-
1
-
-
2542485466
-
The microrevolution: Applications and impacts of microarray technology on molecular biology and medicine (review)
-
Goldsmith ZG, Dhanasekaran N: The microrevolution: applications and impacts of microarray technology on molecular biology and medicine (review). Int J Mol Med 2004, 13(4):483-495.
-
(2004)
Int J Mol Med
, vol.13
, Issue.4
, pp. 483-495
-
-
Goldsmith, Z.G.1
Dhanasekaran, N.2
-
2
-
-
0036211063
-
Analysis of matched mRNA measurements from two different microarray technologies
-
Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS: Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18(3):405-412.
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 405-412
-
-
Kuo, W.P.1
Jenssen, T.K.2
Butte, A.J.3
Ohno-Machado, L.4
Kohane, I.S.5
-
3
-
-
0036773278
-
Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays
-
Li J, Pankratz M, Johnson JA: Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci 2002, 69(2):383-390.
-
(2002)
Toxicol Sci
, vol.69
, Issue.2
, pp. 383-390
-
-
Li, J.1
Pankratz, M.2
Johnson, J.A.3
-
4
-
-
0141905890
-
Evaluation of gene expression measurements from commercial microarray platforms
-
Tan PK, Downey TJ, Spitznagel EL Jr., Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31(19):5676-5684.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.19
, pp. 5676-5684
-
-
Tan, P.K.1
Downey, T.J.2
Spitznagel Jr., E.L.3
Xu, P.4
Fu, D.5
Dimitrov, D.S.6
Lempicki, R.A.7
Raaka, B.M.8
Cam, M.C.9
-
5
-
-
7444234286
-
Getting the noise out of gene arrays
-
Marshall E: Getting the noise out of gene arrays. Science 2004, 306(5696):630-631.
-
(2004)
Science
, vol.306
, Issue.5696
, pp. 630-631
-
-
Marshall, E.1
-
6
-
-
0038486795
-
Spotted long oligonucleotide arrays for human gene expression analysis
-
Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ: Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 2003, 13(7):1775-1785.
-
(2003)
Genome Res
, vol.13
, Issue.7
, pp. 1775-1785
-
-
Barczak, A.1
Rodriguez, M.W.2
Hanspers, K.3
Koth, L.L.4
Tai, Y.C.5
Bolstad, B.M.6
Speed, T.P.7
Erle, D.J.8
-
7
-
-
23644453736
-
Three microarray platforms: An analysis of their concordance in profiling gene expression
-
Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES: Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 2005, 6(1):63.
-
(2005)
BMC Genomics
, vol.6
, Issue.1
, pp. 63
-
-
Petersen, D.1
Chandramouli, G.V.2
Geoghegan, J.3
Hilburn, J.4
Paarlberg, J.5
Kim, C.H.6
Munroe, D.7
Gangi, L.8
Han, J.9
Puri, R.10
Staudt, L.11
Weinstein, J.12
Barrett, J.C.13
Green, J.14
Kawasaki, E.S.15
-
8
-
-
27144529544
-
Patient-based cross-platform comparison of oligonucleotide microarray expression profiles
-
Schlingemann J, Habtemichael N, Ittrich C, Toedt G, Kramer H, Hambek M, Knecht R, Lichter P, Stauber R, Hahn M: Patient-based cross-platform comparison of oligonucleotide microarray expression profiles. Lab Invest 2005, 85(8):1024-1039.
-
(2005)
Lab Invest
, vol.85
, Issue.8
, pp. 1024-1039
-
-
Schlingemann, J.1
Habtemichael, N.2
Ittrich, C.3
Toedt, G.4
Kramer, H.5
Hambek, M.6
Knecht, R.7
Lichter, P.8
Stauber, R.9
Hahn, M.10
-
9
-
-
18244378238
-
Independence and reproducibility across microarray platforms
-
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods 2005, 2(5):337-344.
-
(2005)
Nat Methods
, vol.2
, Issue.5
, pp. 337-344
-
-
Larkin, J.E.1
Frank, B.C.2
Gavras, H.3
Sultana, R.4
Quackenbush, J.5
-
10
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2(5):345-350.
