-
1
-
-
75549087047
-
The IntAct molecular interaction database in 2010
-
Aranda B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian A.T., Kerrien S., Khadake J., Kerssemakers J., Leroy C., Menden M., Michaut M., Montecchi-Palazzi L., Neuhauser S.N., Orchard S., Perreau V., Roechert B., van Eijk K., Hermjakob H. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010, 38:D525-D530.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
Armean, I.4
Bridge, A.5
Derow, C.6
Feuermann, M.7
Ghanbarian, A.T.8
Kerrien, S.9
Khadake, J.10
Kerssemakers, J.11
Leroy, C.12
Menden, M.13
Michaut, M.14
Montecchi-Palazzi, L.15
Neuhauser, S.N.16
Orchard, S.17
Perreau, V.18
Roechert, B.19
van Eijk, K.20
Hermjakob, H.21
more..
-
2
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
3
-
-
0037245913
-
BIND: the Biomolecular Interaction Network Database
-
Bader G.D., Betel D., Hogue C.W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003, 31:248-250.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
4
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings /.. International Conference on Intelligent Systems for Molecular Biology; ISMB
-
Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings /.. International Conference on Intelligent Systems for Molecular Biology; ISMB. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2:28-36.
-
(1994)
Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
5
-
-
0031877016
-
Combining evidence using p-values: application to sequence homology searches
-
Bailey T.L., Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998, 14:48-54.
-
(1998)
Bioinformatics
, vol.14
, pp. 48-54
-
-
Bailey, T.L.1
Gribskov, M.2
-
6
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M., Gatta G.D., di Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 2006, 22:815-822.
-
(2006)
Bioinformatics
, vol.22
, pp. 815-822
-
-
Bansal, M.1
Gatta, G.D.2
di Bernardo, D.3
-
7
-
-
38349107287
-
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
-
Bare J.C., Shannon P.T., Schmid A.K., Baliga N.S. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformat. 2007, 8:456.
-
(2007)
BMC Bioinformat.
, vol.8
, pp. 456
-
-
Bare, J.C.1
Shannon, P.T.2
Schmid, A.K.3
Baliga, N.S.4
-
8
-
-
0242690489
-
Discovering local structure in gene expression data: the order-preserving submatrix problem
-
Ben-Dor A., Chor B., Karp R., Yakhini Z. Discovering local structure in gene expression data: the order-preserving submatrix problem. J. Comput. Biol. 2003, 10:373-384.
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 373-384
-
-
Ben-Dor, A.1
Chor, B.2
Karp, R.3
Yakhini, Z.4
-
9
-
-
79955750055
-
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
-
Bendall S.C., Simonds E.F., Qiu P., Amir el A.D., Krutzik P.O., Finck R., Bruggner R.V., Melamed R., Trejo A., Ornatsky O.I., Balderas R.S., Plevritis S.K., Sachs K., Pe'er D., Tanner S.D., Nolan G.P. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011, 332:687-696.
-
(2011)
Science
, vol.332
, pp. 687-696
-
-
Bendall, S.C.1
Simonds, E.F.2
Qiu, P.3
Amir el, A.D.4
Krutzik, P.O.5
Finck, R.6
Bruggner, R.V.7
Melamed, R.8
Trejo, A.9
Ornatsky, O.I.10
Balderas, R.S.11
Plevritis, S.K.12
Sachs, K.13
Pe'er, D.14
Tanner, S.D.15
Nolan, G.P.16
-
11
-
-
37349099750
-
A predictive model for transcriptional control of physiology in a free living cell
-
Bonneau R., Facciotti M.T., Reiss D.J., Schmid A.K., Pan M., Kaur A., Thorsson V., Shannon P., Johnson M.H., Bare J.C., Longabaugh W., Vuthoori M., Whitehead K., Madar A., Suzuki L., Mori T., Chang D.-E., Diruggiero J., Johnson C.H., Hood L., Baliga N.S. A predictive model for transcriptional control of physiology in a free living cell. Cell 2007, 131:1354-1365.
-
(2007)
Cell
, vol.131
, pp. 1354-1365
-
-
Bonneau, R.1
Facciotti, M.T.2
Reiss, D.J.3
Schmid, A.K.4
Pan, M.5
Kaur, A.6
Thorsson, V.7
Shannon, P.8
Johnson, M.H.9
Bare, J.C.10
Longabaugh, W.11
Vuthoori, M.12
Whitehead, K.13
Madar, A.14
Suzuki, L.15
Mori, T.16
Chang, D.-E.17
Diruggiero, J.18
Johnson, C.H.19
Hood, L.20
Baliga, N.S.21
more..
-
12
-
-
33747813561
-
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
Bonneau R., Reiss D.J., Shannon P., Facciotti M., Hood L., Baliga N.S., Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006, 7:R36.
-
(2006)
Genome Biol.
, vol.7
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
Facciotti, M.4
Hood, L.5
Baliga, N.S.6
Thorsson, V.7
-
13
-
-
4644231028
-
Prolinks: a database of protein functional linkages derived from coevolution
-
Bowers P.M., Pellegrini M., Thompson M.J., Fierro J., Yeates T.O., Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004, 5:R35.
-
(2004)
Genome Biol.
, vol.5
-
-
Bowers, P.M.1
Pellegrini, M.2
Thompson, M.J.3
Fierro, J.4
Yeates, T.O.5
Eisenberg, D.6
-
14
-
-
38549174065
-
The Mouse Genome Database (MGD): mouse biology and model systems
-
Bult C.J., Eppig J.T., Kadin J.A., Richardson J.E., Blake J.A. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 2008, 36:D724-D728.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Bult, C.J.1
Eppig, J.T.2
Kadin, J.A.3
Richardson, J.E.4
Blake, J.A.5
-
15
-
-
0033655775
-
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
-
Butte A.J., Kohane I.S. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Proceedings of the 5th Pacific Symposium on Biocomputing 2000, 418-429.
