-
1
-
-
35748950713
-
Exploring the functional landscape of gene expression: Directed search of large microarray compendia
-
Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, et al. (2007) Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 23: 2692-2699.
-
(2007)
Bioinformatics
, vol.23
, pp. 2692-2699
-
-
Hibbs, M.A.1
Hess, D.C.2
Myers, C.L.3
Huttenhower, C.4
Li, K.5
-
2
-
-
63449085311
-
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis
-
Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, et al. (2009) Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet 5: e1000407.
-
(2009)
PLoS Genet
, vol.5
-
-
Hess, D.C.1
Myers, C.L.2
Huttenhower, C.3
Hibbs, M.A.4
Hayes, A.P.5
-
3
-
-
47549116997
-
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
-
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 9: Suppl 1:S2.
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Pena-Castillo, L.1
Tasan, M.2
Myers, C.L.3
Lee, H.4
Joshi, T.5
-
4
-
-
47549108100
-
Predicting gene function in a hierarchical context with an ensemble of classifiers
-
Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, et al. (2008) Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol 9: Suppl 1: S3.
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Guan, Y.1
Myers, C.L.2
Hess, D.C.3
Barutcuoglu, Z.4
Caudy, A.A.5
-
5
-
-
33845220382
-
IntNetDB v1.0: An integrated protein-protein interaction network database generated by a probabilistic model
-
Xia K, Dong D, Han JD (2006) IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics 7: 508.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 508
-
-
Xia, K.1
Dong, D.2
Han, J.D.3
-
6
-
-
33745113181
-
Discovery of biological networks from diverse functional genomic data
-
Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, et al. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol 6: R114.
-
(2005)
Genome Biol
, vol.6
-
-
Myers, C.L.1
Robson, D.2
Wible, A.3
Hibbs, M.A.4
Chiriac, C.5
-
7
-
-
38649138295
-
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
-
Lee I, Lehner B, Crombie C, Wong W, Fraser AG, et al. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181-188.
-
(2008)
Nat Genet
, vol.40
, pp. 181-188
-
-
Lee, I.1
Lehner, B.2
Crombie, C.3
Wong, W.4
Fraser, A.G.5
-
8
-
-
52949087576
-
A genomewide functional network for the laboratory mouse
-
Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, et al. (2008) A genomewide functional network for the laboratory mouse. PLoS Comput Biol 4: e1000165.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Guan, Y.1
Myers, C.L.2
Lu, R.3
Lemischka, I.R.4
Bult, C.J.5
-
9
-
-
66449120271
-
Exploring the human genome with functional maps
-
Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, et al. (2009) Exploring the human genome with functional maps. Genome Res.
-
(2009)
Genome Res
-
-
Huttenhower, C.1
Haley, E.M.2
Hibbs, M.A.3
Dumeaux, V.4
Barrett, D.R.5
-
10
-
-
33846871449
-
Next-generation sequencing outpaces expectations
-
Shaffer C (2007) Next-generation sequencing outpaces expectations. Nat Biotechnol 25: 149.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 149
-
-
Shaffer, C.1
-
11
-
-
43249117094
-
Functional maps of protein complexes from quantitative genetic interaction data
-
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T (2008) Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4: e1000065.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Bandyopadhyay, S.1
Kelley, R.2
Krogan, N.J.3
Ideker, T.4
-
12
-
-
64249139133
-
The automation of science
-
King RD, Rowland J, Oliver SG, Young M, Aubrey W, et al. (2009) The automation of science. Science 324: 85-89.
-
(2009)
Science
, vol.324
, pp. 85-89
-
-
King, R.D.1
Rowland, J.2
Oliver, S.G.3
Young, M.4
Aubrey, W.5
-
14
-
-
18744413287
-
Estimating misclassification error with small samples via bootstrap cross-validation
-
Fu WJ, Carroll RJ, Wang S (2005) Estimating misclassification error with small samples via bootstrap cross-validation. Bioinformatics 21: 1979-1986.
-
(2005)
Bioinformatics
, vol.21
, pp. 1979-1986
-
-
Fu, W.J.1
Carroll, R.J.2
Wang, S.3
-
15
-
-
0036810412
-
Interplay of TBP inhibitors in global transcriptional control
-
Chitikila C, Huisinga KL, Irvin JD, Basehoar AD, Pugh BF (2002) Interplay of TBP inhibitors in global transcriptional control. Mol Cell 10: 871-882.
-
(2002)
Mol Cell
, vol.10
, pp. 871-882
-
-
Chitikila, C.1
Huisinga, K.L.2
Irvin, J.D.3
Basehoar, A.D.4
Pugh, B.F.5
-
16
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
-
(2002)
Science
, vol.296
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
17
-
-
21644460849
-
Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures
-
Boer VM, Daran JM, Almering MJ, de Winde JH, Pronk JT (2005) Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res 5: 885-897.
