-
1
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
2-s2.0-0028806048
-
Schena M., Shalon D., Davis R. W., Brown P. O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995 270 5235 467 470 2-s2.0-0028806048
-
(1995)
Science
, vol.270
, Issue.5235
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
2
-
-
52949096084
-
Next-generation DNA sequencing methods
-
2-s2.0-52949096084 10.1146/annurev.genom.9.081307.164359
-
Mardis E. R., Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 2008 9 387 402 2-s2.0-52949096084 10.1146/annurev.genom.9.081307.164359
-
(2008)
Annual Review of Genomics and Human Genetics
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
3
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas Network
-
Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 2012 490 61 70
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
4
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
2-s2.0-79959838081 10.1038/nature10166
-
Bell D., Berchuck A., Birrer M., Chien J., Cramer D. W., Dao F., Dhir R., Disaia P., Gabra H., Glenn P., Godwin A. K., Gross J., Hartmann L., Huang M., Huntsman D. G., Iacocca M., Imielinski M., Kalloger S., Karlan B. Y., Levine D. A., Mills G. B., Morrison C., Mutch D., Olvera N., Orsulic S., Park K., Petrelli N., Rabeno B., Rader J. S., Sikic B. I., Smith-Mccune K., Sood A. K., Bowtell D., Penny R., Testa J. R., Chang K., Dinh H. H., Drummond J. A., Fowler G., Gunaratne P., Hawes A. C., Kovar C. L., Lewis L. R., Morgan M. B., Newsham I. F., Santibanez J., Reid J. G., Trevino L. R., Wu Y. Q., Wang M., Muzny D. M., Wheeler D. A., Gibbs R. A., Getz G., Lawrence M. S., Cibulskis K., Sivachenko A. Y., Sougnez C., Voet D., Wilkinson J., Bloom T., Ardlie K., Fennell T., Baldwin J., Gabriel S., Lander E. S., Ding L., Fulton R. S., Koboldt D. C., McLellan M. D., Wylie T., Walker J., O'Laughlin M., Dooling D. J., Fulton L., Abbott R., Dees N. D., Zhang Q., Kandoth C., Wendl M., Schierding W., Shen D., Harris C. C., Schmidt H., Kalicki J., Delehaunty K. D., Fronick C. C., Demeter R., Cook L., Wallis J. W., Lin L., Magrini V. J., Hodges J. S., Eldred J. M., Smith S. M., Pohl C. S., Vandin F., Raphael B. J., Weinstock G. M., Mardis E. R., Wilson R. K., Meyerson M., Winckler W., Getz G., Verhaak R. G. W., Carter S. L., Mermel C. H., Saksena G., Nguyen H., Onofrio R. C., Lawrence M. S., Hubbard D., Gupta S., Crenshaw A., Ramos A. H., Ardlie K., Chin L., Protopopov A., Zhang J., Kim T. M., Perna I., Xiao Y., Zhang H., Ren G., Sathiamoorthy N., Park R. W., Lee E., Park P. J., Kucherlapati R., Absher D. M., Waite L., Sherlock G., Brooks J. D., Li J. Z., Xu J., Myers R. M., Laird P. W., Cope L., Herman J. G., Shen H., Weisenberger D. J., Noushmehr H., Pan F., Triche T., Berman B. P., Van Den Berg D. J., Buckley J., Baylin S. B., Spellman P. T., Purdom E., Neuvial P., Bengtsson H., Jakkula L. R., Durinck S., Han J., Dorton S., Marr H., Choi Y. G., Wang V., Wang N. J., Ngai J., Conboy J. G., Parvin B., Feiler H. S., Speed T. P., Gray J. W., Levine D. A., Socci N. D., Liang Y., Taylor B. S., Schultz N., Borsu L., Lash A. E., Brennan C., Viale A., Sander C., Ladanyi M., Hoadley K. A., Meng S., Du Y., Shi Y., Li L., Turman Y. J., Zang D., Helms E. B., Balu S., Zhou X., Wu J., Topal M. D., Hayes D. N., Perou C. M., Getz G., Voet D., Saksena G., Zhang J., Zhang H., Wu C. J., Shukla S., Cibulskis K., Lawrence M. S., Sivachenko A., Jing R., Park R. W., Liu Y., Park P. J., Noble M., Chin L., Carter H., Kim D., Karchin R., Spellman