-
1
-
-
84868020742
-
Bayesian inference of signaling network topology in a cancer cell line
-
Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics. 2012; 28(21):2804-10.
-
(2012)
Bioinformatics
, vol.28
, Issue.21
, pp. 2804-2810
-
-
Hill, S.M.1
Lu, Y.2
Molina, J.3
Heiser, L.M.4
Spellman, P.T.5
Speed, T.P.6
Gray, J.W.7
Mills, G.B.8
Mukherjee, S.9
-
2
-
-
84964312497
-
Sexually-dimorphic targeting of functionally-related genes in copd
-
Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in copd. BMC Syst Biol. 2014; 8(1):118.
-
(2014)
BMC Syst Biol
, vol.8
, Issue.1
, pp. 118
-
-
Glass, K.1
Quackenbush, J.2
Silverman, E.K.3
Celli, B.4
Rennard, S.I.5
Yuan, G.C.6
DeMeo, D.L.7
-
3
-
-
84928540618
-
A network model for angiogenesis in ovarian cancer
-
Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. BMC Bioinformatics. 2015; 16(1):115.
-
(2015)
BMC Bioinformatics
, vol.16
, Issue.1
, pp. 115
-
-
Glass, K.1
Quackenbush, J.2
Spentzos, D.3
Haibe-Kains, B.4
Yuan, G.C.5
-
4
-
-
84866467177
-
Integrating literature-constrained and data-driven inference of signalling networks
-
Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics. 2012; 28(18):2311-7.
-
(2012)
Bioinformatics
, vol.28
, Issue.18
, pp. 2311-2317
-
-
Eduati, F.1
De Las Rivas, J.2
Di Camillo, B.3
Toffolo, G.4
Saez-Rodriguez, J.5
-
5
-
-
58549083142
-
Input-output behavior of erbb signaling pathways as revealed by a mass action model trained against dynamic data
-
Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, Lauffenburger DA, Sorger PK. Input-output behavior of erbb signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol. 2009; 5:239.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 239
-
-
Chen, W.W.1
Schoeberl, B.2
Jasper, P.J.3
Niepel, M.4
Nielsen, U.B.5
Lauffenburger, D.A.6
Sorger, P.K.7
-
6
-
-
84892763562
-
Perturbation biology: inferring signaling networks in cellular systems
-
Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, et al.Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol. 2013; 9(12):1003290.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.12
, pp. 1003290
-
-
Molinelli, E.J.1
Korkut, A.2
Wang, W.3
Miller, M.L.4
Gauthier, N.P.5
Jing, X.6
Kaushik, P.7
He, Q.8
Mills, G.9
Solit, D.B.10
-
7
-
-
80051692878
-
Comparing signaling networks between normal and transformed hepatocytes using discrete logical models
-
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res. 2011; 71(16):5400-11.
-
(2011)
Cancer Res
, vol.71
, Issue.16
, pp. 5400-5411
-
-
Saez-Rodriguez, J.1
Alexopoulos, L.G.2
Zhang, M.3
Morris, M.K.4
Lauffenburger, D.A.5
Sorger, P.K.6
-
8
-
-
84878605343
-
Passing messages between biological networks to refine predicted interactions
-
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PloS ONE. 2013; 8(5):64832.
-
(2013)
PloS ONE
, vol.8
, Issue.5
, pp. 64832
-
-
Glass, K.1
Huttenhower, C.2
Quackenbush, J.3
Yuan, G.C.4
-
9
-
-
0042706147
-
Genomic analysis of gene expression relationships in transcriptional regulatory networks
-
Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet. 2003; 19(8):422-7.
-
(2003)
Trends Genet
, vol.19
, Issue.8
, pp. 422-427
-
-
Yu, H.1
Luscombe, N.M.2
Qian, J.3
Gerstein, M.4
-
10
-
-
0142179209
-
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
-
Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003; 19(15):1917-26.
-
(2003)
Bioinformatics
, vol.19
, Issue.15
, pp. 1917-1926
-
-
Qian, J.1
Lin, J.2
Luscombe, N.M.3
Yu, H.4
Gerstein, M.5
-
11
-
-
62549128139
-
A census of human transcription factors: function, expression and evolution
-
Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009; 10(4):252.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.4
, pp. 252
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
12
-
-
85038103721
-
Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression
-
Bussemaker HJ, Causton HC, Fazlollahi M, Lee E, Muroff I. Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression. Curr Opin Syst Biol. 2017; 2:98-102.
