-
1
-
-
33745054329
-
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
-
Fermin, D.; Allen, B. B.; Blackwell, T. W.; Menon, R.; Asamski, M.; Xu, Y.; Ulintz, P.; Omenn, G. S.; States, D. J. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol., 2006, 7, R35.
-
(2006)
Genome Biol
, vol.7
-
-
Fermin, D.1
Allen, B.B.2
Blackwell, T.W.3
Menon, R.4
Asamski, M.5
Xu, Y.6
Ulintz, P.7
Omenn, G.S.8
States, D.J.9
-
2
-
-
34249717879
-
A high-quality catalog of the Drosophila melanogaster proteome
-
Brunner, E.; Ahrens, C. H.; Mohanty, S.; Baetschmann, H.; Loevenich, S.; Potthast, F.; Deutsch, E. W.; Panse, C.; de Lichten-berg, U.; Rinner, O.; Lee, H.; Pedrioli P.G.; Malmstrom, J.; Koehler, K.; Schrimpf, S.; Krijgsveld, J.; Kregenow, F.; Hech, A. J.; Hafen, E.; Schlapbach, R.; Aebersold, R. A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol., 2007, 25, 576-583.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 576-583
-
-
Brunner, E.1
Ahrens, C.H.2
Mohanty, S.3
Baetschmann, H.4
Loevenich, S.5
Potthast, F.6
Deutsch, E.W.7
Panse, C.8
de Lichten-berg, U.9
Rinner, O.10
Lee, H.11
Pedrioli, P.G.12
Malmstrom, J.13
Koehler, K.14
Schrimpf, S.15
Krijgsveld, J.16
Kregenow, F.17
Hech, A.J.18
Hafen, E.19
Schlapbach, R.20
Aebersold, R.21
more..
-
3
-
-
33846884410
-
Improving gene annotation using peptide mass spectrometry
-
Tanner, S.; Shen, Z.; Ng, J.; Florea, L.; Guigo, R.; Briggs, S. P.; Bafna, V. Improving gene annotation using peptide mass spectrometry. Genome Res., 2007, 17, 231-239.
-
(2007)
Genome Res
, vol.17
, pp. 231-239
-
-
Tanner, S.1
Shen, Z.2
Ng, J.3
Florea, L.4
Guigo, R.5
Briggs, S.P.6
Bafna, V.7
-
4
-
-
3242792729
-
Review: Structural bioinformatics and its impact to biomedical science
-
Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
-
(2004)
Curr. Med. Chem
, vol.11
, pp. 2105-2134
-
-
Chou, K.C.1
-
5
-
-
1642377868
-
Modelling extracellular domains of GABA-A receptors: Subtypes 1, 2, 3, and 5
-
Chou, K. C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun., 2004, 316, 636-642.
-
(2004)
Biochem. Biophys. Res. Commun
, vol.316
, pp. 636-642
-
-
Chou, K.C.1
-
6
-
-
11144275172
-
Molecular therapeutic target for type-2 diabetes
-
Chou, K. C. Molecular therapeutic target for type-2 diabetes. J. Proteome Res., 2004, 3, 1284-1288.
-
(2004)
J. Proteome Res
, vol.3
, pp. 1284-1288
-
-
Chou, K.C.1
-
7
-
-
39449105071
-
Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms
-
Chou, K. C.; Shen, H. B. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protocols, 2008, 3, 153-162.
-
(2008)
Nat. Protocols
, vol.3
, pp. 153-162
-
-
Chou, K.C.1
Shen, H.B.2
-
8
-
-
34548606295
-
Review: Recent progresses in protein subcellular location prediction
-
Chou, K. C.; Shen, H. B. Review: Recent progresses in protein subcellular location prediction. Analy. Biochem., 2007, 370, 1-16.
-
(2007)
Analy. Biochem
, vol.370
, pp. 1-16
-
-
Chou, K.C.1
Shen, H.B.2
-
9
-
-
34447095147
-
MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM
-
Chou, K. C.; Shen, H. B. MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Comm., 2007, 360, 339-345.