P. T., Purdom E., Neuvial P., Bengtsson H., Durinck S., Han J., Korkola J. E., Heiser L. M., Cho R. J., Hu Z., Parvin B., Speed T. P., Gray J. W., Schultz N., Cerami E., Taylor B. S., Olshen A., Reva B., Antipin Y., Shen R., Mankoo P., Sheridan R., Ciriello G., Chang W. K., Bernanke J. A., Borsu L., Levine D. A., Ladanyi M., Sander C., Haussler D., Benz C. C., Stuart J. M., Benz S. C., Sanborn J. Z., Vaske C. J., Zhu J., Szeto C., Scott G. K., Yau C., Hoadley K. A., Du Y., Balu S., Hayes D. N., Perou C. M., Wilkerson M. D., Zhang N., Akbani R., Baggerly K. A., Yung W. K., Mills G. B., Weinstein J. N., Penny R., Shelton T., Grimm D., Hatfield M., Morris S., Yena P., Rhodes P., Sherman M., Paulauskis J., Millis S., Kahn A., Greene J. M., Sfeir R., Jensen M. A., Chen J., Whitmore J., Alonso S., Jordan J., Chu A., Zhang J., Barker A., Compton C., Eley G., Ferguson M., Fielding P., Gerhard D. S., Myles R., Schaefer C., Mills Shaw K. R., Vaught J., Vockley J. B., Good P. J., Guyer M. S., Ozenberger B., Peterson J., Thomson E., Integrated genomic analyses of ovarian carcinoma. Nature 2011 474 7353 609 615 2-s2.0-79959838081 10.1038/nature10166
-
(2011)
Nature
, vol.474
, Issue.7353
, pp. 609-615
-
-
Bell, D.1
Berchuck, A.2
Birrer, M.3
Chien, J.4
Cramer, D.W.5
Dao, F.6
Dhir, R.7
Disaia, P.8
Gabra, H.9
Glenn, P.10
Godwin, A.K.11
Gross, J.12
Hartmann, L.13
Huang, M.14
Huntsman, D.G.15
Iacocca, M.16
Imielinski, M.17
Kalloger, S.18
Karlan, B.Y.19
Levine, D.A.20
Mills, G.B.21
Morrison, C.22
Mutch, D.23
Olvera, N.24
Orsulic, S.25
Park, K.26
Petrelli, N.27
Rabeno, B.28
Rader, J.S.29
Sikic, B.I.30
Smith-Mccune, K.31
Sood, A.K.32
Bowtell, D.33
Penny, R.34
Testa, J.R.35
Chang, K.36
Dinh, H.H.37
Drummond, J.A.38
Fowler, G.39
Gunaratne, P.40
Hawes, A.C.41
Kovar, C.L.42
Lewis, L.R.43
Morgan, M.B.44
Newsham, I.F.45
Santibanez, J.46
Reid, J.G.47
Trevino, L.R.48
Wu, Y.Q.49
Wang, M.50
Muzny, D.M.51
Wheeler, D.A.52
Gibbs, R.A.53
Getz, G.54
Lawrence, M.S.55
Cibulskis, K.56
Sivachenko, A.Y.57
Sougnez, C.58
Voet, D.59
Wilkinson, J.60
Bloom, T.61
Ardlie, K.62
Fennell, T.63
Baldwin, J.64
Gabriel, S.65
Lander, E.S.66
Ding, L.67
Fulton, R.S.68
Koboldt, D.C.69
McLellan, M.D.70
Wylie, T.71
Walker, J.72
O'Laughlin, M.73
Dooling, D.J.74
Fulton, L.75
Abbott, R.76
Dees, N.D.77
Zhang, Q.78
Kandoth, C.79
Wendl, M.80
Schierding, W.81
Shen, D.82
Harris, C.C.83
Schmidt, H.84
Kalicki, J.85
Delehaunty, K.D.86
Fronick, C.C.87
Demeter, R.88
Cook, L.89
Wallis, J.W.90
Lin, L.91
Magrini, V.J.92
Hodges, J.S.93
Eldred, J.M.94
Smith, S.M.95
Pohl, C.S.96
Vandin, F.97
Raphael, B.J.98
Weinstock, G.M.99
more..
-
5
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
2-s2.0-54549108740 10.1038/nature07385
-
McLendon R., Friedman A., Bigner D., Van Meir E. G., Brat D. J., Mastrogianakis G. M., Olson J. J., Mikkelsen T., Lehman N., Aldape K., Yung W. K. A., Bogler O., Weinstein J. N., VandenBerg S., Berger M., Prados M., Muzny D., Morgan M., Scherer S., Sabo A., Nazareth L., Lewis L., Hall O., Zhu Y., Ren Y., Alvi O., Yao J., Hawes A., Jhangiani S., Fowler G., San Lucas A., Kovar C., Cree A., Dinh H., Santibanez J., Joshi V., Gonzalez-Garay M. L., Miller C. A., Milosavljevic A., Donehower L., Wheeler D. A., Gibbs R. A., Cibulskis K., Sougnez C., Fennell T., Mahan S., Wilkinson J., Ziaugra L., Onofrio R., Bloom T., Nicol R., Ardlie K., Baldwin J., Gabriel S., Lander E. S., Ding L., Fulton R. S., McLellan M. D., Wallis J., Larson D. E., Shi X., Abbott R., Fulton L., Chen K., Koboldt D. C., Wendl M. C., Meyer R., Tang Y., Lin