-
(2005)
Nat Methods
, vol.2
, Issue.5
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.8
Geoghegan, J.9
Germino, G.10
Griffin, C.11
Hilmer, S.C.12
Hoffman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martinez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
11
-
-
27644528185
-
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
-
Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su Z, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong H, Xie Q, Perkins RG, Chen JJ, Casciano DA: Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005, 6 Suppl 2:S12.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 2
-
-
Shi, L.1
Tong, W.2
Fang, H.3
Scherf, U.4
Han, J.5
Puri, R.K.6
Frueh, F.W.7
Goodsaid, F.M.8
Guo, L.9
Su, Z.10
Han, T.11
Fuscoe, J.C.12
Xu, Z.A.13
Patterson, T.A.14
Hong, H.15
Xie, Q.16
Perkins, R.G.17
Chen, J.J.18
Casciano, D.A.19
-
12
-
-
25444514459
-
Comparing independent microarray studies: The case of human embryonic stem cells
-
Suarez-Farinas M, Noggle S, Heke M, Hemmati-Brivanlou A, Magnasco MO: Comparing independent microarray studies: the case of human embryonic stem cells. BMC Genomics 2005, 6:99.
-
(2005)
BMC Genomics
, vol.6
, pp. 99
-
-
Suarez-Farinas, M.1
Noggle, S.2
Heke, M.3
Hemmati-Brivanlou, A.4
Magnasco, M.O.5
-
13
-
-
0002922661
-
Microarray results: How accurate are they?
-
Kothapalli R, Yoder SJ, Mane S, Loughran TP Jr.: Microarray results: how accurate are they? BMC Bioinformatics 2002, 3:22.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 22
-
-
Kothapalli, R.1
Yoder, S.J.2
Mane, S.3
Loughran Jr., T.P.4
-
14
-
-
4344641894
-
Analysis of alternative splicing with microarrays: Successes and challenges
-
Lee C, Roy M: Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol 2004, 5(7):231.
-
(2004)
Genome Biol
, vol.5
, Issue.7
, pp. 231
-
-
Lee, C.1
Roy, M.2
-
15
-
-
14744291858
-
Platform influence on DNA microarray data in postmortem brain research
-
Hollingshead D, Lewis DA, Mirnics K: Platform influence on DNA microarray data in postmortem brain research. Neurobiol Dis 2005, 18(3):649-655.
-
(2005)
Neurobiol Dis
, vol.18
, Issue.3
, pp. 649-655
-
-
Hollingshead, D.1
Lewis, D.A.2
Mirnics, K.3
-
16
-
-
27144486151
-
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
-
Barnes M, Freudenberg J, Thompson S, Aronow B. Pavlidis P: Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 2005, 33(18):5914-5923.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.18
, pp. 5914-5923
-
-
Barnes, M.1
Freudenberg, J.2
Thompson, S.3
Aronow, B.4
Pavlidis, P.5
-
17
-
-
0036545952
-
An assessment of Motorola CodeLink microarray performance for gene expression profiling applications
-
Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, Prokhorova A, Gieser L, Touma E, Lockner R, Tata M, Zhu X, Patterson M, Shippy R, Sendera TJ, Mazumder A: An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res 2002, 30(7):e30.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.7
-
-
Ramakrishnan, R.1
Dorris, D.2
Lublinsky, A.3
Nguyen, A.4
Domanus, M.5
Prokhorova, A.6
Gieser, L.7
Touma, E.8
Lockner, R.9
Tata, M.10
Zhu, X.11
Patterson, M.12
Shippy, R.13
Sendera, T.J.14
Mazumder, A.15
-
18
-
-
0037100632
-
Analysis of repeatability in spotted cDNA microarrays
-
Jenssen TK, Langaas M, Kuo WP, Smith-Sorensen B, Myklebost O, Hovig E: Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 2002, 30(14):3235-3244.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.14
, pp. 3235-3244
-
-
Jenssen, T.K.1
Langaas, M.2
Kuo, W.P.3
Smith-Sorensen, B.4
Myklebost, O.5
Hovig, E.6
-
19
-
-
9144256854
-
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
-
Shippy R, Sendera TJ, Lockner R, Palaniappan C, Kaysser-Kranich T, Watts G, Alsobrook J: Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 2004, 5(1):61.