-
(2000)
Proceedings of the 5th Pacific Symposium on Biocomputing
, pp. 418-429
-
-
Butte, A.J.1
Kohane, I.S.2
-
16
-
-
45349108231
-
Social network analysis with sna
-
Butts C.T. Social network analysis with sna. J. Stat. Softw. 2008, 24:1-51.
-
(2008)
J. Stat. Softw.
, vol.24
, pp. 1-51
-
-
Butts, C.T.1
-
17
-
-
0018236173
-
Long-term human breast carcinoma cell lines of metastatic origin: preliminary characterization
-
Cailleau R., Olive M., Cruciger Q.V. Long-term human breast carcinoma cell lines of metastatic origin: preliminary characterization. In Vitro 1978, 14:911-915.
-
(1978)
In Vitro
, vol.14
, pp. 911-915
-
-
Cailleau, R.1
Olive, M.2
Cruciger, Q.V.3
-
18
-
-
75149195336
-
The transcriptional network for mesenchymal transformation of brain tumours
-
Carro M.S., Lim W.K., Alvarez M.J., Bollo R.J., Zhao X., Snyder E.Y., Sulman E.P., Anne S.L., Doetsch F., Colman H., Lasorella A., Aldape K., Califano A., Iavarone A. The transcriptional network for mesenchymal transformation of brain tumours. Nature 2010, 463:318-325.
-
(2010)
Nature
, vol.463
, pp. 318-325
-
-
Carro, M.S.1
Lim, W.K.2
Alvarez, M.J.3
Bollo, R.J.4
Zhao, X.5
Snyder, E.Y.6
Sulman, E.P.7
Anne, S.L.8
Doetsch, F.9
Colman, H.10
Lasorella, A.11
Aldape, K.12
Califano, A.13
Iavarone, A.14
-
19
-
-
75549083295
-
MINT, the molecular interaction database: 2009 update
-
Ceol A., Aryamontri A.C., Licata L., Peluso D., Briganti L., Perfetto L., Castagnoli L., Cesareni G. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res. 2010, 38:D532-D540.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ceol, A.1
Aryamontri, A.C.2
Licata, L.3
Peluso, D.4
Briganti, L.5
Perfetto, L.6
Castagnoli, L.7
Cesareni, G.8
-
20
-
-
77957695678
-
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks
-
Chaitankar V., Ghosh P., Perkins E.J., Gong P., Zhang C. Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. BMC Bioinformat. 2010, 11(Suppl 6):S19.
-
(2010)
BMC Bioinformat.
, vol.11
, Issue.SUPPL. 6
-
-
Chaitankar, V.1
Ghosh, P.2
Perkins, E.J.3
Gong, P.4
Zhang, C.5
-
21
-
-
78651301312
-
MatrixDB, the extracellular matrix interaction database
-
Chautard E., Fatoux-Ardore M., Ballut L., Thierry-Mieg N., Ricard-Blum S. MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res. 2011, 39:D235-D240.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Chautard, E.1
Fatoux-Ardore, M.2
Ballut, L.3
Thierry-Mieg, N.4
Ricard-Blum, S.5
-
22
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., Wong E., Orlov Y.L., Zhang W., Jiang J., Loh Y.-H., Yeo H.C., Yeo Z.X., Narang V., Govindarajan K.R., Leong B., Shahab A., Ruan Y., Bourque G., Sung W.-K., Clarke N.D., Wei C.-L., Ng H.-H. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
Loh, Y.-H.11
Yeo, H.C.12
Yeo, Z.X.13
Narang, V.14
Govindarajan, K.R.15
Leong, B.16
Shahab, A.17
Ruan, Y.18
Bourque, G.19
Sung, W.-K.20
Clarke, N.D.21
Wei, C.-L.22
Ng, H.-H.23
more..
-
24
-
-
69449094754
-
Incorporating existing network information into gene network inference
-
Christley S., Nie Q., Xie X. Incorporating existing network information into gene network inference. PloS One 2009, 4:e6799.
-
(2009)
PloS One
, vol.4
-
-
Christley, S.1
Nie, Q.2
Xie, X.3
-
25
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
Croft D., O'Kelly G., Wu G., Haw R., Gillespie M., Matthews L., Caudy M., Garapati P., Gopinath G., Jassal B., Jupe S., Kalatskaya I., Mahajan S., May B., Ndegwa N., Schmidt E., Shamovsky V., Yung C., Birney E., Hermjakob H., D'Eustachio P., Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011, 39:D691-D700.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
Matthews, L.6
Caudy, M.7
Garapati, P.8
Gopinath, G.9
Jassal, B.10
Jupe, S.11
Kalatskaya, I.12
Mahajan, S.13
May, B.14
Ndegwa, N.15
Schmidt, E.16
Shamovsky, V.17
Yung, C.18
Birney, E.19
Hermjakob, H.20
D'Eustachio, P.21
Stein, L.22
more..
-
26
-
-
34250727580
-
The relationship between precision-recall and ROC curves
-
Proceedings of the 23rd International Conference on Machine Learning - ICML'06
-
Davis, J., Goadrich, M., 2006. The relationship between precision-recall and ROC curves. Proceedings of the 23rd International Conference on Machine Learning - ICML'06, 233-240.
-
(2006)
, pp. 233-240
-
-
Davis, J.1
Goadrich, M.2
-
27
-
-
77957110013
-
Advantages and limitations of current network inference methods. Nature reviews
-
De Smet R., Marchal K. Advantages and limitations of current network inference methods. Nature reviews. Microbiology 2010, 8:717-729.
-
(2010)
Microbiology
, vol.8
, pp. 717-729
-
-
De Smet, R.1
Marchal, K.2
-
28
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
di Bernardo D., Bansal M., Gatta G.D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 2006, 22:815-822.