L., Osborne J. R., Dunford-Shore B. H., Miner T. L., Delehaunty K., Markovic C., Swift G., Courtney W., Pohl C., Abbott S., Hawkins A., Leong S., Haipek C., Schmidt H., Wiechert M., Vickery T., Scott S., Dooling D. J., Chinwalla A., Weinstock G. M., Mardis E. R., Wilson R. K., Getz G., Winckler W., Verhaak R. G. W., Lawrence M. S., O'Kelly M., Robinson J., Alexe G., Beroukhim R., Carter S., Chiang D., Gould J., Gupta S., Korn J., Mermel C., Mesirov J., Monti S., Nguyen H., Parkin M., Reich M., Stransky N., Weir B. A., Garraway L., Golub T., Meyerson M., Chin L., Protopopov A., Zhang J., Perna I., Aronson S., Sathiamoorthy N., Ren G., Yao J., Wiedemeyer W. R., Kim H., Sek W. K., Xiao Y., Kohane I. S., Seidman J., Park P. J., Kucherlapati R., Laird P. W., Cope L., Herman J. G., Weisenberger D. J., Pan F., Van Den Berg D., Van Neste L., Joo M. Y., Schuebel K. E., Baylin S. B., Absher D. M., Li J. Z., Southwick A., Brady S., Aggarwal A., Chung T., Sherlock G., Brooks J. D., Myers R. M., Spellman P. T., Purdom E., Jakkula L. R., Lapuk A. V., Marr H., Dorton S., Yoon G. C., Han J., Ray A., Wang V., Durinck S., Robinson M., Wang N. J., Vranizan K., Peng V., Van Name E., Fontenay G. V., Ngai J., Conboy J. G., Parvin B., Feiler H. S., Speed T. P., Gray J. W., Brennan C., Socci N. D., Olshen A., Taylor B. S., Lash A., Schultz N., Reva B., Antipin Y., Stukalov A., Gross B., Cerami E., Wei Q. W., Qin L. X., Seshan V. E., Villafania L., Cavatore M., Borsu L., Viale A., Gerald W., Sander C., Ladanyi M., Perou C. M., Hayes D. N., Topal M. D., Hoadley K. A., Qi Y., Balu S., Shi Y., Wu J., Penny R., Bittner M., Shelton T., Lenkiewicz E., Morris S., Beasley D., Sanders S., Kahn A., Sfeir R., Chen J., Nassau D., Feng L., Hickey E., Barker A., Gerhard D. S., Vockley J., Compton C., Vaught J., Fielding P., Ferguson M. L., Schaefer C., Zhang J., Madhavan S., Buetow K. H., Collins F., Good P., Guyer M., Ozenberger B., Peterson J., Thomson E., Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008 455 7216 1061 1068 2-s2.0-54549108740 10.1038/nature07385
-
(2008)
Nature
, vol.455
, Issue.7216
, pp. 1061-1068
-
-
McLendon, R.1
Friedman, A.2
Bigner, D.3
Van Meir, E.G.4
Brat, D.J.5
Mastrogianakis, G.M.6
Olson, J.J.7
Mikkelsen, T.8
Lehman, N.9
Aldape, K.10
Yung, W.K.A.11
Bogler, O.12
Weinstein, J.N.13
Vandenberg, S.14
Berger, M.15
Prados, M.16
Muzny, D.17
Morgan, M.18
Scherer, S.19
Sabo, A.20
Nazareth, L.21
Lewis, L.22
Hall, O.23
Zhu, Y.24
Ren, Y.25
Alvi, O.26
Yao, J.27
Hawes, A.28
Jhangiani, S.29
Fowler, G.30
San Lucas, A.31
Kovar, C.32
Cree, A.33
Dinh, H.34
Santibanez, J.35
Joshi, V.36
Gonzalez-Garay, M.L.37
Miller, C.A.38
Milosavljevic, A.39
Donehower, L.40
Wheeler, D.A.41
Gibbs, R.A.42
Cibulskis, K.43
Sougnez, C.44
Fennell, T.45
Mahan, S.46
Wilkinson, J.47
Ziaugra, L.48
Onofrio, R.49
Bloom, T.50
Nicol, R.51
Ardlie, K.52
Baldwin, J.53
Gabriel, S.54
Lander, E.S.55
Ding, L.56
Fulton, R.S.57
McLellan, M.D.58
Wallis, J.59
Larson, D.E.60
Shi, X.61
Abbott, R.62
Fulton, L.63
Chen, K.64
Koboldt, D.C.65
Wendl, M.C.66
Meyer, R.67
Tang, Y.68
Lin, L.69
Osborne, J.R.70
Dunford-Shore, B.H.71
Miner, T.L.72
Delehaunty, K.73
Markovic, C.74
Swift, G.75
Courtney, W.76
Pohl, C.77
Abbott, S.78
Hawkins, A.79
Leong, S.80
Haipek, C.81
Schmidt, H.82
Wiechert, M.83
Vickery, T.84
Scott, S.85
Dooling, D.J.86
Chinwalla, A.87
Weinstock, G.M.88
Mardis, E.R.89
Wilson, R.K.90
Getz, G.91
Winckler, W.92
Verhaak, R.G.W.93
Lawrence, M.S.94
O'Kelly, M.95
Robinson, J.96
Alexe, G.97
Beroukhim, R.98
Carter, S.99
more..
