-
1
-
-
0033518234
-
From molecular to modular cell biology
-
10.1038/35011540, 10591225
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-52. 10.1038/35011540, 10591225.
-
(1999)
Nature
, vol.402
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
2
-
-
0035830505
-
A biological atlas of functional maps
-
10.1016/S0092-8674(01)00221-5, 11239391
-
Vidal M. A biological atlas of functional maps. Cell 2001, 104:333-339. 10.1016/S0092-8674(01)00221-5, 11239391.
-
(2001)
Cell
, vol.104
, pp. 333-339
-
-
Vidal, M.1
-
3
-
-
19344372271
-
Systems biology: its practice and challenges
-
10.1016/j.cell.2005.04.020, 15907465
-
Aderem A. Systems biology: its practice and challenges. Cell 2005, 121:511-513. 10.1016/j.cell.2005.04.020, 15907465.
-
(2005)
Cell
, vol.121
, pp. 511-513
-
-
Aderem, A.1
-
4
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
10.1126/science.1073374, 12202830
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555. 10.1126/science.1073374, 12202830.
-
(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
-
5
-
-
20844450402
-
Differential network expression during drug and stress response
-
10.1093/bioinformatics/bti440, 15840709
-
Cabusora L, Sutton E, Fulmer A, Forst CV. Differential network expression during drug and stress response. Bioinformatics 2005, 21:2898-2905. 10.1093/bioinformatics/bti440, 15840709.
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
Sutton, E.2
Fulmer, A.3
Forst, C.V.4
-
6
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
10.1093/bioinformatics/btn161, 2718639, 18586718
-
Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24:i223-231. 10.1093/bioinformatics/btn161, 2718639, 18586718.
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Muller, T.5
-
7
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
8
-
-
34248593385
-
Gene expression network analysis and applications to immunology
-
10.1093/bioinformatics/btm019, 17267429
-
Nacu S, Critchley-Thorne R, Lee P, Holmes S. Gene expression network analysis and applications to immunology. Bioinformatics 2007, 23:850-858. 10.1093/bioinformatics/btm019, 17267429.
-
(2007)
Bioinformatics
, vol.23
, pp. 850-858
-
-
Nacu, S.1
Critchley-Thorne, R.2
Lee, P.3
Holmes, S.4
-
9
-
-
67649208263
-
Identification of differentially expressed subnetworks based on multivariate ANOVA
-
10.1186/1471-2105-10-128, 2696448, 19405941
-
Hwang T, Park T. Identification of differentially expressed subnetworks based on multivariate ANOVA. BMC Bioinformatics 2009, 10:128. 10.1186/1471-2105-10-128, 2696448, 19405941.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 128
-
-
Hwang, T.1
Park, T.2
-
10
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
10.1038/msb4100180, 2063581, 17940530
-
Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007, 3:140. 10.1038/msb4100180, 2063581, 17940530.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
11
-
-
34548583420
-
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network
-
10.1093/bioinformatics/btm294, 17545181
-
Guo Z, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D, Wang J. Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics 2007, 23:2121-2128. 10.1093/bioinformatics/btm294, 17545181.
-
(2007)
Bioinformatics
, vol.23
, pp. 2121-2128
-
-
Guo, Z.1
Li, Y.2
Gong, X.3
Yao, C.4
Ma, W.5
Wang, D.6
Li, Y.7
Zhu, J.8
Zhang, M.9
Yang, D.10
Wang, J.11
-
12
-
-
44349093750
-
Uncovering signal transduction networks from high-throughput data by integer linear programming
-
10.1093/nar/gkn145, 2396433, 18411207
-
Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 2008, 36:e48. 10.1093/nar/gkn145, 2396433, 18411207.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Zhao, X.M.1
Wang, R.S.2
Chen, L.3
Aihara, K.4
-
13
-
-
70349331032
-
Identifying responsive functional modules from protein-protein interaction network
-
10.1007/s10059-009-0035-x, 19326072
-
Wu Z, Zhao X, Chen L. Identifying responsive functional modules from protein-protein interaction network. Mol Cells 2009, 27:271-277. 10.1007/s10059-009-0035-x, 19326072.