-
(2017)
Curr Opin Syst Biol
, vol.2
, pp. 98-102
-
-
Bussemaker, H.J.1
Causton, H.C.2
Fazlollahi, M.3
Lee, E.4
Muroff, I.5
-
13
-
-
84930607351
-
Sharing and specificity of co-expression networks across 35 human tissues
-
Pierson E, Koller D, Battle A, Mostafavi S, Consortium G, et al.Sharing and specificity of co-expression networks across 35 human tissues. PLoS Comput Biol. 2015; 11(5):1004220.
-
(2015)
PLoS Comput Biol
, vol.11
, Issue.5
, pp. 1004220
-
-
Pierson, E.1
Koller, D.2
Battle, A.3
Mostafavi, S.4
Consortium, G.5
-
14
-
-
84991270631
-
Identifying gene regulatory network rewiring using latent differential graphical models
-
Tian D, Gu Q, Ma J. Identifying gene regulatory network rewiring using latent differential graphical models. Nucleic Acids Res. 2016; 44(17):140-0.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.17
, pp. 140-140
-
-
Tian, D.1
Gu, Q.2
Ma, J.3
-
15
-
-
85046412751
-
Netdiff-bayesian model selection for differential gene regulatory network inference
-
Thorne T. Netdiff-bayesian model selection for differential gene regulatory network inference. Sci Rep. 2016; 6:39224.
-
(2016)
Sci Rep
, vol.6
, pp. 39224
-
-
Thorne, T.1
-
16
-
-
84907501962
-
Altered gene expression in blood and sputum in copd frequent exacerbators in the eclipse cohort
-
Singh D, Fox SM, Tal-Singer R, Bates S, Riley JH, Celli B. Altered gene expression in blood and sputum in copd frequent exacerbators in the eclipse cohort. PloS ONE. 2014; 9(9):107381.
-
(2014)
PloS ONE
, vol.9
, Issue.9
, pp. 107381
-
-
Singh, D.1
Fox, S.M.2
Tal-Singer, R.3
Bates, S.4
Riley, J.H.5
Celli, B.6
-
17
-
-
42949146028
-
Evaluation of copd longitudinally to identify predictive surrogate end-points (eclipse)
-
Vestbo J, Anderson W, Coxson HO, Crim C, Dawber F, Edwards L, Hagan G, Knobil K, Lomas DA, MacNee W, et al.Evaluation of copd longitudinally to identify predictive surrogate end-points (eclipse). Eur Respir J. 2008; 31(4):869-73.
-
(2008)
Eur Respir J
, vol.31
, Issue.4
, pp. 869-873
-
-
Vestbo, J.1
Anderson, W.2
Coxson, H.O.3
Crim, C.4
Dawber, F.5
Edwards, L.6
Hagan, G.7
Knobil, K.8
Lomas, D.A.9
MacNee, W.10
-
18
-
-
77949363490
-
Genetic epidemiology of copd (copdgene) study design
-
Regan EA, Hokanson JE, Murphy JR, Make B, Lynch DA, Beaty TH, Curran-Everett D, Silverman EK, Crapo JD. Genetic epidemiology of copd (copdgene) study design. COPD J Chronic Obstructive Pulm Dis. 2011; 7(1):32-43.
-
(2011)
COPD J Chronic Obstructive Pulm Dis
, vol.7
, Issue.1
, pp. 32-43
-
-
Regan, E.A.1
Hokanson, J.E.2
Murphy, J.R.3
Make, B.4
Lynch, D.A.5
Beaty, T.H.6
Curran-Everett, D.7
Silverman, E.K.8
Crapo, J.D.9
-
19
-
-
84883185155
-
Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease
-
Bahr TM, Hughes GJ, Armstrong M, Reisdorph R, Coldren CD, Edwards MG, Schnell C, Kedl R, LaFlamme DJ, Reisdorph N, et al.Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 2013; 49(2):316-23.
-
(2013)
Am J Respir Cell Mol Biol
, vol.49
, Issue.2
, pp. 316-323
-
-
Bahr, T.M.1
Hughes, G.J.2
Armstrong, M.3
Reisdorph, R.4
Coldren, C.D.5
Edwards, M.G.6
Schnell, C.7
Kedl, R.8
LaFlamme, D.J.9
Reisdorph, N.10
-
20
-
-
63449101907
-
A genome-wide association study in chronic obstructive pulmonary disease (copd): identification of two major susceptibility loci
-
Pillai SG, Ge D, Zhu G, Kong X, Shianna KV, Need AC, Feng S, Hersh CP, Bakke P, Gulsvik A, et al.A genome-wide association study in chronic obstructive pulmonary disease (copd): identification of two major susceptibility loci. PLoS Genet. 2009; 5(3):1000421.
