflagellate of harmful algal blooms
Leo Lai Chan, Ivor John Hodgkiss, Paul Kwan-Sing Lam, Jennifer Man-Fan Wan, Hong-Nong Chou, John Hon-Kei Lum, Maria Gar-Yee Lo, Abby Sin-Chi Mak, Wai-Hung Sit, Samuel Chun-Lap Lo
PROTEOMICS (2005) 5(6): 1580-1593

Analysis of the Dorsal Spinal Cord Synaptic Architecture by Combined Proteome Analysis and in Situ Hybridization
Mathias Dreger, # Joanna Mika, Annette Bieller, Ricarda Jahnel, Clemens Gillen, Martin K. H. Schaefer, Eberhard Weihe, and Ferdinand Hucho
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 238-249

Morphinome - proteome of the nervous system after morphine treatment
A. Bodzon-Kulakowska, A. Bierczynska-Krzysik, A. Drabik, M. Noga, A. Kraj, P. Suder, J. Silberring
Amino Acids (2005) 28(1): 13-19

Developmental changes in the metabolic protein profiles of wheat endosperm
William H. Vensel, Charlene K. Tanaka, Nick Cai, Joshua H. Wong, Bob B. Buchanan, William J. Hurkman
PROTEOMICS (2005) 5(6): 1594-1611

Effect of High Density Lipoproteins on Protein Expression in Myoblast Cell Lines
Nikolina Babic, Craig Beeson, and Norman J. Dovichi
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 344-348

Maspin alters the carcinoma proteome
Chen EI, Florens L, Axelrod FT, Monosov E, Barbas Iii CF, Yates Iii JR, Felding-Habermann B, Smith JW
FASEB J Early Edition: published 27-Apr-2005

Biomedical and clinical applications

The antiapoptotic effect of fibroblast growth factor-2 is mediated through nuclear factor-kappaB activation induced via interaction between Akt and IkappaB kinase-beta in breast cancer cells
Vandermoere F, El Yazidi-Belkoura I, Adriaenssens E, Lemoine J, Hondermarck H
Oncogene Early Edition: published 25-Apr-2005

Distinct proteomic profiles of amphetamine self-administration transitional states
Freeman WM, Brebner K, Amara SG, Reed MS, Pohl J, Phillips AG
Pharmacogenomics J Early Edition: published 26-Apr-2005

Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease
Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q, Aebersold RH, Montine TJ
J Alzheimers Dis (2005) 7(2): 125-33

Alteration of cancer pain-related signals by radiation: Proteomic analysis in an animal model with cancer bone invasion
Park HC, Seong J, An JH, Kim J, Kim UJ, Lee BW
Int J Radiat Oncol Biol Phys (2005) 61(5): 1523-34

Analysis of cerebellum proteomics in the hydrocephalic H-Tx rat
Li X, Miyajima M, Mineki R, Taka H, Murayama K, Arai H
Neuroreport (2005) 16(6): 571-574

Techniques: Application of systems biology to absorption, distribution, metabolism, excretion and toxicity
Ekins S, Nikolsky Y, Nikolskaya T
Trends Pharmacol Sci (2005) 26(4): 202-9

Proteomic approaches in colon cancer: promising tools for new cancer markers and drug target discovery
Alessandro R, Belluco C, Kohn EC
Clin Colorectal Cancer (2005) 4(6): 396-402

Transcript and proteome analysis reveals reduced expression of calgranulins in head and neck squamous cell carcinoma
Roesch Ely M, Nees M, Karsai S, Magele I, Bogumil R, Vorderwulbecke S, Ruess A, Dietz A, Schnolzer M, Bosch FX
Eur J Cell Biol (2005) 84(2-3): 431-44

Microarray and Proteomics Analyses of Human Intestinal Epithelial Cells Treated with the Aeromonas hydrophila Cytotoxic Enterotoxin
Galindo CL, Fadl AA, Sha J, Pillai L, Gutierrez C Jr, Chopra AK
Infect Immun (2005) 73(5): 2628-43

Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease
Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L
Cancer Res (2005) 65(8): 3081-91