-
(2009)
Mol Cells
, vol.27
, pp. 271-277
-
-
Wu, Z.1
Zhao, X.2
Chen, L.3
-
14
-
-
57749210454
-
An in silico method for detecting overlapping functional modules from composite biological networks
-
10.1186/1752-0509-2-93, 2600641, 18976494
-
Maraziotis IA, Dimitrakopoulou K, Bezerianos A. An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst Biol 2008, 2:93. 10.1186/1752-0509-2-93, 2600641, 18976494.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 93
-
-
Maraziotis, I.A.1
Dimitrakopoulou, K.2
Bezerianos, A.3
-
15
-
-
34347326247
-
Network-based analysis of affected biological processes in type 2 diabetes models
-
10.1371/journal.pgen.0030096, 1904360,1904360, 17571924
-
Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 2007, 3:e96. 10.1371/journal.pgen.0030096, 1904360,1904360, 17571924.
-
(2007)
PLoS Genet
, vol.3
-
-
Liu, M.1
Liberzon, A.2
Kong, S.W.3
Lai, W.R.4
Park, P.J.5
Kohane, I.S.6
Kasif, S.7
-
16
-
-
3042514191
-
Coexpression analysis of human genes across many microarray data sets
-
10.1101/gr.1910904, 419787, 15173114
-
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14:1085-1094. 10.1101/gr.1910904, 419787, 15173114.
-
(2004)
Genome Res
, vol.14
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
17
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
10.1126/science.1087447, 12934013
-
Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255. 10.1126/science.1087447, 12934013.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
18
-
-
25144498379
-
A human protein-protein interaction network: a resource for annotating the proteome
-
10.1016/j.cell.2005.08.029, 16169070
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968. 10.1016/j.cell.2005.08.029, 16169070.
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
-
19
-
-
44249113841
-
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth
-
10.1126/science.1152662, 2776723, 18487186
-
Bromberg KD, Ma'ayan A, Neves SR, Iyengar R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 2008, 320:903-909. 10.1126/science.1152662, 2776723, 18487186.
-
(2008)
Science
, vol.320
, pp. 903-909
-
-
Bromberg, K.D.1
Ma'ayan, A.2
Neves, S.R.3
Iyengar, R.4
-
20
-
-
70350452758
-
Understanding modularity in molecular networks requires dynamics
-
10.1126/scisignal.281pe44, 19638611
-
Alexander RP, Kim PM, Emonet T, Gerstein MB. Understanding modularity in molecular networks requires dynamics. Sci Signal 2009, 2:pe44. 10.1126/scisignal.281pe44, 19638611.
-
(2009)
Sci Signal
, vol.2
-
-
Alexander, R.P.1
Kim, P.M.2
Emonet, T.3
Gerstein, M.B.4
-
21
-
-
32244436305
-
Angiopoietin-2 sensitizes endothelial cells to TNF-alpha and has a crucial role in the induction of inflammation
-
10.1038/nm1351, 16462802
-
Fiedler U, Reiss Y, Scharpfenecker M, Grunow V, Koidl S, Thurston G, Gale NW, Witzenrath M, Rosseau S, Suttorp N, et al. Angiopoietin-2 sensitizes endothelial cells to TNF-alpha and has a crucial role in the induction of inflammation. Nat Med 2006, 12:235-239. 10.1038/nm1351, 16462802.
-
(2006)
Nat Med
, vol.12
, pp. 235-239
-
-
Fiedler, U.1
Reiss, Y.2
Scharpfenecker, M.3
Grunow, V.4
Koidl, S.5
Thurston, G.6
Gale, N.W.7
Witzenrath, M.8
Rosseau, S.9
Suttorp, N.10
-
22
-
-
32244447827
-
Angiogenesis and inflammation face off
-
10.1038/nm0206-171, 16462798
-
Imhof BA, Aurrand-Lions M. Angiogenesis and inflammation face off. Nat Med 2006, 12:171-172. 10.1038/nm0206-171, 16462798.
-
(2006)
Nat Med
, vol.12
, pp. 171-172
-
-
Imhof, B.A.1
Aurrand-Lions, M.2
-
23
-
-
34748914299
-
Evolving functions of endothelial cells in inflammation
-
10.1038/nri2171, 17893694
-
Pober JS, Sessa WC. Evolving functions of endothelial cells in inflammation. Nat Rev Immunol 2007, 7:803-815. 10.1038/nri2171, 17893694.
-
(2007)
Nat Rev Immunol
, vol.7
, pp. 803-815
-
-
Pober, J.S.1
Sessa, W.C.2
-
24
-
-
0037180757
-
Inflammation and cancer
-
10.1038/nature01322, 2803035, 12490959
-
Coussens LM, Werb Z. Inflammation and cancer. Nature 2002, 420:860-867. 10.1038/nature01322, 2803035, 12490959.