-
(2006)
Bioinformatics
, vol.22
, pp. 815-822
-
-
di Bernardo, D.1
Bansal, M.2
Gatta, G.D.3
-
29
-
-
21444452397
-
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
-
di Bernardo D., Thompson M.J., Gardner T.S., Chobot S.E., Eastwood E.L., Wojtovich A.P., Elliott S.J., Schaus S.E., Collins J.J. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat. Biotechnol. 2005, 23:377-383.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 377-383
-
-
di Bernardo, D.1
Thompson, M.J.2
Gardner, T.S.3
Chobot, S.E.4
Eastwood, E.L.5
Wojtovich, A.P.6
Elliott, S.J.7
Schaus, S.E.8
Collins, J.J.9
-
30
-
-
57949105676
-
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
-
DiMaggio P.A., McAllister S.R., Floudas C.A., Feng X.J., Rabinowitz J.D., Rabitz H.A. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. BMC Bioinformat. 2008, 9:458.
-
(2008)
BMC Bioinformat.
, vol.9
, pp. 458
-
-
DiMaggio, P.A.1
McAllister, S.R.2
Floudas, C.A.3
Feng, X.J.4
Rabinowitz, J.D.5
Rabitz, H.A.6
-
31
-
-
0036081355
-
Gene expression omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R., Domrachev M., Lash A.E. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
33
-
-
22344437987
-
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
-
Elemento O., Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 2005, 6:R18.
-
(2005)
Genome Biol.
, vol.6
-
-
Elemento, O.1
Tavazoie, S.2
-
34
-
-
38549134505
-
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
-
Faith J.J., Driscoll M.E., Fusaro V.A., Cosgrove E.J., Hayete B., Juhn F.S., Schneider S.J., Gardner T.S. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 2008, 36:D866-D870.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Faith, J.J.1
Driscoll, M.E.2
Fusaro, V.A.3
Cosgrove, E.J.4
Hayete, B.5
Juhn, F.S.6
Schneider, S.J.7
Gardner, T.S.8
-
35
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith J.J., Hayete B., Thaden J.T., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins J.J., Gardner T.S. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007, 5:54-66.
-
(2007)
PLoS Biol.
, vol.5
, pp. 54-66
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
36
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N., Linial M., Nachman I. Using Bayesian networks to analyze expression data. J. Comput. Biol. 2000, 7:601-620.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
-
37
-
-
2442461510
-
-
UAI, San Fransisco, CA
-
Friedman N., Nachman I. Learning Bayesian Network Structure from Massive Datasets: The " Sparse Candidate" Algorithm 1999, UAI, San Fransisco, CA, pp. 206-215.
-
(1999)
Learning Bayesian Network Structure from Massive Datasets: The " Sparse Candidate" Algorithm
, pp. 206-215
-
-
Friedman, N.1
Nachman, I.2
-
38
-
-
43849109594
-
Discovering biclusters in gene expression data based on high-dimensional linear geometries
-
Gan X., Liew A.W., Yan H. Discovering biclusters in gene expression data based on high-dimensional linear geometries. BMC Bioinformat. 2008, 9:209.
-
(2008)
BMC Bioinformat.
, vol.9
, pp. 209
-
-
Gan, X.1
Liew, A.W.2
Yan, H.3
-
39
-
-
34548538013
-
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
-
Geier F., Timmer J., Fleck C. Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst. Biol. 2007, 11.
-
(2007)
BMC Syst. Biol.
, pp. 11
-
-
Geier, F.1
Timmer, J.2
Fleck, C.3
-
40
-
-
36248991815
-
A framework for elucidating regulatory networks based on prior information and expression data
-
Gevaert O., Van Vooren S., De Moor B. A framework for elucidating regulatory networks based on prior information and expression data. Ann. N Y Acad. Sci. 2007, 1115:240-248.
-
(2007)
Ann. N Y Acad. Sci.
, vol.1115
, pp. 240-248
-
-
Gevaert, O.1
Van Vooren, S.2
De Moor, B.3
-
41
-
-
48249112175
-
MPIDB: the microbial protein interaction database
-
Goll J., Rajagopala S.V., Shiau S.C., Wu H., Lamb B.T., Uetz P. MPIDB: the microbial protein interaction database. Bioinformatics 2008, 24:1743-1744.
-
(2008)
Bioinformatics
, vol.24
, pp. 1743-1744
-
-
Goll, J.1
Rajagopala, S.V.2
Shiau, S.C.3
Wu, H.4
Lamb, B.T.5
Uetz, P.6
-
42
-
-
78149421254
-
DREAM4: combining genetic and dynamic information to identify biological networks and dynamical models
-
Greenfield A., Madar A., Ostrer H., Bonneau R. DREAM4: combining genetic and dynamic information to identify biological networks and dynamical models. PLoS ONE 2010, 5:e13397.
-
(2010)
PLoS ONE
, vol.5
-
-
Greenfield, A.1
Madar, A.2
Ostrer, H.3
Bonneau, R.4
-
43
-
-
38649119730
-
Signaling networks assembled by oncogenic EGFR and c-Met
-
Guo A., Villen J., Kornhauser J., Lee K.A., Stokes M.P., Rikova K., Possemato A., Nardone J., Innocenti G., Wetzel R., Wang Y., MacNeill J., Mitchell J., Gygi S.P., Rush J., Polakiewicz R.D., Comb M.J. Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U S A 2008, 105:692-697.
-
(2008)
Proc. Natl. Acad. Sci. U S A
, vol.105
, pp. 692-697
-
-
Guo, A.1
Villen, J.2
Kornhauser, J.3
Lee, K.A.4
Stokes, M.P.5
Rikova, K.6
Possemato, A.7
Nardone, J.8
Innocenti, G.9
Wetzel, R.10
Wang, Y.11
MacNeill, J.12
Mitchell, J.13
Gygi, S.P.14
Rush, J.15
Polakiewicz, R.D.16
Comb, M.J.17
-
44
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell 2000, 100:57-70.
-
(2000)
Cell
, vol.100
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
45
-
-
79952284127
-
Hallmarks of cancer: the next generation
-
Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
-
(2011)
Cell
, vol.144
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.A.2
-
46
-
-
84927511887
-
Direct clustering of a data matrix
-
Hartigan J.A. Direct clustering of a data matrix. J. Amer. Statist. Assoc. 1972, 67:123-129.
