-
1
-
-
84861643512
-
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
-
Martin F, Thomson TM, Sewer A, Drubin DA, Mathis C, Weisensee D, Pratt D, Hoeng J, Peitsch MC: Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. BMC Syst Biol 2012, 6:54.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 54
-
-
Martin, F.1
Thomson, T.M.2
Sewer, A.3
Drubin, D.A.4
Mathis, C.5
Weisensee, D.6
Pratt, D.7
Hoeng, J.8
Peitsch, M.C.9
-
2
-
-
84893009656
-
Methods and approaches in the topology-based analysis of biological pathways
-
Mitrea C, Taghavi Z, Bokanizad B, Hanoudi S, Tagett R, Donato M, Voichita C, Draghici S: Methods and approaches in the topology-based analysis of biological pathways. Front Physiol 2013, 4:278.
-
(2013)
Front Physiol
, vol.4
, pp. 278
-
-
Mitrea, C.1
Taghavi, Z.2
Bokanizad, B.3
Hanoudi, S.4
Tagett, R.5
Donato, M.6
Voichita, C.7
Draghici, S.8
-
3
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
4
-
-
33644873677
-
Pathguide: A pathway resource list
-
Bader GD, Cary MP, Sander C: Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34(Database issue):D504-D506.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
, pp. D504-D506
-
-
Bader, G.D.1
Cary, M.P.2
Sander, C.3
-
5
-
-
84860698978
-
A network-based approach to quantifying the impact of biologically active substances
-
Hoeng J, Deehan R, Pratt D, Martin F, Sewer A, Thomson TM, Drubin DA, Waters CA, de Graaf D, Peitsch MC: A network-based approach to quantifying the impact of biologically active substances. Drug Discov Today 2012, 17(9-10):413-418.
-
(2012)
Drug Discov Today
, vol.17
, Issue.9-10
, pp. 413-418
-
-
Hoeng, J.1
Deehan, R.2
Pratt, D.3
Martin, F.4
Sewer, A.5
Thomson, T.M.6
Drubin, D.A.7
Waters, C.A.8
De Graaf, D.9
Peitsch, M.C.10
-
6
-
-
79959759890
-
Construction of a computable cell proliferation network focused on non-diseased lung cells
-
Westra JW, Schlage WK, Frushour BP, Gebel S, Catlett NL, Han W, Eddy SF, Hengstermann A, Matthews AL, Mathis C, Lichtner RB, Poussin C, Talikka M, Veljkovic E, Van Hooser AA, Wong B, Maria MJ, Peitsch MC, Deehan R, Hoeng J: Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst Biol 2011, 5:105.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 105
-
-
Westra, J.W.1
Schlage, W.K.2
Frushour, B.P.3
Gebel, S.4
Catlett, N.L.5
Han, W.6
Eddy, S.F.7
Hengstermann, A.8
Matthews, A.L.9
Mathis, C.10
Lichtner, R.B.11
Poussin, C.12
Talikka, M.13
Veljkovic, E.14
Van Hooser, A.A.15
Wong, B.16
Maria, M.J.17
Peitsch, M.C.18
Deehan, R.19
Hoeng, J.20
more..
-
7
-
-
77957766590
-
SnapShot: Network motifs
-
Shoval O, Alon U: SnapShot: network motifs. Cell 2010, 143(2):326-e321.
-
(2010)
Cell
, vol.143
, Issue.2
, pp. e321-e326
-
-
Shoval, O.1
Alon, U.2
-
8
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R: A novel signaling pathway impact analysis. Bioinformatics 2009, 25(1):75-82.
-
(2009)
Bioinformatics
, vol.25
, Issue.1
, pp. 75-82
-
-
Tarca, A.L.1
Draghici, S.2
Khatri, P.3
Hassan, S.S.4
Mittal, P.5
Kim, J.S.6
Kim, C.J.7
Kusanovic, J.P.8
Romero, R.9
-
9
-
-
84894571860
-
Causal analysis approaches in ingenuity pathway analysis
-
Kramer A, Green J, Pollard J Jr, Tugendreich S: Causal analysis approaches in ingenuity pathway analysis. Bioinformatics 2014, 30(4):523-530.