-
6
-
-
0034680102
-
Molecular portraits of human breast tumours
-
10.1038/35021093
-
Perou C. M., Sørile T., Eisen M. B., Van De Rijn M., Jeffrey S. S., Ress C. A., Pollack J. R., Ross D. T., Johnsen H., Akslen L. A., Fluge Ø., Pergammenschlkov A., Williams C., Zhu S. X., Lønning P. E., Børresen-Dale A.-L., Brown P. O., Botstein D., Molecular portraits of human breast tumours. Nature 2000 406 6797 747 752 10.1038/35021093
-
(2000)
Nature
, vol.406
, Issue.6797
, pp. 747-752
-
-
Perou, C.M.1
Sørile, T.2
Eisen, M.B.3
Van De Rijn, M.4
Jeffrey, S.S.5
Ress, C.A.6
Pollack, J.R.7
Ross, D.T.8
Johnsen, H.9
Akslen, L.A.10
Fluge Ø11
Pergammenschlkov, A.12
Williams, C.13
Zhu, S.X.14
Lønning, P.E.15
Børresen-Dale, A.-L.16
Brown, P.O.17
Botstein, D.18
-
7
-
-
9144251970
-
Gene expression profiling identifies clinically relevant subtypes of prostate cancer
-
DOI 10.1073/pnas.0304146101
-
Lapointe J., Li C., Higgins J. P., Van De Rijn M., Bair E., Montgomery K., Ferrari M., Egevad L., Rayford W., Bergerheim U., Ekman P., DeMarzo A. M., Tibshiran R., Botstein D., Brown P. O., Brooks J. D., Pollack J. R., Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America 2004 101 3 811 816 2-s2.0-9144251970 10.1073/pnas.0304146101 (Pubitemid 38121040)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.3
, pp. 811-816
-
-
Lapointe, J.1
Li, C.2
Higgins, J.P.3
Van De Rijn, M.4
Bair, E.5
Montgomery, K.6
Ferrari, M.7
Egevad, L.8
Rayford, W.9
Bergerheim, U.10
Ekman, P.11
DeMarzo, A.M.12
Tibshiran, R.13
Botstein, D.14
Brown, P.O.15
Brooks, J.D.16
Pollack, J.R.17
-
8
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
DOI 10.1073/pnas.95.25.14863
-
Eisen M. B., Spellman P. T., Brown P. O., Botstein D., Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 1998 95 25 14863 14868 2-s2.0-0032441150 10.1073/pnas.95.25.14863 (Pubitemid 29003722)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
9
-
-
45149101194
-
Current approaches to gene regulatory network modelling
-
DOI 10.1186/1471-2105-8-S6-S9
-
Schlitt T., Brazma A., Current approaches to gene regulatory network modelling. BMC Bioinformatics 2007 8 supplement 6, article S9 2-s2.0-45149101194 10.1186/1471-2105-8-S6-S9 (Pubitemid 351833845)
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 6
-
-
Schlitt, T.1
Brazma, A.2
-
10
-
-
68349161006
-
Reverse engineering of gene regulatory networks: A comparative study
-
2-s2.0-68149164746 10.1155/2009/617281 617281
-
Hache H., Lehrach H., Herwig R., Reverse engineering of gene regulatory networks: a comparative study. Eurasip Journal on Bioinformatics and Systems Biology 2009 2009 2-s2.0-68149164746 10.1155/2009/617281 617281
-
(2009)
Eurasip Journal on Bioinformatics and Systems Biology
, vol.2009
-
-
Hache, H.1
Lehrach, H.2
Herwig, R.3
-
11
-
-
67449095889
-
Computational methods for discovering gene networks from expression data
-
2-s2.0-67449095889 10.1093/bib/bbp028
-
Lee W. P., Tzou W. S., Computational methods for discovering gene networks from expression data. Briefings in Bioinformatics 2009 10 4 408 423 2-s2.0-67449095889 10.1093/bib/bbp028
-
(2009)
Briefings in Bioinformatics
, vol.10
, Issue.4
, pp. 408-423
-
-
Lee, W.P.1
Tzou, W.S.2
-
12
-
-
70549083891
-
Inference of gene regulatory networks using time-series data: A survey
-
2-s2.0-70549083891 10.2174/138920209789177610
-
Sima C., Hua J., Jung S., Inference of gene regulatory networks using time-series data: a survey. Current Genomics 2009 10 6 416 429 2-s2.0-70549083891 10.2174/138920209789177610
-
(2009)
Current Genomics
, vol.10
, Issue.6
, pp. 416-429
-
-
Sima, C.1
Hua, J.2
Jung, S.3
-
13
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
DOI 10.1126/science.1087447
-
Stuart J. M., Segal E., Koller D., Kim S. K., A gene-coexpression network for global discovery of conserved genetic modules. Science 2003 302 5643 249 255 2-s2.0-0141993704 10.1126/science.1087447 (Pubitemid 37248749)
-
(2003)
Science
, vol.302
, Issue.5643
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
14
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
DOI 10.1186/1471-2105-7-S1-S7
-
Margolin A. A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Favera R. D., Califano A., ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006 7 supplement 1, article S7 2-s2.0-33947305781 10.1186/1471-2105-7-S1-S7 (Pubitemid 46437495)
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL.1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
15
-
-
0034302007
-
Coefficient of determination in nonlinear signal processing
-
2-s2.0-0034302007 10.1016/S0165-1684(00)00079-7
-
Dougherty E. R., Kim S., Chen Y., Coefficient of determination in nonlinear signal processing. Signal Processing 2000 80 10 2219 2235 2-s2.0-0034302007 10.1016/S0165-1684(00)00079-7
-
(2000)
Signal Processing
, vol.80
, Issue.10
, pp. 2219-2235
-
-
Dougherty, E.R.1
Kim, S.2
Chen, Y.3
-
16
-
-
0034661192
-
Multivariate measurement of gene expression relationships
-
DOI 10.1006/geno.2000.6241
-
Kim S., Dougherty E. R., Chen Y., Sivakumar K., Meltzer P., Trent J. M., Bittner M., Multivariate measurement of gene expression relationships. Genomics 2000 67 2 201 209 10.1006/geno.2000.6241 (Pubitemid 30614588)
-
(2000)
Genomics
, vol.67
, Issue.2
, pp. 201-209
-
-
Kim, S.1
Dougherty, E.R.2
Chen, Y.3
Sivakumar, K.4
Meltzer, P.5
Trent, J.M.6
Bittner, M.7
-
17
-
-
33751356890
-
BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network
-
DOI 10.1093/bioinformatics/btl491
-
Chen X., Chen M., Ning K., BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network. Bioinformatics 2006 22 23 2952 2954 2-s2.0-33751356890 10.1093/bioinformatics/ btl491 (Pubitemid 44811571)