-
(1972)
J. Amer. Statist. Assoc.
, vol.67
, pp. 123-129
-
-
Hartigan, J.A.1
-
47
-
-
38449110386
-
Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networks. Computational systems bioinformatics/Life Sciences Society
-
Husmeier D., Werhli A.V. Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networks. Computational systems bioinformatics/Life Sciences Society. Comput. Syst. Bioinformat. Conf. 2007, 6:85-95.
-
(2007)
Comput. Syst. Bioinformat. Conf.
, vol.6
, pp. 85-95
-
-
Husmeier, D.1
Werhli, A.V.2
-
48
-
-
75849134576
-
Detailing regulatory networks through large scale data integration
-
Huttenhower C., Mutungu K.T., Indik N., Yang W., Schroeder M., Forman J.J., Troyanskaya O.G., Coller H.A. Detailing regulatory networks through large scale data integration. Bioinformatics 2009, 25:3267-3274.
-
(2009)
Bioinformatics
, vol.25
, pp. 3267-3274
-
-
Huttenhower, C.1
Mutungu, K.T.2
Indik, N.3
Yang, W.4
Schroeder, M.5
Forman, J.J.6
Troyanskaya, O.G.7
Coller, H.A.8
-
49
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu V.A., Irrthum A., Wehenkel L., Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 2010, 5:e12776.
-
(2010)
PLoS ONE
, vol.5
-
-
Huynh-Thu, V.A.1
Irrthum, A.2
Wehenkel, L.3
Geurts, P.4
-
50
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
Ideker T., Thorsson V., Ranish J.a., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (New York, NY) 2001, 292:929-934.
-
(2001)
Science (New York, NY)
, vol.292
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
51
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program
-
Ihmels J., Bergmann S., Berman J., Barkai N. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet. 2005, 1:e39.
-
(2005)
PLoS Genet.
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
52
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H., Tombor B., Albert R., Oltvai Z.N., Barabási a.L. The large-scale organization of metabolic networks. Nature 2000, 407:651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabási, A.5
-
53
-
-
84855265559
-
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
-
Kacmarczyk T., Waltman P., Bate A., Eichenberger P., Bonneau R. Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters. PLoS computational biology 2011, 7:e1002228.
-
(2011)
PLoS computational biology
, vol.7
-
-
Kacmarczyk, T.1
Waltman, P.2
Bate, A.3
Eichenberger, P.4
Bonneau, R.5
-
54
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
55
-
-
0037399130
-
Spectral biclustering of microarray data: coclustering genes and conditions
-
Kluger Y., Basri R., Chang J.T., Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Res. 2003, 13:703-716.
-
(2003)
Genome Res.
, vol.13
, pp. 703-716
-
-
Kluger, Y.1
Basri, R.2
Chang, J.T.3
Gerstein, M.4
-
56
-
-
78651287426
-
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs
-
Knox C., Law V., Jewison T., Liu P., Ly S., Frolkis A., Pon A., Banco K., Mak C., Neveu V., Djoumbou Y., Eisner R., Guo A.C., Wishart D.S. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011, 39:D1035-D1040.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Knox, C.1
Law, V.2
Jewison, T.3
Liu, P.4
Ly, S.5
Frolkis, A.6
Pon, A.7
Banco, K.8
Mak, C.9
Neveu, V.10
Djoumbou, Y.11
Eisner, R.12
Guo, A.C.13
Wishart, D.S.14
-
57
-
-
0036012349
-
Plaid models for gene expression data
-
Lazzeroni L., Owen A. Plaid models for gene expression data. Statistica Sinica 1999, 12:61-86.
-
(1999)
Statistica Sinica
, vol.12
, pp. 61-86
-
-
Lazzeroni, L.1
Owen, A.2
-
58
-
-
59249086642
-
Learning a prior on regulatory potential from eQTL data
-
Lee S.-I., Dudley A.M., Drubin D., Silver P.A., Krogan N.J., Pe'er D., Koller D. Learning a prior on regulatory potential from eQTL data. PLoS Genet. 2009, 5:e1000358.
-
(2009)
PLoS Genet.
, vol.5
-
-
Lee, S.-I.1
Dudley, A.M.2
Drubin, D.3
Silver, P.A.4
Krogan, N.J.5
Pe'er, D.6
Koller, D.7
-
59
-
-
48849090016
-
Gene regulatory network reconstruction using conditional mutual information
-
Liang K.-C., Wang X. Gene regulatory network reconstruction using conditional mutual information. EURASIP J. Bioinformat. Syst. Biol. 2008, 2008:253894.
-
(2008)
EURASIP J. Bioinformat. Syst. Biol.
, vol.2008
, pp. 253894
-
-
Liang, K.-C.1
Wang, X.2
-
60
-
-
66349116028
-
Cross species analysis of microarray expression data
-
Lu Y., Huggins P., Bar-Joseph Z. Cross species analysis of microarray expression data. Bioinformatics 2009, 25:1476-1483.
-
(2009)
Bioinformatics
, vol.25
, pp. 1476-1483
-
-
Lu, Y.1
Huggins, P.2
Bar-Joseph, Z.3
-
61
-
-
51049113607
-
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
-
Lynn D.J., Winsor G.L., Chan C., Richard N., Laird M.R., Barsky A., Gardy J.L., Roche F.M., Chan T.H.W., Shah N., Lo R., Naseer M., Que J., Yau M., Acab M., Tulpan D., Whiteside M.D., Chikatamarla A., Mah B., Munzner T., Hokamp K., Hancock R.E.W., Brinkman F.S.L. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol. Syst. Biol. 2008, 4:218.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 218
-
-
Lynn, D.J.1
Winsor, G.L.2
Chan, C.3
Richard, N.4
Laird, M.R.5
Barsky, A.6
Gardy, J.L.7
Roche, F.M.8
Chan, T.H.W.9
Shah, N.10
Lo, R.11
Naseer, M.12
Que, J.13
Yau, M.14
Acab, M.15
Tulpan, D.16
Whiteside, M.D.17
Chikatamarla, A.18
Mah, B.19
Munzner, T.20
Hokamp, K.21
Hancock, R.E.W.22
Brinkman, F.S.L.23
more..