-
(2002)
Nature
, vol.420
, pp. 860-867
-
-
Coussens, L.M.1
Werb, Z.2
-
25
-
-
66449123068
-
The notch ligands Dll4 and Jagged1 have opposing effects on angiogenesis
-
10.1016/j.cell.2009.03.025, 19524514
-
Benedito R, Roca C, Sorensen I, Adams S, Gossler A, Fruttiger M, Adams RH. The notch ligands Dll4 and Jagged1 have opposing effects on angiogenesis. Cell 2009, 137:1124-1135. 10.1016/j.cell.2009.03.025, 19524514.
-
(2009)
Cell
, vol.137
, pp. 1124-1135
-
-
Benedito, R.1
Roca, C.2
Sorensen, I.3
Adams, S.4
Gossler, A.5
Fruttiger, M.6
Adams, R.H.7
-
26
-
-
0030576517
-
Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis
-
10.1016/S0092-8674(00)80108-7, 8756718
-
Hanahan D, Folkman J. Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis. Cell 1996, 86:353-364. 10.1016/S0092-8674(00)80108-7, 8756718.
-
(1996)
Cell
, vol.86
, pp. 353-364
-
-
Hanahan, D.1
Folkman, J.2
-
27
-
-
0034648765
-
Angiogenesis in cancer and other diseases
-
10.1038/35025220, 11001068
-
Carmeliet P, Jain RK. Angiogenesis in cancer and other diseases. Nature 2000, 407:249-257. 10.1038/35025220, 11001068.
-
(2000)
Nature
, vol.407
, pp. 249-257
-
-
Carmeliet, P.1
Jain, R.K.2
-
28
-
-
34547891037
-
Transcriptional network governing the angiogenic switch in human pancreatic cancer
-
10.1073/pnas.0705505104, 1931565, 17652168
-
Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, et al. Transcriptional network governing the angiogenic switch in human pancreatic cancer. Proc Natl Acad Sci USA 2007, 104:12890-12895. 10.1073/pnas.0705505104, 1931565, 17652168.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 12890-12895
-
-
Abdollahi, A.1
Schwager, C.2
Kleeff, J.3
Esposito, I.4
Domhan, S.5
Peschke, P.6
Hauser, K.7
Hahnfeldt, P.8
Hlatky, L.9
Debus, J.10
-
29
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
10.1101/gr.1680803, 403728, 14525934
-
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13:2363-2371. 10.1101/gr.1680803, 403728, 14525934.
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
Kristiansen, T.Z.4
Jonnalagadda, C.K.5
Surendranath, V.6
Niranjan, V.7
Muthusamy, B.8
Gandhi, T.K.9
Gronborg, M.10
-
30
-
-
58149193222
-
Human Protein Reference Database--2009 update
-
10.1093/nar/gkn892, 2686490, 18988627
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009, 37:D767-772. 10.1093/nar/gkn892, 2686490, 18988627.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
-
31
-
-
33644877439
-
Human protein reference database--2006 update
-
10.1093/nar/gkj141, 1347503, 16381900
-
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, et al. Human protein reference database--2006 update. Nucleic Acids Res 2006, 34:D411-414. 10.1093/nar/gkj141, 1347503, 16381900.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Mishra, G.R.1
Suresh, M.2
Kumaran, K.3
Kannabiran, N.4
Suresh, S.5
Bala, P.6
Shivakumar, K.7
Anuradha, N.8
Reddy, R.9
Raghavan, T.M.10
-
32
-
-
77953360504
-
KEGG
-
KEGG. , http://www.genome.jp/kegg/
-
-
-
-
33
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
10.1016/j.cell.2004.12.035, 15652477
-
Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
34
-
-
34250805982
-
MicroRNA targeting specificity in mammals: determinants beyond seed pairing
-
10.1016/j.molcel.2007.06.017, 17612493
-
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105. 10.1016/j.molcel.2007.06.017, 17612493.
