-
1
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
10.1126/science.270.5235.467 7569999
-
Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995 270 467-470 10.1126/science.270.5235.467 7569999
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
2
-
-
0026108692
-
Light-directed, spatially addressable parallel chemical synthesis
-
10.1126/science.1990438 1990438
-
Fodor SP Read JL Pirrung MC Stryer L Lu AT Solas D Light-directed, spatially addressable parallel chemical synthesis. Science 1991 251 767-773 10.1126/science.1990438 1990438
-
(1991)
Science
, vol.251
, pp. 767-773
-
-
Fodor, S.P.1
Read, J.L.2
Pirrung, M.C.3
Stryer, L.4
Lu, A.T.5
Solas, D.6
-
3
-
-
0042121254
-
ExpressYourself: A modular platform for processing and visualizing microarray data
-
169034 12824348 10.1093/nar/gkg628
-
Luscombe NM Royce TE Bertone P Echols N Horak CE Chang JT Snyder M Gerstein M ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res 2003 31 3477-3482 169034 12824348 10.1093/nar/gkg628
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3477-3482
-
-
Luscombe, N.M.1
Royce, T.E.2
Bertone, P.3
Echols, N.4
Horak, C.E.5
Chang, J.T.6
Snyder, M.7
Gerstein, M.8
-
4
-
-
0037311919
-
TM4: A free, open-source system for microarray data management and analysis
-
12613259
-
Saeed AI Sharov V White J Li J Liang W Bhagabati N Braisted J Klapa M Currier T Thiagarajan M et al TM4: A free, open-source system for microarray data management and analysis. Biotechniques 2003 34 374-378 12613259
-
(2003)
Biotechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
-
6
-
-
0036852098
-
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
-
187555 12421762 10.1101/gr.362402
-
Nuwaysir EF Huang W Albert TJ Singh J Nuwaysir K Pitas A Richmond T Gorski T Berg JP Ballin J et al Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 2002 12 1749-1755 187555 12421762 10.1101/gr.362402
-
(2002)
Genome Res
, vol.12
, pp. 1749-1755
-
-
Nuwaysir, E.F.1
Huang, W.2
Albert, T.J.3
Singh, J.4
Nuwaysir, K.5
Pitas, A.6
Richmond, T.7
Gorski, T.8
Berg, J.P.9
Ballin, J.10
-
7
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
10.1126/science.1103388 15539566
-
Bertone P Stolc V Royce TE Rozowsky JS Urban AE Zhu X Rinn JL Tongprasit W Samanta M Weissman S et al Global identification of human transcribed sequences with genome tiling arrays. Science 2004 306 2242-2246 10.1126/ science.1103388 15539566
-
(2004)
Science
, vol.306
, pp. 2242-2246
-
-
Bertone, P.1
Stolc, V.2
Royce, T.E.3
Rozowsky, J.S.4
Urban, A.E.5
Zhu, X.6
Rinn, J.L.7
Tongprasit, W.8
Samanta, M.9
Weissman, S.10
-
8
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
10.1126/science.1101312 15499012
-
Stolc V Gauhar Z Mason C Halasz G van Batenburg MF Rifkin SA Hua S Herreman T Tongprasit W Barbano PE et al A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 2004 306 655-660 10.1126/science.1101312 15499012
-
(2004)
Science
, vol.306
, pp. 655-660
-
-
Stolc, V.1
Gauhar, Z.2
Mason, C.3
Halasz, G.4
van Batenburg, M.F.5
Rifkin, S.A.6
Hua, S.7
Herreman, T.8
Tongprasit, W.9
Barbano, P.E.10
-
9
-
-
20144386497
-
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
-
555476 15755812 10.1073/pnas.0408203102
-
Stolc V Samanta MP Tongprasit W Sethi H Liang S Nelson DC Hegeman A Nelson C Rancour D Bednarek S et al Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA 2005 102 4453-4458 555476 15755812 10.1073/pnas.0408203102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4453-4458
-
-
Stolc, V.1
Samanta, M.P.2
Tongprasit, W.3
Sethi, H.4
Liang, S.5
Nelson, D.C.6
Hegeman, A.7
Nelson, C.8
Rancour, D.9
Bednarek, S.10
-
10
-
-
12144287461
-
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
-
353210 14993201 10.1101/gr.2094104
-
Kampa D Cheng J Kapranov P Yamanaka M Brubaker S Cawley S Drenkow J Piccolboni A Bekiranov S Helt G et al Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004 14 331-342 353210 14993201 10.1101/gr.2094104