Application of Isotope Coded Affinity Tag (ICAT) Analysis for the Identification of Differentially Expressed Proteins Following Infection of Atlantic Salmon (Salmo salar) with Infectious Hematopoietic Necrosis Virus (IHNV) or Renibacterium salmoninarum (BKD)
A. T. Booy, J. D. Haddow, L. B. Ohlund, D. B. Hardie, and R. W. Olafson
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 325-334

Proteomic Characterization of Rat Liver Exposed to 2,3,7,8-Tetrachlorobenzo-p-dioxin
Sung-Han Lee, Do-Youn Lee, Won-Kyu Son, Won-A Joo, and Chan-Wha Kim
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 335-343

Discovery of biomarkers in human urine and cerebrospinal fluid by capillary electrophoresis coupled to mass spectrometry: Towards new diagnostic and therapeutic approaches
Stefan Wittke, Harald Mischak, Michael Walden, Walter Kolch, Thomas Rädler, Klaus Wiedemann
ELECTROPHORESIS (2005) 26(7-8): 1476-1487

Depletion of High-Abundant Proteins in Body Fluids Prior to Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Margareta Ramström, Charlotte Hagman, Jennifer K. Mitchell, Peter J. Derrick, Per Håkansson, and Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 410-416

Proteomic analysis of progressive factors in uterine cervical cancer
Yoon Pyo Choi, Suki Kang, Sunghee Hong, Xianhe Xie, Nam Hoon Cho
PROTEOMICS (2005) 5(6): 1481-1493

Post-translational processing of beta-secretase in Alzheimer's disease
Christina Sidera, Richard Parsons, Brian Austen
PROTEOMICS (2005) 5(6): 1533-1543

Proteomic identification of human neutrophil alpha-defensins in chronic lung allograft rejection
Gary L. Nelsestuen, Michael B. Martinez, Marshall I. Hertz, Kay Savik, Christine H. Wendt
PROTEOMICS (2005) 5(6): 1705-1713

Proteomic Analysis of Serum Cytokine Levels in Response to Highly Active Antiretroviral Therapy (HAART)
Karen I. Relucio, Hans T. Beernink, Donna Chen, Dennis M. Israelski, Raymond Kim, and Mark Holodniy #
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 227-231

Search for Cancer Markers from Endometrial Tissues Using Differentially Labeled Tags iTRAQ and cICAT with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry
Leroi DeSouza, Georg Diehl, Mary Joe Rodrigues, Jingzhong Guo, Alexander D. Romaschin, Terence J. Colgan, and K. W. Michael Siu
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 377-386

Identification of the Thrombin Light Chain A as the Single Best Mass for Differentiation of Gastric Cancer Patients from Individuals with Dyspepsia by Proteome Analysis
Matthias P. A. Ebert, Stephanie Lamer, Jörn Meuer, Peter Malfertheiner, Marc Reymond, Thomas Buschmann, Christoph Röcken, and Volker Seibert
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 586-590

Genistein Reverses Changes of the Proteome Induced by Oxidized-LDL in EA·hy 926 Human Endothelial Cells
Dagmar Fuchs, Petra Erhard, Rufus Turner, Gerald Rimbach, Hannelore Daniel, and Uwe Wenzel
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 369-376

Proteome Analysis of Antiproliferative Mechanism of 12-O-Tetradecanoylphorbol 13-Acetate on Cultured Nasopharyngeal Carcinoma CNE2 Cells
Peizhou Jiang, Ming Gan, Hua Huang, Xinming Shen, Shuang Wang, and Kaitai Yao
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 599-605

Diagnostic Potential of Tear Proteomic Patterns in Sjögren's Syndrome
Naohisa Tomosugi, Kazuko Kitagawa, Nobuo Takahashi, Susumu Sugai, and Isao Ishikawa
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/08/2005

Proteomic analysis of urine in patients with intestinal segments transposed into the urinary tract
Ghulam Nabi, James N'Dow, Tahseen S. Hasan, Ian R. Booth, Phil Cash
PROTEOMICS (2005) 5(6): 1729-1733

Eukaryotic Cells And Tissues

Proteomic analysis of the proteins expressed by hydrogen peroxide treated cultured human dermal microvascular endothelial cells
Moon Kyung Ha, Kee Yang Chung, Dongsik Bang, Yoon Kee Park, Kwang Hoon Lee
PROTEOMICS (2005) 5(6): 1507-1519