-
62
-
-
77950991905
-
The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models. Conference proceedings:.. Annual International Conference of the IEEE Engineering in Medicine and Biology Society
-
Madar A., Greenfield A., Ostrer H., Vanden-Eijnden E., Bonneau R. The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models. Conference proceedings:.. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Eng. Med. Biol. Soc. Conf. 2009, 1:5448-5451.
-
(2009)
IEEE Eng. Med. Biol. Soc. Conf.
, vol.1
, pp. 5448-5451
-
-
Madar, A.1
Greenfield, A.2
Ostrer, H.3
Vanden-Eijnden, E.4
Bonneau, R.5
-
63
-
-
78149461178
-
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator
-
Madar A., Greenfield A., Vanden-Eijnden E., Bonneau R. DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS ONE 2010, 5:e9803.
-
(2010)
PLoS ONE
, vol.5
-
-
Madar, A.1
Greenfield, A.2
Vanden-Eijnden, E.3
Bonneau, R.4
-
64
-
-
84859351639
-
Wisdom of crowds for gene network inference
-
submitted
-
Marbach, D., Costello, J., Küffner, R., Vega, N., Prill, R., Camacho, D., Allison, K., Consortium, T.D., Kellis, M., Collins, J., Stolovitzky, G., submitted. Wisdom of crowds for gene network inference.
-
-
-
Marbach, D.1
Costello J2
Küffner R3
Vega N4
Prill R5
Camacho D6
Allison K7
Consortium T.D8
Kellis M9
Collins J10
Stolovitzky, G.11
-
65
-
-
63849258962
-
Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge
-
Marbach D., Mattiussi C., Floreano D. Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge. Ann. N Y Acad. Sci. 2009, 1158:102-113.
-
(2009)
Ann. N Y Acad. Sci.
, vol.1158
, pp. 102-113
-
-
Marbach, D.1
Mattiussi, C.2
Floreano, D.3
-
66
-
-
59649096341
-
Replaying the evolutionary tape: biomimetic reverse engineering of gene networks
-
Marbach D., Mattiussi C., Floreano D. Replaying the evolutionary tape: biomimetic reverse engineering of gene networks. Ann. N Y Acad. Sci. 2009, 1158:234-245.
-
(2009)
Ann. N Y Acad. Sci.
, vol.1158
, pp. 234-245
-
-
Marbach, D.1
Mattiussi, C.2
Floreano, D.3
-
67
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach D., Prill R.J., Schaffter T., Mattiussi C., Floreano D., Stolovitzky G. Revealing strengths and weaknesses of methods for gene network inference. Proc. Natl. Acad. Sci. U S A 2010, 107:6286-6291.
-
(2010)
Proc. Natl. Acad. Sci. U S A
, vol.107
, pp. 6286-6291
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
Mattiussi, C.4
Floreano, D.5
Stolovitzky, G.6
-
68
-
-
59649110273
-
Generating realistic in silico gene networks for performance assessment of reverse engineering methods
-
Marbach D., Schaffter T., Mattiussi C., Floreano D. Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J. Comput. Biol. 2009, 16:229-239.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 229-239
-
-
Marbach, D.1
Schaffter, T.2
Mattiussi, C.3
Floreano, D.4
-
69
-
-
33947305781
-
ARACNE: an algorithm for the reoncstruction of gene regulatory networks in a mammalian cellular context
-
Margolin A.A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Favera R.D., Califano A. ARACNE: an algorithm for the reoncstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformat. 2006, 15:1-15.
-
(2006)
BMC Bioinformat.
, vol.15
, pp. 1-15
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
70
-
-
75649151459
-
Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling
-
Mazur J., Ritter D., Reinelt G., Kaderali L. Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling. BMC Bioinformat. 2009, 10:448.
-
(2009)
BMC Bioinformat.
, vol.10
, pp. 448
-
-
Mazur, J.1
Ritter, D.2
Reinelt, G.3
Kaderali, L.4
-
71
-
-
0036081482
-
Predictome: a database of putative functional links between proteins
-
Mellor J.C., Yanai I., Clodfelter K.H., Mintseris J., DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 2002, 30:306-309.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 306-309
-
-
Mellor, J.C.1
Yanai, I.2
Clodfelter, K.H.3
Mintseris, J.4
DeLisi, C.5
-
72
-
-
47049085481
-
InteroPORC: automated inference of highly conserved protein interaction networks
-
Michaut M., Kerrien S., Montecchi-Palazzi L., Chauvat F., Cassier-Chauvat C., Aude J.-C., Legrain P., Hermjakob H. InteroPORC: automated inference of highly conserved protein interaction networks. Bioinformatics 2008, 24:1625-1631.
-
(2008)
Bioinformatics
, vol.24
, pp. 1625-1631
-
-
Michaut, M.1
Kerrien, S.2
Montecchi-Palazzi, L.3
Chauvat, F.4
Cassier-Chauvat, C.5
Aude, J.-C.6
Legrain, P.7
Hermjakob, H.8
-
74
-
-
0006178946
-
Problems in the analysis of survey data, and a proposal
-
Morgan J.N., Sonquist J.A. Problems in the analysis of survey data, and a proposal. J. Amer. Stat. Assoc. 1963, 415-434.
-
(1963)
J. Amer. Stat. Assoc.
, pp. 415-434
-
-
Morgan, J.N.1
Sonquist, J.A.2
-
76
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 2002, 1:376-386.
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
Mann, M.7
-
77
-
-
79952775180
-
Transcriptomes of the B and T lineages compared by multiplatform microarray profiling
-
Painter M.W., Davis S., Hardy R.R., Mathis D., Benoist C. Transcriptomes of the B and T lineages compared by multiplatform microarray profiling. J. Immunol. 2011, 186:3047-3057.