-
(2004)
Genome Res
, vol.14
, pp. 331-342
-
-
Kampa, D.1
Cheng, J.2
Kapranov, P.3
Yamanaka, M.4
Brubaker, S.5
Cawley, S.6
Drenkow, J.7
Piccolboni, A.8
Bekiranov, S.9
Helt, G.10
-
11
-
-
0036270889
-
ChIP-chip: A genomic approach for identifying transcription factor binding sites
-
12073330
-
Horak CE Snyder M ChIP-chip: A genomic approach for identifying transcription factor binding sites. Methods Enzymol 2002 350 469-483 12073330
-
(2002)
Methods Enzymol
, vol.350
, pp. 469-483
-
-
Horak, C.E.1
Snyder, M.2
-
12
-
-
33645243394
-
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays
-
1450206 16537408 10.1073/pnas.0511340103
-
Urban AE Korbel JO Selzer R Richmond T Hacker A Popescu GV Cubells JF Green R Emanuel BS Gerstein MB et al High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci USA 2006 103 4534-4539 1450206 16537408 10.1073/pnas.0511340103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 4534-4539
-
-
Urban, A.E.1
Korbel, J.O.2
Selzer, R.3
Richmond, T.4
Hacker, A.5
Popescu, G.V.6
Cubells, J.F.7
Green, R.8
Emanuel, B.S.9
Gerstein, M.B.10
-
13
-
-
23944462969
-
Genome-wide map of nucleosome acetylation and methylation in yeast
-
10.1016/j.cell.2005.06.026 16122420
-
Pokholok DK Harbison CT Levine S Cole M Hannett NM Lee TI Bell GW Walker K Rolfe PA Herbolsheimer E Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 2005 122 517-527 10.1016/j.cell.2005.06.026 16122420
-
(2005)
Cell
, vol.122
, pp. 517-527
-
-
Pokholok, D.K.1
Harbison, C.T.2
Levine, S.3
Cole, M.4
Hannett, N.M.5
Lee, T.I.6
Bell, G.W.7
Walker, K.8
Rolfe, P.A.9
Herbolsheimer, E.10
-
15
-
-
22144467302
-
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
-
10.1016/j.tig.2005.06.007 15979196 1855044
-
Royce TE Rozowsky JS Bertone P Samanta M Stolc V Weissman S Snyder M Gerstein M Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005 21 466-475 10.1016/ j.tig.2005.06.007 15979196 1855044
-
(2005)
Trends Genet
, vol.21
, pp. 466-475
-
-
Royce, T.E.1
Rozowsky, J.S.2
Bertone, P.3
Samanta, M.4
Stolc, V.5
Weissman, S.6
Snyder, M.7
Gerstein, M.8
-
17
-
-
33747856481
-
Transcript mapping with high-density oligonucleotide tiling arrays
-
10.1093/bioinformatics/btl289 16787969
-
Huber W Toedling J Steinmetz LM Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 2006 22 1963-1970 10.1093/ bioinformatics/btl289 16787969
-
(2006)
Bioinformatics
, vol.22
, pp. 1963-1970
-
-
Huber, W.1
Toedling, J.2
Steinmetz, L.M.3
-
22
-
-
0034786939
-
Unfolding of microarray data
-
10.1089/106652701752236232 11571077
-
Goryachev AB Macgregor PF Edwards AM Unfolding of microarray data. J Comput Biol 2001 8 443-461 10.1089/106652701752236232 11571077
-
(2001)
J Comput Biol
, vol.8
, pp. 443-461
-
-
Goryachev, A.B.1
Macgregor, P.F.2
Edwards, A.M.3
-
23
-
-
0036376993
-
Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments
-
Dudoit S Yang YH Callow MJ Speed TP Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Stat Sin 2002 12 111-139
-
(2002)
Stat Sin
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
24
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
10.1093/bioinformatics/19.2.185 12538238
-
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 19 185-193 10.1093/bioinformatics/19.2.185 12538238
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
25
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
10.1016/S0092-8674(04)00127-8 14980218
-
Cawley S Bekiranov S Ng HH Kapranov P Sekinger EA Kampa D Piccolboni A Sementchenko V Cheng J Williams AJ et al Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004 116 499-509 10.1016/S0092-8674(04)00127-8 14980218
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
Kampa, D.6
Piccolboni, A.7
Sementchenko, V.8
Cheng, J.9
Williams, A.J.10
-
26
-
-
0036856209
-
Nonparametric methods for identifying differentially expressed genes in microarray data
-
10.1093/bioinformatics/18.11.1454 12424116
