-
1
-
-
0003206867
-
Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry
-
Adkins,J.N. et al. (2002) Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell Proteomics, 1, 947-955.
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 947-955
-
-
Adkins, J.N.1
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
3
-
-
0001644020
-
The human plasma proteome: History, character, and diagnostic prospects
-
Anderson,N.L. and Anderson,N.G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 1, 845-867.
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 845-867
-
-
Anderson, N.L.1
Anderson, N.G.2
-
4
-
-
0011542799
-
The Pfam protein families database
-
Bateman,A. et al. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 276-280
-
-
Bateman, A.1
-
5
-
-
25444441166
-
Prediction of twin-arginine signal peptides
-
Bendtsen,J.D. et al. (2005) Prediction of twin-arginine signal peptides. BMC Biomformatics, 6, 167.
-
(2005)
BMC Biomformatics
, vol.6
, pp. 167
-
-
Bendtsen, J.D.1
-
6
-
-
24744435534
-
Kernel methods for predicting protein-protein interactions
-
Ben-Hur,A. and Noble,W.S. (2005) Kernel methods for predicting protein-protein interactions. Biomformatics, 21 (Suppl. 1), i38-i46.
-
(2005)
Biomformatics
, vol.21
, Issue.SUPPL. 1
-
-
Ben-Hur, A.1
Noble, W.S.2
-
7
-
-
2542458612
-
Classification of nuclear receptors based on amino acid composition and dipeptide composition
-
Bhasin,M. and Raghava,G.P. (2004) Classification of nuclear receptors based on amino acid composition and dipeptide composition. J. Biol. Chem., 279, 23262-23266.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 23262-23266
-
-
Bhasin, M.1
Raghava, G.P.2
-
8
-
-
33748510186
-
The sweet side of biomarker discovery
-
Bosques,C.J. et al. (2006) The sweet side of biomarker discovery. Nat. Biotechnol., 24, 1100-1101.
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 1100-1101
-
-
Bosques, C.J.1
-
9
-
-
33751326131
-
Molecular markers of prostate cancer
-
Bradford,T.J. et al. (2006) Molecular markers of prostate cancer. Urol. Oncol., 24, 538-551.
-
(2006)
Urol. Oncol
, vol.24
, pp. 538-551
-
-
Bradford, T.J.1
-
10
-
-
0032053823
-
The unique physiology of solid tumors: Opportunities (and problems) for cancer therapy
-
Brown,J.M. and Giaccia,A.J. (1998) The unique physiology of solid tumors: Opportunities (and problems) for cancer therapy. Cancer Res. 58, 1408-1416.
-
(1998)
Cancer Res
, vol.58
, pp. 1408-1416
-
-
Brown, J.M.1
Giaccia, A.J.2
-
11
-
-
0035477337
-
Secreted and cell surface genes expressed in benign and malignant colorectal tumors
-
Buckhaults,P. et al. (2001) Secreted and cell surface genes expressed in benign and malignant colorectal tumors. Cancer Res., 61, 6996-7001.
-
(2001)
Cancer Res
, vol.61
, pp. 6996-7001
-
-
Buckhaults, P.1
-
12
-
-
0034740222
-
Drug design by machine learning: Support vector machines for pharmaceutical data analysis
-
Burbidge,R. et al. (2001) Drug design by machine learning: Support vector machines for pharmaceutical data analysis. Comput. Chem., 26, 5-14.
-
(2001)
Comput. Chem
, vol.26
, pp. 5-14
-
-
Burbidge, R.1
-
13
-
-
0042622243
-
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
-
Cai,C.Z. et al. (2003) SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res., 31, 3692-3697.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3692-3697
-
-
Cai, C.Z.1
-
14
-
-
13444269483
-
SPD - a web-based secreted protein database
-
Chen,Y. et al. (2005) SPD - a web-based secreted protein database. Nucleic Acids Res., 33, D169-D173.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Chen, Y.1
-
15
-
-
33748199236
-
Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties
-
Cui,J. et al. (2007a) Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Mol. Immunol., 44, 514-520.