The human brain mannose 6-phosphate glycoproteome: A complex mixture composed of multiple isoforms of many soluble lysosomal proteins
David E. Sleat, Henry Lackland, Yanhong Wang, Istvan Sohar, Gang Xiao, Hong Li, Peter Lobel
PROTEOMICS (2005) 5(6): 1520-1532

Comparative proteomic analysis identifies protein disulfide isomerase and peroxiredoxin 1 as new players involved in embryonic interdigital cell death
Shan SW, Tang MK, Cai DQ, Chui YL, Chow PH, Grotewold L, Lee KK
Dev Dyn Early Edition: published 27-Apr-2005

Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism
Lafaye A, Junot C, Pereira Y, Lagniel G, Tabet JC, Ezan E, Labarre J
J Biol Chem Early Edition: published 26-Apr-2005

Proteomic analysis of protein nitration in aging skeletal muscle and identification of nitrotyrosine-containing sequences in vivo by nanoelectrospray ionization tandem mass spectrometry
Kanski J, Hong SJ, Schoneich C
J Biol Chem Early Edition: published 25-Apr-2005

The wheat (Triticum aestivum L.) leaf proteome
Bryna E. Donnelly, Robin D. Madden, Patricia Ayoubi, David R. Porter, Jack W. Dillwith
PROTEOMICS (2005) 5(6): 1624-1633

Differential proteome analysis of aging in rat skeletal muscle
Piec I, Listrat A, Alliot J, Chambon C, Taylor RG, Bechet D
FASEB J Early Edition: published 14-Apr-2005

Proteomic Analysis of Phagocytosis in the Enteric Protozoan Parasite Entamoeba histolytica
Okada M, Huston CD, Mann BJ, Petri WA Jr, Kita K, Nozaki T
Eukaryot Cell (2005) 4(4): 827-31

Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards
Ishihama Y, Sato T, Tabata T, Miyamoto N, Sagane K, Nagasu T, Oda Y
Nat Biotechnol Early Edition: published 17-Apr-2005

Proteomic Profiling of Erythrocyte Proteins by Proteolytic Digestion Chip and Identification Using Two-dimensional Electrospray Ionization Tandem Mass Spectrometry
Yu-Chang Tyan, Shiang-Bin Jong, Jiunn-Der Liao, Pao-Chi Liao, Ming-Hui Yang, Chia-Yuan Liu, Ruth Klauser, # Michael Himmelhaus, and Michael Grunze
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/22/2005

Metabolic Labeling of Human Primary Retinal Pigment Epithelial Cells for Accurate Comparative Proteomics
Yetrib Hathout, Jessica Flippin, Chenguang Fan, Pinghu Liu, and Karl Csaky
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 620-627

Phosphoproteomic Analysis of Synaptosomes from Human Cerebral Cortex
Joseph A. DeGiorgis, Howard Jaffe, Jorge E. Moreira, Carlos G. Carlotti Jr., João P. Leite, # Harish C. Pant, and Ayse Dosemeci
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 306-315

The first two-dimensional reference map of the fission yeast, Schizosaccharomyces pombe proteins
Namkyu Sun, Jaewon Jang, Seunghee Lee, Sunkyung Kim, Seunghyun Lee, Kwang-Lae Hoe, Kyung-Sook Chung, Dong-Uk Kim, Hyang-Sook Yoo, Misun Won, Kyung Bin Song
PROTEOMICS (2005) 5(6): 1574-1579

Quantitative Proteomic Analysis of the Secretory Proteins from Rat Adipose Cells Using a 2D Liquid Chromatography-MS/MS Approach
Xiaoli Chen, Samuel W. Cushman, Lewis K. Pannell, and Sonja Hess
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 570-577

Protein Profiling of Human Pancreatic Islets by Two-Dimensional Gel Electrophoresis and Mass Spectrometry
Meftun Ahmed, Jens Forsberg, and Peter Bergsten
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/29/2005

Prokaryotes

Effect of Biofilm Model, Mode of Growth, and Strain on Streptococcus mutans Protein Expression as Determined by Two-Dimensional Difference Gel Electrophoresis
Suzanne B. I. Luppens and Jacob M. ten Cate
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 232-237

Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species
Matthias Trost, Dirk Wehmhöner, Uwe Kärst, Guido Dieterich, Jürgen Wehland, Lothar Jänsch
PROTEOMICS (2005) 5(6): 1544-1557

Shotgun proteomic analysis of Chlamydia trachomatis
Paul Skipp, Jo Robinson, C. David O'Connor, Ian N. Clarke
PROTEOMICS (2005) 5(6): 1558-1573

Proteome Analysis of Membrane and Cell Wall Associated Proteins from Staphylococcus aureus
Renu Nandakumar, M. P. Nandakumar, Mark R. Marten, and Julia M. Ross
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 250-257

Pharmacology and Toxicology

Proteomic Analysis of Lipid Microdomains from Lipopolysaccharide-Activated Human Endothelial Cells
Aly Karsan, Josip Blonder, Jennifer Law, Elisa Yaquian, David A. Lucas, Thomas P. Conrads, and Timothy Veenstra
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 349-357

Proteomic Profiling of Surface Proteins on Th1 and Th2 Cells
Kelly M. Loyet, Wenjun Ouyang, Dan L. Eaton, and John T. Stults
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 400-409

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Protein Characterization / PTMs

Posttranslational processing of mouse and human BMP-15: Potential implication in the determination of ovulation quota
Osamu Hashimoto, R. Kelly Moore, and Shunichi Shimasaki
PNAS (2005) 102(15): 5426-5431

Application of metal-chelate affinity chromatography to the study of the phosphoproteome
N. Imam-Sghiouar, R. Joubert-Caron, M. Caron
Amino Acids (2005) 28(1): 105-109

Mapping Sites of Protein Phosphorylation by Mass Spectrometry Utilizing a Chemical-Enzymatic Approach: Characterization of Products from -S1Casein Phosphopeptides
Daniel J. McCormick, ^, Michael W. Holmes, David C. Muddiman, and Benjamin J. Madden
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 424-434

A new approach for sequencing human IRS1 phosphotyrosine-containing peptides using CapLC-Q-TOFmicro
Xiao-Ming Lu, Mary Y. Lu, Alan J. Fischman, Ronald G. Tompkins
Journal of Mass Spectrometry (2005) 40(5): 599-607

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Protein-protein interaction

Proteomic analysis of complexes formed by human topoisomerase I
Czubaty A, Girstun A, Kowalska-Loth B, Trzcinska AM, Purta E, Winczura A, Grajkowski W, Staron K
Biochim Biophys Acta (2005) 1749(1): 133-41

Scanning the human proteome for calmodulin-binding proteins
Xinchun Shen, C. Alexander Valencia, Jack Szostak, Biao Dong, and Rihe Liu
PNAS (2005) 102(17): 5969-5974

Ontological visualization of protein-protein interactions
Harold J Drabkin, Christopher Hollenbeck, David P Hill and Judith A Blake
BMC Bioinformatics (2005) 6: 29

Simple Protein Complex Purification and Identification Method for High-Throughput Mapping of Protein Interaction Networks
Lye Meng Markillie, Chiann-Tso Lin, Joshua N. Adkins, Deanna L. Auberry, Eric A. Hill, Brian S. Hooker, Priscilla A. Moore, Ronald J. Moore, Liang Shi, H. Steven Wiley, and Vladimir Kery
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 268-274

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Quantitation

Assessing Reproducibility of a Protein Dynamics Study Using in Vivo Labeling and Liquid Chromatography Tandem Mass Spectrometry
Molina H, Parmigiani G, Pandey A
Anal Chem (2005) 77(9): 2739-2744

Quantitative Profiling of the Detergent-Resistant Membrane Proteome of Iota-b Toxin Induced Vero Cells
Josip Blonder, Martha L. Hale, King C. Chan, Li-Rong Yu, David A. Lucas, Thomas P. Conrads, Ming Zhou, Michel R. Popoff, Haleem J. Issaq, Bradley G. Stiles, and Timothy D. Veenstra
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 523-531

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Review

Proteomics in prostate cancer
Banez LL, Srivastava S, Moul JW
Curr Opin Urol (2005) 15(3): 151-6

