-
1
-
-
0034598746
-
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
-
Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson, J., Jr., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Staudt, L.M., et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511.
-
(2000)
Nature
, vol.403
, pp. 503-511
-
-
Alizadeh, A.A.1
Eisen, M.B.2
Davis, R.E.3
Ma, C.4
Lossos, I.S.5
Rosenwald, A.6
Boldrick, J.C.7
Sabet, H.8
Tran, T.9
Yu, X.10
Powell, J.I.11
Yang, L.12
Marti, G.E.13
Moore, T.14
Hudson, J.15
Lu, L.16
Lewis, D.B.17
Tibshirani, R.18
Sherlock, G.19
Chan, W.C.20
Greiner, T.C.21
Weisenburger, D.D.22
Armitage, J.O.23
Warnke, R.24
Staudt, L.M.25
more..
-
2
-
-
0033536012
-
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
-
Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D., and Levine, A.J. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96, 6745-6750.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 6745-6750
-
-
Alon, U.1
Barkai, N.2
Notterman, D.A.3
Gish, K.4
Ybarra, S.5
Mack, D.6
Levine, A.J.7
-
3
-
-
0034703060
-
Global gene expression profiling in Esherichia coli K12: The effects of integration host factor
-
Arfin, S.M., Long, A.D., Ito, E.T., Tolleri, L., Riehle, M.M., Paegle, E.S., and Hatfield, G.W. 2000. Global gene expression profiling in Esherichia coli K12: The effects of integration host factor. J. Biol. Chem. 275, 29672-29684.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 29672-29684
-
-
Arfin, S.M.1
Long, A.D.2
Ito, E.T.3
Tolleri, L.4
Riehle, M.M.5
Paegle, E.S.6
Hatfield, G.W.7
-
4
-
-
0035687492
-
Identifying differentially expressed genes in cDNA microarray experiments
-
Baggerly, K.A., Coombes, K.R., Hess, K.R., Stivers, D.N., Abruzzo, L.V., and Zhang, W. 2001. Identifying differentially expressed genes in cDNA microarray experiments. J. Comp. Biol. 8, 639-659.
-
(2001)
J. Comp. Biol
, vol.8
, pp. 639-659
-
-
Baggerly, K.A.1
Coombes, K.R.2
Hess, K.R.3
Stivers, D.N.4
Abruzzo, L.V.5
Zhang, W.6
-
5
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
-
Baldi, P., and Long, A.D. 2001. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
6
-
-
0034176929
-
Development of a toxicological gene array and quantitative assessment of this technology
-
Bartosiewicz, M., Trounstine, M., Barker, D., Johnston, R., and Buckpitt, A. 2000. Development of a toxicological gene array and quantitative assessment of this technology. Arch. Biochem. Biophys. 376, 66-73.
-
(2000)
Arch. Biochem. Biophys
, vol.376
, pp. 66-73
-
-
Bartosiewicz, M.1
Trounstine, M.2
Barker, D.3
Johnston, R.4
Buckpitt, A.5
-
7
-
-
0032850660
-
Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples
-
Bertucci, F., Bernard, K., Loriod, B., Chang, Y.C., Granjeaud, S., Birnbaum, D., Nguyen, C., Peck, K., and Jordan, B.R. 1999. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Human Mol. Genet. 8, 1715-1722.
-
(1999)
Human Mol. Genet
, vol.8
, pp. 1715-1722
-
-
Bertucci, F.1
Bernard, K.2
Loriod, B.3
Chang, Y.C.4
Granjeaud, S.5
Birnbaum, D.6
Nguyen, C.7
Peck, K.8
Jordan, B.R.9
-
8
-
-
0034601455
-
Molecular classification of cutaneous malignant melanoma by gene expression profiling
-
Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., Sampas, N., Dougherty, E., Wang, E., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P., Carpten, J., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C., Berens, M., Alberts, D., and Sondak, V. 2000. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406, 536-540.
-
(2000)
Nature
, vol.406
, pp. 536-540
-
-
Bittner, M.1
Meltzer, P.2
Chen, Y.3
Jiang, Y.4
Seftor, E.5
Hendrix, M.6
Radmacher, M.7
Simon, R.8
Yakhini, Z.9
Ben-Dor, A.10
Sampas, N.11
Dougherty, E.12
Wang, E.13
Marincola, F.14
Gooden, C.15
Lueders, J.16
Glatfelter, A.17
Pollock, P.18
Carpten, J.19
Gillanders, E.20
Leja, D.21
Dietrich, K.22
Beaudry, C.23
Berens, M.24
Alberts, D.25
Sondak, V.26
more..
