-
1
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467-70.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
2
-
-
17344371740
-
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
-
Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998;20:207-11.
-
(1998)
Nat Genet
, vol.20
, pp. 207-211
-
-
Pinkel, D.1
Segraves, R.2
Sudar, D.3
Clark, S.4
Poole, I.5
Kowbel, D.6
Collins, C.7
Kuo, W.L.8
Chen, C.9
Zhai, Y.10
Dairkee, S.H.11
Ljung, B.M.12
Gray, J.W.13
Albertson, D.G.14
-
3
-
-
0033031437
-
DNA arrays for analysis of gene expression
-
Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999;303:179-205.
-
(1999)
Methods Enzymol
, vol.303
, pp. 179-205
-
-
Eisen, M.B.1
Brown, P.O.2
-
4
-
-
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;13:1775-85.
-
(2003)
Genome Res
, vol.13
, 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
-
6
-
-
35748982895
-
Getting started in tiling microarray analysis
-
Liu XS. Getting started in tiling microarray analysis. PLoS Comput Biol. 2007;3:1842-4.
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 1842-1844
-
-
Liu, X.S.1
-
7
-
-
33748491718
-
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
-
Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006;24:1140-50.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1140-1150
-
-
Patterson, T.A.1
Lobenhofer, E.K.2
Fulmer-Smentek, S.B.3
Collins, P.J.4
Chu, T.M.5
Bao, W.6
Fang, H.7
Kawasaki, E.S.8
Hager, J.9
Tikhonova, I.R.10
Walker, S.J.11
Zhang, L.12
Hurban, P.13
de Longueville, F.14
Fuscoe, J.C.15
Tong, W.16
Shi, L.17
Wolfinger, R.D.18
-
8
-
-
16544386180
-
Experimental design and low-level analysis of microarray data
-
Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental design and low-level analysis of microarray data. Int Rev Neurobiol. 2004;60:25-58.
-
(2004)
Int Rev Neurobiol
, vol.60
, pp. 25-58
-
-
Bolstad, B.M.1
Collin, F.2
Simpson, K.M.3
Irizarry, R.A.4
Speed, T.P.5
-
10
-
-
28644440465
-
Combined static and dynamic analysis for determining the quality of time-series expression profiles
-
Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol. 2005;23:1503-8.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1503-1508
-
-
Simon, I.1
Siegfried, Z.2
Ernst, J.3
Bar-Joseph, Z.4
-
11
-
-
0041336612
-
Effects of atmospheric ozone on microarray data quality
-
Fare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y. Effects of atmospheric ozone on microarray data quality. Anal Chem. 2003;75:4672-5.
-
(2003)
Anal Chem
, vol.75
, pp. 4672-4675
-
-
Fare, T.L.1
Coffey, E.M.2
Dai, H.3
He, Y.D.4
Kessler, D.A.5
Kilian, K.A.6
Koch, J.E.7
LeProust, E.8
Marton, M.J.9
Meyer, M.R.10
Stoughton, R.B.11
Tokiwa, G.Y.12
Wang, Y.13
-
13
-
-
1342294092
-
Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002;30:e15.
-
(2002)
Nucleic Acids Res
, vol.30
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
-
14
-
-
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;19:185-93.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
15
-
-
2942601439
-
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
-
Wang J, Bo TH, Jonassen I, Myklebost O, Hovig E. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 2003;4:60.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 60
-
-
Wang, J.1
Bo, T.H.2
Jonassen, I.3
Myklebost, O.4
Hovig, E.5
-
16
-
-
2942511784
-
Clustering of the SOM easily reveals distinct gene expression patterns: Results of a reanalysis of lymphoma study
-
Wang J, Delabie J, Aasheim H, Smeland E, Myklebost O. Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics. 2002;3:36.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 36
-
-
Wang, J.1
Delabie, J.2
Aasheim, H.3
Smeland, E.4
Myklebost, O.5
-
17
-
-
0034598746
-
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
-
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503-11.
-
(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 Jr, 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
Levy, R.25
Wilson, W.26
Grever, M.R.27
Byrd, J.C.28
Botstein, D.29
Brown, P.O.30
Staudt, L.M.31
more..
-
19
-
-
34147104969
-
A faster circular binary segmentation algorithm for the analysis of array CGH data
-
Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007;23:657-63.
-
(2007)
Bioinformatics
, vol.23
, pp. 657-663
-
-
Venkatraman, E.S.1
Olshen, A.B.2
-
20
-
-
0345327603
-
MGraph: Graphical models for microarray data analysis
-
Wang J, Myklebost O, Hovig E. MGraph: graphical models for microarray data analysis. Bioinformatics. 2003;19:2210-1.