Metabolomics, genomics, proteomics, and the identification of enzymes and their substrates and products
Fridman E, Pichersky E
Curr Opin Plant Biol (2005) 8(3): 242-8

The use of genetically modified Saccharomyces cerevisiae strains in the wine industry
Schuller D, Casal M
Appl Microbiol Biotechnol Early Edition: published 26-Apr-2005

In vitro methods to study chemically-induced hepatotoxicity: a literature review
Farkas D, Tannenbaum SR
Curr Drug Metab (2005) 6(2): 111-25

From proteomics to biomarker discovery in Alzheimer's disease
Ho L, Sharma N, Blackman L, Festa E, Reddy G, Pasinetti GM
Brain Res Brain Res Rev (2005) 48(2): 360-9

Difference Gel Electrophoresis: Application in Quantitative Proteomics Research
Deb N. Chakravarti; Sean Gallagher; Bulbul Chakravarti
Current Proteomics (2004) 1(4): 261-271

Advanced Capillary and Microchip Electrophoretic Techniques for Proteomics
Huan-Tsung Changa; Yu-Fen Huanga; Shin-Huei Chiou; Tai-Chia Chiu; Ming-Mu Hsieh
Current Proteomics (2004) 1(4): 325-347

Drug Discovery Using Yeast as a Model System: A Functional Genomic and Proteomic View
Auerbach Daniel; Arnoldo Anthony; Bogdan Boris; Fetchko Michael; Stagljar Igor
Current Proteomics (2005) 2(1): 1-13

The Application of Proteomics in Neurology
Tsuji Teruyuki; Shiozaki Aiko; Shimohama Shun
Current Proteomics (2005) 2(1): 41-53

Combining capillary electrophoresis with mass spectrometry for applications in proteomics
David C. Simpson, Richard D. Smith
ELECTROPHORESIS (2005) 26(7-8): 1291-1305

Pathway proteomics: global and focused approaches
Marko-Varga G
Am J Pharmacogenomics (2005) 5(2): 113-22

Nitrosylation of thiols in vascular homeostasis and disease
Martinez-Ruiz A, Lamas S
Curr Atheroscler Rep (2005) 7(3): 213-8

Laser-assisted microdissection, techniques and applications in pathology (Review)
Okuducu AF, Hahne JC, Von Deimling A, Wernert N
Int J Mol Med (2005) 15(5): 763-9

Peptides in body fluids and tissues as markers of disease
Schulte I, Tammen H, Selle H, Schulz-Knappe P
Expert Rev Mol Diagn (2005) 5(2): 145-57

Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry
Ishihama Y
J Chromatogr A (2005) 1067(1-2): 73-83

Global approach to perinatal medicine: functional genomics and proteomics
Kralj M, Kraljevic S, Sedic M, Kurjak A, Pavelic K
J Perinat Med (2005) 33(1): 5-16

Advancing Cancer Biotherapy with Proteomics
Stroncek DF, Burns C, Martin BM, Rossi L, Marincola FM, Panelli MC
J Immunother (2005) 28(3): 183-192

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories
Manuel Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David Juan and Alfonso Valencia
Lecture Notes in Computer Science (2005) 3380: 1-13

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Methodology

Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments
Xinping Li, Matthias Wilm, Thomas Franz
PROTEOMICS (2005) 5(6): 1460-1471

Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease
Arora PS, Yamagiwa H, Srivastava A, Bolander ME, Sarkar G
J Orthop Sci (2005) 10(2): 160-6

Fast, comprehensive two-dimensional HPLC separation of tryptic peptides based on high-temperature HPLC
Stoll DR, Carr PW
J Am Chem Soc (2005) 127(14): 5034-5

Robotic cloning and protein production platform of the northeast structural genomics consortium
Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GV, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT
Methods Enzymol (2005) 394: 210-43

The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales
Hu Jianhua; Coombes Kevin R.; Morris Jeffrey S.; Baggerly Keith A
Briefings in Functional Genomics and Proteomics (2005) 3(4): 322-331

The dynamics of the proteome: Strategies for measuring protein turnover on a proteome-wide scale
Beynon Robert J
Briefings in Functional Genomics and Proteomics (2005) 3(4): 382-390

Protein profiling by capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry
Feng Zhou, Murray V. Johnston
ELECTROPHORESIS (2005) 26(7-8): 1383-1388