-
(2009)
PLoS Genet
, vol.5
, Issue.3
, pp. 1000421
-
-
Pillai, S.G.1
Ge, D.2
Zhu, G.3
Kong, X.4
Shianna, K.V.5
Need, A.C.6
Feng, S.7
Hersh, C.P.8
Bakke, P.9
Gulsvik, A.10
-
21
-
-
85038083168
-
-
Accessed 2 Feb 2016
-
Lung genomics research consortium (lgrc). 2015. http://www.lung-genomics.org/. Accessed 2 Feb 2016.
-
(2015)
-
-
-
22
-
-
84988823479
-
Network analysis of gene expression in severe COPD lung tissue samples
-
Qiu W, DeMeo DL, Houston I, Pinto-Plata VM, Celli BR, Marchetti N, Criner GJ, Bueno R, Morrow G, Washko K, et al. Network analysis of gene expression in severe COPD lung tissue samples. Am J Respir Crit Care Med. 2015; 191:A1253.
-
(2015)
Am J Respir Crit Care Med
, vol.191
, pp. A1253
-
-
Qiu, W.1
DeMeo, D.L.2
Houston, I.3
Pinto-Plata, V.M.4
Celli, B.R.5
Marchetti, N.6
Criner, G.J.7
Bueno, R.8
Morrow, G.9
Washko, K.10
-
23
-
-
33947305781
-
Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A. Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 2006; 7(Suppl 1):7.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
24
-
-
33846400424
-
Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007; 5(1):8.
-
(2007)
PLoS Biol
, vol.5
, Issue.1
, pp. 8
-
-
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
-
25
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005; 4(1):Article17.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
, Issue.1
-
-
Zhang, B.1
Horvath, S.2
-
26
-
-
34247634108
-
E2f4 is required for normal development of the airway epithelium
-
Danielian PS, Kim CFB, Caron AM, Vasile E, Bronson RT, Lees JA. E2f4 is required for normal development of the airway epithelium. Dev Biol. 2007; 305(2):564-76.
-
(2007)
Dev Biol
, vol.305
, Issue.2
, pp. 564-576
-
-
Danielian, P.S.1
Kim, C.F.B.2
Caron, A.M.3
Vasile, E.4
Bronson, R.T.5
Lees, J.A.6
-
27
-
-
84975129723
-
Bridging lung development with chronic obstructive pulmonary disease. relevance of developmental pathways in chronic obstructive pulmonary disease pathogenesis
-
Boucherat O, Morissette M, Provencher S, Bonnet S, F M.Bridging lung development with chronic obstructive pulmonary disease. relevance of developmental pathways in chronic obstructive pulmonary disease pathogenesis. Am J Respir Crit Care Med. 2016; 193(4):362-75.
-
(2016)
Am J Respir Crit Care Med
, vol.193
, Issue.4
, pp. 362-375
-
-
Boucherat, O.1
Morissette, M.2
Provencher, S.3
Bonnet, S.4
-
28
-
-
84863279822
-
Identification of a chronic obstructive pulmonary disease genetic determinant that regulates hhip
-
Zhou X, Baron RM, Hardin M, Cho MH, Zielinski J, Hawrylkiewicz I, Sliwinski P, Hersh CP, Mancini JD, Lu K, et al.Identification of a chronic obstructive pulmonary disease genetic determinant that regulates hhip. Hum Mol Genet. 2012; 21(6):1325-35.
-
(2012)
Hum Mol Genet
, vol.21
, Issue.6
, pp. 1325-1335
-
-
Zhou, X.1
Baron, R.M.2
Hardin, M.3
Cho, M.H.4
Zielinski, J.5
Hawrylkiewicz, I.6
Sliwinski, P.7
Hersh, C.P.8
Mancini, J.D.9
Lu, K.10
-
29
-
-
0033550316
-
Transcription factors of the sp1 family: interaction with e2f and regulation of the murine thymidine kinase promoter
-
Rotheneder H, Geymayer S, Haidweger E. Transcription factors of the sp1 family: interaction with e2f and regulation of the murine thymidine kinase promoter. J Mol Biol. 1999; 293(5):1005-15.
-
(1999)
J Mol Biol
, vol.293
, Issue.5
, pp. 1005-1015
-
-
Rotheneder, H.1
Geymayer, S.2
Haidweger, E.3
-
30
-
-
0029926303
-
Interaction of sp1 with the growth-and cell cycle-regulated transcription factor e2f
-
Karlseder J, Rotheneder H, Wintersberger E. Interaction of sp1 with the growth-and cell cycle-regulated transcription factor e2f. Mol Cell Biol. 1996; 16(4):1659-67.