-
(2003)
Bioinformatics
, vol.19
, pp. 2210-2211
-
-
Wang, J.1
Myklebost, O.2
Hovig, E.3
-
21
-
-
0345928693
-
Building and analysing genome-wide gene disruption networks
-
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Building and analysing genome-wide gene disruption networks. Bioinformatics. 2002;18 Suppl 2:S202-10.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Rung, J.1
Schlitt, T.2
Brazma, A.3
Freivalds, K.4
Vilo, J.5
-
22
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 2004;306:655-60.
-
(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
Bussemaker, H.J.11
White, K.P.12
-
23
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics. 2001;2:183-201.
-
(2001)
Biostatistics
, vol.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
24
-
-
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;77:123-8.
-
(2001)
Genet Res
, vol.77
, pp. 123-128
-
-
Kerr, M.K.1
Churchill, G.A.2
-
25
-
-
0037114470
-
Power and sample size for DNA microarray studies
-
Lee ML, Whitmore, G.A. Power and sample size for DNA microarray studies. Stat Med. 2002;21:3543-70.
-
(2002)
Stat Med
, vol.21
, pp. 3543-3570
-
-
Lee, M.L.1
Whitmore, G.A.2
-
26
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet. 2002;3:579-88.
-
(2002)
Nat Rev Genet
, vol.3
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
27
-
-
34547665470
-
Microarray data analysis: An overview of design, methodology, and analysis
-
Weeraratna AT, Taub DD. Microarray data analysis: an overview of design, methodology, and analysis. Methods Mol Biol. 2007;377:1-16.
-
(2007)
Methods Mol Biol
, vol.377
, pp. 1-16
-
-
Weeraratna, A.T.1
Taub, D.D.2
-
28
-
-
0036678784
-
MArray: Analysing single, replicated or reversed microarray experiments
-
Wang J, Nygaard V, Smith-Sorensen B, Hovig E, Myklebost O. MArray: analysing single, replicated or reversed microarray experiments. Bioinformatics. 2002;18:1139-40.
-
(2002)
Bioinformatics
, vol.18
, pp. 1139-1140
-
-
Wang, J.1
Nygaard, V.2
Smith-Sorensen, B.3
Hovig, E.4
Myklebost, O.5
-
29
-
-
85036949117
-
-
The R Project for Statistical Computing. http://www.r-project.org/
-
-
-
-
30
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
31
-
-
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:e15.
-
(2003)
Nucleic Acids Res
, vol.31
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
32
-
-
0033957466
-
Database resources of the National Center for Biotechnology Information
-
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2000;28:10-4.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 10-14
-
-
Wheeler, D.L.1
Chappey, C.2
Lash, A.E.3
Leipe, D.D.4
Madden, T.L.5
Schuler, G.D.6
Tatusova, T.A.7
Rapp, B.A.8
-
33
-
-
34547840228
-
Continuous hidden process model for time series expression experiments
-
Shi Y, Klustein M, Simon I, Mitchell T, Bar-Joseph Z. Continuous hidden process model for time series expression experiments. Bioinformatics. 2007;23:i459-67.
-
(2007)
Bioinformatics
, vol.23
, Issue.I459-67
-
-
Shi, Y.1
Klustein, M.2
Simon, I.3
Mitchell, T.4
Bar-Joseph, Z.5
-
34
-
-
13844250828
-
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
-
Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002;99:12963-8.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12963-12968
-
-
Pollack, J.R.1
Sorlie, T.2
Perou, C.M.3
Rees, C.A.4
Jeffrey, S.S.5
Lonning, P.E.6
Tibshirani, R.7
Botstein, D.8
Borresen-Dale, A.L.9
Brown, P.O.10
-
35
-
-
33748272115
-
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
-
Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 2006;16:1136-48.
-
(2006)
Genome Res
, vol.16
, pp. 1136-1148
-
-
Peiffer, D.A.1
Le, J.M.2
Steemers, F.J.3
Chang, W.4
Jenniges, T.5
Garcia, F.6
Haden, K.7
Li, J.8
Shaw, C.A.9
Belmont, J.10
Cheung, S.W.11
Shen, R.M.12
Barker, D.L.13
Gunderson, K.L.14
-
36
-
-
38049123402
-
MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia
-
Mi S, Lu J, Sun M, Li Z, Zhang H, Neilly MB, Wang Y, Qian Z, Jin J, Zhang Y, Bohlander SK, Le Beau MM, Larson RA, Golub TR, Rowley JD, Chen J. MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc Natl Acad Sci USA. 2007;104:19971-6.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19971-19976
-
-
Mi, S.1
Lu, J.2
Sun, M.3
Li, Z.4
Zhang, H.5
Neilly, M.B.6
Wang, Y.7
Qian, Z.8
Jin, J.9
Zhang, Y.10
Bohlander, S.K.11
Le Beau, M.M.12
Larson, R.A.13
Golub, T.R.14
Rowley, J.D.15
Chen, J.16
-
37
-
-
35448950862
-
Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites
-
Zhang C, Hastings ML, Krainer AR, Zhang MQ. Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites. Proc Natl Acad Sci USA. 2007;104:15028-33.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 15028-15033
-
-
Zhang, C.1
Hastings, M.L.2
Krainer, A.R.3
Zhang, M.Q.4
-
38
-
-
84860506529
-
Mining ChIP-chip data for transcription factor and cofactor binding sites
-
Smith AD, Sumazin P, Das D, Zhang MQ. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics. 2005;21 Suppl 1:i403-12.