-
(2011)
J. Immunol.
, vol.186
, pp. 3047-3057
-
-
Painter, M.W.1
Davis, S.2
Hardy, R.R.3
Mathis, D.4
Benoist, C.5
-
78
-
-
78149429509
-
From knockouts to networks: establishing direct cause-effect relationships through graph analysis
-
Pinna A., Soranzo N., de la Fuente A. From knockouts to networks: establishing direct cause-effect relationships through graph analysis. PloS ONE 2010, 5:e12912.
-
(2010)
PloS ONE
, vol.5
-
-
Pinna, A.1
Soranzo, N.2
de la Fuente, A.3
-
79
-
-
33846681447
-
Sungear: interactive visualization and functional analysis of genomic datasets
-
Poultney C.S., Gutiérrez R.a., Katari M.S., Gifford M.L., Paley W.B., Coruzzi G.M., Shasha D.E. Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (Oxford, England) 2007, 23:259-261.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, pp. 259-261
-
-
Poultney, C.S.1
Gutiérrez, R.2
Katari, M.S.3
Gifford, M.L.4
Paley, W.B.5
Coruzzi, G.M.6
Shasha, D.E.7
-
80
-
-
33747853260
-
APID: agile protein interaction dataanalyzer
-
Prieto C., Rivas J.D.L. APID: agile protein interaction dataanalyzer. Nucleic Acids Res. 2006, 34:W298-W302.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Prieto, C.1
Rivas, J.D.L.2
-
81
-
-
77949644952
-
Towards a rigorous assessment of systems biology models: the DREAM3 challenges
-
Prill R.J., Marbach D., Saez-Rodriguez J., Sorger P.K., Alexopoulos L.G., Xue X., Clarke N.D., Altan-Bonnet G., Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PloS ONE 2010, 5:e9202.
-
(2010)
PloS ONE
, vol.5
-
-
Prill, R.J.1
Marbach, D.2
Saez-Rodriguez, J.3
Sorger, P.K.4
Alexopoulos, L.G.5
Xue, X.6
Clarke, N.D.7
Altan-Bonnet, G.8
Stolovitzky, G.9
-
82
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
83
-
-
54949127160
-
IRefIndex: a consolidated protein interaction database with provenance
-
Razick S., Magklaras G., Donaldson I.M. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformat. 2008, 9:405.
-
(2008)
BMC Bioinformat.
, vol.9
, pp. 405
-
-
Razick, S.1
Magklaras, G.2
Donaldson, I.M.3
-
84
-
-
33746067911
-
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
-
Reiss D.J., Baliga N.S., Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformat. 2006, 7:280.
-
(2006)
BMC Bioinformat.
, vol.7
, pp. 280
-
-
Reiss, D.J.1
Baliga, N.S.2
Bonneau, R.3
-
85
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M., Storm C.E., Sonnhammer E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314:1041-1052.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
86
-
-
78651271733
-
Integrative genomics viewer
-
Robinson J.T., Thorvaldsdottir H., Winckler W., Guttman M., Lander E.S., Getz G., Mesirov J.P. Integrative genomics viewer. Nat. Biotechnol. 2011, 29:24-26.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
87
-
-
4043054669
-
Bayesian network approach to cell signaling pathway modeling
-
Science's STKE: signal transduction knowledge environment 2002, pe38.
-
Sachs, K., Gifford, D., Jaakkola, T., Sorger, P., Lauffenburger, D.A., 2002. Bayesian network approach to cell signaling pathway modeling. Science's STKE: signal transduction knowledge environment 2002, pe38.
-
(2002)
-
-
Sachs, K.1
Gifford, D.2
Jaakkola, T.3
Sorger, P.4
Lauffenburger, D.A.5
-
88
-
-
17644427718
-
Causal protein-signaling networks derived from multiparameter single-cell data
-
Sachs K., Perez O., Pe'er D., Lauffenburger D.A., Nolan G.P. Causal protein-signaling networks derived from multiparameter single-cell data. Science (New York, NY) 2005, 308:523-529.
-
(2005)
Science (New York, NY)
, vol.308
, pp. 523-529
-
-
Sachs, K.1
Perez, O.2
Pe'er, D.3
Lauffenburger, D.A.4
Nolan, G.P.5
-
89
-
-
0037311919
-
TM4: a free, open-source system for microarray data management and analysis
-
Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V., Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. BioTechniques 2003, 34:374-378.
-
(2003)
BioTechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Ryltsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
90
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res. 2004, 32:D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
91
-
-
4444352289
-
Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data
-
Schmitt W.A., Raab R.M., Stephanopoulos G. Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res. 2004, 14:1654-1663.
-
(2004)
Genome Res.
, vol.14
, pp. 1654-1663
-
-
Schmitt, W.A.1
Raab, R.M.2
Stephanopoulos, G.3
-
92
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 2003, 34:166-176.
-
(2003)
Nat. Genet.
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
93
-
-
84856043672
-
A mathematical theory of communication
-
Shannon C. A mathematical theory of communication. Bell Syst.Tech. J. 1948, 27:379-423.
-
(1948)
Bell Syst.Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.1
-
94
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, 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
-
95
-
-
33646743767
-
The Gaggle: an open-source software system for integrating bioinformatics software and data sources
-
Shannon P.T., Reiss D.J., Bonneau R., Baliga N.S. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformat. 2006, 7:176.
-
(2006)
BMC Bioinformat.
, vol.7
, pp. 176
-
-
Shannon, P.T.1
Reiss, D.J.2
Bonneau, R.3
Baliga, N.S.4
-
96
-
-
44949168530
-
Modularity of stress response evolution
-
Singh A.H., Wolf D.M., Wang P., Arkin A.P. Modularity of stress response evolution. Proc. Natl. Acad. Sci. U S A 2008, 105:7500-7505.
