-
2
-
-
34250713877
-
Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures
-
Baker,E.S. et al. (2007) Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures. J. Amer. Soc. Mass Spectrom., 18, 1176-1187.
-
(2007)
J. Amer. Soc. Mass Spectrom.
, vol.18
, pp. 1176-1187
-
-
Baker, E.S.1
-
3
-
-
76149102921
-
An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies
-
Baker,E.S. et al. (2009) An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res., 9, 997-1006.
-
(2009)
J. Proteome Res.
, vol.9
, pp. 997-1006
-
-
Baker, E.S.1
-
4
-
-
0035023445
-
Predicting protein-protein interactions from primary structure
-
Bock,J.R. and Gough,D.A. (2001) Predicting protein-protein interactions from primary structure. Bioinformatics, 17, 455-460.
-
(2001)
Bioinformatics
, vol.17
, pp. 455-460
-
-
Bock, J.R.1
Gough, D.A.2
-
5
-
-
0032555696
-
Prediction of local structure in proteins using a library of sequence-structure motifs
-
Bystroff,C. and Baker,D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 565-577
-
-
Bystroff, C.1
Baker, D.2
-
6
-
-
77954187780
-
-
LIBSVM: a library for support vector machines. Available at (last accessed date May 14, 2010)
-
Chang,C.-C. and Lin,C.-J. (2001) LIBSVM: a library for support vector machines. Available at http://www.csie.ntu.edu.tw/~cjlin/libsvm (last accessed date May 14, 2010).
-
(2001)
-
-
Chang, C.-C.1
Lin, C.-J.2
-
7
-
-
0346250790
-
Practical selection of SVM parameters and noise estimation for SVM regression
-
Cherkassky,V. and Ma,Y. (2004) Practical selection of SVM parameters and noise estimation for SVM regression. Neural Netw., 17, 113-126.
-
(2004)
Neural Netw.
, vol.17
, pp. 113-126
-
-
Cherkassky, V.1
Ma, Y.2
-
8
-
-
0000929505
-
The hydrophobic moment detects periodicity in protein hydrophobicity
-
Eisenberg,D. et al. (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl Acad. Sci. USA, 81, 140-144.
-
(1984)
Proc. Natl Acad. Sci. USA
, vol.81
, pp. 140-144
-
-
Eisenberg, D.1
-
9
-
-
67649666679
-
SubCellProt: predicting subcellular localization using machine learning approaches
-
Garg,P. et al. (2009) SubCellProt: predicting subcellular localization using machine learning approaches. In Silico Biol., 9, 35-44.
-
(2009)
In Silico Biol.
, vol.9
, pp. 35-44
-
-
Garg, P.1
-
11
-
-
34548567232
-
POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
-
Hirose,S. et al. (2007) POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics, 23, 2046-2053.
-
(2007)
Bioinformatics
, vol.23
, pp. 2046-2053
-
-
Hirose, S.1
-
12
-
-
0033556190
-
ESI/Ion Trap/Ion Mobility/Time-of-Flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures
-
Henderson,S.C. et al. (1998) ESI/Ion Trap/Ion Mobility/Time-of-Flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures. Anal. Chem., 71, 291-301.
-
(1998)
Anal. Chem.
, vol.71
, pp. 291-301
-
-
Henderson, S.C.1
-
13
-
-
0002161961
-
Application of ridge analysis to regression problems
-
Hoerl,A.E. (1962) Application of ridge analysis to regression problems. Chem. Eng. Prog., 58, 54-59.
-
(1962)
Chem. Eng. Prog.
, vol.58
, pp. 54-59
-
-
Hoerl, A.E.1
-
14
-
-
0020623947
-
A computer program for predicting protein antigenic determinants
-
Hopp,T.P. and Woods,K.R. (1983) A computer program for predicting protein antigenic determinants. Mol. Immunol., 20, 483-489.
-
(1983)
Mol. Immunol.
, vol.20
, pp. 483-489
-
-
Hopp, T.P.1
Woods, K.R.2
-
15
-
-
62149121444
-
Decon2LS: an open source software package for automated processing and visualization of high resolution mass spectrometry data
-
Jaitly,N. et al. (2009) Decon2LS: an open source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics, 10, 87.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 87
-
-
Jaitly, N.1
-
16
-
-
33750743755
-
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline
-
Jaitly,N. et al. (2006) Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal. Chem., 78, 7397-7409.
-
(2006)
Anal. Chem.
, vol.78
, pp. 7397-7409
-
-
Jaitly, N.1
-
17
-
-
14044266328
-
Profile-based string kernels for remote homology detection and motif extraction
-
IEEE Computer Society, Stanford, CA
-
Kuang,R. et al. (2004) Profile-based string kernels for remote homology detection and motif extraction. In Computational Systems Bioinformatics Conference (CSB'04). IEEE Computer Society, Stanford, CA, pp. 152-160.