-
(2007)
Biochem. Biophys. Res. Comm
, vol.360
, pp. 339-345
-
-
Chou, K.C.1
Shen, H.B.2
-
10
-
-
52149087297
-
Predicting membrane protein types by the LLDA algorithm. Protein Pept
-
Wang, T.; Yang, J.; Shen, H. B.; Chou, K. C. Predicting membrane protein types by the LLDA algorithm. Protein Pept. Lett., 2008, 15, 915-921.
-
(2008)
Lett
, vol.15
, pp. 915-921
-
-
Wang, T.1
Yang, J.2
Shen, H.B.3
Chou, K.C.4
-
11
-
-
34247544233
-
Signal-CF: A subsite-coupled and window-fusing approach for predicting signal peptides
-
Chou, K. C.; Shen, H. B. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem. Bio-phys. Res. Comm., 2007, 357, 633-640.
-
(2007)
Biochem. Bio-phys. Res. Comm
, vol.357
, pp. 633-640
-
-
Chou, K.C.1
Shen, H.B.2
-
12
-
-
34748902270
-
Signal-3L: A 3-layer approach for predicting signal peptide
-
Shen, H. B.; Chou, K. C. Signal-3L: a 3-layer approach for predicting signal peptide. Biochem. Biophys. Res. Comm., 2007, 363, 297-303.
-
(2007)
Biochem. Biophys. Res. Comm
, vol.363
, pp. 297-303
-
-
Shen, H.B.1
Chou, K.C.2
-
13
-
-
0030049315
-
Review: Prediction of HIV protease cleavage sites in proteins
-
Chou, K. C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
-
(1996)
Anal. Biochem
, vol.233
, pp. 1-14
-
-
Chou, K.C.1
-
14
-
-
0027219970
-
A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins
-
Chou, K. C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
-
(1993)
J. Biol. Chem
, vol.268
, pp. 16938-16948
-
-
Chou, K.C.1
-
15
-
-
0032997217
-
The essence of SNPs
-
Brookes, A.J. The essence of SNPs. Gene, 1999, 234, 177-186.
-
(1999)
Gene
, vol.234
, pp. 177-186
-
-
Brookes, A.J.1
-
16
-
-
0035865322
-
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
-
Sachidanandam, R.; Weissman, D.; Schmidt, S.C.; Kakol, J.M.; Stein, L.D.; Marth, G.; Sherry, S.; Mullikin, J.C.; Mortimore, B.J.; Willey, D.L.; Hunt, S.E.; Cole, C.G.; Coggill, P.C.; Rice, C.M.; Ning, Z.; Rogers, J.; Bentley, D.R.; Kwok, P.Y.; Mardis, E.R.; Yeh, R.T.; Schultz, B.; Cook, L.; Davenport, R.; Dante, M.; Fulton, L.; Hillie, L.; Waterston, R.H.; McPherson, J.D.; Gilman, B.; Schaffner, S.; Van Etten, W.J.; Reich, D.; Higgins, J.; Daly, M.J.; Blumenstiel, B.; Baldwin, J.; Stange-Thomann, N.; Zody, M.C.; Linton, L.; Lander, E.S.; Altshuler, D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 2001, 409, 928-933.
-
(2001)
Nature
, vol.409
, pp. 928-933
-
-
Sachidanandam, R.1
Weissman, D.2
Schmidt, S.C.3
Kakol, J.M.4
Stein, L.D.5
Marth, G.6
Sherry, S.7
Mullikin, J.C.8
Mortimore, B.J.9
Willey, D.L.10
Hunt, S.E.11
Cole, C.G.12
Coggill, P.C.13
Rice, C.M.14
Ning, Z.15
Rogers, J.16
Bentley, D.R.17
Kwok, P.Y.18
Mardis, E.R.19
Yeh, R.T.20
Schultz, B.21
Cook, L.22
Davenport, R.23
Dante, M.24
Fulton, L.25
Hillie, L.26
Waterston, R.H.27
McPherson, J.D.28
Gilman, B.29
Schaffner, S.30
van Etten, W.J.31
Reich, D.32
Higgins, J.33
Daly, M.J.34
Blumenstiel, B.35
Baldwin, J.36
Stange-Thomann, N.37
Zody, M.C.38
Linton, L.39
Lander, E.S.40
Altshuler, D.41
more..