-
(2007)
Mol. Immunol
, vol.44
, pp. 514-520
-
-
Cui, J.1
-
16
-
-
34249291647
-
Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology
-
Cui,J. et al. (2007b) Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology. Curr. Bioinformatics, 2, 95-112.
-
(2007)
Curr. Bioinformatics
, vol.2
, pp. 95-112
-
-
Cui, J.1
-
17
-
-
3943099373
-
Structural insights into the signal recognition particle
-
Doudna,J.A. and Batey,R.T. (2004) Structural insights into the signal recognition particle. Annu. Rev. Biochem., 73, 539-557.
-
(2004)
Annu. Rev. Biochem
, vol.73
, pp. 539-557
-
-
Doudna, J.A.1
Batey, R.T.2
-
18
-
-
0029047319
-
Prediction of protein folding class using global description of amino acid sequence
-
Dubchak,I. et al. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc. Natl Acad. Sci. USA 92, 8700-8704.
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 8700-8704
-
-
Dubchak, I.1
-
19
-
-
0029946575
-
Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods
-
Eisenhaber,F. et al. (1996) Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins, 25, 157-168.
-
(1996)
Proteins
, vol.25
, pp. 157-168
-
-
Eisenhaber, F.1
-
20
-
-
0033781978
-
Prediction of membrane protein types based on the hydrophobic index of amino acids
-
Feng,Z.P. and Zhang,C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. J. Protein Chem., 19, 269-275.
-
(2000)
J. Protein Chem
, vol.19
, pp. 269-275
-
-
Feng, Z.P.1
Zhang, C.T.2
-
21
-
-
33747375161
-
pTARGET: A web server for predicting protein subcellular localization
-
Guda,C. (2006) pTARGET: A web server for predicting protein subcellular localization. Nucleic Acids Res., 34, W210-W213.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Guda, C.1
-
22
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan,D. and Weinberg,R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
-
(2000)
Cell
, vol.100
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
23
-
-
34547560275
-
WoLF PSORT: Protein localization predictor
-
Horton,P. et al. (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res., 35, W585-W587.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Horton, P.1
-
24
-
-
0035957531
-
A novel method ofprotein secondary structure prediction with high segment overlap measure: Support vector machine approach
-
Hua,S. and Sun,Z. (2001) A novel method ofprotein secondary structure prediction with high segment overlap measure: Support vector machine approach. J. Mol. Biol., 308, 397-407.
-
(2001)
J. Mol. Biol
, vol.308
, pp. 397-407
-
-
Hua, S.1
Sun, Z.2
-
25
-
-
34247170626
-
Proteomics-based identification of secreted protein dihydrodiol dehydrogenase as a novel serum markers of non-small cell lung cancer
-
Huang,L.J. et al. (2006) Proteomics-based identification of secreted protein dihydrodiol dehydrogenase as a novel serum markers of non-small cell lung cancer. Lung Cancer, 54, 87-94.
-
(2006)
Lung Cancer
, vol.54
, pp. 87-94
-
-
Huang, L.J.1
-
26
-
-
0000545946
-
Improvements to Platt's SMO algorithm for SVM classifier design
-
Keerthi,S.S. et al. (2001) Improvements to Platt's SMO algorithm for SVM classifier design. Neural Comput., 13, 637-649.
-
(2001)
Neural Comput
, vol.13
, pp. 637-649
-
-
Keerthi, S.S.1
-
27
-
-
0037012469
-
Osteopontin as a potential diagnostic biomarker for ovarian cancer
-
Kim,J.H. et al. (2002) Osteopontin as a potential diagnostic biomarker for ovarian cancer. J. Am. Med. Assoc., 287, 1671-1679.
-
(2002)
J. Am. Med. Assoc
, vol.287
, pp. 1671-1679
-
-
Kim, J.H.1
-
28
-
-
19944425959
-
Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells
-
Kim,J.M. et al. (2005) Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells. Clin. Cancer Res., 11, 473-482.
-
(2005)
Clin. Cancer Res
, vol.11
, pp. 473-482
-
-
Kim, J.M.1
-
29
-
-
0035987843
-
Synthesis of factor D by gastric cancer-derived cell lines
-
Kitano,E. and Kitamura,H. (2002) Synthesis of factor D by gastric cancer-derived cell lines. Int. Immunopharmacol., 2, 843-848.