-
(2005)
Bioinformatics
, Issue.SUPPL. 1 i403-12
, pp. 21
-
-
Smith, A.D.1
Sumazin, P.2
Das, D.3
Zhang, M.Q.4
-
39
-
-
33845290262
-
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1
-
Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1. Genome Res. 2006;16:1585-95.
-
(2006)
Genome Res
, vol.16
, pp. 1585-1595
-
-
Jin, V.X.1
Rabinovich, A.2
Squazzo, S.L.3
Green, R.4
Farnham, P.J.5
-
40
-
-
36949023082
-
A nucleosome-guided map of transcription factor binding sites in yeast
-
Narlikar L, Gordan R, Hartemink AJ. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol. 2007;3:e215.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Narlikar, L.1
Gordan, R.2
Hartemink, A.J.3
-
41
-
-
0033027794
-
Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
-
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA. 1999;96:2907-12.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2907-2912
-
-
Tamayo, P.1
Slonim, D.2
Mesirov, J.3
Zhu, Q.4
Kitareewan, S.5
Dmitrovsky, E.6
Lander, E.S.7
Golub, T.R.8
-
42
-
-
27544451127
-
Simple decision rules for classifying human cancers from gene expression profiles
-
Tan AC, Naiman DQ, Xu L, Winslow RL, Geman D. Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics. 2005;21:3896-904.
-
(2005)
Bioinformatics
, vol.21
, pp. 3896-3904
-
-
Tan, A.C.1
Naiman, D.Q.2
Xu, L.3
Winslow, R.L.4
Geman, D.5
-
43
-
-
33847665105
-
Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
-
Price ND, Trent J, El-Naggar AK, Cogdell D, Taylor E, Hunt KK, Pollock RE, Hood L, Shmulevich I, Zhang W. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci USA. 2007;104:3414-9.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 3414-3419
-
-
Price, N.D.1
Trent, J.2
El-Naggar, A.K.3
Cogdell, D.4
Taylor, E.5
Hunt, K.K.6
Pollock, R.E.7
Hood, L.8
Shmulevich, I.9
Zhang, W.10
-
44
-
-
15844413351
-
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
-
Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics. 2005;21:631-43.
-
(2005)
Bioinformatics
, vol.21
, pp. 631-643
-
-
Statnikov, A.1
Aliferis, C.F.2
Tsamardinos, I.3
Hardin, D.4
Levy, S.5
-
45
-
-
33749499031
-
Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas
-
Meza-Zepeda LA, Kresse SH, Barragan-Polania AH, Bjerkehagen B, Ohnstad, HO, Namlos HM, Wang J, Kristiansen BE, Myklebost O. Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas. Cancer Res. 2006;66:8984-93.
-
(2006)
Cancer Res
, vol.66
, pp. 8984-8993
-
-
Meza-Zepeda, L.A.1
Kresse, S.H.2
Barragan-Polania, A.H.3
Bjerkehagen, B.4
Ohnstad, H.O.5
Namlos, H.M.6
Wang, J.7
Kristiansen, B.E.8
Myklebost, O.9
-
46
-
-
10744231187
-
Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation
-
Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, West JA, Rostan S, Nguyen KC, Powers S, Ye KQ, Olshen A, Venkatraman E, Norton L, Wigler M. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003;13:2291-305.
-
(2003)
Genome Res
, vol.13
, pp. 2291-2305
-
-
Lucito, R.1
Healy, J.2
Alexander, J.3
Reiner, A.4
Esposito, D.5
Chi, M.6
Rodgers, L.7
Brady, A.8
Sebat, J.9
Troge, J.10
West, J.A.11
Rostan, S.12
Nguyen, K.C.13
Powers, S.14
Ye, K.Q.15
Olshen, A.16
Venkatraman, E.17
Norton, L.18
Wigler, M.19
-
47
-
-
37349084293
-
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data
-
Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA. Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. BMC Bioinformatics. 2007;8:368.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 368
-
-
Baross, A.1
Delaney, A.D.2
Li, H.I.3
Nayar, T.4
Flibotte, S.5
Qian, H.6
Chan, S.Y.7
Asano, J.8
Ally, A.9
Cao, M.10
Birch, P.11
Brown-John, M.12
Fernandes, N.13
Go, A.14
Kennedy, G.15
Langlois, S.16
Eydoux, P.17
Friedman, J.M.18
Marra, M.A.19
-
48
-
-
22244453416
-
A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays
-
Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Ogawa S. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 2005;65:6071-9.