-
(2004)
BMC Genomics
, vol.5
, Issue.1
, pp. 61
-
-
Shippy, R.1
Sendera, T.J.2
Lockner, R.3
Palaniappan, C.4
Kaysser-Kranich, T.5
Watts, G.6
Alsobrook, J.7
-
20
-
-
17844379157
-
A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
-
Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G: A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 2004, 15(4):276-284.
-
(2004)
J Biomol Tech
, vol.15
, Issue.4
, pp. 276-284
-
-
Woo, Y.1
Affourtit, J.2
Daigle, S.3
Viale, A.4
Johnson, K.5
Naggert, J.6
Churchill, G.7
-
21
-
-
33744804832
-
Comparison of the latest commercial short and long oligonucleotide microarray technologies
-
de Reynies A, Geromin D, Cayuela JM, Petel F, Dessen P, Sigaux F, Rickman DS: Comparison of the latest commercial short and long oligonucleotide microarray technologies. BMC Genomics 2006, 7(1):51.
-
(2006)
BMC Genomics
, vol.7
, Issue.1
, pp. 51
-
-
de Reynies, A.1
Geromin, D.2
Cayuela, J.M.3
Petel, F.4
Dessen, P.5
Sigaux, F.6
Rickman, D.S.7
-
22
-
-
33646369893
-
Strategies for comparing gene expression profiles from different microarray platforms: Application to a case-control experiment
-
Severgnini M, Bicciato S, Mangano E, Scarlatti F, Mezzelani A, Mattioli M, Ghidoni R, Peano C, Bonnal R, Viti F, Milanesi L, De Bellis G, Battaglia C: Strategies for comparing gene expression profiles from different microarray platforms: Application to a case-control experiment. Anal Biochem 2006, 353(1):43-56.
-
(2006)
Anal Biochem
, vol.353
, Issue.1
, pp. 43-56
-
-
Severgnini, M.1
Bicciato, S.2
Mangano, E.3
Scarlatti, F.4
Mezzelani, A.5
Mattioli, M.6
Ghidoni, R.7
Peano, C.8
Bonnal, R.9
Viti, F.10
Milanesi, L.11
De Bellis, G.12
Battaglia, C.13
-
23
-
-
0037095769
-
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays
-
Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC: Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 2002, 30(10):e48.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.10
-
-
Yuen, T.1
Wurmbach, E.2
Pfeffer, R.L.3
Ebersole, B.J.4
Sealfon, S.C.5
-
24
-
-
4143151607
-
Current issues for DNA microarrays: Platform comparison, double linear amplification, and universal RNA reference
-
Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S: Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol 2004, 112(3):225-245.
-
(2004)
J Biotechnol
, vol.112
, Issue.3
, pp. 225-245
-
-
Park, P.J.1
Cao, Y.A.2
Lee, S.Y.3
Kim, J.W.4
Chang, M.S.5
Hart, R.6
Choi, S.7
-
25
-
-
33645473195
-
Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells
-
Ali-Seyed M, Laycock N, Karanam S, Xiao W, Blair ET, Moreno CS: Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells. BMC Cancer 2006, 6:54.
-
(2006)
BMC Cancer
, vol.6
, pp. 54
-
-
Ali-Seyed, M.1
Laycock, N.2
Karanam, S.3
Xiao, W.4
Blair, E.T.5
Moreno, C.S.6
-
26
-
-
33645808222
-
Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays
-
Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR: Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 2006, 7:59.
-
(2006)
BMC Genomics
, vol.7
, pp. 59
-
-
Wang, Y.1
Barbacioru, C.2
Hyland, F.3
Xiao, W.4
Hunkapiller, K.L.5
Blake, J.6
Chan, F.7
Gonzalez, C.8
Zhang, L.9
Samaha, R.R.10
-
27
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.
-
(2003)
Biostatistics
, vol.4
, Issue.2
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
28
-
-
1342330572
-
A benchmark for Affymetrix GeneChip expression measures
-
Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP: A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004, 20(3):323-331.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 323-331
-
-
Cope, L.M.1
Irizarry, R.A.2
Jaffee, H.A.3
Wu, Z.4
Speed, T.P.5
-
29
-
-
9144268360
-
Empirical evaluation of data transformations and ranking statistics for microarray analysis
-
Qin LX, Kerr KF: Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32(18):5471-5479.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.18
, pp. 5471-5479
-
-
Qin, L.X.1
Kerr, K.F.2
-
30
-
-
4844222268
-
Increased measurement accuracy for sequence-verified microarray probes
-
Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ: Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics 2004, 18(3):308-315.