-
(2007)
Mol Cell
, vol.27
, pp. 91-105
-
-
Grimson, A.1
Farh, K.K.2
Johnston, W.K.3
Garrett-Engele, P.4
Lim, L.P.5
Bartel, D.P.6
-
35
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
-
(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
-
36
-
-
77953358508
-
Time course gene expression of HUVEC after TNF-alpha treatment
-
Kodama T, Xu M, Ohta Y, Minami T, Tsutsumi S, Komura D, Inoue K, Kobayashi M, Izumi A, Miura M, et al. Time course gene expression of HUVEC after TNF-alpha treatment. , http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE9055
-
-
-
Kodama, T.1
Xu, M.2
Ohta, Y.3
Minami, T.4
Tsutsumi, S.5
Komura, D.6
Inoue, K.7
Kobayashi, M.8
Izumi, A.9
Miura, M.10
-
37
-
-
70849129503
-
A wave of nascent transcription on activated human genes
-
10.1073/pnas.0902573106, 2761237, 19826084
-
Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, Kitakami J, Oshida N, Papantonis A, et al. A wave of nascent transcription on activated human genes. Proc Natl Acad Sci USA 2009, 106:18357-18361. 10.1073/pnas.0902573106, 2761237, 19826084.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 18357-18361
-
-
Wada, Y.1
Ohta, Y.2
Xu, M.3
Tsutsumi, S.4
Minami, T.5
Inoue, K.6
Komura, D.7
Kitakami, J.8
Oshida, N.9
Papantonis, A.10
-
38
-
-
0027971199
-
Induction of endothelial cell apoptosis by TNF alpha: modulation by inhibitors of protein synthesis
-
10.1006/excr.1994.1296, 7925652
-
Polunovsky VA, Wendt CH, Ingbar DH, Peterson MS, Bitterman PB. Induction of endothelial cell apoptosis by TNF alpha: modulation by inhibitors of protein synthesis. Exp Cell Res 1994, 214:584-594. 10.1006/excr.1994.1296, 7925652.
-
(1994)
Exp Cell Res
, vol.214
, pp. 584-594
-
-
Polunovsky, V.A.1
Wendt, C.H.2
Ingbar, D.H.3
Peterson, M.S.4
Bitterman, P.B.5
-
39
-
-
0026093190
-
Tumor necrosis factor induces apoptosis (programmed cell death) in normal endothelial cells in vitro
-
1886201, 1992769
-
Robaye B, Mosselmans R, Fiers W, Dumont JE, Galand P. Tumor necrosis factor induces apoptosis (programmed cell death) in normal endothelial cells in vitro. Am J Pathol 1991, 138:447-453. 1886201, 1992769.
-
(1991)
Am J Pathol
, vol.138
, pp. 447-453
-
-
Robaye, B.1
Mosselmans, R.2
Fiers, W.3
Dumont, J.E.4
Galand, P.5
-
40
-
-
55749105944
-
TLR2 expression in astrocytes is induced by TNF-alpha- and NF-kappa B-dependent pathways
-
2649826, 18768838
-
Phulwani NK, Esen N, Syed MM, Kielian T. TLR2 expression in astrocytes is induced by TNF-alpha- and NF-kappa B-dependent pathways. J Immunol 2008, 181:3841-3849. 2649826, 18768838.
-
(2008)
J Immunol
, vol.181
, pp. 3841-3849
-
-
Phulwani, N.K.1
Esen, N.2
Syed, M.M.3
Kielian, T.4
-
41
-
-
35448954337
-
Tumor necrosis factor-alpha (TNF-alpha) regulates Toll-like receptor 2 (TLR2) expression in microglia
-
10.1111/j.1471-4159.2007.04838.x, 2423670, 17961202
-
Syed MM, Phulwani NK, Kielian T. Tumor necrosis factor-alpha (TNF-alpha) regulates Toll-like receptor 2 (TLR2) expression in microglia. J Neurochem 2007, 103:1461-1471. 10.1111/j.1471-4159.2007.04838.x, 2423670, 17961202.
-
(2007)
J Neurochem
, vol.103
, pp. 1461-1471
-
-
Syed, M.M.1
Phulwani, N.K.2
Kielian, T.3
-
42
-
-
0032521284
-
Induction of Jak/STAT signaling by activation of the type 1 TNF receptor
-
Guo D, Dunbar JD, Yang CH, Pfeffer LM, Donner DB. Induction of Jak/STAT signaling by activation of the type 1 TNF receptor. J Immunol 1998, 160:2742-2750.