-
(2005)
Cancer Res
, vol.65
, pp. 6071-6079
-
-
Nannya, Y.1
Sanada, M.2
Nakazaki, K.3
Hosoya, N.4
Wang, L.5
Hangaishi, A.6
Kurokawa, M.7
Chiba, S.8
Bailey, D.K.9
Kennedy, G.C.10
Ogawa, S.11
-
49
-
-
2342453338
-
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays
-
Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 2004;64:3060-71.
-
(2004)
Cancer Res
, vol.64
, pp. 3060-3071
-
-
Zhao, X.1
Li, C.2
Paez, J.G.3
Chin, K.4
Janne, P.A.5
Chen, T.H.6
Girard, L.7
Minna, J.8
Christiani, D.9
Leo, C.10
Gray, J.W.11
Sellers, W.R.12
Meyerson, M.13
-
50
-
-
10844232112
-
Whole genome DNA copy number changes identified by high density oligonucleotide arrays
-
Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics. 2004;1:287-99.
-
(2004)
Hum Genomics
, vol.1
, pp. 287-299
-
-
Huang, J.1
Wei, W.2
Zhang, J.3
Liu, G.4
Bignell, G.R.5
Stratton, M.R.6
Futreal, P.A.7
Wooster, R.8
Jones, K.W.9
Shapero, M.H.10
-
51
-
-
35948984173
-
PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
-
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665-74.
-
(2007)
Genome Res
, vol.17
, pp. 1665-1674
-
-
Wang, K.1
Li, M.2
Hadley, D.3
Liu, R.4
Glessner, J.5
Grant, S.F.6
Hakonarson, H.7
Bucan, M.8
-
52
-
-
0033707946
-
-
Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol. 2000;7:601-20.
-
Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol. 2000;7:601-20.
-
-
-
-
53
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 2002;9:67-103.
-
(2002)
J Comput Biol
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
54
-
-
0037461033
-
Dynamic modeling of genetic networks using genetic algorithm and S-system
-
Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics. 2003;19:643-50.
-
(2003)
Bioinformatics
, vol.19
, pp. 643-650
-
-
Kikuchi, S.1
Tominaga, D.2
Arita, M.3
Takahashi, K.4
Tomita, M.5
-
55
-
-
28744449703
-
New probabilistic graphical models for genetic regulatory networks studies
-
Wang J, Cheung LW, Delabie J. New probabilistic graphical models for genetic regulatory networks studies. J Biomed Inform. 2005;38:443-55.
-
(2005)
J Biomed Inform
, vol.38
, pp. 443-455
-
-
Wang, J.1
Cheung, L.W.2
Delabie, J.3
-
56
-
-
0142179209
-
Prediction of regulatory networks: Genome-wide identification of transcription factor targets from gene expression data
-
Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003;19:1917-26.
-
(2003)
Bioinformatics
, vol.19
, pp. 1917-1926
-
-
Qian, J.1
Lin, J.2
Luscombe, N.M.3
Yu, H.4
Gerstein, M.5
-
57
-
-
36049002205
-
A new framework for identifying combinatorial regulation of transcription factors: A case study of the yeast cell cycle
-
Wang J. A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle. J Biomed Inform. 2007;40:707-25.
-
(2007)
J Biomed Inform
, vol.40
, pp. 707-725
-
-
Wang, J.1
-
58
-
-
0035733752
-
The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
-
Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet. 2001;29:389-95.
-
(2001)
Nat Genet
, vol.29
, pp. 389-395
-
-
Jin, W.1
Riley, R.M.2
Wolfinger, R.D.3
White, K.P.4
Passador-Gurgel, G.5
Gibson, G.6
-
59
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003;21:1337-42.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
60
-
-
13844253637
-
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
-
Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL. A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics. 2005;21:349-56.
-
(2005)
Bioinformatics
, vol.21
, pp. 349-356
-
-
Beal, M.J.1
Falciani, F.2
Ghahramani, Z.3
Rangel, C.4
Wild, D.L.5
-
61
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
Werhli AV, Grzegorczyk M, Husmeier D. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics. 2006;22:2523-31.
-
(2006)
Bioinformatics
, vol.22
, pp. 2523-2531
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
62
-
-
29244456166
-
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
-
Yugi K, Nakayama Y, Kojima S, Kitayama T, Tomita M. A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. BMC Bioinformatics. 2005;6:299.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 299
-
-
Yugi, K.1
Nakayama, Y.2
Kojima, S.3
Kitayama, T.4
Tomita, M.5
-
63
-
-
33745440791
-
-
Das D, Nahle Z, Zhang MQ. Adaptively inferring human transcriptional subnetworks. Mol Syst Biol. 2006;2:2006.0029.
-
Das D, Nahle Z, Zhang MQ. Adaptively inferring human transcriptional subnetworks. Mol Syst Biol. 2006;2:2006.0029.