-
Troyanskaya OG Garber ME Brown PO Botstein D Altman RB Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 2002 18 1454-1461 10.1093/bioinformatics/18.11.1454 12424116
-
(2002)
Bioinformatics
, vol.18
, pp. 1454-1461
-
-
Troyanskaya, O.G.1
Garber, M.E.2
Brown, P.O.3
Botstein, D.4
Altman, R.B.5
-
27
-
-
33845369532
-
A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: Systematically incorporating validated biological knowledge
-
10.1093/bioinformatics/btl515 17038339
-
Du J Rozowsky JS Korbel JO Zhang ZD Royce TE Schultz MH Snyder M Gerstein M A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: Systematically incorporating validated biological knowledge. Bioinformatics 2006 22 3016-3024 10.1093/bioinformatics/ btl515 17038339
-
(2006)
Bioinformatics
, vol.22
, pp. 3016-3024
-
-
Du, J.1
Rozowsky, J.S.2
Korbel, J.O.3
Zhang, Z.D.4
Royce, T.E.5
Schultz, M.H.6
Snyder, M.7
Gerstein, M.8
-
28
-
-
34250376888
-
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
-
Emanuelsson O Nagalakshmi U Zheng D Rozowsky JS Urban AE Du J Lian Z Stolc V Weissman S Snyder M et al Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res 2007
-
(2007)
Genome Res
-
-
Emanuelsson, O.1
Nagalakshmi, U.2
Zheng, D.3
Rozowsky, J.S.4
Urban, A.E.5
Du, J.6
Lian, Z.7
Stolc, V.8
Weissman, S.9
Snyder, M.10
-
29
-
-
33745295639
-
A hidden Markov model approach for determining expression from genomic tiling micro arrays
-
1481622 16672042 10.1186/1471-2105-7-239
-
Munch K Gardner PP Arctander P Krogh A A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics 2006 7 239 1481622 16672042 10.1186/1471-2105-7-239
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 239
-
-
Munch, K.1
Gardner, P.P.2
Arctander, P.3
Krogh, A.4
-
30
-
-
24644438062
-
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
-
10.1093/bioinformatics/bti1046 15961467
-
Li W Meyer CA Liu XS A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005 21 Suppl 1 i274-i282 10.1093/ bioinformatics/bti1046 15961467
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Li, W.1
Meyer, C.A.2
Liu, X.S.3
-
31
-
-
24644462724
-
TileMap: Create chromosomal map of tiling array hybridizations
-
10.1093/bioinformatics/bti593 16046496
-
Ji H Wong WH TileMap: Create chromosomal map of tiling array hybridizations. Bioinformatics 2005 21 3629-3636 10.1093/bioinformatics/ bti593 16046496
-
(2005)
Bioinformatics
, vol.21
, pp. 3629-3636
-
-
Ji, H.1
Wong, W.H.2
-
32
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: An overview
-
10.1093/bioinformatics/16.5.412 10871264
-
Baldi P Brunak S Chauvin Y Andersen CA Nielsen H Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics 2000 16 412-424 10.1093/bioinformatics/16.5.412 10871264
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.4
Nielsen, H.5
-
33
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
1180967
-
Matthews BW Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975 405 442-451 1180967
-
(1975)
Biochim Biophys Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
34
-
-
1942425486
-
Improving profile HMM discrimination by adapting transition probabilities
-
10.1016/j.jmb.2004.03.023 15099750
-
Wistrand M Sonnhammer EL Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol 2004 338 847-854 10.1016/ j.jmb.2004.03.023 15099750
-
(2004)
J Mol Biol
, vol.338
, pp. 847-854
-
-
Wistrand, M.1
Sonnhammer, E.L.2
-
35
-
-
46049120549
-
-
Tilescope http://tilescope.gersteinlab.org/
-
-
-
-
36
-
-
46049109833
-
-
Tilescope Download http://tilescope.gersteinlab.org/download.html
-
-
-
-
37
-
-
46049097879
-
-
Bioconductor http://www.bioconductor.org/
-
-
-
-
38
-
-
46049098273
-
-
TAS http://www.affymetrix.com/support/developer/downloads/ TilingArrayTools/index.affx
-
-
-
-
39
-
-
46049120736
-
-
MAT http://chip.dfci.harvard.edu/~wli/MAT/
-
-
-
-
40
-
-
46049114801
-
-
TileMap http://biogibbs.stanford.edu/~jihk/TileMap/index.htm
-
-
-
|