-
(2004)
Physiol Genomics
, vol.18
, Issue.3
, pp. 308-315
-
-
Mecham, B.H.1
Wetmore, D.Z.2
Szallasi, Z.3
Sadovsky, Y.4
Kohane, I.5
Mariani, T.J.6
-
31
-
-
23844483247
-
A study of inter-lab and inter-platform agreement of DNA microarray data
-
Wang H, He X, Band M, Wilson C, Liu L: A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 2005, 6(1):71.
-
(2005)
BMC Genomics
, vol.6
, Issue.1
, pp. 71
-
-
Wang, H.1
He, X.2
Band, M.3
Wilson, C.4
Liu, L.5
-
32
-
-
30544444095
-
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis
-
Magnusson NE, Cardozo AK, Kruhoffer M, Eizirik DL, Orntoft TF, Jensen JL: Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis. BMC Bioinformatics 2005, 6:311.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 311
-
-
Magnusson, N.E.1
Cardozo, A.K.2
Kruhoffer, M.3
Eizirik, D.L.4
Orntoft, T.F.5
Jensen, J.L.6
-
33
-
-
33644778724
-
Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
-
Walker SJ, Wang Y, Grant KA, Chan F, Hellmann GM: Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. J Neurosci Methods 2006, 152(1-2):179-189.
-
(2006)
J Neurosci Methods
, vol.152
, Issue.1-2
, pp. 179-189
-
-
Walker, S.J.1
Wang, Y.2
Grant, K.A.3
Chan, F.4
Hellmann, G.M.5
-
34
-
-
0037015215
-
Comparison of different labeling methods for two-channel high-density microarray experiments
-
Manduchi E, Scearce LM, Brestelli JE, Grant GR, Kaestner KH, Stoeckert CJ Jr.: Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol Genomics 2002, 10(3):169-179.
-
(2002)
Physiol Genomics
, vol.10
, Issue.3
, pp. 169-179
-
-
Manduchi, E.1
Scearce, L.M.2
Brestelli, J.E.3
Grant, G.R.4
Kaestner, K.H.5
Stoeckert Jr., C.J.6
-
35
-
-
0037944217
-
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs
-
He YD, Dai H, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB: Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics 2003, 19(8):956-965.
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 956-965
-
-
He, Y.D.1
Dai, H.2
Schadt, E.E.3
Cavet, G.4
Edwards, S.W.5
Stepaniants, S.B.6
Duenwald, S.7
Kleinhanz, R.8
Jones, A.R.9
Shoemaker, D.D.10
Stoughton, R.B.11
-
36
-
-
18244389201
-
Standardizing global gene expression analysis between laboratories and across platforms
-
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'Malley J P, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H: Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005, 2(5):351-356.
-
(2005)
Nat Methods
, vol.2
, Issue.5
, pp. 351-356
-
-
Bammler, T.1
Beyer, R.P.2
Bhattacharya, S.3
Boorman, G.A.4
Boyles, A.5
Bradford, B.U.6
Bumgarner, R.E.7
Bushel, P.R.8
Chaturvedi, K.9
Choi, D.10
Cunningham, M.L.11
Deng, S.12
Dressman, H.K.13
Fannin, R.D.14
Farin, F.M.15
Freedman, J.H.16
Fry, R.C.17
Harper, A.18
Humble, M.C.19
Hurban, P.20
Kavanagh, T.J.21
Kaufmann, W.K.22
Kerr, K.F.23
Jing, L.24
Lapidus, J.A.25
Lasarev, M.R.26
Li, J.27
Li, Y.J.28
Lobenhofer, E.K.29
Lu, X.30
Malek, R.L.31
Milton, S.32
Nagalla, S.R.33
O'Malley, J.P.34
Palmer, V.S.35
Pattee, P.36
Paules, R.S.37
Perou, C.M.38
Phillips, K.39
Qin, L.X.40
Qiu, Y.41
Quigley, S.D.42
Rodland, M.43
Rusyn, I.44
Samson, L.D.45
Schwartz, D.A.46
Shi, Y.47
Shin, J.L.48
Sieber, S.O.49
Slifer, S.50
Speer, M.C.51
Spencer, P.S.52
Sproles, D.I.53
Swenberg, J.A.54
Suk, W.A.55
Sullivan, R.C.56
Tian, R.57
Tennant, R.W.58
Todd, S.A.59
Tucker, C.J.60
Van Houten, B.61
Weis, B.K.62
Xuan, S.63
Zarbl, H.64
more..