-
9
-
-
0034714421
-
Gene expression data analysis
-
Brazma, A., and Vilo, J. 2000. Gene expression data analysis. FEBS Lett. 480, 17-24.
-
(2000)
FEBS Lett
, vol.480
, pp. 17-24
-
-
Brazma, A.1
Vilo, J.2
-
10
-
-
17044450862
-
Development of a prostate cDNA microarray and statistical gene expression analysis package
-
Carlisle, A.J., Prabhu, V.V., Elkahloun, A., Hudson, J., Trent, J.M., Linehan, W.M., Williams, E.D., Emmert-Buck, M.R., Liotta, L.A., Munson, P.J., and Krizman, D.B. 2000. Development of a prostate cDNA microarray and statistical gene expression analysis package. Mol. Carcinog. 28, 12-22.
-
(2000)
Mol. Carcinog
, vol.28
, pp. 12-22
-
-
Carlisle, A.J.1
Prabhu, V.V.2
Elkahloun, A.3
Hudson, J.4
Trent, J.M.5
Linehan, W.M.6
Williams, E.D.7
Emmert-Buck, M.R.8
Liotta, L.A.9
Munson, P.J.10
Krizman, D.B.11
-
11
-
-
0031246430
-
Ratio-based decisions and the quantitative analysis of cDNA microarray images
-
Chen, Y., Dougherty, E.R., and Bittner, M.R. 1997. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 2, 364-374.
-
(1997)
J. Biomed. Opt
, vol.2
, pp. 364-374
-
-
Chen, Y.1
Dougherty, E.R.2
Bittner, M.R.3
-
12
-
-
0032837252
-
Computational methods for the identification of differential and coordinated gene expression
-
Claverie, J.M. 1999. Computational methods for the identification of differential and coordinated gene expression. Human Mol. Genet. 8, 1821-1832.
-
(1999)
Human Mol. Genet
, vol.8
, pp. 1821-1832
-
-
Claverie, J.M.1
-
14
-
-
85007266222
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit, S., Yang, Y.H., Callow, M.J., and Speed, T.P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica. In press.
-
Statistica Sinica
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
15
-
-
0029995095
-
From hybridization image to numerical values: A practical, high throughput quantification system for high density filter hybridizations
-
Granjeaud, S., Nguyen, C., Rocha, D., Luton, R., and Jordan, B.R. 1996. From hybridization image to numerical values: A practical, high throughput quantification system for high density filter hybridizations. Genet. Anal. 12, 151-162.
-
(1996)
Genet. Anal
, vol.12
, pp. 151-162
-
-
Granjeaud, S.1
Nguyen, C.2
Rocha, D.3
Luton, R.4
Jordan, B.R.5
-
16
-
-
0035931947
-
Gene-expression profiles in hereditary breast cancer
-
Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O.P., Wilfond, B., Borg, A., and Trent, J. 2001. Gene-expression profiles in hereditary breast cancer. N. Engl. J. Med. 344, 539-548.
-
(2001)
N. Engl. J. Med
, vol.344
, pp. 539-548
-
-
Hedenfalk, I.1
Duggan, D.2
Chen, Y.3
Radmacher, M.4
Bittner, M.5
Simon, R.6
Meltzer, P.7
Gusterson, B.8
Esteller, M.9
Kallioniemi, O.P.10
Wilfond, B.11
Borg, A.12
Trent, J.13
-
17
-
-
0033818954
-
A concise guide to cDNA microarray analysis
-
552-554, 556 passim
-
Hegde, P., Qi, R., Abernathy, K., Gay, C., Dharap, S., Gaspard, R., Hughes, J.E., Snesrud, E., Lee, N., and Quackenbush, J. 2000. A concise guide to cDNA microarray analysis. Biotechniques 29, 548-550, 552-554, 556 passim.
-
(2000)
Biotechniques
, vol.29
, pp. 548-550
-
-
Hegde, P.1
Qi, R.2
Abernathy, K.3
Gay, C.4
Dharap, S.5
Gaspard, R.6
Hughes, J.E.7
Snesrud, E.8
Lee, N.9
Quackenbush, J.10
-
18
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S.H. 2000. Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
Meyer, M.R.13
Slade, D.14
Lum, P.Y.15
Stepaniants, S.B.16
Shoemaker, D.D.17
Gachotte, D.18
Chakraburtty, K.19
Simon, J.20
Bard, M.21
Friend, S.H.22
more..