-
-
-
-
64
-
-
38849171836
-
Reliable prediction of regulator targets using 12 Drosophila genomes
-
Kheradpour P, Stark A, Roy S, Kellis M. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res. 2007;17:1919-31.
-
(2007)
Genome Res
, vol.17
, pp. 1919-1931
-
-
Kheradpour, P.1
Stark, A.2
Roy, S.3
Kellis, M.4
-
65
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617-24.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
66
-
-
14044252090
-
Conservation and evolution of cis-regulatory systems in ascomycete fungi
-
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2004;2:e398.
-
(2004)
PLoS Biol
, vol.2
-
-
Gasch, A.P.1
Moses, A.M.2
Chiang, D.Y.3
Fraser, H.B.4
Berardini, M.5
Eisen, M.B.6
-
67
-
-
1242316281
-
ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 2004;83:349-60.
-
(2004)
Genomics
, vol.83
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
68
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nat Genet. 2001;27:167-71.
-
(2001)
Nat Genet
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
69
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel Y, Sudarsanam P, Church, GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001;29:153-9.
-
(2001)
Nat Genet
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
70
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
-
Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics. 2006;22:e141-9.
-
(2006)
Bioinformatics
, vol.22
-
-
Foat, B.C.1
Morozov, A.V.2
Bussemaker, H.J.3
-
71
-
-
33747072322
-
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
-
Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci USA. 2006;103:12027-32.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12027-12032
-
-
Moorman, C.1
Sun, L.V.2
Wang, J.3
de Wit, E.4
Talhout, W.5
Ward, L.D.6
Greil, F.7
Lu, X.J.8
White, K.P.9
Bussemaker, H.J.10
van Steensel, B.11
-
72
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 2006;16:962-72.
-
(2006)
Genome Res
, vol.16
, pp. 962-972
-
-
Tanay, A.1
-
73
-
-
34547653033
-
Predictive models of gene regulation: Application of regression methods to microarray data
-
Das D, Zhang MQ. Predictive models of gene regulation: application of regression methods to microarray data. Methods Mol Biol. 2007;377:95-110.
-
(2007)
Methods Mol Biol
, vol.377
, pp. 95-110
-
-
Das, D.1
Zhang, M.Q.2
-
74
-
-
9244257298
-
Interacting models of cooperative gene regulation
-
Das D, Banerjee N, Zhang MQ. Interacting models of cooperative gene regulation. Proc Natl Acad Sci USA. 2004;101:16234-9.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 16234-16239
-
-
Das, D.1
Banerjee, N.2
Zhang, M.Q.3
-
75
-
-
34347237542
-
Predictive modeling of genome-wide mRNA expression: From modules to molecules
-
Bussemaker HJ, Foat BC, Ward LD. Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annu Rev Biophys Biomol Struct. 2007;36:329-47.
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 329-347
-
-
Bussemaker, H.J.1
Foat, B.C.2
Ward, L.D.3
-
76
-
-
0345743695
-
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
-
Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci USA. 2004;101:641-6.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 641-646
-
-
Kao, K.C.1
Yang, Y.L.2
Boscolo, R.3
Sabatti, C.4
Roychowdhury, V.5
Liao, J.C.6
-
77
-
-
27744485351
-
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
-
Lin LH, Lee HC, Li WH, Chen BS. Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics. 2005;6:258.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 258
-
-
Lin, L.H.1
Lee, H.C.2
Li, W.H.3
Chen, B.S.4
-
78
-
-
23744491001
-
Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach
-
Boulesteix AL, Strimmer K. Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model. 2005;2:23.
-
(2005)
Theor Biol Med Model
, vol.2
, pp. 23
-
-
Boulesteix, A.L.1
Strimmer, K.2
-
79
-
-
33645108505
-
Using a state-space model with hidden variables to infer transcription factor activities
-
Li Z, Shaw SM, Yedwabnick MJ, Chan C. Using a state-space model with hidden variables to infer transcription factor activities. Bioinformatics. 2006;22:747-54.
-
(2006)
Bioinformatics
, vol.22
, pp. 747-754
-
-
Li, Z.1
Shaw, S.M.2
Yedwabnick, M.J.3
Chan, C.4
-
80
-
-
33745038921
-
Ranked prediction of p53 targets using hidden variable dynamic modeling
-
Barenco M, Tomescu D, Brewer D, Callard R, Stark J, Hubank M. Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biol. 2006;7:R25.
-
(2006)
Genome Biol
, vol.7
-
-
Barenco, M.1
Tomescu, D.2
Brewer, D.3
Callard, R.4
Stark, J.5
Hubank, M.6
-
81
-
-
85036935302
-
Quantitative Model for inferring dynamic regulation of the tumor suppressor gene p53
-
In preparation
-
Wang JT, Tian TH. Quantitative Model for inferring dynamic regulation of the tumor suppressor gene p53. In preparation.