-
37
-
-
0036004157
-
Comparison of methods for image analysis on cDNA microarray data
-
Yang YH, Buckley MJ, Dudoit S, Speed TP: Comparison of methods for image analysis on cDNA microarray data. J Computational Graphical Stats 2002, 11:108-136.
-
(2002)
J Computational Graphical Stats
, vol.11
, pp. 108-136
-
-
Yang, Y.H.1
Buckley, M.J.2
Dudoit, S.3
Speed, T.P.4
-
38
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth GK, Speed TP: Normalization of cDNA microarray data. Methods 2003, 31(4):265-273.
-
(2003)
Methods
, vol.31
, Issue.4
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.P.2
-
39
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.4
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
40
-
-
32644439684
-
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
-
Harr B, Schlotterer C: Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res 2006, 34(2):e8.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.2
-
-
Harr, B.1
Schlotterer, C.2
-
41
-
-
33745291926
-
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
-
Verhaak RG, Staal FJ, Valk PJ, Lowenberg B, Reinders MJ, De Ridder D: The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. BMC Bioinformatics 2006, 7(1):105.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 105
-
-
Verhaak, R.G.1
Staal, F.J.2
Valk, P.J.3
Lowenberg, B.4
Reinders, M.J.5
De Ridder, D.6
-
42
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-140.
-
(2002)
Statistica Sinica
, vol.12
, pp. 111-140
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
43
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
44
-
-
84870640374
-
Supplementary material
-
Supplementary material [http://bioinf.wehi.edu.au/resources]
-
-
-
-
46
-
-
18744378315
-
Evaluation of the gene-specific dye bias in cDNA microarray experiments
-
Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ: Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 2005, 21(9):1995-2000.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1995-2000
-
-
Martin-Magniette, M.L.1
Aubert, J.2
Cabannes, E.3
Daudin, J.J.4
-
47
-
-
0038314004
-
Direct and indirect hybridizations for cDNA microarray experiments
-
Yang YH, Speed TP: Direct and indirect hybridizations for cDNA microarray experiments. Sankhya Series A 2002, 64:707-721.
-
(2002)
Sankhya Series A
, vol.64
, pp. 707-721
-
-
Yang, Y.H.1
Speed, T.P.2
-
48
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang YH, Speed T: Design issues for cDNA microarray experiments. Nat Rev Genet 2002, 3(8):579-588.
-
(2002)
Nat Rev Genet
, vol.3
, Issue.8
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
49
-
-
0003463572
-
Introduction to linear regression analysis
-
In 3rd edition. New York, Wiley; xvi
-
Montgomery DC, Peck EA, Vining GG: Introduction to linear regression analysis. In Wiley series in probability and mathematical statistics Applied probability and statistics, 3rd edition. New York, Wiley; 2001:xvi, 641 p..
-
(2001)
Wiley Series in Probability and Mathematical Statistics Applied Probability and Statistics
, pp. 641
-
-
Montgomery, D.C.1
Peck, E.A.2
Vining, G.G.3
-
50
-
-
2442691827
-
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
-
Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z: Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 2004, 32(9):e74.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.9
-
-
Mecham, B.H.1
Klus, G.T.2
Strovel, J.3
Augustus, M.4
Byrne, D.5
Bozso, P.6
Wetmore, D.Z.7
Mariani, T.J.8
Kohane, I.S.9
Szallasi, Z.10
-
51
-
-
84874661025
-
-
GeneChip Operating Software
-
GeneChip Operating Software [http://www.affymetrix.com]
-
-
-
-
52
-
-
0015762456
-
A human cell line from a pleural effusion derived from a breast carcinoma
-
Soule HD, Vazguez J, Long A, Albert S, Brennan M: A human cell line from a pleural effusion derived from a breast carcinoma. J Natl Cancer Inst 1973, 51(5):1409-1416.
