-
1
-
-
10644247621
-
Applications of DNA tiling arrays for whole-genome analysis
-
Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, et al.(2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85: 1-15.
-
(2005)
Genomics
, vol.85
, pp. 1-15
-
-
Mockler, T.C.1
Chan, S.2
Sundaresan, A.3
Chen, H.4
Jacobsen, S.E.5
-
2
-
-
23444440190
-
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
-
Bertone P, Gerstein M, Snyder M, (2005) Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res 13: 259-274.
-
(2005)
Chromosome Res
, vol.13
, pp. 259-274
-
-
Bertone, P.1
Gerstein, M.2
Snyder, M.3
-
3
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al.(2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
-
4
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al.(2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
-
5
-
-
12344291073
-
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments
-
Johnson JM, Edwards S, Shoemaker D, Schadt EE, (2005) Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 21: 93-102.
-
(2005)
Trends Genet
, vol.21
, pp. 93-102
-
-
Johnson, J.M.1
Edwards, S.2
Shoemaker, D.3
Schadt, E.E.4
-
6
-
-
0033664358
-
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
-
Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, et al.(2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18: 1262-1268.
-
(2000)
Nat Biotechnol
, vol.18
, pp. 1262-1268
-
-
Selinger, D.W.1
Cheung, K.J.2
Mei, R.3
Johansson, E.M.4
Richmond, C.S.5
-
7
-
-
0141483023
-
Probe selection for high-density oligonucleotide arrays
-
Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, et al.(2003) Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci U S A 100: 11237-11242.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 11237-11242
-
-
Mei, R.1
Hubbell, E.2
Bekiranov, S.3
Mittmann, M.4
Christians, F.C.5
-
8
-
-
0141966130
-
Statistical Algorithms Description Document
-
Affymetrix, Technical report, Affymetrix Inc Discontinued support by Affymetrix: Available:
-
Affymetrix(2002) Statistical Algorithms Description Document. Technical report, Affymetrix Inc Discontinued support by Affymetrix: Available:http://www.lrgc.ca/Reading/Affymetrix20Statistical20Algorithm20Description.pdf.
-
(2002)
-
-
-
9
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al.(2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
-
10
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
-
Li C, Wong WH, (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 98: 31-36.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
11
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu Z, Irizarry R, Gentlemen R, Martinez-Murillo F, Spencer F, (2004) A model-based background adjustment for oligonucleotide expression arrays. J Am Statist Assoc 99: 909-917.
-
(2004)
J Am Statist Assoc
, vol.99
, pp. 909-917
-
-
Wu, Z.1
Irizarry, R.2
Gentlemen, R.3
Martinez-Murillo, F.4
Spencer, F.5
-
12
-
-
33747856481
-
Transcript mapping with high-density oligonucleotide tiling arrays
-
Huber W, Toedling J, Steinmetz LM, (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22: 1963-1970.
-
(2006)
Bioinformatics
, vol.22
, pp. 1963-1970
-
-
Huber, W.1
Toedling, J.2
Steinmetz, L.M.3
-
13
-
-
33747587864
-
Model-based analysis of tiling-arrays for ChIP-chip
-
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, et al.(2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A 103: 12457-12462.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 12457-12462
-
-
Johnson, W.E.1
Li, W.2
Meyer, C.A.3
Gottardo, R.4
Carroll, J.S.5
-
14
-
-
33845369532
-
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
-
Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, et al.(2006) A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics 22: 3016-3024.
-
(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
-
15
-
-
84875399359
-
Affymetrix NimbleExpress Array Program
-
Available:
-
Affymetrix NimbleExpress Array Program. Available:http://www.affymetrix.com/products/arrays/specific/nimble.affx.
-
-
-
-
16
-
-
0037394734
-
Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays
-
Albert TJ, Norton J, Ott M, Richmond T, Nuwaysir K, et al.(2003) Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays. Nucleic Acids Res 31: e35.
-
(2003)
Nucleic Acids Res
, vol.31
-
-
Albert, T.J.1
Norton, J.2
Ott, M.3
Richmond, T.4
Nuwaysir, K.5
-
17
-
-
0036852098
-
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
-
Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, et al.(2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12: 1749-1755.