-
(2002)
Int. Immunopharmacol
, vol.2
, pp. 843-848
-
-
Kitano, E.1
Kitamura, H.2
-
30
-
-
33847274230
-
Computational classification of classically secreted proteins
-
Klee,E.W. and Sosa,C.P. (2007) Computational classification of classically secreted proteins. Drug Discov. Today, 12, 234-240.
-
(2007)
Drug Discov. Today
, vol.12
, pp. 234-240
-
-
Klee, E.W.1
Sosa, C.P.2
-
31
-
-
40249103182
-
Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis
-
Lo,K.C. et al. (2008) Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis. Lung Cancer, 59 315-331.
-
(2008)
Lung Cancer
, vol.59
, pp. 315-331
-
-
Lo, K.C.1
-
32
-
-
0036630603
-
Areas beneath the relative operating characteristics (ROC) and levels (ROL) curves: Statistical significance and interpretation
-
Mason,S.J. and Graham,N.E. (2002) Areas beneath the relative operating characteristics (ROC) and levels (ROL) curves: Statistical significance and interpretation. Q. J. Roy. Meteorol. Soc., 128, 2145-2166.
-
(2002)
Q. J. Roy. Meteorol. Soc
, vol.128
, pp. 2145-2166
-
-
Mason, S.J.1
Graham, N.E.2
-
33
-
-
0033738137
-
A comparison of signal sequence prediction methods using a test set of signal peptides
-
Menne,K.M. et al. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics, 16, 741-742.
-
(2000)
Bioinformatics
, vol.16
, pp. 741-742
-
-
Menne, K.M.1
-
34
-
-
0035802183
-
Prostasin, a potential serum marker for ovarian cancer: Identification through microarray technology
-
Mok,S.C. et al. (2001) Prostasin, a potential serum marker for ovarian cancer: Identification through microarray technology. J. Natl Cancer Inst., 93, 1458-1464.
-
(2001)
J. Natl Cancer Inst
, vol.93
, pp. 1458-1464
-
-
Mok, S.C.1
-
35
-
-
0036677029
-
Predicting protein cellular localization using a domain projection method
-
Moft,R. et al. (2002) Predicting protein cellular localization using a domain projection method. Genome Res., 12, 1168-1174.
-
(2002)
Genome Res
, vol.12
, pp. 1168-1174
-
-
Moft, R.1
-
36
-
-
16244398103
-
Mimicking cellular sorting improves prediction of subeellular localization
-
Nair,R. and Rost,B. (2005) Mimicking cellular sorting improves prediction of subeellular localization. J. Mol. Biol., 348, 85-100.
-
(2005)
J. Mol. Biol
, vol.348
, pp. 85-100
-
-
Nair, R.1
Rost, B.2
-
37
-
-
23944492134
-
Overview of the HUPO plasma proteome project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
-
Omenn,G.S. et al. (2005) Overview of the HUPO plasma proteome project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics, 5, 3226-3245.
-
(2005)
Proteomics
, vol.5
, pp. 3226-3245
-
-
Omenn, G.S.1
-
38
-
-
29144523534
-
A human transporter protein that mediates the final excretion step for toxic organic cations
-
Otsuka,M. et al. (2005) A human transporter protein that mediates the final excretion step for toxic organic cations. Proc. Natl Acad. Sci. USA, 102, 17923-17928.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 17923-17928
-
-
Otsuka, M.1
-
39
-
-
34547217974
-
Biomarker discovery from uveal melanoma secretomes: Identification of gp100 and cathepsin D in patient serum
-
Pardo,M. et al. (2007) Biomarker discovery from uveal melanoma secretomes: Identification of gp100 and cathepsin D in patient serum. J. Proteome Res., 6, 2802-2811.
-
(2007)
J. Proteome Res
, vol.6
, pp. 2802-2811
-
-
Pardo, M.1
-
40
-
-
12444339443
-
The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins
-
Pieper,R. et al. (2003) The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics, 3, 1345-1364.