-
-
-
Wang, J.T.1
Tian, T.H.2
-
82
-
-
33745605801
-
Stochastic transcriptional regulatory systems with time delays: A mean-field approximation
-
Goutsias J, Kim S. Stochastic transcriptional regulatory systems with time delays: a mean-field approximation. J Comput Biol. 2006;13:1049-76.
-
(2006)
J Comput Biol
, vol.13
, pp. 1049-1076
-
-
Goutsias, J.1
Kim, S.2
-
83
-
-
34249856850
-
Bayesian model-based inference of transcription factor activity
-
Rogers S, Khanin R, Girolami M. Bayesian model-based inference of transcription factor activity. BMC Bioinformatics. 2007;8 Suppl 2:S2.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 2
-
-
Rogers, S.1
Khanin, R.2
Girolami, M.3
-
84
-
-
0035236830
-
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
-
Chiang DY, Brown PO, Eisen MB. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics. 2001;17 Suppl 1:S49-55.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Chiang, D.Y.1
Brown, P.O.2
Eisen, M.B.3
-
85
-
-
33745434510
-
-
Bussemaker HJ. Modeling gene expression control using Omes Law. Mol Syst Biol. 2006;2:2006.0013.
-
Bussemaker HJ. Modeling gene expression control using Omes Law. Mol Syst Biol. 2006;2:2006.0013.
-
-
-
-
86
-
-
33845365903
-
A Gibbs sampler for the identification of gene expression and network connectivity consistency
-
Brynildsen MP, Tran LM, Liao JC. A Gibbs sampler for the identification of gene expression and network connectivity consistency. Bioinformatics. 2006;22:3040-6.
-
(2006)
Bioinformatics
, vol.22
, pp. 3040-3046
-
-
Brynildsen, M.P.1
Tran, L.M.2
Liao, J.C.3
-
87
-
-
33947359083
-
A classification-based framework for predicting and analyzing gene regulatory response
-
Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics. 2006;7 Suppl 1:S5.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 1
-
-
Kundaje, A.1
Middendorf, M.2
Shah, M.3
Wiggins, C.H.4
Freund, Y.5
Leslie, C.6
-
88
-
-
14744275223
-
Predicting genetic regulatory response using classification
-
Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification. Bioinformatics. 2004;20 Suppl 1:i232-40.
-
(2004)
Bioinformatics
, Issue.SUPPL. 1 i232-40
, pp. 20
-
-
Middendorf, M.1
Kundaje, A.2
Wiggins, C.3
Freund, Y.4
Leslie, C.5
-
89
-
-
36949030484
-
Predicting gene expression from sequence: A reexamination
-
Yuan Y, Guo L, Shen L, Liu JS. Predicting gene expression from sequence: a reexamination. PLoS Comput Biol. 2007;3:e243.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yuan, Y.1
Guo, L.2
Shen, L.3
Liu, J.S.4
-
90
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
Segal E, Yelensky R, Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics. 2003;19 Suppl 1:i273-82.
-
(2003)
Bioinformatics
, Issue.SUPPL. 1 i273-82
, pp. 19
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
91
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 2004;117:185-98.
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
92
-
-
38749127589
-
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature. 2008.
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature. 2008.
-
-
-
-
93
-
-
13544254744
-
Identifying combinatorial regulation of transcription factors and binding motifs
-
Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 2004;5:R56.
-
(2004)
Genome Biol
, vol.5
-
-
Kato, M.1
Hata, N.2
Banerjee, N.3
Futcher, B.4
Zhang, M.Q.5
-
94
-
-
33748694308
-
Identification of transcription factor cooperativity via stochastic system model
-
Chang YH, Wang YC, Chen BS. Identification of transcription factor cooperativity via stochastic system model. Bioinformatics. 2006;22:2276-82.
-
(2006)
Bioinformatics
, vol.22
, pp. 2276-2282
-
-
Chang, Y.H.1
Wang, Y.C.2
Chen, B.S.3
-
95
-
-
33745449162
-
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
-
Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol. 2006;360:213-27.
-
(2006)
J Mol Biol
, vol.360
, pp. 213-227
-
-
Balaji, S.1
Babu, M.M.2
Iyer, L.M.3
Luscombe, N.M.4
Aravind, L.5
-
96
-
-
22344434546
-
Discovering functional transcription-factor combinations in the human cell cycle
-
Zhu Z, Shendure J, Church, G.M. Discovering functional transcription-factor combinations in the human cell cycle. Genome Res 2005;15:848-55.
-
(2005)
Genome Res
, vol.15
, pp. 848-855
-
-
Zhu, Z.1
Shendure, J.2
Church, G.M.3
-
97
-
-
33750217984
-
Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues
-
Yu X, Lin J, Zack DJ, Qian J. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 2006;34:4925-36.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4925-4936
-
-
Yu, X.1
Lin, J.2
Zack, D.J.3
Qian, J.4
-
99
-
-
85036943272
-
-
Microarray Software Suite
-
Microarray Software Suite: http://www.tm4.org/index.html.