-
(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
-
19
-
-
0038239283
-
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
-
Rouillard JM, Zuker M, Gulari E, (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31: 3057-3062.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3057-3062
-
-
Rouillard, J.M.1
Zuker, M.2
Gulari, E.3
-
20
-
-
27244449595
-
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
-
Li X, He Z, Zhou J, (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 33: 6114-6123.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 6114-6123
-
-
Li, X.1
He, Z.2
Zhou, J.3
-
21
-
-
0043123142
-
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
-
Nielsen HB, Wernersson R, Knudsen S, (2003) Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31: 3491-3496.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3491-3496
-
-
Nielsen, H.B.1
Wernersson, R.2
Knudsen, S.3
-
22
-
-
23144447636
-
OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes
-
Wernersson R, Nielsen HB, (2005) OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res 33: W611-615.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Wernersson, R.1
Nielsen, H.B.2
-
23
-
-
32044460122
-
Design optimization methods for genomic DNA tiling arrays
-
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, et al.(2006) Design optimization methods for genomic DNA tiling arrays. Genome Res 16: 271-281.
-
(2006)
Genome Res
, vol.16
, pp. 271-281
-
-
Bertone, P.1
Trifonov, V.2
Rozowsky, J.S.3
Schubert, F.4
Emanuelsson, O.5
-
24
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
25
-
-
39149084716
-
Probe selection for DNA microarrays using OligoWiz
-
Wernersson R, Juncker AS, Nielsen HB, (2007) Probe selection for DNA microarrays using OligoWiz. Nat Protoc 2: 2677-2691.
-
(2007)
Nat Protoc
, vol.2
, pp. 2677-2691
-
-
Wernersson, R.1
Juncker, A.S.2
Nielsen, H.B.3
-
26
-
-
27244450872
-
Sequence dependence of cross-hybridization on short oligo microarrays
-
Wu C, Carta R, Zhang L, (2005) Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res 33: e84.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Wu, C.1
Carta, R.2
Zhang, L.3
-
27
-
-
8844269509
-
In control: systematic assessment of microarray performance
-
van Bakel H, Holstege FC, (2004) In control: systematic assessment of microarray performance. EMBO Rep 5: 964-969.
-
(2004)
EMBO Rep
, vol.5
, pp. 964-969
-
-
van Bakel, H.1
Holstege, F.C.2
-
28
-
-
11144290527
-
GeneChip® CustomExpress™ Array Design Guide
-
Affymetrix, Available:
-
Affymetrix(2003) GeneChip® CustomExpress™ Array Design Guide. Available:www.affymetrix.com/support/technical/other/custom_design_manual.pdf.
-
(2003)
-
-
-
29
-
-
34547840248
-
Optimized design and assessment of whole genome tiling arrays
-
Graf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, et al.(2007) Optimized design and assessment of whole genome tiling arrays. Bioinformatics 23: i195-204.
-
(2007)
Bioinformatics
, vol.23
-
-
Graf, S.1
Nielsen, F.G.2
Kurtz, S.3
Huynen, M.A.4
Birney, E.5
-
30
-
-
55949114130
-
Efficient algorithms for the computational design of optimal tiling arrays
-
Schliep A, Krause R, (2008) Efficient algorithms for the computational design of optimal tiling arrays. IEEE/ACM Trans Comput Biol Bioinform 5: 557-567.
-
(2008)
IEEE/ACM Trans Comput Biol Bioinform
, vol.5
, pp. 557-567
-
-
Schliep, A.1
Krause, R.2
-
31
-
-
64549125944
-
An evaluation of custom microarray applications: the oligonucleotide design challenge
-
Lemoine S, Combes F, Le Crom S, (2009) An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res 37: 1726-1739.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1726-1739
-
-
Lemoine, S.1
Combes, F.2
Le Crom, S.3
-
32
-
-
0027681165
-
Suffix Arrays - a New Method for Online String Searches
-
Manber U, Myers G, (1993) Suffix Arrays- a New Method for Online String Searches. SIAM J Comput 22: 935-938.
-
(1993)
SIAM J Comput
, vol.22
, pp. 935-938
-
-
Manber, U.1
Myers, G.2
-
33
-
-
60649100664
-
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis
-
Skotheim RI, Thomassen GO, Eken M, Lind GE, Micci F, et al.(2009) A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Mol Cancer 8: 5.
