-
1
-
-
33644860299
-
A multi-step approach to time series analysis and gene expression clustering
-
Amato R, Ciaramella A, Deniskina N, Del Mondo C, di Bernardo D, Donalek C, Longo G, Mangano G, Miele G, Raiconi G, Staiano A, Tagliaferri R (2006) A multi-step approach to time series analysis and gene expression clustering. Bioinformatics 22: 589-596
-
(2006)
Bioinformatics
, vol.22
, pp. 589-596
-
-
Amato, R.1
Ciaramella, A.2
Deniskina, N.3
Del Mondo, C.4
di Bernardo, D.5
Donalek, C.6
Longo, G.7
Mangano, G.8
Miele, G.9
Raiconi, G.10
Staiano, A.11
Tagliaferri, R.12
-
2
-
-
33751238890
-
Computational biology and drug discovery: From single-target to network drugs
-
Ambesi A, di Bernardo D (2006) Computational biology and drug discovery: From single-target to network drugs. Curr Bioinform 1: 3-13
-
(2006)
Curr Bioinform
, vol.1
, pp. 3-13
-
-
Ambesi, A.1
di Bernardo, D.2
-
3
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M, Della Gatta G, di Bernardo D (2006) Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22: 815-822
-
(2006)
Bioinformatics
, vol.22
, pp. 815-822
-
-
Bansal, M.1
Della Gatta, G.2
di Bernardo, D.3
-
4
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37: 382-390
-
(2005)
Nat Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
5
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117: 185-198
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
6
-
-
33747813561
-
The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
Bonneau R, Reiss D, Shannon P, Facciotti M, Hood L, Baliga N, Thorsson V (2006) The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7: R36
-
(2006)
Genome Biol
, vol.7
-
-
Bonneau, R.1
Reiss, D.2
Shannon, P.3
Facciotti, M.4
Hood, L.5
Baliga, N.6
Thorsson, V.7
-
7
-
-
2942694772
-
Artificial gene networks for objective comparison of analysis algorithms
-
Brazhnik P, de la Fuente A, Mendes P (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19 (Suppl 2): II122-II129
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Brazhnik, P.1
de la Fuente, A.2
Mendes, P.3
-
9
-
-
0033655775
-
Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
-
Butte A, Kohane I (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 418-429
-
(2000)
Pac Symp Biocomput
, pp. 418-429
-
-
Butte, A.1
Kohane, I.2
-
10
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comp Biol 9: 67-103
-
(2002)
J Comp Biol
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
12
-
-
21444452397
-
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
-
di Bernardo D, Thompson M, Gardner T, Chobot S, Eastwood E, Wojtovich A, Elliott S, Schaus S, Collins J (2005) Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol 23: 377-383
-
(2005)
Nat Biotechnol
, vol.23
, pp. 377-383
-
-
di Bernardo, D.1
Thompson, M.2
Gardner, T.3
Chobot, S.4
Eastwood, E.5
Wojtovich, A.6
Elliott, S.7
Schaus, S.8
Collins, J.9
-
14
-
-
14844286390
-
Reverse-engineering transcription control networks
-
Faith J, Gardner T (2005) Reverse-engineering transcription control networks. Phys Life Rev 2: 65-88
-
(2005)
Phys Life Rev
, vol.2
, pp. 65-88
-
-
Faith, J.1
Gardner, T.2
-
15
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce
-
Foat B, Morozov A, Bussemaker HJ (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce. Bioinformatics 22: e141-e149
-
(2006)
Bioinformatics
, vol.22
-
-
Foat, B.1
Morozov, A.2
Bussemaker, H.J.3
-
17
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner T, di Bernardo D, Lorenz D, Collins J (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.4
-
18
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH (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
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
Meyer, M.R.13
Slade, D.14
Lum, P.Y.15
Stepaniants, S.B.16
Shoemaker, D.D.17
Gachotte, D.18
Chakraburtty, K.19
Simon, J.20
Bard, M.21
Friend, S.H.22
more..
-
19
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisae
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne J-B, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisae. Science 298: 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.-B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
20
-
-
33947305781
-
-
Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Della Favera R, Califano A (2006) Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics S1 (arXiv: q-bio.MN/0410037)
-
Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Della Favera R, Califano A (2006) Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics S1 (arXiv: q-bio.MN/0410037)
-
-
-
-
21
-
-
0003229133
-
The bayes net toolbox for matlab
-
Murphy K (2001) The bayes net toolbox for matlab. Comput Sci Stat 33
-
(2001)
Comput Sci Stat
, vol.33
-
-
Murphy, K.1
-
23
-
-
27144476523
-
Discovery of regulatory elements in vertebrates through comparative genomics
-
Prakash A, Tompa M (2005) Discovery of regulatory elements in vertebrates through comparative genomics. Nat Biotechnol 23: 1249-1256
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1249-1256
-
-
Prakash, A.1
Tompa, M.2
-
24
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga N,Wang J, Ramage D, Amin D, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.4
Wang, J.5
Ramage, D.6
Amin, D.7
Schwikowski, B.8
Ideker, T.9
-
25
-
-
0042526388
-
The mutual information: Detecting and evaluating dependencies between variables
-
Evaluation Stud
-
Steuer R, Kurths J, Daub CO, Weise J, Selbig J (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18 (Suppl 2): 231-240, Evaluation Stud
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
, pp. 231-240
-
-
Steuer, R.1
Kurths, J.2
Daub, C.O.3
Weise, J.4
Selbig, J.5
-
26
-
-
8844262539
-
Identification of DNA regulatory motifs using bayesian variable selection
-
Tadesse M, Vannucci M, Lio P (2004) Identification of DNA regulatory motifs using bayesian variable selection. Bioinformatics 20: 2556-2561
-
(2004)
Bioinformatics
, vol.20
, pp. 2556-2561
-
-
Tadesse, M.1
Vannucci, M.2
Lio, P.3
-
27
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
Tegner J, Yeung MK, Hasty J, Collins JJ (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci USA 100: 5944-5949
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
28
-
-
32544457104
-
Least absolute regression network analysis of the murine osteoblast differentiation network
-
van Someren E, Vaes B, Steegenga W, Sijbers A, Dechering K, Reinders M (2006) Least absolute regression network analysis of the murine osteoblast differentiation network. Bioinformatics 22: 477-484
-
(2006)
Bioinformatics
, vol.22
, pp. 477-484
-
-
van Someren, E.1
Vaes, B.2
Steegenga, W.3
Sijbers, A.4
Dechering, K.5
Reinders, M.6
-
29
-
-
33646748283
-
A systems approach to mapping DNA damage response pathways
-
Workman C, Mak H, McCuine S, Tagne J, Agarwal M, Ozier O, Begley T, Samson L, T I (2006) A systems approach to mapping DNA damage response pathways. Science 312: 1054-1059
-
(2006)
Science
, vol.312
, pp. 1054-1059
-
-
Workman, C.1
Mak, H.2
McCuine, S.3
Tagne, J.4
Agarwal, M.5
Ozier, O.6
Begley, T.7
Samson, L.T.I.8
-
30
-
-
12344259602
-
Advances to bayesian network inference for generating causal networks from observational biological data
-
Yu J, Smith VA,Wang PP, Hartemink AJ, Jarvis ED (2004) Advances to bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20: 3594-3603
-
(2004)
Bioinformatics
, vol.20
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
Hartemink, A.J.4
Jarvis, E.D.5
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