-
19
-
-
0032903908
-
The transcriptional program in the response of human fibroblasts to serum
-
Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C., Trent, J.M., Staudt, L.M., Hudson, J., Jr., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D., and Brown, P.O. 1999. The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-87.
-
(1999)
Science
, vol.283
, pp. 83-87
-
-
Iyer, V.R.1
Eisen, M.B.2
Ross, D.T.3
Schuler, G.4
Moore, T.5
Lee, J.C.6
Trent, J.M.7
Staudt, L.M.8
Hudson, J.9
Boguski, M.S.10
Lashkari, D.11
Shalon, D.12
Botstein, D.13
Brown, P.O.14
-
20
-
-
2542426171
-
Statistical analysis of a gene expression microarray experiment with replication
-
Kerr, M.K., Afshari, C.A., Bennett, L., Bushel, P., Martinez, J., Walker, N.J., and Churchill, G.A. Statistical analysis of a gene expression microarray experiment with replication. Statistica Sinica. in press.
-
Statistica Sinica
-
-
Kerr, M.K.1
Afshari, C.A.2
Bennett, L.3
Bushel, P.4
Martinez, J.5
Walker, N.J.6
Churchill, G.A.7
-
21
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr, M.K., and Churchill, G.A. 2001. Experimental design for gene expression microarrays. Biostatistics 2, 183-201.
-
(2001)
Biostatistics
, vol.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
22
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr, M.K., Martin, M., and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7, 819-837.
-
(2000)
J. Comput. Biol
, vol.7
, pp. 819-837
-
-
Kerr, M.K.1
Martin, M.2
Churchill, G.A.3
-
23
-
-
0034661192
-
Multivariate measurement of gene expression relationships
-
Kim, S., Dougherty, E.R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J.M., and Bittner, M. 2000. Multivariate measurement of gene expression relationships. Genomics 67, 201-209.
-
(2000)
Genomics
, vol.67
, pp. 201-209
-
-
Kim, S.1
Dougherty, E.R.2
Chen, Y.3
Sivakumar, K.4
Meltzer, P.5
Trent, J.M.6
Bittner, M.7
-
24
-
-
0033610079
-
Gene expression profile of aging and its retardation by caloric restriction
-
Lee, C.K., Klopp, R.G., Weindruch, R., and Prolla, T.A. 1999. Gene expression profile of aging and its retardation by caloric restriction. Science 285, 1390-1393.
-
(1999)
Science
, vol.285
, pp. 1390-1393
-
-
Lee, C.K.1
Klopp, R.G.2
Weindruch, R.3
Prolla, T.A.4
-
25
-
-
0034730124
-
Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
-
Lee, M.L., Kuo, F.C., Whitmore, G.A., and Sklar, J. 2000. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97, 9834-9839.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 9834-9839
-
-
Lee, M.L.1
Kuo, F.C.2
Whitmore, G.A.3
Sklar, J.4
-
26
-
-
0035827588
-
Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12
-
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. 2001. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276, 19937-19944.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 19937-19944
-
-
Long, A.D.1
Mangalam, H.J.2
Chan, B.Y.3
Tolleri, L.4
Hatfield, G.W.5
Baldi, P.6
-
28
-
-
0034923013
-
On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data
-
Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R., and Tsui, K.W. 2001. On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. J. Comp. Biol. 8, 37-52.
-
(2001)
J. Comp. Biol
, vol.8
, pp. 37-52
-
-
Newton, M.A.1
Kendziorski, C.M.2
Richmond, C.S.3
Blattner, F.R.4
Tsui, K.W.5
-
29
-
-
0034680102
-
Molecular portraits of human breast tumours
-
Perou, C.M., Sorlie, T., Eisen, M.B., van de Rijm, M., Jeffrey, S.S., Rees, C.A., Pollack, J.R., Ross, D.T., Johnsen, H., Akslen, L.A., Fluge, O., Pergamenschikov, A., Williams, C., Zhu, S.X., Lonning, P.E., Borresen-Dale, A.L., Brown, P.O., and Botstein, D. 2000. Molecular portraits of human breast tumours. Nature 406, 747-752.