-
(2006)
Bioinformatics
, vol.22
, Issue.23
, pp. 2952-2954
-
-
Chen, X.1
Chen, M.2
Ning, K.3
-
18
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
DOI 10.1093/bioinformatics/btl391
-
Werhli A. V., Grzegorczyk M., Husmeier D., Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 2006 22 20 2523 2531 2-s2.0-33749825955 10.1093/bioinformatics/btl391 (Pubitemid 44560759)
-
(2006)
Bioinformatics
, vol.22
, Issue.20
, pp. 2523-2531
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
19
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
Shmulevich I., Dougherty E. R., Kim S., Zhang W., Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002 18 2 261 274 2-s2.0-0036184629 (Pubitemid 34183104)
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
20
-
-
80054689794
-
An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma
-
10.1016/j.cell.2011.09.041
-
Sumazin P., Yang X., Chiu H.-S., Chung W.-J., Llobet-Navas D., Rajbhandari P., Bansal M., Guarnieri P., Silva J., Califano A., An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011 147 2 370 381 10.1016/j.cell.2011. 09.041
-
(2011)
Cell
, vol.147
, Issue.2
, pp. 370-381
-
-
Sumazin, P.1
Yang, X.2
Chiu, H.-S.3
Chung, W.-J.4
Llobet-Navas, D.5
Rajbhandari, P.6
Bansal, M.7
Guarnieri, P.8
Silva, J.9
Califano, A.10
-
21
-
-
80054700538
-
Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs
-
10.1016/j.cell.2011.09.029
-
Tay Y., Kats L., Salmena L., Weiss D., Tan S. M., Ala U., Karreth F., Poliseno L., Provero P., Di Cunto F., Lieberman J., Rigoutsos I., Pandolfi P. P., Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011 147 2 344 357 10.1016/j.cell.2011.09.029
-
(2011)
Cell
, vol.147
, Issue.2
, pp. 344-357
-
-
Tay, Y.1
Kats, L.2
Salmena, L.3
Weiss, D.4
Tan, S.M.5
Ala, U.6
Karreth, F.7
Poliseno, L.8
Provero, P.9
Di Cunto, F.10
Lieberman, J.11
Rigoutsos, I.12
Pandolfi, P.P.13
-
22
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
2-s2.0-58249088751 10.1016/j.cell.2009.01.002
-
Bartel D. P., MicroRNAs: target recognition and regulatory functions. Cell 2009 136 2 215 233 2-s2.0-58249088751 10.1016/j.cell.2009.01.002
-
(2009)
Cell
, vol.136
, Issue.2
, pp. 215-233
-
-
Bartel, D.P.1
-
23
-
-
85032751589
-
Understanding MicroRNA regulation: A computational perspective
-
6105465 10.1109/MSP.2011.943013
-
Yue D., Meng J., Lu M., Chen C. L. P., Guo M., Huang Y., Understanding MicroRNA regulation: a computational perspective. IEEE Signal Processing Magazine 2012 29 1 77 88 6105465 10.1109/MSP.2011.943013
-
(2012)
IEEE Signal Processing Magazine
, vol.29
, Issue.1
, pp. 77-88
-
-
Yue, D.1
Meng, J.2
Lu, M.3
Chen, C.L.P.4
Guo, M.5
Huang, Y.6
-
24
-
-
2942672580
-
Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA
-
DOI 10.1016/j.molcel.2004.05.027, PII S1097276504003284
-
Jones-Rhoades M. W., Bartel D. P., Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Molecular Cell 2004 14 6 787 799 2-s2.0-2942672580 10.1016/j.molcel.2004.05.027 (Pubitemid 38780852)
-
(2004)
Molecular Cell
, vol.14
, Issue.6
, pp. 787-799
-
-
Jones-Rhoades, M.W.1
Bartel, D.P.2
-
25
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan D., Weinberg R. A., The hallmarks of cancer. Cell 2000 100 1 57 70 2-s2.0-0034614637 (Pubitemid 30046295)
-
(2000)
Cell
, vol.100
, Issue.1
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
26
-
-
78149341677
-
Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1 α and HIF-2 α target genes
-
2-s2.0-78149341677 10.1186/1476-4598-9-293
-
Chun S. Y., Johnson C., Washburn J. G., Cruz-Correa M. R., Dang D. T., Dang L. H., Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1 α and HIF-2 α target genes. Molecular Cancer 2010 9, article 293 2-s2.0-78149341677 10.1186/1476-4598-9-293
-
(2010)
Molecular Cancer
, vol.9293
-
-
Chun, S.Y.1
Johnson, C.2
Washburn, J.G.3
Cruz-Correa, M.R.4
Dang, D.T.5
Dang, L.H.6
-
27
-
-
67049159812
-
A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
-
2-s2.0-67049159812 10.1371/journal.pcbi.1000382 e1000382
-
Hudson N. J., Reverter A., Dalrymple B. P., A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Computational Biology 2009 5 5 2-s2.0-67049159812 10.1371/journal.pcbi.1000382 e1000382
-
(2009)
PLoS Computational Biology
, vol.5
, Issue.5
-
-
Hudson, N.J.1
Reverter, A.2
Dalrymple, B.P.3
-
28
-
-
84864831454
-
Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS
-
601 10.1038/msb.2012.32
-
Stelniec-Klotz I., Legewie S., Tchernitsa O., Witzel F., Klinger B., Sers C., Herzel H., Blüthgen N., Schäfer R., Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. Molecular Systems Biology 2012 8 601 10.1038/msb.2012.32
-
(2012)
Molecular Systems Biology
, vol.8
-
-
Stelniec-Klotz, I.1
Legewie, S.2
Tchernitsa, O.3
Witzel, F.4
Klinger, B.5
Sers, C.6
Herzel, H.7
Blüthgen, N.8
Schäfer, R.9
-
29
-
-
79955690126
-
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer
-
2-s2.0-79955690126 10.1186/1752-0509-5-67
-
Shen C., Huang Y., Liu Y., Wang G., Zhao Y., Wang Z., Teng M., Wang Y., Flockhart D. A., Skaar T. C., Yan P., Nephew K. P., Huang T. H. M., Li L., A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Systems Biology 2011 5, article 67 2-s2.0-79955690126 10.1186/1752-0509-5-67
-
(2011)
BMC Systems Biology
, vol.567
-
-
Shen, C.1
Huang, Y.2
Liu, Y.3
Wang, G.4
Zhao, Y.5
Wang, Z.6
Teng, M.7
Wang, Y.8
Flockhart, D.A.9
Skaar, T.C.10
Yan, P.11
Nephew, K.P.12
Huang, T.H.M.13
Li, L.14
-
30
-
-
4544326058
-
Recent translational research: Microarray expression profiling of breast cancer - Beyond classification and prognostic markers?