-
(2014)
Bioinformatics
, vol.30
, Issue.4
, pp. 523-530
-
-
Kramer, A.1
Green, J.2
Pollard, J.3
Tugendreich, S.4
-
10
-
-
80054106639
-
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue
-
Schlage W, Westra J, Gebel S, Catlett N, Mathis C, Frushour B, Hengstermann A, Van Hooser A, Poussin C, Wong B, Lietz M, Park J, Drubin D, Veljkovic E, Peitsch MC, Hoeng J, Deehan R: A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. BMC Syst Biol 2011, 5(1):168.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.1
, pp. 168
-
-
Schlage, W.1
Westra, J.2
Gebel, S.3
Catlett, N.4
Mathis, C.5
Frushour, B.6
Hengstermann, A.7
Van Hooser, A.8
Poussin, C.9
Wong, B.10
Lietz, M.11
Park, J.12
Drubin, D.13
Veljkovic, E.14
Peitsch, M.C.15
Hoeng, J.16
Deehan, R.17
-
11
-
-
84874921123
-
Construction of a computable network model for DNA Damage, autophagy, cell death, and senescence
-
Gebel S, Lichtner RB, Frushour BP, Schlage WK, Hoang V, Talikka M, Hengstermann A, Mathis C, Veljkovic E, Peck M, Peitsch MC, Deehan R, Hoeng J, Westra JW: Construction of a computable network model for DNA Damage, autophagy, cell death, and senescence. Bioinform Biol Insights 2013, 7:1-21.
-
(2013)
Bioinform Biol Insights
, vol.7
, pp. 1-21
-
-
Gebel, S.1
Lichtner, R.B.2
Frushour, B.P.3
Schlage, W.K.4
Hoang, V.5
Talikka, M.6
Hengstermann, A.7
Mathis, C.8
Veljkovic, E.9
Peck, M.10
Peitsch, M.C.11
Deehan, R.12
Hoeng, J.13
Westra, J.W.14
-
12
-
-
84879307956
-
A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue
-
Westra JW, Schlage WK, Hengstermann A, Gebel S, Mathis C, Thomson T, Wong B, Hoang V, Veljkovic E, Peck M, Lichtner RB, Weisensee D, Talikka M, Deehan R, Hoeng J, Peitsch MC: A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue. Bioinform Biol Insights 2013, 7:167-192.
-
(2013)
Bioinform Biol Insights
, vol.7
, pp. 167-192
-
-
Westra, J.W.1
Schlage, W.K.2
Hengstermann, A.3
Gebel, S.4
Mathis, C.5
Thomson, T.6
Wong, B.7
Hoang, V.8
Veljkovic, E.9
Peck, M.10
Lichtner, R.B.11
Weisensee, D.12
Talikka, M.13
Deehan, R.14
Hoeng, J.15
Peitsch, M.C.16
-
14
-
-
84962331939
-
-
Spanning tree. http://en.wikipedia.org/wiki/Spanning-tree.
-
Spanning Tree
-
-
-
15
-
-
0000052835
-
The random walk construction of uniform spanning trees and uniform labelled trees
-
Aldous DJ: The random walk construction of uniform spanning trees and uniform labelled trees. SIAM J Discret Math 1990, 3(4):450-465.
-
(1990)
SIAM J Discret Math
, vol.3
, Issue.4
, pp. 450-465
-
-
Aldous, D.J.1
-
16
-
-
84884695502
-
Quantitative assessment of biological impact using transcriptomic data and mechanistic network models
-
Thomson TM, Sewer A, Martin F, Belcastro V, Frushour BP, Gebel S, Park J, Schlage WK, Talikka M, Vasilyev DM, Westra JW, Hoeng J, Peitsch MC: Quantitative assessment of biological impact using transcriptomic data and mechanistic network models. Toxicol Appl Pharmacol 2013, 272(3):863-878.