-
(2004)
Computational Systems Bioinformatics Conference (CSB'04)
, pp. 152-160
-
-
Kuang, R.1
-
18
-
-
17444378757
-
Simple probabilistic predictions for support vector regression
-
National Taiwan University
-
Lin,C.-J. and Weng,R.C. (2004) Simple probabilistic predictions for support vector regression. Technical Report, Department of Computer Science, National Taiwan University.
-
(2004)
Technical Report, Department of Computer Science
-
-
Lin, C.-J.1
Weng, R.C.2
-
19
-
-
76049109467
-
Prediction of ion drift times for a proteome-wide peptide set using partial least squares regression, least-squares support vector machine and Gaussian process
-
Liu,X. et al. (2009) Prediction of ion drift times for a proteome-wide peptide set using partial least squares regression, least-squares support vector machine and Gaussian process. QSAR Comb. Sci., 28, 1386-1393.
-
(2009)
QSAR Comb. Sci.
, vol.28
, pp. 1386-1393
-
-
Liu, X.1
-
22
-
-
34548136221
-
VIPER: an advanced software package to support highthroughput LC-MS peptide identification
-
Monroe,M.E. et al. (2007) VIPER: an advanced software package to support highthroughput LC-MS peptide identification. Bioinformatics, 23, 2021-2023.
-
(2007)
Bioinformatics
, vol.23
, pp. 2021-2023
-
-
Monroe, M.E.1
-
23
-
-
33646871614
-
An ensemble of K-local hyperplanes for predicting protein-protein interactions
-
Nanni,L. and Lumini,A. (2006) An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics, 22, 1207-1210.
-
(2006)
Bioinformatics
, vol.22
, pp. 1207-1210
-
-
Nanni, L.1
Lumini, A.2
-
24
-
-
31044454399
-
Sensitivity and specificity of PLS-class modelling for five sensory characteristics of dry-cured ham using visible and near infrared spectroscopy
-
Ortiz,M.C. et al. (2006) Sensitivity and specificity of PLS-class modelling for five sensory characteristics of dry-cured ham using visible and near infrared spectroscopy. Anal. Chim. Acta, 558, 125-131.
-
(2006)
Anal. Chim. Acta
, vol.558
, pp. 125-131
-
-
Ortiz, M.C.1
-
25
-
-
6344280371
-
Proteomic analyses using an accurate mass and time tag strategy
-
626-633, 636 passim
-
Pasa-Tolic,L. et al. (2004) Proteomic analyses using an accurate mass and time tag strategy. Biotechniques, 37, 621-624, 626-633, 636 passim.
-
(2004)
Biotechniques
, vol.37
, pp. 621-624
-
-
Pasa-Tolic, L.1
-
26
-
-
12444272753
-
Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses
-
Medium: X
-
Petritis,K. et al. (2003) Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal. Chem., 75, 1039-1048, Medium: X.
-
(2003)
Anal. Chem.
, vol.75
, pp. 1039-1048
-
-
Petritis, K.1
-
27
-
-
33746448330
-
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information
-
Petritis,K. et al. (2006) Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal. Chem., 78, 5026-5039.
-
(2006)
Anal. Chem.
, vol.78
, pp. 5026-5039
-
-
Petritis, K.1
-
28
-
-
84952503562
-
Thirteen ways to look at the correlation coefficient
-
Rodgers,J.L. and Nicewander,W.A. (1988) Thirteen ways to look at the correlation coefficient. Am. Statist., 42, 59-66.
-
(1988)
Am. Statist.
, vol.42
, pp. 59-66
-
-
Rodgers, J.L.1
Nicewander, W.A.2
-
29
-
-
0024278757
-
Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group
-
Roseman,M.A. (1988) Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group. J. Mol. Biol., 201, 621-623.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 621-623
-
-
Roseman, M.A.1
-
30
-
-
3242885293
-
The PredictProtein server
-
Rost,B. et al. (2004) The PredictProtein server. Nucleic Acids Res., 32, W321-W326.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Rost, B.1
-
31
-
-
0036684871
-
Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry
-
Ruotolo,B.T. et al. (2002) Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry. Int. J. Mass Spectrom., 219, 253-267.
-
(2002)
Int. J. Mass Spectrom.
, vol.219
, pp. 253-267
-
-
Ruotolo, B.T.1
-
32
-
-
27144463192
-
On comparing classifiers: pitfalls to avoid and a recommended approach
-
Salzberg,S. (1997) On comparing classifiers: pitfalls to avoid and a recommended approach. Data Min Knowl. Discov., 1, 317-328.
-
(1997)
Data Min Knowl. Discov.