-
DOI 10.1186/bcr917
-
Wilson C. A., Dering J., Recent translational research: microarray expression profiling of breast cancer. Beyond classification and prognostic markers? Breast Cancer Research 2004 6 5 192 200 2-s2.0-4544326058 10.1186/bcr917 (Pubitemid 39220373)
-
(2004)
Breast Cancer Research
, vol.6
, Issue.5
, pp. 192-200
-
-
Wilson, C.A.1
Dering, J.2
-
31
-
-
0242442571
-
The Gene Expression Response of Breast Cancer to Growth Regulators: Patterns and Correlation with Tumor Expression Profiles
-
Cunliffe H. E., Ringnér M., Bilke S., Walker R. L., Cheung J. M., Chen Y., Meltzer P. S., The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles. Cancer Research 2003 63 21 7158 7166 2-s2.0-0242442571 (Pubitemid 37413453)
-
(2003)
Cancer Research
, vol.63
, Issue.21
, pp. 7158-7166
-
-
Cunliffe, H.E.1
Ringner, M.2
Bilke, S.3
Walker, R.L.4
Cheung, J.M.5
Chen, Y.6
Meltzer, P.S.7
-
32
-
-
1242338758
-
Selective Estrogen Receptor Modulators: Discrimination of Agonistic versus Antagonistic Activities by Gene Expression Profiling in Breast Cancer Cells
-
DOI 10.1158/0008-5472.CAN-03-3326
-
Frasor J., Stossi F., Danes J. M., Komm B., Lyttle C. R., Katzenellenbogen B. S., Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells. Cancer Research 2004 64 4 1522 1533 2-s2.0-1242338758 10.1158/0008-5472.CAN-03-3326 (Pubitemid 38235626)
-
(2004)
Cancer Research
, vol.64
, Issue.4
, pp. 1522-1533
-
-
Frasor, J.1
Stossi, F.2
Danes, J.M.3
Komm, B.4
Lyttle, C.R.5
Katzenellenbogen, B.S.6
-
33
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
DOI 10.1038/415530a
-
van't Veer L. J., Dai H., van de Vijver M. J., He Y. D., Hart A. A. M., Mao M., Peterse H. L., Van Der Kooy K., Marton M. J., Witteveen A. T., Schreiber G. J., Kerkhoven R. M., Roberts C., Linsley P. S., Bernards R., Friend S. H., Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002 415 6871 530 536 2-s2.0-18244409687 10.1038/415530a (Pubitemid 34130608)
-
(2002)
Nature
, vol.415
, Issue.6871
, pp. 530-536
-
-
Van't Veer, L.J.1
Dai, H.2
Van De Vijver, M.J.3
He, Y.D.4
Hart, A.A.M.5
Mao, M.6
Peterse, H.L.7
Van Der Kooy, K.8
Marton, M.J.9
Witteveen, A.T.10
Schreiber, G.J.11
Kerkhoven, R.M.12
Roberts, C.13
Linsley, P.S.14
Bernards, R.15
Friend, S.H.16
-
35
-
-
84855846735
-
Comparing statistical methods for constructing large scale gene networks
-
e29348 10.1371/journal.pone.0029348
-
Allen J. D., Xie Y., Chen M., Girard L., Xiao G., Comparing statistical methods for constructing large scale gene networks. PLoS ONE 2012 7 1 e29348 10.1371/journal.pone.0029348
-
(2012)
PLoS ONE
, vol.7
, Issue.1
-
-
Allen, J.D.1
Xie, Y.2
Chen, M.3
Girard, L.4
Xiao, G.5
-
36
-
-
85032751772
-
Reverse engineering gene regulatory networks: A survey of statistical models
-
2-s2.0-61549115055 10.1109/MSP.2008.930647
-
Huang Y., Tienda-Luna I. M., Wang Y., Reverse engineering gene regulatory networks: a survey of statistical models. IEEE Signal Processing Magazine 2009 26 1 76 97 2-s2.0-61549115055 10.1109/MSP.2008.930647
-
(2009)
IEEE Signal Processing Magazine
, vol.26
, Issue.1
, pp. 76-97
-
-
Huang, Y.1
Tienda-Luna, I.M.2
Wang, Y.3
-
37
-
-
0014937223
-
Central dogma of molecular biology
-
2-s2.0-0014937223 10.1038/227561a0
-
Crick F., Central dogma of molecular biology. Nature 1970 227 5258 561 563 2-s2.0-0014937223 10.1038/227561a0
-
(1970)
Nature
, vol.227
, Issue.5258
, pp. 561-563
-
-
Crick, F.1
-
38
-
-
0033744498
-
The contribution of molecular markers to the prediction of response in the treatment of breast cancer: A review of the literature on HER-2, p53 and BCL-2
-
2-s2.0-0033744498 10.1023/A:1008390429428
-
Hamilton A., Piccart M., The contribution of molecular markers to the prediction of response in the treatment of breast cancer: a review of the literature on HER-2, p53 and BCL-2. Annals of Oncology 2000 11 6 647 663 2-s2.0-0033744498 10.1023/A:1008390429428
-
(2000)
Annals of Oncology
, vol.11
, Issue.6
, pp. 647-663
-
-
Hamilton, A.1
Piccart, M.2