-
(2008)
Proc. Natl. Acad. Sci. U S A
, vol.105
, pp. 7500-7505
-
-
Singh, A.H.1
Wolf, D.M.2
Wang, P.3
Arkin, A.P.4
-
97
-
-
0242498780
-
Surface plasmon resonance imaging as a tool to monitor biomolecular interactions in an array based format
-
Smith E.A., Corn R.M. Surface plasmon resonance imaging as a tool to monitor biomolecular interactions in an array based format. Appl. Spectrosc. 2003, 57:320A-332A.
-
(2003)
Appl. Spectrosc.
, vol.57
-
-
Smith, E.A.1
Corn, R.M.2
-
98
-
-
0034666108
-
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
-
Snel B., Lehmann G., Bork P., Huynen M.A. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000, 28:3442-3444.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3442-3444
-
-
Snel, B.1
Lehmann, G.2
Bork, P.3
Huynen, M.A.4
-
99
-
-
0025129726
-
Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10
-
Soule H.D., Maloney T.M., Wolman S.R., Peterson W.D., Brenz R., McGrath C.M., Russo J., Pauley R.J., Jones R.F., Brooks S.C. Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. Cancer Res. 1990, 50:6075-6086.
-
(1990)
Cancer Res.
, vol.50
, pp. 6075-6086
-
-
Soule, H.D.1
Maloney, T.M.2
Wolman, S.R.3
Peterson, W.D.4
Brenz, R.5
McGrath, C.M.6
Russo, J.7
Pauley, R.J.8
Jones, R.F.9
Brooks, S.C.10
-
100
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
Stark C., Breitkreutz B.-J., Chatr-Aryamontri A., Boucher L., Oughtred R., Livstone M.S., Nixon J., Auken K.V., Wang X., Shi X., Reguly T., Rust J.M., Winter A., Dolinski K., Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39:D698-D700.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Stark, C.1
Breitkreutz, B.-J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
Livstone, M.S.6
Nixon, J.7
Auken, K.V.8
Wang, X.9
Shi, X.10
Reguly, T.11
Rust, J.M.12
Winter, A.13
Dolinski, K.14
Tyers, M.15
-
101
-
-
36249019789
-
Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference
-
Stolovitzky G., Monroe D., Califano A. Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann. N Y Acad. Sci. 2007, 1115:1-22.
-
(2007)
Ann. N Y Acad. Sci.
, vol.1115
, pp. 1-22
-
-
Stolovitzky, G.1
Monroe, D.2
Califano, A.3
-
102
-
-
35748941236
-
EDISA: extracting biclusters from multiple time-series of gene expression profiles
-
Supper J., Strauch M., Wanke D., Harter K., Zell A. EDISA: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformat. 2007, 8:334.
-
(2007)
BMC Bioinformat.
, vol.8
, pp. 334
-
-
Supper, J.1
Strauch, M.2
Wanke, D.3
Harter, K.4
Zell, A.5
-
103
-
-
65149083962
-
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
-
Suzuki H., Forrest A.R.R., van Nimwegen E., Daub C.O., Balwierz P.J., Irvine K.M., Lassmann T., Ravasi T., Hasegawa Y., de Hoon M.J.L., Katayama S., Schroder K., Carninci P., Tomaru Y., Kanamori-Katayama M., Kubosaki A., Akalin A., Ando Y., Arner E., Asada M., Asahara H., Bailey T., Bajic V.B., Bauer D., Beckhouse A.G., Bertin N., Björkegren J., Brombacher F., Bulger E., Chalk A.M., Chiba J., Cloonan N., Dawe A., Dostie J., Engström P.G., Essack M., Faulkner G.J., Fink J.L., Fredman D., Fujimori K., Furuno M., Gojobori T., Gough J., Grimmond S.M., Gustafsson M., Hashimoto M., Hashimoto T., Hatakeyama M., Heinzel S., Hide W., Hofmann O., Hörnquist M., Huminiecki L., Ikeo K., Imamoto N., Inoue S., Inoue Y., Ishihara R., Iwayanagi T., Jacobsen A., Kaur M., Kawaji H., Kerr M.C., Kimura R., Kimura S., Kimura Y., Kitano H., Koga H., Kojima T., Kondo S., Konno T., Krogh A., Kruger A., Kumar A., Lenhard B., Lennartsson A., Lindow M., Lizio M., Macpherson C., Maeda N., Maher C.A., Maqungo M., Mar J., Matigian N.A., Matsuda H., Mattick J.S., Meier S., Miyamoto S., Miyamoto-Sato E., Nakabayashi K., Nakachi Y., Nakano M., Nygaard S., Okayama T., Okazaki Y., Okuda-Yabukami H., Orlando V., Otomo J., Pachkov M., Petrovsky N., Plessy C., Quackenbush J., Radovanovic A., Rehli M., Saito R., Sandelin A., Schmeier S., Schönbach C., Schwartz A.S., Semple C.A., Sera M., Severin J., Shirahige K., Simons C., St Laurent G., Suzuki M., Suzuki T., Sweet M.J., Taft R.J., Takeda S., Takenaka Y., Tan K., Taylor M.S., Teasdale R.D., Tegnér J., Teichmann S., Valen E., Wahlestedt C., Waki K., Waterhouse A., Wells C.A., Winther O., Wu L., Yamaguchi K., Yanagawa H., Yasuda J., Zavolan M., Hume D.A., Arakawa T., Fukuda S., Imamura K., Kai C., Kaiho A., Kawashima T., Kawazu C., Kitazume Y., Kojima M., Miura H., Murakami K., Murata M., Ninomiya N., Nishiyori H., Noma S., Ogawa C., Sano T., Simon C., Tagami M., Takahashi Y., Kawai J., Hayashizaki Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. 2009, 41:553-562.
-
(2009)
Nat. Genet.