-
-
-
-
100
-
-
0037099005
-
-
Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 2002;3:SOFTWARE0003.
-
Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 2002;3:SOFTWARE0003.
-
-
-
-
101
-
-
0038005018
-
DAVID: Database for Annotation, Visualization, and Integrated Discovery
-
Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003;4:P3.
-
(2003)
Genome Biol
, vol.4
-
-
Dennis Jr, G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
Lempicki, R.A.7
-
102
-
-
0037208157
-
NetAffx: Affymetrix probesets and annotations
-
Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp, D, Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003;31:82-6.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 82-86
-
-
Liu, G.1
Loraine, A.E.2
Shigeta, R.3
Cline, M.4
Cheng, J.5
Valmeekam, V.6
Sun, S.7
Kulp, D.8
Siani-Rose, M.A.9
-
103
-
-
36549052737
-
A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R
-
Alvord, WG, Roayaei JA, Quinones OA, Schneider KT. A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R. Brief Bioinform. 2007;8:415-31.
-
(2007)
Brief Bioinform
, vol.8
, pp. 415-431
-
-
Alvord, W.G.1
Roayaei, J.A.2
Quinones, O.A.3
Schneider, K.T.4
-
104
-
-
33750354315
-
Back to the future: Education for systems-level biologists
-
Wingreen N, Botstein D. Back to the future: education for systems-level biologists. Nat Rev Mol Cell Biol. 2006;7:829-32.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 829-832
-
-
Wingreen, N.1
Botstein, D.2
-
105
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823-37.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
106
-
-
34147098535
-
An expression atlas of rice mRNAs and small RNAs
-
Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang GL, Meyers BC. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 2007;25:473-7.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 473-477
-
-
Nobuta, K.1
Venu, R.C.2
Lu, C.3
Belo, A.4
Vemaraju, K.5
Kulkarni, K.6
Wang, W.7
Pillay, M.8
Green, P.J.9
Wang, G.L.10
Meyers, B.C.11
-
107
-
-
36049018312
-
-
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007;450:219-32.
-
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007;450:219-32.
-
-
-
-
108
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi, M, Birren, B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003;423:241-54.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
109
-
-
33750314698
-
Collecting and organizing systematic sets of protein data
-
Albeck JG, MacBeath G, White FM, Sorger PK, Lauffenburger DA, Gaudet S. Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol. 2006;7:803-12.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 803-812
-
-
Albeck, J.G.1
MacBeath, G.2
White, F.M.3
Sorger, P.K.4
Lauffenburger, D.A.5
Gaudet, S.6
-
110
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007;448:553-60.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
111
-
-
38049054726
-
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
-
Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res. 2008;18:46-59.
-
(2008)
Genome Res
, vol.18
, pp. 46-59
-
-
Barrera, L.O.1
Li, Z.2
Smith, A.D.3
Arden, K.C.4
Cavenee, W.K.5
Zhang, M.Q.6
Green, R.D.7
Ren, B.8
-
112
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39:311-8.
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
Wang, W.11
Weng, Z.12
Green, R.D.13
Crawford, G.E.14
Ren, B.15
-
113
-
-
34250359062
-
ENCODE: More genomic empowerment
-
Weinstock GM. ENCODE: more genomic empowerment. Genome Res. 2007;17:667-8.
-
(2007)
Genome Res
, vol.17
, pp. 667-668
-
-
Weinstock, G.M.1
-
114
-
-
38349118310
-
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species
-
Wang X, Gu J, Zhang MQ, Li Y. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics. 2008;24:165-71.
-
(2008)
Bioinformatics
, vol.24
, pp. 165-171
-
-
Wang, X.1
Gu, J.2
Zhang, M.Q.3
Li, Y.4
-
115
-
-
37548999369
-
Computational epigenetics
-
Bock C, Lengauer, T Computational epigenetics. Bioinformatics. 2008;24:1-10.
-
(2008)
Bioinformatics
, vol.24
, pp. 1-10
-
-
Bock, C.1
Lengauer, T.2
-
116
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast species. Science. 2007;317:815-9.
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
Gianoulis, T.A.2
Zhang, Z.D.3
Yu, H.4
Rozowsky, J.5
Seringhaus, M.R.6
Wang, L.Y.7
Gerstein, M.8
Snyder, M.9
-
117
-
-
34548359013
-
Transcription factor binding site identification in yeast: A comparison of high-density oligonucleotide and PCR-based microarray platforms
-
Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007;7:7335-45.
-
(2007)
Funct Integr Genomics
, vol.7
, pp. 7335-7345
-
-
Borneman, A.R.1
Zhang, Z.D.2
Rozowsky, J.3
Seringhaus, M.R.4
Gerstein, M.5
Snyder, M.6
-
118
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005;434:338-45.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
119
-
-
40549121344
-
Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast
-
Lusk RW, Eisen,MB. Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. Pac Symp Biocomput 2008, 489-500.