-
39
-
-
0042838307
-
Breast cancer classification and prognosis based on gene expression profiles from a population-based study
-
DOI 10.1073/pnas.1732912100
-
Sotiriou C., Neo S. Y., McShane L. M., Korn E. L., Long P. M., Jazaeri A., Martiat P., Fox S. B., Harris A. L., Liu E. T., Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proceedings of the National Academy of Sciences of the United States of America 2003 100 18 10393 10398 2-s2.0-0042838307 10.1073/pnas.1732912100 (Pubitemid 37071889)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.18
, pp. 10393-10398
-
-
Sotiriou, C.1
Neo, S.-Y.2
McShane, L.M.3
Korn, E.L.4
Long, P.M.5
Jazaeri, A.6
Martiat, P.7
Fox, S.B.8
Harris, A.L.9
Liu, E.T.10
-
40
-
-
0035845511
-
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
-
DOI 10.1073/pnas.191367098
-
Sørlie T., Perou C. M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M. B., Van De Rijn M., Jeffrey S. S., Thorsen T., Quist H., Matese J. C., Brown P. O., Botstein D., Lønning P. E., Børresen-Dale A. L., Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences of the United States of America 2001 98 19 10869 10874 2-s2.0-0035845511 10.1073/pnas.191367098 (Pubitemid 32878711)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.19
, pp. 10869-10874
-
-
Sorlie, T.1
Perou, C.M.2
Tibshirani, R.3
Aas, T.4
Geisler, S.5
Johnsen, H.6
Hastie, T.7
Eisen, M.B.8
Van De Rijn, M.9
Jeffrey, S.S.10
Thorsen, T.11
Quist, H.12
Matese, J.C.13
Brown, P.O.14
Botstein, D.15
Lonning, P.E.16
Borresen-Dale, A.-L.17
-
41
-
-
33750442923
-
Genome-wide analysis of estrogen receptor binding sites
-
DOI 10.1038/ng1901, PII NG1901
-
Carroll J. S., Meyer C. A., Song J., Li W., Geistlinger T. R., Eeckhoute J., Brodsky A. S., Keeton E. K., Fertuck K. C., Hall G. F., Wang Q., Bekiranov S., Sementchenko V., Fox E. A., Silver P. A., Gingeras T. R., Liu X. S., Brown M., Genome-wide analysis of estrogen receptor binding sites. Nature Genetics 2006 38 11 1289 1297 10.1038/ng1901 (Pubitemid 44646291)
-
(2006)
Nature Genetics
, vol.38
, Issue.11
, pp. 1289-1297
-
-
Carroll, J.S.1
Meyer, C.A.2
Song, J.3
Li, W.4
Geistlinger, T.R.5
Eeckhoute, J.6
Brodsky, A.S.7
Keeton, E.K.8
Fertuck, K.C.9
Hall, G.F.10
Wang, Q.11
Bekiranov, S.12
Sementchenko, V.13
Fox, E.A.14
Silver, P.A.15
Gingeras, T.R.16
Liu, X.S.17
Brown, M.18
-
42
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
2-s2.0-16844376909 10.1038/ng1532
-
Basso K., Margolin A. A., Stolovitzky G., Klein U., Dalla-Favera R., Califano A., Reverse engineering of regulatory networks in human B cells. Nature Genetics 2005 37 4 382 390 2-s2.0-16844376909 10.1038/ng1532
-
(2005)
Nature Genetics
, vol.37
, Issue.4
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
43
-
-
48849090016
-
Gene regulatory network reconstruction using conditional mutual information
-
2-s2.0-48849090016 10.1155/2008/253894 253894
-
Liang K. C., Wang X., Gene regulatory network reconstruction using conditional mutual information. Eurasip Journal on Bioinformatics and Systems Biology 2008 2008 2-s2.0-48849090016 10.1155/2008/253894 253894
-
(2008)
Eurasip Journal on Bioinformatics and Systems Biology
, vol.2008
-
-
Liang, K.C.1
Wang, X.2
-
44
-
-
70249108504
-
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
-
10.1038/nbt.1563
-
Wang K., Bisikirska B. C., Alvarez M. J., Lim W. K., Rajbhandari P., Shen Q., Nemenman I., Basso K., Margolin A. A., Klein U., Dalla-Favera R., Califano A., Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology 2009 27 9 829 837 10.1038/nbt.1563
-
(2009)
Nature Biotechnology
, vol.27
, Issue.9
, pp. 829-837
-
-
Wang, K.1
Bisikirska, B.C.2
Alvarez, M.J.3
Lim, W.K.4
Rajbhandari, P.5
Shen, Q.6
Nemenman, I.7
Basso, K.8
Margolin, A.A.9
Klein, U.10
Dalla-Favera, R.11
Califano, A.12
-
45
-
-
77249109446
-
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
-
ARTICLE 4 2-s2.0-77249109446 10.1186/1748-7188-5-4
-