-
17
-
-
0035065485
-
SNPs, protein structure, and disease
-
Wang, Z.; Moult, J. SNPs, protein structure, and disease. Human Mutation, 2001, 17, 263-270.
-
(2001)
Human Mutation
, vol.17
, pp. 263-270
-
-
Wang, Z.1
Moult, J.2
-
18
-
-
0034191958
-
Towards a structural basis of human non-synonymous single nucleotide polymorphisms
-
Sunyaev, S.; Ramensky, V.; Bork, P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet, 2000, 16,198-200.
-
(2000)
Trends Genet
, vol.16
, pp. 198-200
-
-
Sunyaev, S.1
Ramensky, V.2
Bork, P.3
-
19
-
-
0035026704
-
Predicting deleterious amino acid substitutions
-
Ng, P.C.; Henikoff, S. Predicting deleterious amino acid substitutions. Genome Res., 2001, 11, 863-874.
-
(2001)
Genome Res
, vol.11
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
20
-
-
0032903821
-
Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat
-
Howell, W.M.; Jobs, M.; Gyllensten, U.; Brookes, A.J. Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat. Biotechnol., 1999, 17, 87-88.
-
(1999)
Biotechnol
, vol.17
, pp. 87-88
-
-
Howell, W.M.1
Jobs, M.2
Gyllensten, U.3
Brookes, A.J.4
-
22
-
-
0032998425
-
Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes
-
Lyamichev, V.; Mast, A.L.; Hall, J.G.; Prudent, J.R.; Kaiser, M.W.; Takova, T.; Kwiatkowski, R.W.; Sander, T.J.; de Arruda, M.; Arco, D.A.; Neri, B.P.; Brow, M.A. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol., 1999, 17, 292-296.
-
(1999)
Nat Biotechnol
, vol.17
, pp. 292-296
-
-
Lyamichev, V.1
Mast, A.L.2
Hall, J.G.3
Prudent, J.R.4
Kaiser, M.W.5
Takova, T.6
Kwiatkowski, R.W.7
Sander, T.J.8
de Arruda, M.9
Arco, D.A.10
Neri, B.P.11
Brow, M.A.12
-
23
-
-
0037098634
-
High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology
-
Olivier, M.; Chuang, L.M.; Chang, M.S.; Chen, Y.T.; Pei, D.; Ranade, K.; de Witte, A.; Allen, J.; Tran, N.; Curb, D.; Pratt, R.; Neefs, H.; de Arruda Indig, M.; Law, S.; Neri, B.; Wang, L.; Cox, D.R. High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res., 2002, 30, e53.
-
(2002)
Nucleic Acids Res
, vol.e53
, pp. 30
-
-
Olivier, M.1
Chuang, L.M.2
Chang, M.S.3
Chen, Y.T.4
Pei, D.5
Ranade, K.6
de Witte, A.7
Allen, J.8
Tran, N.9
Curb, D.10
Pratt, R.11
Neefs, H.12
de Arruda Indig, M.13
Law, S.14
Neri, B.15
Wang, L.16
Cox, D.R.17
-
24
-
-
0030914509
-
Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA. Rapid Commun
-
Tsuneyoshi, T.; Ishikawa, K.; Koga Naito, Y.; Baba, S.; Terunuma, H.; Arakawa, R.; Prockop, D.J. Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA. Rapid Commun. Mass Spectrom., 1997, 11, 719-722.
-
(1997)
Mass Spectrom
, vol.11
, pp. 719-722
-
-
Tsuneyoshi, T.1
Ishikawa, K.2
Koga Naito, Y.3
Baba, S.4
Terunuma, H.5
Arakawa, R.6
Prockop, D.J.7
-
25
-
-
0033032090
-
Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry
-
Griffin, T.J.; Hall, J.G.; Prudent, J.R.; Smith, L.M. Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc. Natl. Acad. Sci. USA, 1999, 96, 6301-6306.