-
(1998)
J Immunol
, vol.160
, pp. 2742-2750
-
-
Guo, D.1
Dunbar, J.D.2
Yang, C.H.3
Pfeffer, L.M.4
Donner, D.B.5
-
43
-
-
70450158562
-
Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells
-
IEEE Computer Society
-
Gu J, Li S, Chen Y, Li Y. Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells. Bioinformatics, Systems Biology and Intelligent Computing, International Joint Conference on; Shanghai 2009, 422-427. IEEE Computer Society.
-
(2009)
Bioinformatics, Systems Biology and Intelligent Computing, International Joint Conference on; Shanghai
, pp. 422-427
-
-
Gu, J.1
Li, S.2
Chen, Y.3
Li, Y.4
-
44
-
-
34447632218
-
Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis
-
10.1161/CIRCRESAHA.107.153916, 17540974
-
Kuehbacher A, Urbich C, Zeiher AM, Dimmeler S. Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ Res 2007, 101:59-68. 10.1161/CIRCRESAHA.107.153916, 17540974.
-
(2007)
Circ Res
, vol.101
, pp. 59-68
-
-
Kuehbacher, A.1
Urbich, C.2
Zeiher, A.M.3
Dimmeler, S.4
-
45
-
-
33751173635
-
MicroRNAs modulate the angiogenic properties of HUVECs
-
10.1182/blood-2006-01-012369, 16849646
-
Poliseno L, Tuccoli A, Mariani L, Evangelista M, Citti L, Woods K, Mercatanti A, Hammond S, Rainaldi G. MicroRNAs modulate the angiogenic properties of HUVECs. Blood 2006, 108:3068-3071. 10.1182/blood-2006-01-012369, 16849646.
-
(2006)
Blood
, vol.108
, pp. 3068-3071
-
-
Poliseno, L.1
Tuccoli, A.2
Mariani, L.3
Evangelista, M.4
Citti, L.5
Woods, K.6
Mercatanti, A.7
Hammond, S.8
Rainaldi, G.9
-
46
-
-
20444467290
-
A microRNA polycistron as a potential human oncogene
-
10.1038/nature03552, 15944707
-
He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM. A microRNA polycistron as a potential human oncogene. Nature 2005, 435:828-833. 10.1038/nature03552, 15944707.
-
(2005)
Nature
, vol.435
, pp. 828-833
-
-
He, L.1
Thomson, J.M.2
Hemann, M.T.3
Hernando-Monge, E.4
Mu, D.5
Goodson, S.6
Powers, S.7
Cordon-Cardo, C.8
Lowe, S.W.9
Hannon, G.J.10
Hammond, S.M.11
-
47
-
-
68449097267
-
MiR-145 and miR-143 regulate smooth muscle cell fate and plasticity
-
2769203, 19578358
-
Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN, Lee TH, Miano JM, Ivey KN, Srivastava D. miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 2009, 460:705-710. 2769203, 19578358.
-
(2009)
Nature
, vol.460
, pp. 705-710
-
-
Cordes, K.R.1
Sheehy, N.T.2
White, M.P.3
Berry, E.C.4
Morton, S.U.5
Muth, A.N.6
Lee, T.H.7
Miano, J.M.8
Ivey, K.N.9
Srivastava, D.10
-
48
-
-
67349149082
-
MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells
-
10.1016/j.cell.2009.02.038, 19409607
-
Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell 2009, 137:647-658. 10.1016/j.cell.2009.02.038, 19409607.
-
(2009)
Cell
, vol.137
, pp. 647-658
-
-
Xu, N.1
Papagiannakopoulos, T.2
Pan, G.3
Thomson, J.A.4
Kosik, K.S.5
-
49
-
-
70449347212
-
The VEGF-induced transcriptional response comprises gene clusters at the crossroad of angiogenesis and inflammation
-
Schweighofer B, Testori J, Sturtzel C, Sattler S, Mayer H, Wagner O, Bilban M, Hofer E. The VEGF-induced transcriptional response comprises gene clusters at the crossroad of angiogenesis and inflammation. Thromb Haemost 2009, 102:544-554.
-
(2009)
Thromb Haemost
, vol.102
, pp. 544-554
-
-
Schweighofer, B.1
Testori, J.2
Sturtzel, C.3
Sattler, S.4
Mayer, H.5
Wagner, O.6
Bilban, M.7
Hofer, E.8
-
50
-
-
58249094059
-
Nrarp coordinates endothelial Notch and Wnt signaling to control vessel density in angiogenesis
-
10.1016/j.devcel.2008.12.009, 19154719
-
Phng LK, Potente M, Leslie JD, Babbage J, Nyqvist D, Lobov I, Ondr JK, Rao S, Lang RA, Thurston G, Gerhardt H. Nrarp coordinates endothelial Notch and Wnt signaling to control vessel density in angiogenesis. Dev Cell 2009, 16:70-82. 10.1016/j.devcel.2008.12.009, 19154719.