-
(2003)
Proteomics
, vol.3
, pp. 1345-1364
-
-
Pieper, R.1
-
41
-
-
0003120218
-
Fast training of support vector machines using sequential minimal optimization
-
MIT Press, Cambridge, MA, USA, pp
-
Platt,J.C. (1999) Fast training of support vector machines using sequential minimal optimization. In Advances in Kernel Methods: Support Vector Learning. MIT Press, Cambridge, MA, USA, pp. 185-208.
-
(1999)
Advances in Kernel Methods: Support Vector Learning
, pp. 185-208
-
-
Platt, J.C.1
-
42
-
-
0027997161
-
The DEF database of sequence based protein fold class predictions
-
Reczko,M. and Bohr,H. (1994) The DEF database of sequence based protein fold class predictions. Nucleic Acids Res., 22, 3616-3619.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3616-3619
-
-
Reczko, M.1
Bohr, H.2
-
43
-
-
0037387176
-
Use of serological proteomic methods to find biomarkers associated with breast cancer
-
Rui,Z. et al. (2003) Use of serological proteomic methods to find biomarkers associated with breast cancer. Proteomics, 3, 433-439.
-
(2003)
Proteomics
, vol.3
, pp. 433-439
-
-
Rui, Z.1
-
44
-
-
0002652573
-
Peptidomics technologies for human body fluids
-
Schrader,M. and Schulz-Knappe,P. (2001) Peptidomics technologies for human body fluids. Trends Biotechnol., 19, S55-S60.
-
(2001)
Trends Biotechnol
, vol.19
-
-
Schrader, M.1
Schulz-Knappe, P.2
-
45
-
-
35748966976
-
Protein solubility: Sequence based prediction and experimental verification
-
Smialowski,R et al. (2007) Protein solubility: Sequence based prediction and experimental verification. Bioinformatics, 23 2536-2542.
-
(2007)
Bioinformatics
, vol.23
, pp. 2536-2542
-
-
Smialowski, R.1
-
46
-
-
0021958679
-
Autocrine growth factors and cancer
-
Sporn,M.B. and Roberts,A.B. (1985) Autocrine growth factors and cancer. Nature, 313, 745-747.
-
(1985)
Nature
, vol.313
, pp. 745-747
-
-
Sporn, M.B.1
Roberts, A.B.2
-
47
-
-
35448970604
-
Protein subcellular localization prediction based on compartment-specific features and structure conservation
-
Su,E.C. et al. (2007) Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics, 8, 330.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 330
-
-
Su, E.C.1
-
48
-
-
35448932757
-
Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation
-
Tang,Z.Q. et al. (2007) Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation. Cancer Res. 67, 9996-10003.
-
(2007)
Cancer Res
, vol.67
, pp. 9996-10003
-
-
Tang, Z.Q.1
-
49
-
-
37349103372
-
TATPred: A Bayesian method for the identification of twin arginine translocation pathway signal sequences
-
Taylor,P.D. et al. (2006) TATPred: A Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation, 1, 184-187.
-
(2006)
Bioinformation
, vol.1
, pp. 184-187
-
-
Taylor, P.D.1
-
50
-
-
0033818171
-
Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome
-
Tjalsma,H. et al. (2000) Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome. Microbiol. Mol. Biol. Rev., 64, 515-547.
-
(2000)
Microbiol. Mol. Biol. Rev
, vol.64
, pp. 515-547
-
-
Tjalsma, H.1
-
51
-
-
0037250739
-
Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinoma
-
Unwin,R.D. et al. (2003) Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinoma. Proteomics, 3, 45-55.
-
(2003)
Proteomics
, vol.3
, pp. 45-55
-
-
Unwin, R.D.1
-
52
-
-
0035970050
-
Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer
-
Welsh,J.B. et al. (2001) Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc. Natl Acad. Sci. USA, 98, 1176-118l.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
-
-
Welsh, J.B.1
-
53
-
-
0037452997
-
Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum
-
Welsh,J.B. et al. (2003) Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc. Natl Acad. Sci. USA, 100, 3410-3415.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 3410-3415
-
-
Welsh, J.B.1
|