An automated, sheathless capillary electrophoresis-mass spectrometry platform for discovery of biomarkers in human serum
Alexander P. Sassi, Frank Andel III, Hans-Marcus L. Bitter, Michael P.S. Brown, Robert G. Chapman, Jeraldine Espiritu, Alfred C. Greenquist, Isabelle Guyon, Mariana Horchi-Alegre, Kathy L. Stults, Ann Wainright, Jonathan C. Heller, John T. Stults
ELECTROPHORESIS (2005) 26(7-8): 1500-1512

Affinity chromatographic selection of carbonylated proteins followed by identification of oxidation sites using tandem mass spectrometry
Mirzaei H, Regnier F
Anal Chem (2005) 77(8): 2386-92

High-Speed, High-Resolution Monolithic Capillary LC-MALDI MS Using an Off-Line Continuous Deposition Interface for Proteomic Analysis
Chen HS, Rejtar T, Andreev V, Moskovets E, Karger BL
Anal Chem (2005) 77(8): 2323-31

Evaluation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry proteomic profiling: identification of alpha 2-HS glycoprotein B-chain as a biomarker of diet
Mitchell BL, Yasui Y, Lampe JW, Gafken PR, Lampe PD
Proteomics Early Edition: published 19-Apr-2005

Standardized Approach to Proteome Profiling of Human Serum Based on Magnetic Bead Separation and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Baumann S, Ceglarek U, Fiedler GM, Lembcke J, Leichtle A, Thiery J
Clin Chem Early Edition: published 21-Apr-2005

Replaceable Cross-Linked Polyacrylamide for High Performance Separation of Proteins
Joann J. Lu, Shaorong Liu, and Qiaosheng Pu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/22/2005

Differential Detergent Fractionation for Non-electrophoretic Eukaryote Cell Proteomics
Fiona M. McCarthy, Shane C. Burgess, Bart H. J. van den Berg, Marek D. Koter, and G. Todd Pharr
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 316-324

Identification of degradation products formed during performic oxidation of peptides and proteins by high-performance liquid chromatography with matrix-assisted laser desorption/ionization and tandem mass spectrometry
Jingquan Dai, Yangjun Zhang, Jinglan Wang, Xiaohai Li, Zhuang Lu, Yun Cai, Xiaohong Qian
Rapid Communications in Mass Spectrometry (2005) 19(9): 1130-1138

Denaturation of metalloproteins with EDTA to facilitate enzymatic digestion and mass fingerprinting
Dariusz J. Janecki, James P. Reilly
Rapid Communications in Mass Spectrometry (2005) 19(10): 1268-1272

Trypsin-Based Monolithic Bioreactor Coupled On-Line with LC/MS/MS System for Protein Digestion and Variant Identification in Standard Solutions and Serum Samples
Enrica Calleri, Caterina Temporini, Eleonora Perani, Antonella De Palma, Dieter Lubda, Giorgio Mellerio, Alberto Sala, Monica Galliano, Gabriele Caccialanza, and Gabriella Massolini
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 481-490

Proteolytic 18O Labeling by Peptidyl-Lys Metalloendopeptidase for Comparative Proteomics
K. C. Sekhar Rao, Ryan T. Carruth, and Masaru Miyagi
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 507-514

Novel Approach for Peptide Quantitation and Sequencing Based on 15N and 13C Metabolic Labeling
Ambrosius P. L. Snijders, Marjon G. J. de Vos, and Phillip C. Wright
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 578-585

Reproducibility of Tryptic Digestion Investigated by Quantitative Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Charlotte Hagman, Margareta Ramström, Maria Jansson, Peter James, Per Håkansson, and Jonas Bergquist
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 394-399

SCAPE: A New Tool for the Selective CApture of PEptides in Protein Identification
Lazaro Betancourt, Jeovanis Gil, Vladimir Besada, Luis J. González, Jorge Fernández-de-Cossio, Liudy García, Rolando Pajón, Aniel Sanchez, Félix Alvarez, and Gabriel Padrón
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 491-496

Analysis of Shotgun Proteomics and RNA Profiling Data from Arabidopsis thaliana Chloroplasts
Sacha Baginsky, Torsten Kleffmann, Anne von Zychlinski, and Wilhelm Gruissem
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 637-640