, vol.1
, pp. 317-328
-
-
Salzberg, S.1
-
33
-
-
0035527773
-
Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues
-
Shvartsburg,A.A. et al. (2001) Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues. J. Am. Soc. Mass Spectrom., 12, 885-888.
-
(2001)
J. Am. Soc. Mass Spectrom.
, vol.12
, pp. 885-888
-
-
Shvartsburg, A.A.1
-
34
-
-
4043137356
-
A tutorial on support vector regression
-
Smola,A.J. and Scholkopf,B. (2004) A tutorial on support vector regression. Stat. Comput., 14, 199-222.
-
(2004)
Stat. Comput.
, vol.14
, pp. 199-222
-
-
Smola, A.J.1
Scholkopf, B.2
-
35
-
-
0032638628
-
Least squares support vector machine classifiers
-
Suykens,J.A.K. and Vandewalle,J. (1999) Least squares support vector machine classifiers. Neural Proc. Lett., 9, 293-300.
-
(1999)
Neural Proc. Lett.
, vol.9
, pp. 293-300
-
-
Suykens, J.A.K.1
Vandewalle, J.2
-
36
-
-
46049118177
-
AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices
-
Tantoso,E. and Li,K.-B. (2008) AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices. Amino Acids, 35, 345-353.
-
(2008)
Amino Acids
, vol.35
, pp. 345-353
-
-
Tantoso, E.1
Li, K.-B.2
-
37
-
-
33750313595
-
Promoter prediction using physico-chemical properties of DNA
-
Lecture Notes in Computer Science, Springer, Berlin, New York
-
Uren,P. et al. (2006) Promoter prediction using physico-chemical properties of DNA. In Computational Life Sciences II. Vol. 4216 of Lecture Notes in Bioinformatics, Lecture Notes in Computer Science, Springer, Berlin, New York, pp. 21-31.
-
(2006)
Computational Life Sciences II. Vol. 4216 of Lecture Notes in Bioinformatics
, pp. 21-31
-
-
Uren, P.1
-
38
-
-
0032238909
-
Gas-phase separations of protease digests
-
Valentine,S.J. et al. (1998) Gas-phase separations of protease digests. J. Amer. Soc. Mass Spectrom., 9, 1213-1216.
-
(1998)
J. Amer. Soc. Mass Spectrom.
, vol.9
, pp. 1213-1216
-
-
Valentine, S.J.1
-
39
-
-
0033473749
-
A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections
-
Valentine,S.J. et al. (1999a) A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections. J. Am. Soc. Mass Spectrom., 10, 1188-1211.
-
(1999)
J. Am. Soc. Mass Spectrom.
, vol.10
, pp. 1188-1211
-
-
Valentine, S.J.1
-
40
-
-
16644396658
-
Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions
-
Valentine,S.J. et al. (1999b) Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions. J. Phys. Chem. B, 103, 1203-1207.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 1203-1207
-
-
Valentine, S.J.1
-
42
-
-
67650539034
-
Prediction of peptide drift time in ion mobility-mass spectrometry
-
Wang,B. et al. (2009) Prediction of peptide drift time in ion mobility-mass spectrometry. BMC Bioinformatics, 10, A1.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Wang, B.1
-
43
-
-
46349085804
-
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
-
Webb-Robertson,B.-J.M. et al. (2008) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics, 24, 1503-1509.
-
(2008)
Bioinformatics
, vol.24
, pp. 1503-1509
-
-
Webb-Robertson, B.-J.1
-
44
-
-
0035965476
-
PLS-regression: a basic tool of chemometrics
-
Wold,S. et al. (2001) PLS-regression: a basic tool of chemometrics. Chemometrics Intell. Lab. Syst., 58, 109-130.
-
(2001)
Chemometrics Intell. Lab. Syst.
, vol.58
, pp. 109-130
-
-
Wold, S.1
-
45
-
-
41949092513
-
Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties
-
Yang,Y. et al. (2008) Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. J. Theor. Biol., 252, 145-154.
-
(2008)
J. Theor. Biol.
, vol.252
, pp. 145-154
-
-
Yang, Y.1
-
46
-
-
3242660851
-
Prediction of low-energy collision-induced dissociation spectra of peptides
-
Zhang,Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem., 76, 3908-3922.
-
(2004)
Anal. Chem.
, vol.76
, pp. 3908-3922
-
-
Zhang, Z.1
-
47
-
-
0014349825
-
The characterization of amino acid sequences in proteins by statistical methods
-
Zimmerman,J.M. et al. (1968) The characterization of amino acid sequences in proteins by statistical methods. J. Theor. Biol., 21, 170-201.
-
(1968)
J. Theor. Biol.
, vol.21
, pp. 170-201
-
-
Zimmerman, J.M.1
|