-
1
-
-
1542399989
-
FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
-
Al-Shahrour, F., az-Uriarte, R. and Dopazo, J. (2004). FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20 578-580.
-
(2004)
Bioinformatics
, vol.20
, pp. 578-580
-
-
Al-Shahrour, F.1
Az-Uriarte, R.2
Dopazo, J.3
-
2
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 57 289300.
-
(1995)
Journal of the Royal Statistical Society
, vol.57
, pp. 289300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
3
-
-
0037106398
-
Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatographytandem mass spectrometry
-
Bondarenko, P. V., Chelius, D. and Shaler, T. A. (2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatographytandem mass spectrometry. Anal. Chem. 74 4741-4749.
-
(2002)
Anal. Chem
, vol.74
, pp. 4741-4749
-
-
Bondarenko, P.V.1
Chelius, D.2
Shaler, T.A.3
-
4
-
-
3142555412
-
Clustering analysis of SAGE data using aPoisson approach
-
Cai, L., Huang, H., Blackshaw, S., Liu, J. S., Cepko, C. and Wong, W. H. (2004). Clustering analysis of SAGE data using aPoisson approach. Genome Biol. 5 R51.
-
(2004)
Genome Biol
, vol.5
-
-
Cai, L.1
Huang, H.2
Blackshaw, S.3
Liu, J.S.4
Cepko, C.5
Wong, W.H.6
-
5
-
-
0036665581
-
Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
-
Chelius, D. and Bondarenko, P. V. (2002). Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome. Res. 1 317-323.
-
(2002)
J. Proteome. Res
, vol.1
, pp. 317-323
-
-
Chelius, D.1
Bondarenko, P.V.2
-
6
-
-
58149299336
-
Significance analysis of spectral count data in label-free shotgun proteomics. Mol
-
Choi, H., Fermin, D. and Nesvizhskii, A. I. (2008). Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell Proteomics 7 2373-2385.
-
(2008)
Cell Proteomics
, vol.7
, pp. 2373-2385
-
-
Choi, H.1
Fermin, D.2
Nesvizhskii, A.I.3
-
7
-
-
74049132731
-
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
-
Griffin, N. M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J. A. and Schnitzer, J. E. (2010). Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 28 83-89.
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 83-89
-
-
Griffin, N.M.1
Yu, J.2
Long, F.3
Oh, P.4
Shore, S.5
Li, Y.6
Koziol, J.A.7
Schnitzer, J.E.8
-
8
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H. and Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 994-999.
-
(1999)
Nat. Biotechnol
, vol.17
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
9
-
-
0025066941
-
More powerful procedures for multiple significance testing
-
Hochberg, Y. and Benjamini, Y. (1990). More powerful procedures for multiple significance testing. Stat. Med. 9 811-818.
-
(1990)
Stat. Med
, vol.9
, pp. 811-818
-
-
Hochberg, Y.1
Benjamini, Y.2
-
10
-
-
41649108679
-
Clustering analysisof SAGE transcription profiles using a Poisson approach
-
Huang, H., Cai, L. and Wong, W. H. (2008). Clustering analysisof SAGE transcription profiles using a Poisson approach. Methods Mol. Biol. 387 185-198.
-
(2008)
Methods Mol. Biol.
, vol.387
, pp. 185-198
-
-
Huang, H.1
Cai, L.2
Wong, W.H.3
-
11
-
-
77955458799
-
Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling
-
Li, M., Gray, W., Zhang, H., Chung, C. H., Billheimer, D., Yarbrough, W. G., Liebler, D. C., Shyr, Y. and Slebos, R. J. (2010). Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling. J. Proteome Res. 9 4295-4305.
-
(2010)
J. Proteome Res
, vol.9
, pp. 4295-4305
-
-
Li, M.1
Gray, W.2
Zhang, H.3
Chung, C.H.4
Billheimer, D.5
Yarbrough, W.G.6
Liebler, D.C.7
Shyr, Y.8
Slebos, R.J.9
-
12
-
-
0033051101
-
Direct analysis of protein complexes using mass spectrometry
-
Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M. and Yates, J. R., III (1999). Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17 676-682.
-
(1999)
Nat. Biotechnol
, vol.17
, pp. 676-682
-
-
Link, A.J.1
Eng, J.2
Schieltz, D.M.3
Carmack, E.4
Mize, G.J.5
Morris, D.R.6
Garvik, B.M.7
Yates III, J.R.8
-
13
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
Liu, H., Sadygov, R. G. and Yates, J. R., III (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76 4193-4201.
-
(2004)
Anal. Chem.
, vol.76
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
14
-
-
37649006805
-
Inference in regression models of heavily skewed alcohol use data: A comparison of ordinary least squares, generalized linear models, and bootstrap resampling. Psychol
-
Neal, D. J. and Simons, J. S. (2007). Inference in regression models of heavily skewed alcohol use data: A comparison of ordinary least squares, generalized linear models, and bootstrap resampling. Psychol. Addict. Behav. 21 441-452.
-
(2007)
Addict. Behav
, vol.21
, pp. 441-452
-
-
Neal, D.J.1
Simons, J.S.2
-
15
-
-
27644543078
-
Comparison of label-free methods for quantifying human proteins by shotgun proteomics
-
Old, W. M., Meyer-Arendt, K., veline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A. and Ahn, N. G. (2005). Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell Proteomics. 4 1487-1502.