-
(1999)
Proc. Natl. Acad. Sci. Usa
, vol.96
, pp. 6301-6306
-
-
Griffin, T.J.1
Hall, J.G.2
Prudent, J.R.3
Smith, L.M.4
-
26
-
-
12944281622
-
Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins
-
Savas, S.; Ahmad, F. M.; Shariff, M.; Kim, D.Y.; Ozcelik, H. Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins. Proteins, 2005, 58, 697-705.
-
(2005)
Proteins
, vol.58
, pp. 697-705
-
-
Savas, S.1
Ahmad, F.M.2
Shariff, M.3
Kim, D.Y.4
Ozcelik, H.5
-
27
-
-
33847232891
-
Mouse SNP Miner: An annotated database of mouse functional single nucleotide polymorphisms
-
Reuveni, E.; Ramensky, V. E.; Gross, C. Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. BMC Genomics, 2007, 8, 24.
-
(2007)
Bmc Genomics
, vol.8
, pp. 24
-
-
Reuveni, E.1
Ramensky, V.E.2
Gross, C.3
-
28
-
-
34250873383
-
Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data
-
Bunger, M.K.; Cargile, B.J.; Sevinsky, J.R.; Deyanova, E.; Yates, N.A.; Hendrickson, R.C.; Stephenson Jr, J.L. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data. J. Proteome Res., 2007, 6, 2331-2340
-
(2007)
J. Proteome Res
, vol.6
, pp. 2331-2340
-
-
Bunger, M.K.1
Cargile, B.J.2
Sevinsky, J.R.3
Deyanova, E.4
Yates, N.A.5
Hendrickson, R.C.6
Stephenson, J.L.7
-
29
-
-
41949118839
-
Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions
-
Teng, S.; Michonova-Alexova E, Alexov, E. Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr. Pharm. Biotechnol., 2008, 9(2): 123-133.
-
(2008)
Curr. Pharm. Biotechnol
, vol.9
, Issue.2
, pp. 123-133
-
-
Teng, S.1
Michonova-Alexova, E.2
Alexov, E.3
-
30
-
-
0035860293
-
PicSNP: A browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Bio-chem
-
Chang, H.; Fujita, T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Bio-chem. Biophys. Res. Commun., 2001, 287, 288-291.
-
(2001)
Biophys. Res. Commun
, vol.287
, pp. 288-291
-
-
Chang, H.1
Fujita, T.2
-
31
-
-
0036119504
-
Accounting for human polymorphisms predicted to affect protein function
-
Ng, P.C.; Henikoff, S. Accounting for human polymorphisms predicted to affect protein function. Genome Res., 2002, 12, 436-446.
-
(2002)
Genome Res
, vol.12
, pp. 436-446
-
-
Ng, P.C.1
Henikoff, S.2
-
32
-
-
1542405868
-
-
Zhu, Y.; Spitz, M.R.; Amos, C.I.; Lin, J.; Schabath, M.B.; Wu, X. An evolutionary perspective on single-nucleotide polymorphism screening in molecular cancer epidemiology Cancer Res., 2004, 64, 2251-2257.
-
(2004)
An Evolutionary Perspective On Single-nucleotide Polymorphism Screening In Molecular Cancer Epidemiology Cancer Res
, vol.64
, pp. 2251-2257
-
-
Zhu, Y.1
Spitz, M.R.2
Amos, C.I.3
Lin, J.4
Schabath, M.B.5
Wu, X.6
-
33
-
-
1642554457
-
Identification and characterization of mouse TRMU gene encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase
-
Yan, Q.; Guan, M.X. Identification and characterization of mouse TRMU gene encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase. Biochim. Biophys. Acta, 2004, 1676, 119-126.
-
(2004)
Biochim. Biophys. Acta
, vol.1676
, pp. 119-126
-
-
Yan, Q.1
Guan, M.X.2
-
34
-
-
18544364500
-
Screening for deleterious nonsynonymous single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response. Cancer Epidemiol
-
Johnson, M.M.; Houck, J.; Chen, C. Screening for deleterious nonsynonymous single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response. Cancer Epidemiol. Biomarkers Prev., 2005, 14, 1326-1329.