-
(1973)
J Natl Cancer Inst
, vol.51
, Issue.5
, pp. 1409-1416
-
-
Soule, H.D.1
Vazguez, J.2
Long, A.3
Albert, S.4
Brennan, M.5
-
53
-
-
0017702412
-
Characterization of EBV-genome negative "null" and "T" cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non-Hodgkin lymphoma
-
Schneider U, Schwenk HU, Bornkamm G: Characterization of EBV-genome negative "null" and "T" cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non-Hodgkin lymphoma. Int J Cancer 1977, 19(5):621-626.
-
(1977)
Int J Cancer
, vol.19
, Issue.5
, pp. 621-626
-
-
Schneider, U.1
Schwenk, H.U.2
Bornkamm, G.3
-
54
-
-
33748865331
-
Empirical array quality weights in the analysis of microarray data
-
Ritchie ME, Diyagama D, Neilson J, van Laar R, Dobrovic A, Holloway A, Smyth GK: Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics 2006, 7(1):261.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 261
-
-
Ritchie, M.E.1
Diyagama, D.2
Neilson, J.3
van Laar, R.4
Dobrovic, A.5
Holloway, A.6
Smyth, G.K.7
-
55
-
-
0035032570
-
Statistical design and the analysis of gene expression microarray data
-
Kerr MK, Churchill GA: Statistical design and the analysis of gene expression microarray data. Genet Res 2001, 77(2):123-128.
-
(2001)
Genet Res
, vol.77
, Issue.2
, pp. 123-128
-
-
Kerr, M.K.1
Churchill, G.A.2
-
56
-
-
33644872577
-
Limma: Linear models for microarray data
-
In Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York, Springer
-
Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York, Springer; 2005:397-420.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
57
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
58
-
-
18244409933
-
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
-
Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR: Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 2002, 8(1):68-74.
-
(2002)
Nat Med
, vol.8
, Issue.1
, pp. 68-74
-
-
Shipp, M.A.1
Ross, K.N.2
Tamayo, P.3
Weng, A.P.4
Kutok, J.L.5
Aguiar, R.C.6
Gaasenbeek, M.7
Angelo, M.8
Reich, M.9
Pinkus, G.S.10
Ray, T.S.11
Koval, M.A.12
Last, K.W.13
Norton, A.14
Lister, T.A.15
Mesirov, J.16
Neuberg, D.S.17
Lander, E.S.18
Aster, J.C.19
Golub, T.R.20
more..
-
59
-
-
0035041657
-
Verification and initial annotation of the NIA mouse 15K cDNA clone set
-
Kargul GJ, Dudekula DB, Qian Y, Lim MK, Jaradat SA, Tanaka TS, Carter MG, Ko MS: Verification and initial annotation of the NIA mouse 15K cDNA clone set. Nat Genet 2001, 28(1):17-18.
-
(2001)
Nat Genet
, vol.28
, Issue.1
, pp. 17-18
-
-
Kargul, G.J.1
Dudekula, D.B.2
Qian, Y.3
Lim, M.K.4
Jaradat, S.A.5
Tanaka, T.S.6
Carter, M.G.7
Ko, M.S.8
-
60
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302(5653):2141-2144.
-
(2003)
Science
, vol.302
, Issue.5653
, pp. 2141-2144
-
-
Johnson, J.M.1
Castle, J.2
Garrett-Engele, P.3
Kan, Z.4
Loerch, P.M.5
Armour, C.D.6
Santos, R.7
Schadt, E.E.8
Stoughton, R.9
Shoemaker, D.D.10
-
61
-
-
14244263334
-
Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells
-
Relogio A, Ben-Dov C, Baum M, Ruggiu M, Gemund C, Benes V, Darnell RB, Valcarcel J: Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J Biol Chem 2005, 280(6):4779-4784.