-
(2013)
Toxicol Appl Pharmacol
, vol.272
, Issue.3
, pp. 863-878
-
-
Thomson, T.M.1
Sewer, A.2
Martin, F.3
Belcastro, V.4
Frushour, B.P.5
Gebel, S.6
Park, J.7
Schlage, W.K.8
Talikka, M.9
Vasilyev, D.M.10
Westra, J.W.11
Hoeng, J.12
Peitsch, M.C.13
-
17
-
-
84887870659
-
Reverse causal reasoning: Applying qualitative causal knowledge to the interpretation of high-throughput data
-
Catlett NL, Bargnesi AJ, Ungerer S, Seagaran T, Ladd W, Elliston KO, Pratt D: Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. BMC Bioinformatics 2013, 14:340.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 340
-
-
Catlett, N.L.1
Bargnesi, A.J.2
Ungerer, S.3
Seagaran, T.4
Ladd, W.5
Elliston, K.O.6
Pratt, D.7
-
18
-
-
19644375686
-
Molecular mechanism of TNF signaling and beyond
-
Liu ZG: Molecular mechanism of TNF signaling and beyond. Cell Res 2005, 15(1):24-27.
-
(2005)
Cell Res
, vol.15
, Issue.1
, pp. 24-27
-
-
Liu, Z.G.1
-
19
-
-
84896364353
-
Systems biology approach for evaluating the biological impact of environmental toxicants in Vitro
-
Gonzalez-Suarez I, Sewer A, Walker P, Mathis C, Ellis S, Woodhouse H, Guedj E, Dulize R, Marescotti D, Acali S, Martin F, Ivanov NV, Hoeng J, Peitsch MC: Systems biology approach for evaluating the biological impact of environmental toxicants in Vitro. Chem Res Toxicol 2014, 27(3):367-376.
-
(2014)
Chem Res Toxicol
, vol.27
, Issue.3
, pp. 367-376
-
-
Gonzalez-Suarez, I.1
Sewer, A.2
Walker, P.3
Mathis, C.4
Ellis, S.5
Woodhouse, H.6
Guedj, E.7
Dulize, R.8
Marescotti, D.9
Acali, S.10
Martin, F.11
Ivanov, N.V.12
Hoeng, J.13
Peitsch, M.C.14
-
20
-
-
84857136306
-
Assessing statistical significance in causal graphs
-
Chindelevitch L, Loh PR, Enayetallah A, Berger B, Ziemek D: Assessing statistical significance in causal graphs. BMC Bioinformatics 2012, 13:35.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 35
-
-
Chindelevitch, L.1
Loh, P.R.2
Enayetallah, A.3
Berger, B.4
Ziemek, D.5
-
21
-
-
84859748911
-
Causal reasoning on biological networks: Interpreting transcriptional changes
-
Chindelevitch L, Ziemek D, Enayetallah A, Randhawa R, Sidders B, Brockel C, Huang ES: Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics 2012, 28(8):1114-1121.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1114-1121
-
-
Chindelevitch, L.1
Ziemek, D.2
Enayetallah, A.3
Randhawa, R.4
Sidders, B.5
Brockel, C.6
Huang, E.S.7
-
22
-
-
84989166578
-
-
Signed graph. http://en.wikipedia.org/wiki/Signed-graph.
-
Signed Graph
-
-
-
23
-
-
0000989134
-
On the notion of balance of a signed graph
-
Harary F: On the notion of balance of a signed graph. Michigan Math J 1953, 2(2):143-146.
-
(1953)
Michigan Math J
, vol.2
, Issue.2
, pp. 143-146
-
-
Harary, F.1
-
24
-
-
84855504473
-
Computing global structural balance in large-scale signed social networks
-
Facchetti G, Iacono G, Altafini C: Computing global structural balance in large-scale signed social networks. Proc Natl Acad Sci U S A 2011, 108(52):20953-20958.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.52
, pp. 20953-20958
-
-
Facchetti, G.1
Iacono, G.2
Altafini, C.3
-
25
-
-
84880838585
-
Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset
-
Belcastro V, Poussin C, Gebel S, Mathis C, Schlage WK, Lichtner RB, Quadt-Humme S, Wagner S, Hoeng J, Peitsch MC: Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset. Bioinform Biol Insights 2013, 7:217-230.
-
(2013)
Bioinform Biol Insights
, vol.7
, pp. 217-230
-
-
Belcastro, V.1
Poussin, C.2
Gebel, S.3
Mathis, C.4
Schlage, W.K.5
Lichtner, R.B.6
Quadt-Humme, S.7
Wagner, S.8
Hoeng, J.9
Peitsch, M.C.10
|