-
(2008)
Pac Symp Biocomput
, pp. 489-500
-
-
Lusk, R.W.1
Eisen, M.B.2
-
120
-
-
40549105160
-
-
Gordan R, HA. Using DNA duplex stability information for transcription factor binding site discovery. Presented at Pac Symp Biocomput. 2008 (In press).
-
Gordan R, HA. Using DNA duplex stability information for transcription factor binding site discovery. Presented at Pac Symp Biocomput. 2008 (In press).
-
-
-
-
121
-
-
40549122037
-
-
M, MRaB Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Presented at Pac Symp Biocompute. 2008 (In press).
-
M, MRaB Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Presented at Pac Symp Biocompute. 2008 (In press).
-
-
-
-
122
-
-
32144452542
-
Sequence features of DNA binding sites reveal structural class of associated transcription factor
-
Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics. 2006;22:157-63.
-
(2006)
Bioinformatics
, vol.22
, pp. 157-163
-
-
Narlikar, L.1
Hartemink, A.J.2
-
123
-
-
35348955882
-
A universal framework for regulatory element discovery across all genomes and data types
-
Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007;28:337-50.
-
(2007)
Mol Cell
, vol.28
, pp. 337-350
-
-
Elemento, O.1
Slonim, N.2
Tavazoie, S.3
-
124
-
-
34547540506
-
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting
-
Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci USA. 2007;104:6305-10.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 6305-6310
-
-
Sosinsky, A.1
Honig, B.2
Mann, R.S.3
Califano, A.4
-
125
-
-
34249080596
-
Theoretical analysis of epigenetic cell memory by nucleosome modification
-
Dodd IB, Micheelsen MA, Sneppen K, Thon G. Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell. 2007;129:813-22.
-
(2007)
Cell
, vol.129
, pp. 813-822
-
-
Dodd, I.B.1
Micheelsen, M.A.2
Sneppen, K.3
Thon, G.4
-
126
-
-
37349024107
-
Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae
-
Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol. 2007;3:153.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 153
-
-
Pham, H.1
Ferrari, R.2
Cokus, S.J.3
Kurdistani, S.K.4
Pellegrini, M.5
-
127
-
-
33846351302
-
Precise physical models of protein-DNA interaction from high-throughput data
-
Kinney JB, Tkacik G, Callan CG Jr. Precise physical models of protein-DNA interaction from high-throughput data. Proc Natl Acad Sci U S A. 2007;104:501-6.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 501-506
-
-
Kinney, J.B.1
Tkacik, G.2
Callan Jr., C.G.3
-
128
-
-
34548758543
-
Splicing in disease: Disruption of the splicing code and the decoding machinery
-
Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet. 2007;8:749-61.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 749-761
-
-
Wang, G.S.1
Cooper, T.A.2
-
129
-
-
34347260600
-
Living with noisy genes: How cells function reliably with inherent variability in gene expression
-
Maheshri N, O'Shea EK. Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu Rev Biophys Biomol Struct. 2007;36:413-34.
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 413-434
-
-
Maheshri, N.1
O'Shea, E.K.2
-
130
-
-
37549013383
-
The effects of molecular noise and size control on variability in the budding yeast cell cycle
-
Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007;450:1272.
-
(2007)
Nature
, vol.450
, pp. 1272
-
-
Di Talia, S.1
Skotheim, J.M.2
Bean, J.M.3
Siggia, E.D.4
Cross, F.R.5
-
131
-
-
25444468618
-
Noise in gene expression: Origins, consequences, and control
-
Raser JM, O'Shea EK. Noise in gene expression: origins, consequences, and control. Science. 2005;309:2010-3.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
133
-
-
34548411011
-
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells
-
Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet. 2007;3:e145.
-
(2007)
PLoS Genet
, vol.3
-
-
Grskovic, M.1
Chaivorapol, C.2
Gaspar-Maia, A.3
Li, H.4
Ramalho-Santos, M.5
-
134
-
-
37349050790
-
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression
-
Hon LS, Zhang Z. The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol. 2007;8:R166.
-
(2007)
Genome Biol
, vol.8
-
-
Hon, L.S.1
Zhang, Z.2
-
135
-
-
34748821761
-
The role of site accessibility in microRNA target recognition
-
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet. 2007;39:1278-84.
-
(2007)
Nat Genet
, vol.39
, pp. 1278-1284
-
-
Kertesz, M.1
Iovino, N.2
Unnerstall, U.3
Gaul, U.4
Segal, E.5
-
136
-
-
34547555796
-
Global and local architecture of the mammalian microRNA-transcription factor regulatory network
-
Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol. 2007;3:e131.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shalgi, R.1
Lieber, D.2
Oren, M.3
Pilpel, Y.4
-
137
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
SShannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498-504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
SShannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
|