-
(2000)
Nature
, vol.406
, pp. 747-752
-
-
Perou, C.M.1
Sorlie, T.2
Eisen, M.B.3
Van de Rijm, M.4
Jeffrey, S.S.5
Rees, C.A.6
Pollack, J.R.7
Ross, D.T.8
Johnsen, H.9
Akslen, L.A.10
Fluge, O.11
Pergamenschikov, A.12
Williams, C.13
Zhu, S.X.14
Lonning, P.E.15
Borresen-Dale, A.L.16
Brown, P.O.17
Botstein, D.18
-
30
-
-
0034603061
-
Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles
-
Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., Tyers, M., Boone, C., and Friend, S.H. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880.
-
(2000)
Science
, vol.287
, pp. 873-880
-
-
Roberts, C.J.1
Nelson, B.2
Marton, M.J.3
Stoughton, R.4
Meyer, M.R.5
Bennett, H.A.6
He, Y.D.7
Dai, H.8
Walker, W.L.9
Hughes, T.R.10
Tyers, M.11
Boone, C.12
Friend, S.H.13
-
31
-
-
0034050902
-
Systematic variation in gene expression patterns in human cancer cell lines
-
Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S.S., Van, de R.M., Waltham, M., Pergamenschikov, A., Lee, J.C., Lashkari, D., Shalon, D., Myers, T.G., Weinstein, J.N., Botstein, D., and Brown, P.O. 2000. Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet. 24, 227-235.
-
(2000)
Nat. Genet
, vol.24
, pp. 227-235
-
-
Ross, D.T.1
Scherf, U.2
Eisen, M.B.3
Perou, C.M.4
Rees, C.5
Spellman, P.6
Iyer, V.7
Jeffrey, S.S.8
Van, D.R.M.9
Waltham, M.10
Pergamenschikov, A.11
Lee, J.C.12
Lashkari, D.13
Shalon, D.14
Myers, T.G.15
Weinstein, J.N.16
Botstein, D.17
Brown, P.O.18
-
32
-
-
0034656561
-
Normalization strategies for cDNA microarrays
-
Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickhoff, H., Lehrach, H., and Herzel, H. 2000. Normalization strategies for cDNA microarrays. Nucl. Acids Res. 28, E47.
-
(2000)
Nucl. Acids Res
, vol.28
, pp. E47
-
-
Schuchhardt, J.1
Beule, D.2
Malik, A.3
Wolski, E.4
Eickhoff, H.5
Lehrach, H.6
Herzel, H.7
-
33
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V.G., Tibshirani, R., and Chu, G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci USA 98, 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
34
-
-
0003895851
-
-
Springer-Verlag, New York
-
Venables, W.N., and Ripley, B.D. 1997. Modern Applied Statistics with S-PLUS, 2nd ed., Springer-Verlag, New York.
-
(1997)
Modern Applied Statistics with S-PLUS, 2nd Ed
-
-
Venables, W.N.1
Ripley, B.D.2
-
35
-
-
0034717076
-
Gene expression profiling in human peripheral blood mononuclear cells using highdensity filter-based cDNA microarrays
-
Walker, J., and Rigley, K. 2000. Gene expression profiling in human peripheral blood mononuclear cells using highdensity filter-based cDNA microarrays. J. Immunol. Methods 239, 167-179.
-
(2000)
J. Immunol. Methods
, vol.239
, pp. 167-179
-
-
Walker, J.1
Rigley, K.2
-
36
-
-
0035229170
-
Maximization of signal derived from cDNA microarrays
-
Wildsmith, S.E., Archer, G.E., Winkley, A.J., Lane, P.W., and Bugelski, P.J. 2001. Maximization of signal derived from cDNA microarrays. Biotechniques 30, 202-6, 208.
-
(2001)
Biotechniques
, vol.30
, pp. 202-206
-
-
Wildsmith, S.E.1
Archer, G.E.2
Winkley, A.J.3
Lane, P.W.4
Bugelski, P.J.5
-
37
-
-
0003576793
-
Normalization for cDNA microarray data
-
Bittner, M.L., Chen, Y., Dorsel, A.N., and Dougherty, E.R., eds., SPIE, Bellingham, WA
-
Yang, Y.-H., Dudoit, S., Luu, P., and Speed, T.P. 2001. Normalization for cDNA microarray data. In Bittner, M.L., Chen, Y., Dorsel, A.N., and Dougherty, E.R., eds., Microarrays: Optical Technologies and Informatics, SPIE, Bellingham, WA.
-
(2001)
Microarrays: Optical Technologies and Informatics
-
-
Yang, Y.-H.1
Dudoit, S.2
Luu, P.3
Speed, T.P.4
|