Hansen M., Everett L., Singh L., Hannenhalli S., Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular Biology 2010 5 1, article 4 2-s2.0-77249109446 10.1186/1748-7188-5-4
-
(2010)
Algorithms for Molecular Biology
, vol.5
, Issue.1
-
-
Hansen, M.1
Everett, L.2
Singh, L.3
Hannenhalli, S.4
-
46
-
-
77957226956
-
Discovering modulators of gene expression
-
2-s2.0-77957226956 10.1093/nar/gkq287 gkq287
-
Babur O., Demir E., Gönen M., Sander C., Dogrusoz U., Discovering modulators of gene expression. Nucleic Acids Research 2010 38 17 5648 5656 2-s2.0-77957226956 10.1093/nar/gkq287 gkq287
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.17
, pp. 5648-5656
-
-
Babur, O.1
Demir, E.2
Gönen, M.3
Sander, C.4
Dogrusoz, U.5
-
47
-
-
79958139080
-
A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition
-
2-s2.0-79958139080 10.1371/journal.pone.0020804 e20804
-
Shimamura T., Imoto S., Shimada Y., Hosono Y., Niida A., Nagasaki M., Yamaguchi R., Takahashi T., Miyano S., A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS ONE 2011 6 6 2-s2.0-79958139080 10.1371/journal.pone.0020804 e20804
-
(2011)
PLoS ONE
, vol.6
, Issue.6
-
-
Shimamura, T.1
Imoto, S.2
Shimada, Y.3
Hosono, Y.4
Niida, A.5
Nagasaki, M.6
Yamaguchi, R.7
Takahashi, T.8
Miyano, S.9
-
48
-
-
84876079151
-
A modulator based regulatory network for ERalpha signaling pathway
-
Supplement 6, article S6
-
Wu H. Y., A modulator based regulatory network for ERalpha signaling pathway. BMC Genomics 2012 13 Supplement 6, article S6
-
(2012)
BMC Genomics
, vol.13
-
-
Wu, H.Y.1
-
49
-
-
81355164253
-
Construction and analysis of an integrated regulatory network derived from High-Throughput sequencing data
-
e1002190 10.1371/journal.pcbi.1002190
-
Yan K.-K., Hwang W., Qian J., Bhardwaj N., Rozowsky J., Lu Z. J., Niu W., Alves P., Kato M., Snyder M., Gerstein M., Construction and analysis of an integrated regulatory network derived from High-Throughput sequencing data. PLoS Computational Biology 2011 7 11 e1002190 10.1371/journal.pcbi.1002190
-
(2011)
PLoS Computational Biology
, vol.7
, Issue.11
-
-
Yan, K.-K.1
Hwang, W.2
Qian, J.3
Bhardwaj, N.4
Rozowsky, J.5
Lu, Z.J.6
Niu, W.7
Alves, P.8
Kato, M.9
Snyder, M.10
Gerstein, M.11
-
51
-
-
78651266827
-
MiRTarBase: A database curates experimentally validated microRNA-target interactions
-
2-s2.0-78651266827 10.1093/nar/gkq1107
-
Hsu S. D., Lin F. M., Wu W. Y., Liang C., Huang W. C., Chan W. L., Tsai W. T., Chen G. Z., Lee C. J., Chiu C. M., Chien C. H., Wu M. C., Huang C. Y., Tsou A. P., Huang H. D., MiRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Research 2011 39 1 D163 D169 2-s2.0-78651266827 10.1093/nar/gkq1107
-
(2011)
Nucleic Acids Research
, vol.39
, Issue.1
-
-
Hsu, S.D.1
Lin, F.M.2
Wu, W.Y.3
Liang, C.4
Huang, W.C.5
Chan, W.L.6
Tsai, W.T.7
Chen, G.Z.8
Lee, C.J.9
Chiu, C.M.10
Chien, C.H.11
Wu, M.C.12
Huang, C.Y.13
Tsou, A.P.14
Huang, H.D.15
-
52
-
-
77956846500
-
Improving performance of mammalian microRNA target prediction
-
2-s2.0-77956846500 10.1186/1471-2105-11-476
-
Liu H., Yue D., Chen Y., Gao S. J., Huang Y., Improving performance of mammalian microRNA target prediction. BMC Bioinformatics 2010 11, article 476 2-s2.0-77956846500 10.1186/1471-2105-11-476
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Liu, H.1
Yue, D.2
Chen, Y.3
Gao, S.J.4
Huang, Y.5
-
53
-
-
84878800712
-
A Bayesian decision fusion approach for microRNA target prediction
-
Dong Y., A Bayesian decision fusion approach for microRNA target prediction. BMC Genomics 2012 13
-
(2012)
BMC Genomics
, vol.13
-
-
Dong, Y.1
-
54
-
-
0034795617
-
-
Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval 2001 New Orleans, La, USA la 10.1145/383952.384007
-
Asm J. A., Montague M., Models for Metasearch. Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval 2001 New Orleans, La, USA la 276 284 10.1145/383952.384007
-
Models for Metasearch
, pp. 276-284
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Asm, J.A.1
Montague, M.2
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