, vol.41
, pp. 553-562
-
-
Suzuki, H.1
Forrest, A.R.R.2
van Nimwegen, E.3
Daub, C.O.4
Balwierz, P.J.5
Irvine, K.M.6
Lassmann, T.7
Ravasi, T.8
Hasegawa, Y.9
de Hoon, M.J.L.10
Katayama, S.11
Schroder, K.12
Carninci, P.13
Tomaru, Y.14
Kanamori-Katayama, M.15
Kubosaki, A.16
Akalin, A.17
Ando, Y.18
Arner, E.19
Asada, M.20
Asahara, H.21
Bailey, T.22
Bajic, V.B.23
Bauer, D.24
Beckhouse, A.G.25
Bertin, N.26
Björkegren, J.27
Brombacher, F.28
Bulger, E.29
Chalk, A.M.30
Chiba, J.31
Cloonan, N.32
Dawe, A.33
Dostie, J.34
Engström, P.G.35
Essack, M.36
Faulkner, G.J.37
Fink, J.L.38
Fredman, D.39
Fujimori, K.40
Furuno, M.41
Gojobori, T.42
Gough, J.43
Grimmond, S.M.44
Gustafsson, M.45
Hashimoto, M.46
Hashimoto, T.47
Hatakeyama, M.48
Heinzel, S.49
Hide, W.50
Hofmann, O.51
Hörnquist, M.52
Huminiecki, L.53
Ikeo, K.54
Imamoto, N.55
Inoue, S.56
Inoue, Y.57
Ishihara, R.58
Iwayanagi, T.59
Jacobsen, A.60
Kaur, M.61
Kawaji, H.62
Kerr, M.C.63
Kimura, R.64
Kimura, S.65
Kimura, Y.66
Kitano, H.67
Koga, H.68
Kojima, T.69
Kondo, S.70
Konno, T.71
Krogh, A.72
Kruger, A.73
Kumar, A.74
Lenhard, B.75
Lennartsson, A.76
Lindow, M.77
Lizio, M.78
Macpherson, C.79
Maeda, N.80
Maher, C.A.81
Maqungo, M.82
Mar, J.83
Matigian, N.A.84
Matsuda, H.85
Mattick, J.S.86
Meier, S.87
Miyamoto, S.88
Miyamoto-Sato, E.89
Nakabayashi, K.90
Nakachi, Y.91
Nakano, M.92
Nygaard, S.93
Okayama, T.94
Okazaki, Y.95
Okuda-Yabukami, H.96
Orlando, V.97
Otomo, J.98
Pachkov, M.99
more..
-
104
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., Doerks T., Stark M., Muller J., Bork P., Jensen L.J., von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39:D561-D568.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
Jensen, L.J.11
von Mering, C.12
-
105
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay A., Sharan R., Kupiec M., Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc. Natl. Acad. Sci. U S A 2004, 101:2981-2986.
-
(2004)
Proc. Natl. Acad. Sci. U S A
, vol.101
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
106
-
-
0033956060
-
The COG database: a tool for genome-scale analysis of protein functions and evolution
-
Tatusov R.L., Galperin M.Y., Natale D.A., Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28:33-36.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
107
-
-
34548527460
-
Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
-
Tirosh I., Barkai N. Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol. 2007, 8:R50.
-
(2007)
Genome Biol.
, vol.8
-
-
Tirosh, I.1
Barkai, N.2
-
108
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U S A 2001, 98:5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U S A
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
109
-
-
0041620271
-
Regulatory sequence analysis tools
-
van Helden J. Regulatory sequence analysis tools. Nucleic Acids Res. 2003, 31:3593-3596.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3593-3596
-
-
van Helden, J.1
-
110
-
-
77957126815
-
Multi-species integrative biclustering
-
Waltman P., Kacmarczyk T., Bate A.R., Kearns D.B., Reiss D.J., Eichenberger P., Bonneau R. Multi-species integrative biclustering. Genome Biol. 2010, 11:R96.
-
(2010)
Genome Biol.
, vol.11
-
-
Waltman, P.1
Kacmarczyk, T.2
Bate, A.R.3
Kearns, D.B.4
Reiss, D.J.5
Eichenberger, P.6
Bonneau, R.7
-
111
-
-
0013188149
-
Node-deletion problems on bipartite graphs
-
Yannakakis M. Node-deletion problems on bipartite graphs. SIAM J. Comput. 1981, 10:310-327.
-
(1981)
SIAM J. Comput.
, vol.10
, pp. 310-327
-
-
Yannakakis, M.1
-
112
-
-
77749264188
-
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data
-
Yip K.Y., Alexander R.P., Yan K.-K., Gerstein M. Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data. PLoS ONE 2010, 5:e8121.
-
(2010)
PLoS ONE
, vol.5
-
-
Yip, K.Y.1
Alexander, R.P.2
Yan, K.-K.3
Gerstein, M.4
-
113
-
-
84859346483
-
Adaptive least absolute regression network analysis improves genetic network reconstruction by employing prior knowledge
-
Yong-a-poi J., Someren E.V., Bellomo D., Reinders M. Adaptive least absolute regression network analysis improves genetic network reconstruction by employing prior knowledge. Commun. Theory 2008, 1-14.
-
(2008)
Commun. Theory
, pp. 1-14
-
-
Yong-a-poi, J.1
Someren, E.V.2
Bellomo, D.3
Reinders, M.4
-
114
-
-
79952136790
-
Functional molecular ecological networks
-
e00169-00110
-
Zhou J., Deng Y., Luo F., He Z., Tu Q., Zhi X. Functional molecular ecological networks. mBio 2010, 1. e00169-00110.
-
(2010)
mBio
, vol.1
-
-
Zhou, J.1
Deng, Y.2
Luo, F.3
He, Z.4
Tu, Q.5
Zhi, X.6
-
115
-
-
33846114377
-
The adaptive lasso and its oracle properties
-
Zou H. The adaptive lasso and its oracle properties. J. Amer. Statis. Assoc. 2006, 101:1418-1429.
-
(2006)
J. Amer. Statis. Assoc.
, vol.101
, pp. 1418-1429
-
-
Zou, H.1
|