-
(2009)
Mol Cancer
, vol.8
, pp. 5
-
-
Skotheim, R.I.1
Thomassen, G.O.2
Eken, M.3
Lind, G.E.4
Micci, F.5
-
34
-
-
34249730556
-
Assessing the need for sequence-based normalization in tiling microarray experiments
-
Royce TE, Rozowsky JS, Gerstein MB, (2007) Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 23: 988-997.
-
(2007)
Bioinformatics
, vol.23
, pp. 988-997
-
-
Royce, T.E.1
Rozowsky, J.S.2
Gerstein, M.B.3
-
35
-
-
22144467302
-
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
-
Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, et al.(2005) Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 21: 466-475.
-
(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
-
36
-
-
84875405209
-
Roche NimbleGen Probe Design Fundamentals, Technical Note TN-ARAY0100
-
Available:
-
Roche NimbleGen Probe Design Fundamentals, Technical Note TN-ARAY0100. Available:http://www.nimblegen.com/products/lit/probe_design_2007_2011_2013.pdf.
-
-
-
-
37
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al.(2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
-
(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
-
38
-
-
0036713509
-
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
-
Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, et al.(2002) Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 30: 3732-3738.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3732-3738
-
-
Tjaden, B.1
Saxena, R.M.2
Stolyar, S.3
Haynor, D.R.4
Kolker, E.5
-
39
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
David L, Huber W, Granovskaia M, Toedling J, Palm CJ, et al.(2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103: 5320-5325.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5320-5325
-
-
David, L.1
Huber, W.2
Granovskaia, M.3
Toedling, J.4
Palm, C.J.5
-
40
-
-
29444438757
-
Genome-wide transcription analyses in rice using tiling microarrays
-
Li L, Wang X, Stolc V, Li X, Zhang D, et al.(2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129.
-
(2006)
Nat Genet
, vol.38
, pp. 124-129
-
-
Li, L.1
Wang, X.2
Stolc, V.3
Li, X.4
Zhang, D.5
-
41
-
-
24944497900
-
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription
-
Jiao Y, Jia P, Wang X, Su N, Yu S, et al.(2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17: 1641-1657.
-
(2005)
Plant Cell
, vol.17
, pp. 1641-1657
-
-
Jiao, Y.1
Jia, P.2
Wang, X.3
Su, N.4
Yu, S.5
-
42
-
-
20144386497
-
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
-
Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, et al.(2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A 102: 4453-4458.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 4453-4458
-
-
Stolc, V.1
Samanta, M.P.2
Tongprasit, W.3
Sethi, H.4
Liang, S.5
-
43
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M, (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 (Suppl 1): S96-104.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
, pp. 96-104
-
-
Huber, W.1
von Heydebreck, A.2
Sultmann, H.3
Poustka, A.4
Vingron, M.5
-
44
-
-
1342303735
-
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
-
Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, et al.(2003) Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 4: R9.
-
(2003)
Genome Biol
, vol.4
-
-
Bozdech, Z.1
Zhu, J.2
Joachimiak, M.P.3
Cohen, F.E.4
Pulliam, B.5
-
45
-
-
4544355898
-
Fast optimal genome tiling with applications to microarray design and homology search
-
Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, et al.(2004) Fast optimal genome tiling with applications to microarray design and homology search. J Comput Biol 11: 766-785.
-
(2004)
J Comput Biol
, vol.11
, pp. 766-785
-
-
Berman, P.1
Bertone, P.2
Dasgupta, B.3
Gerstein, M.4
Kao, M.Y.5
-
46
-
-
0345600083
-
Oligo Design: a computer program for development of probes for oligonucleotide microarrays
-
Herold KE, Rasooly A, (2003) Oligo Design: a computer program for development of probes for oligonucleotide microarrays. Biotechniques 35: 1216-1221.
-
(2003)
Biotechniques
, vol.35
, pp. 1216-1221
-
-
Herold, K.E.1
Rasooly, A.2
-
47
-
-
84870532154
-
Gene Expression Omnibus GSE13829
-
Available:, 3829
-
(3829) Gene Expression Omnibus GSE13829. Available:http://www.ncbi.nlm.nih.gov/geo/.
-
-
-
|