-
(2005)
J Biol Chem
, vol.280
, Issue.6
, pp. 4779-4784
-
-
Relogio, A.1
Ben-Dov, C.2
Baum, M.3
Ruggiu, M.4
Gemund, C.5
Benes, V.6
Darnell, R.B.7
Valcarcel, J.8
-
62
-
-
27944431759
-
Detecting tissue-specific alternative splicing and disease-associated aberrant splicing of the PTCH gene with exon junction microarrays
-
Nagao K, Togawa N, Fujii K, Uchikawa H, Kohno Y, Yamada M, Miyashita T: Detecting tissue-specific alternative splicing and disease-associated aberrant splicing of the PTCH gene with exon junction microarrays. Hum Mol Genet 2005, 14(22):3379-3388.
-
(2005)
Hum Mol Genet
, vol.14
, Issue.22
, pp. 3379-3388
-
-
Nagao, K.1
Togawa, N.2
Fujii, K.3
Uchikawa, H.4
Kohno, Y.5
Yamada, M.6
Miyashita, T.7
-
63
-
-
27944446829
-
Detection and measurement of alternative splicing using splicing-sensitive microarrays
-
Srinivasan K, Shiue L, Hayes JD, Centers R, Fitzwater S, Loewen R, Edmondson LR, Bryant J, Smith M, Rommelfanger C, Welch V, Clark TA, Sugnet CW, Howe KJ, Mandel-Gutfreund Y, Ares M Jr.: Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 2005, 37(4):345-359.
-
(2005)
Methods
, vol.37
, Issue.4
, pp. 345-359
-
-
Srinivasan, K.1
Shiue, L.2
Hayes, J.D.3
Centers, R.4
Fitzwater, S.5
Loewen, R.6
Edmondson, L.R.7
Bryant, J.8
Smith, M.9
Rommelfanger, C.10
Welch, V.11
Clark, T.A.12
Sugnet, C.W.13
Howe, K.J.14
Mandel-Gutfreund, Y.15
Ares Jr., M.16
-
64
-
-
33644542406
-
Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays
-
Li C, Kato M, Shiue L, Shively JE, Ares M Jr., Lin RJ: Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Cancer Res 2006, 66(4):1990-1999.
-
(2006)
Cancer Res
, vol.66
, Issue.4
, pp. 1990-1999
-
-
Li, C.1
Kato, M.2
Shiue, L.3
Shively, J.E.4
Ares Jr., M.5
Lin, R.J.6
-
65
-
-
0038576352
-
Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer
-
Boussioutas A, Li H, Liu J, Waring P, Lade S, Holloway AJ, Taupin D, Gorringe K, Haviv I, Desmond PV, Bowtell DD: Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer. Cancer Res 2003, 63(10):2569-2577.
-
(2003)
Cancer Res
, vol.63
, Issue.10
, pp. 2569-2577
-
-
Boussioutas, A.1
Li, H.2
Liu, J.3
Waring, P.4
Lade, S.5
Holloway, A.J.6
Taupin, D.7
Gorringe, K.8
Haviv, I.9
Desmond, P.V.10
Bowtell, D.D.11
-
66
-
-
84886754344
-
-
The Spot User's Guide [http://www.cmis.csiro.au/iap/Spot/spotmanual.htm]
-
The Spot User's Guide
-
-
-
67
-
-
28444445926
-
R: A language and environment for statistical computing
-
R Core Development Team: Vienna, Austria, R Foundation for Statistical Computing
-
R Core Development Team: R: A language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing; 2005.
-
(2005)
-
-
-
68
-
-
0038048164
-
Statistical issues in cDNA microarray data analysis
-
Smyth GK, Yang YH, Speed T: Statistical issues in cDNA microarray data analysis. Methods Mol Biol 2003, 224:111-136.
-
(2003)
Methods Mol Biol
, vol.224
, pp. 111-136
-
-
Smyth, G.K.1
Yang, Y.H.2
Speed, T.3
-
69
-
-
33645847377
-
Nonlinear models
-
In Edited by: Chambers JM, Hastie TJ. Boca Raton, Chapman & Hall/CRC
-
Bates DM, Chambers JM: Nonlinear models. In Statistical Models in S Edited by: Chambers JM, Hastie TJ. Boca Raton, Chapman & Hall/CRC; 1992:421-454.
-
(1992)
Statistical Models in S
, pp. 421-454
-
-
Bates, D.M.1
Chambers, J.M.2
|