Direct MS/MS Analysis of Proteins Blotted on Membranes by a Matrix-Assisted Laser Desorption/Ionization-Quadrupole Ion Trap-Time-of-Flight Tandem Mass Spectrometer
Tsuyoshi Nakanishi, Iwao Ohtsu, Masaru Furuta, Eiji Ando, and Osamu Nishimura
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/08/2005

Proteomic Characterization of A Triton-Insoluble Fraction from Chloroplasts Defines A Novel Group of Proteins Associated with Macromolecular Structures
Brett S. Phinney and Jay J. Thelen
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 497-506

Nanoliter Sample Handling Combined with Microspot MALDI-MS for Detection of Gel-Separated Phosphoproteins
Jacek Stupak, Huaizhi Liu, Zhengping Wang, Brenda J. Brix, Larry Fliegel, and Liang Li
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 515-522

High Resolution "Ultra Performance" Liquid Chromatography Coupled to oa-TOF Mass Spectrometry as a Tool for Differential Metabolic Pathway Profiling in Functional Genomic Studies
Ian D. Wilson, Jeremy K. Nicholson, Jose Castro-Perez, Jennifer H. Granger, Kelly A. Johnson, Brian W. Smith, and Robert S. Plumb
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 591-598

Statistical design of experiments as a tool in mass spectrometry
Leah S. Riter, Olga Vitek, Karen M. Gooding, Barry D. Hodge, Randall K. Julian Jr
Journal of Mass Spectrometry (2005) 40(5): 565-579

Global Proteome Discovery Using an Online Three-Dimensional LC-MS/MS
Jing Wei, Jun Sun, Wen Yu, Arianna Jones, Paul Oeller, Martin Keller, Gary Woodnutt, and Jay Short
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/08/2005

Robust Method for Proteome Analysis by MS/MS Using an Entire Translated Genome: Demonstration on the Ciliome of Tetrahymena thermophila
Jeffrey C. Smith, Julian G. B. Northey, Jyoti Garg, Ronald E. Pearlman, and K. W. Michael Siu
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/15/2005

Correcting Common Errors in Identifying Cancer-Specific Serum Peptide Signatures
Josep Villanueva, John Philip, Carlos A. Chaparro, Yongbiao Li, Ricardo Toledo-Crow, Lin DeNoyer, Martin Fleisher, Richard J. Robbins, # and Paul Tempst
JOURNAL OF PROTEOME RESEARCH Early Edition: published 04/15/2005

Targeted biomarker detection via whole protein ion trap tandem mass spectrometry: thymosin ?4 in a human lung cancer cell line
Fang Yan, Min He, Jason M. Hogan, Sandra S. Rossie, Scott A. McLuckey
Journal of Mass Spectrometry (2005) 40(4): 444-451

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Meeting

Meeting News: Report from the NIH Standards in Proteomics Workshop
Katie Cottingham
JOURNAL OF PROTEOME RESEARCH (2005) 4(2): 220

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Other

Proteomic response of the biological control fungus Trichoderma atroviride to growth on the cell walls of Rhizoctonia solani
Grinyer J, Hunt S, McKay M, Herbert BR, Nevalainen H
Curr Genet Early Edition: published 27-Apr-2005

Universal biases in protein composition of model prokaryotes
Pascal G, Medigue C, Danchin A
Proteins Early Edition: published 22-Apr-2005

Proteomic Profiling of Recombinant Escherichia coli in High-Cell-Density Fermentations for Improved Production of an Antibody Fragment Biopharmaceutical
Aldor IS, Krawitz DC, Forrest W, Chen C, Nishihara JC, Joly JC, Champion KM
Appl Environ Microbiol (2005) 71(4): 1717-28

Functional ingredient production: application of global metabolic models
Smid EJ, Molenaar D, Hugenholtz J, Vos WM, Teusink B
Curr Opin Biotechnol (2005) 16(2): 190-7

The end of "naive reductionism": rise of systems biology or renaissance of physiology?
Strange K
Am J Physiol Cell Physiol (2005) 288(5): C968-74

New on the market: Bioinformatics
Nat Biotechnol (2005) 23(4): 493

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