-
(2005)
FEMS Yeast Res
, vol.5
, pp. 885-897
-
-
Boer, V.M.1
Daran, J.M.2
Almering, M.J.3
de Winde, J.H.4
Pronk, J.T.5
-
19
-
-
13444306165
-
The landscape of genetic complexity across 5,700 gene expression traits in yeast
-
Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 102: 1572-1577.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 1572-1577
-
-
Brem, R.B.1
Kruglyak, L.2
-
20
-
-
0042856391
-
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
-
Yvert G, Brem RB, Whittle J, Akey JM, Foss E, et al. (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57-64.
-
(2003)
Nat Genet
, vol.35
, pp. 57-64
-
-
Yvert, G.1
Brem, R.B.2
Whittle, J.3
Akey, J.M.4
Foss, E.5
-
21
-
-
12844281816
-
Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae
-
Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, et al. (2005) Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437-447.
-
(2005)
J Biol Chem
, vol.280
, pp. 437-447
-
-
Tai, S.L.1
Boer, V.M.2
Daran-Lapujade, P.3
Walsh, M.C.4
de Winde, J.H.5
-
22
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
-
(1998)
Mol Biol Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
-
23
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
-
24
-
-
0035807884
-
A second iron-regulatory system in yeast independent of Aft1p
-
Rutherford JC, Jaron S, Ray E, Brown PO, Winge DR (2001) A second iron-regulatory system in yeast independent of Aft1p. Proc Natl Acad Sci U S A 98: 14322-14327.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 14322-14327
-
-
Rutherford, J.C.1
Jaron, S.2
Ray, E.3
Brown, P.O.4
Winge, D.R.5
-
25
-
-
0347355518
-
Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure
-
Fernandes PM, Domitrovic T, Kao CM, Kurtenbach E (2004) Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure. FEBS Lett 556: 153-160.
-
(2004)
FEBS Lett
, vol.556
, pp. 153-160
-
-
Fernandes, P.M.1
Domitrovic, T.2
Kao, C.M.3
Kurtenbach, E.4
-
26
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
-
27
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
-
28
-
-
33748513704
-
Finding function: Evaluation methods for functional genomic data
-
Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics 7: 187.
-
(2006)
BMC Genomics
, vol.7
, pp. 187
-
-
Myers, C.L.1
Barrett, D.R.2
Hibbs, M.A.3
Huttenhower, C.4
Troyanskaya, O.G.5
-
29
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
30
-
-
19344374050
-
Similarities and differences in genome-wide expression data of six organisms
-
Bergmann S, Ihmels J, Barkai N (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2: E9.
-
(2004)
PLoS Biol
, vol.2
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
31
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: Application to the Candida albicans transcription program
-
Ihmels J, Bergmann S, Berman J, Barkai N (2005) Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1: e39.
-
(2005)
PLoS Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
32
-
-
33846039701
-
ArrayExpress-a public database of microarray experiments and gene expression profiles
-
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, et al. (2007) ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35: D747-750.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Parkinson, H.1
Kapushesky, M.2
Shojatalab, M.3
Abeygunawardena, N.4
Coulson, R.5
-
33
-
-
0035165508
-
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
-
Ball CA, Jin H, Sherlock G, Weng S, Matese JC, et al. (2001) Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res 29: 80-81.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 80-81
-
-
Ball, C.A.1
Jin, H.2
Sherlock, G.3
Weng, S.4
Matese, J.C.5
-
34
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
35
-
-
0036088110
-
yMGV: Helping biologists with yeast microarray data mining
-
Le Crom S, Devaux F, Jacq C, Marc P (2002) yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res 30: 76-79.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 76-79
-
-
Le Crom, S.1
Devaux, F.2
Jacq, C.3
Marc, P.4
-
36
-
-
38549107989
-
The Stanford Tissue Microarray Database
-
Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, et al. (2008) The Stanford Tissue Microarray Database. Nucleic Acids Res 36: D871-877.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Marinelli, R.J.1
Montgomery, K.2
Liu, C.L.3
Shah, N.H.4
Prapong, W.5
-
37
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, et al. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525.
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
-
40
-
-
0001165055
-
Frequency distribution of the values of the correlation coefficients in samples from an indefinitely large population
-
Fisher RA (1915) Frequency distribution of the values of the correlation coefficients in samples from an indefinitely large population. Biometrika 10: 507-521.
-
(1915)
Biometrika
, vol.10
, pp. 507-521
-
-
Fisher, R.A.1
|