-
(1996)
Mol Cell Biol
, vol.16
, Issue.4
, pp. 1659-1667
-
-
Karlseder, J.1
Rotheneder, H.2
Wintersberger, E.3
-
31
-
-
53749087325
-
Egr-1 regulates autophagy in cigarette smoke-induced chronic obstructive pulmonary disease
-
Chen ZH, Kim HP, Sciurba FC, Lee SJ, Feghali-Bostwick C, Stolz DB, Dhir R, Landreneau RJ, Schuchert MJ, Yousem SA, et al.Egr-1 regulates autophagy in cigarette smoke-induced chronic obstructive pulmonary disease. PloS ONE. 2008; 3(10):3316.
-
(2008)
PloS ONE
, vol.3
, Issue.10
, pp. 3316
-
-
Chen, Z.H.1
Kim, H.P.2
Sciurba, F.C.3
Lee, S.J.4
Feghali-Bostwick, C.5
Stolz, D.B.6
Dhir, R.7
Landreneau, R.J.8
Schuchert, M.J.9
Yousem, S.A.10
-
32
-
-
84957428592
-
Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice
-
Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, et al.Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med. 2016; 22(2):163-74.
-
(2016)
Nat Med.
, vol.22
, Issue.2
, pp. 163-174
-
-
Cloonan, S.M.1
Glass, K.2
Laucho-Contreras, M.E.3
Bhashyam, A.R.4
Cervo, M.5
Pabón, M.A.6
Konrad, C.7
Polverino, F.8
Siempos, I.I.9
Perez, E.10
-
33
-
-
0029051835
-
Structure, expression, and chromosomal assignment of the human gene encoding nuclear respiratory factor 1
-
Gopalakrishnan L, Scarpulla RC. Structure, expression, and chromosomal assignment of the human gene encoding nuclear respiratory factor 1. J Biol Chem. 1995; 270(30):18019-25.
-
(1995)
J Biol Chem
, vol.270
, Issue.30
, pp. 18019-18025
-
-
Gopalakrishnan, L.1
Scarpulla, R.C.2
-
34
-
-
0035830950
-
Sp1 and sp3 physically interact and co-operate with gabp for the activation of the utrophin promoter
-
Galvagni F, Capo S, Oliviero S. Sp1 and sp3 physically interact and co-operate with gabp for the activation of the utrophin promoter. J Mol Biol. 2001; 306(5):985-96.
-
(2001)
J Mol Biol
, vol.306
, Issue.5
, pp. 985-996
-
-
Galvagni, F.1
Capo, S.2
Oliviero, S.3
-
35
-
-
77649176945
-
Comparison of evolutionary algorithms in gene regulatory network model inference
-
Sîrbu A, Ruskin HJ, Crane M. Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinformatics. 2010; 11(1):1.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 1
-
-
Sîrbu, A.1
Ruskin, H.J.2
Crane, M.3
-
36
-
-
84896257145
-
Switching on cilia: transcriptional networks regulating ciliogenesis
-
Choksi SP, Lauter G, Swoboda P, Roy S. Switching on cilia: transcriptional networks regulating ciliogenesis. Development. 2014; 141(7):1427-41.
-
(2014)
Development
, vol.141
, Issue.7
, pp. 1427-1441
-
-
Choksi, S.P.1
Lauter, G.2
Swoboda, P.3
Roy, S.4
-
37
-
-
84904785682
-
Intraflagellar transport gene expression associated with short cilia in smoking and copd
-
Hessel J, Heldrich J, Fuller J, Staudt MR, Radisch S, Hollmann C, Harvey BG, Kaner RJ, Salit J, Yee-Levin J, et al.Intraflagellar transport gene expression associated with short cilia in smoking and copd. PloS ONE. 2014; 9(1):85453.
-
(2014)
PloS ONE
, vol.9
, Issue.1
, pp. 85453
-
-
Hessel, J.1
Heldrich, J.2
Fuller, J.3
Staudt, M.R.4
Radisch, S.5
Hollmann, C.6
Harvey, B.G.7
Kaner, R.J.8
Salit, J.9
Yee-Levin, J.10
-
38
-
-
4344675455
-
Pathophysiology of airflow limitation in chronic obstructive pulmonary disease
-
Hogg JC. Pathophysiology of airflow limitation in chronic obstructive pulmonary disease. The Lancet. 2004; 364(9435):709-21.
-
(2004)
The Lancet
, vol.364
, Issue.9435
, pp. 709-721
-
-
Hogg, J.C.1
-
39
-
-
78649735324
-
Airway mucus function and dysfunction
-
Fahy JV, Dickey BF. Airway mucus function and dysfunction. N Engl J Med. 2010; 363(23):2233-47.
-
(2010)
N Engl J Med
, vol.363
, Issue.23
, pp. 2233-2247
-
-
Fahy, J.V.1
Dickey, B.F.2
|