-
(2005)
Biomarkers Prev
, vol.14
, pp. 1326-1329
-
-
Johnson, M.M.1
Houck, J.2
Chen, C.3
-
35
-
-
0036589948
-
Code developments to improve the efficiency of automated MS/MS spectra interpretation
-
Sadygov, R. G.; Eng, J.; Durr, E.; Saraf, A.; McDonald, H.; Mac-Coss, M. J.; Yates, J. R. Code developments to improve the efficiency of automated MS/MS spectra interpretation. J. Proteome Res., 2002, 1, 211-215.
-
(2002)
J. Proteome Res
, vol.1
, pp. 211-215
-
-
Sadygov, R.G.1
Eng, J.2
Durr, E.3
Saraf, A.4
McDonald, H.5
Mac-Coss, M.J.6
Yates, J.R.7
-
36
-
-
24944544077
-
Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol
-
Roth, M.J.; Forbes, A.J.; Boyne, M.T.; Kim, Y.B.; Robinson, D.E.; Kelleher, N.L. Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol. Cell Proteomics., 2005, 4, 1002-1008.
-
(2005)
Cell Proteomics
, vol.4
, pp. 1002-1008
-
-
Roth, M.J.1
Forbes, A.J.2
Boyne, M.T.3
Kim, Y.B.4
Robinson, D.E.5
Kelleher, N.L.6
-
37
-
-
2442636680
-
Molecular-level description of proteins from saccharomyces cerevisiae using quadrupole FT hybrid mass spec-trometry for top down proteomics
-
Meng, F; Du, Y.; Miller, L.M.; Patrie, S.M.; Robinson, D.E.; Kelleher NL. Molecular-level description of proteins from saccharomyces cerevisiae using quadrupole FT hybrid mass spec-trometry for top down proteomics. Anal. Chem., 2004, 76, 2852-2858.
-
(2004)
Anal Chem
, vol.76
, pp. 2852-2858
-
-
Meng, F.1
Du, Y.2
Miller, L.M.3
Patrie, S.M.4
Robinson, D.E.5
Kelleher, N.L.6
-
38
-
-
34249807325
-
A mass spectrometry-friendly database for cSNP identification
-
Schandorff, S.; Olsen, J.V.; Bunkenborg, J. A mass spectrometry-friendly database for cSNP identification. Nat. Methods, 2007, 4, 465-466.
-
(2007)
Nat. Methods
, vol.4
, pp. 465-466
-
-
Schandorff, S.1
Olsen, J.V.2
Bunkenborg, J.3
-
39
-
-
0035869223
-
-
Sunyaev, S.; Ramensky, V.; Koch, I.; Lathe, W. 3rd.; Kondrashov, A.S.; Bork, P. Prediction of deleterious human alleles. Hum. Mol. Genet., 2001, 10, 591-597.
-
(2001)
Prediction of Deleterious Human Alleles. Hum. Mol. Genet
, vol.10
, pp. 591-597
-
-
Sunyaev, S.1
Ramensky, V.2
Koch, I.3
Lathe, W.4
-
40
-
-
0037432532
-
Structural location of disease-associated single-nucleotide polymorphisms
-
Stitziel, N.O.; Tseng, Y.Y.; Pervouchine, D.; Goddeau, D.; Kasif, S.; Liang, J. Structural location of disease-associated single-nucleotide polymorphisms. J. Mol. Biol., 2003, 327, 1021-1030.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 1021-1030
-
-
Stitziel, N.O.1
Tseng, Y.Y.2
Pervouchine, D.3
Goddeau, D.4
Kasif, S.5
Liang, J.6
-
41
-
-
0003385172
-
Selective constraint in protein polymorphism: Study of the effectively neutral mutation model by using an improved pseudosampling method
-
Kimura, M. and Takahata, N. Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method. Proc. Natl. Acad. Sci. USA, 1983, 80, 1048-1052.
-
(1983)
Proc. Natl. Acad. Sci. Usa
, vol.80
, pp. 1048-1052
-
-
Kimura, M.1
Takahata, N.2
|