-
(2005)
Mol. Cell Proteomics
, vol.4
, pp. 1487-1502
-
-
Old, W.M.1
Meyer-Arendt, K.2
veline-Wolf, L.3
Pierce, K.G.4
Mendoza, A.5
Sevinsky, J.R.6
Resing, K.A.7
Ahn, N.G.8
-
16
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A. and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics. 1 376-386.
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
Mann, M.7
-
17
-
-
34247642450
-
Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors
-
Paoletti, A. C., Parmely, T. J., Tomomori-Sato, C., Sato, S., Zhu, D., Conaway, R. C., Conaway, J. W., Florens, L. and Washburn, M. P. (2006). Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc. Natl. Acad. Sci. U.S.A 103 18928-18933.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, pp. 18928-18933
-
-
Paoletti, A.C.1
Parmely, T.J.2
Tomomori-Sato, C.3
Sato, S.4
Zhu, D.5
Conaway, R.C.6
Conaway, J.W.7
Florens, L.8
Washburn, M.P.9
-
18
-
-
42649131100
-
Statistical similarities between transcriptomics and quantitative shotgun proteomics data
-
Pavelka, N., Fournier, M. L., Swanson, S. K., Pelizzola, M., Ricciardi-Castagnoli, P., Florens, L. and Washburn, M. P. (2008). Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol. Cell Proteomics 7 631-644.
-
(2008)
Mol. Cell Proteomics
, vol.7
, pp. 631-644
-
-
Pavelka, N.1
Fournier, M.L.2
Swanson, S.K.3
Pelizzola, M.4
Ricciardi-Castagnoli, P.5
Florens, L.6
Washburn, M.P.7
-
19
-
-
13244292335
-
A power law global error model for the identification of differentially expressed genes in microarray data
-
Pavelka, N., Pelizzola, M., Vizzardelli, C., Capozzoli, M., Splendiani, A., Granucci, F. and Ricciardi-Castagnoli, P. (2004). A power law global error model for the identification of differentially expressed genes in microarray data. BMC. Bioinformatics 5 203.
-
(2004)
BMC. Bioinformatics
, vol.5
, pp. 203
-
-
Pavelka, N.1
Pelizzola, M.2
Vizzardelli, C.3
Capozzoli, M.4
Splendiani, A.5
Granucci, F.6
Ricciardi-Castagnoli, P.7
-
20
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet- Jones, M., He, F., Jacobson, A. and Pappin, D. J. (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics. 3 1154-1169.
-
(2004)
Mol. Cell Proteomics
, vol.3
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
Williamson, B.4
Parker, K.5
Hattan, S.6
Khainovski, N.7
Pillai, S.8
Dey, S.9
Daniels, S.10
Purkayastha, S.11
Juhasz, P.12
Martin, S.13
Bartlet-Jones, M.14
He, F.15
Jacobson, A.16
Pappin, D.J.17
-
21
-
-
65549119729
-
Statistical quality assessment and outlier detection for liquid chromatographymass spectrometry experiments
-
Schulz-Trieglaff, O., Machtejevas, E., Reinert, K., Schluter, H., Thiemann, J. and Unger, K. (2009). Statistical quality assessment and outlier detection for liquid chromatographymass spectrometry experiments. BioData. Min. 2 4.
-
(2009)
BioData. Min.
, vol.2
, pp. 4
-
-
Schulz-Trieglaff, O.1
Machtejevas, E.2
Reinert, K.3
Schluter, H.4
Thiemann, J.5
Unger, K.6
-
22
-
-
77956873951
-
An effi-cient data format for mass spectrometry-based proteomics
-
Shah, A. R., Davidson, J., Monroe, M. E., Mayampurath, A. M., Danielson, W. F., Shi, Y., Robinson, A. C., Clowers, B. H., Belov, M. E., Anderson, G. A. and Smith, R. D. (2010). An effi-cient data format for mass spectrometry-based proteomics. J. Am. Soc. Mass Spectrom.
-
(2010)
J. Am. Soc. Mass Spectrom
-
-
Shah, A.R.1
Davidson, J.2
Monroe, M.E.3
Mayampurath, A.M.4
Danielson, W.F.5
Shi, Y.6
Robinson, A.C.7
Clowers, B.H.8
Belov, M.E.9
Anderson, G.A.10
Smith, R.D.11
-
23
-
-
38449113722
-
Quasi-Poisson vs. negative binomial regression: How should we model overdispersed count data?
-
Ver Hoef, J. M. and Boveng, P. L. (2007). Quasi-Poisson vs. negative binomial regression: How should we model overdispersed count data? Ecology 88 2766-2772.
-
(2007)
Ecology
, vol.88
, pp. 2766-2772
-
-
Ver Hoef, J.M.1
Boveng, P.L.2
-
24
-
-
51649124498
-
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
-
Vogel, C. and Marcotte, E. M. (2008). Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat. Protoc. 3 1444-1451.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1444-1451
-
-
Vogel, C.1
Marcotte, E.M.2
-
25
-
-
33748319353
-
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
-
Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K., Florens, L. and Washburn, M. P. (2006). Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 5 2339-2347.
-
(2006)
J. Proteome Res
, vol.5
, pp. 2339-2347
-
-
Zybailov, B.1
Mosley, A.L.2
Sardiu, M.E.3
Coleman, M.K.4
Florens, L.5
Washburn, M.P.6
-
26
-
-
84864384498
-
Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors
-
Zybailov, B. L., Florens, L. and Washburn, M. P. (2011). Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol. Biosyst.
-
(2011)
Mol. Biosyst
-
-
Zybailov, B.L.1
Florens, L.2
Washburn, M.P.3
|