-
(2009)
Dev Cell
, vol.16
, pp. 70-82
-
-
Phng, L.K.1
Potente, M.2
Leslie, J.D.3
Babbage, J.4
Nyqvist, D.5
Lobov, I.6
Ondr, J.K.7
Rao, S.8
Lang, R.A.9
Thurston, G.10
Gerhardt, H.11
-
51
-
-
68149168790
-
Inhibition of VEGF or TGF-{beta} signaling activates endothelium and increases leukocyte rolling
-
10.1161/ATVBAHA.109.186742, 19461051
-
Walshe TE, Dole VS, Maharaj AS, Patten IS, Wagner DD, D'Amore PA. Inhibition of VEGF or TGF-{beta} signaling activates endothelium and increases leukocyte rolling. Arterioscler Thromb Vasc Biol 2009, 29:1185-1192. 10.1161/ATVBAHA.109.186742, 19461051.
-
(2009)
Arterioscler Thromb Vasc Biol
, vol.29
, pp. 1185-1192
-
-
Walshe, T.E.1
Dole, V.S.2
Maharaj, A.S.3
Patten, I.S.4
Wagner, D.D.5
D'Amore, P.A.6
-
53
-
-
70349145414
-
MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer
-
10.1101/gad.1820109, 2751988, 19759263
-
Olson P, Lu J, Zhang H, Shai A, Chun MG, Wang Y, Libutti SK, Nakakura EK, Golub TR, Hanahan D. MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer. Genes Dev 2009, 23:2152-2165. 10.1101/gad.1820109, 2751988, 19759263.
-
(2009)
Genes Dev
, vol.23
, pp. 2152-2165
-
-
Olson, P.1
Lu, J.2
Zhang, H.3
Shai, A.4
Chun, M.G.5
Wang, Y.6
Libutti, S.K.7
Nakakura, E.K.8
Golub, T.R.9
Hanahan, D.10
-
54
-
-
46749123975
-
TNF primes endothelial cells for angiogenic sprouting by inducing a tip cell phenotype
-
10.1182/blood-2007-08-108597, 2384130, 18337563
-
Sainson RC, Johnston DA, Chu HC, Holderfield MT, Nakatsu MN, Crampton SP, Davis J, Conn E, Hughes CC. TNF primes endothelial cells for angiogenic sprouting by inducing a tip cell phenotype. Blood 2008, 111:4997-5007. 10.1182/blood-2007-08-108597, 2384130, 18337563.
-
(2008)
Blood
, vol.111
, pp. 4997-5007
-
-
Sainson, R.C.1
Johnston, D.A.2
Chu, H.C.3
Holderfield, M.T.4
Nakatsu, M.N.5
Crampton, S.P.6
Davis, J.7
Conn, E.8
Hughes, C.C.9
-
55
-
-
33847046849
-
Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis
-
10.1038/nature05571, 17259973
-
Hellstrom M, Phng LK, Hofmann JJ, Wallgard E, Coultas L, Lindblom P, Alva J, Nilsson AK, Karlsson L, Gaiano N, et al. Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis. Nature 2007, 445:776-780. 10.1038/nature05571, 17259973.
-
(2007)
Nature
, vol.445
, pp. 776-780
-
-
Hellstrom, M.1
Phng, L.K.2
Hofmann, J.J.3
Wallgard, E.4
Coultas, L.5
Lindblom, P.6
Alva, J.7
Nilsson, A.K.8
Karlsson, L.9
Gaiano, N.10
-
56
-
-
48349129069
-
Blocking VEGFR-3 suppresses angiogenic sprouting and vascular network formation
-
10.1038/nature07083, 18594512
-
Tammela T, Zarkada G, Wallgard E, Murtomaki A, Suchting S, Wirzenius M, Waltari M, Hellstrom M, Schomber T, Peltonen R, et al. Blocking VEGFR-3 suppresses angiogenic sprouting and vascular network formation. Nature 2008, 454:656-660. 10.1038/nature07083, 18594512.
-
(2008)
Nature
, vol.454
, pp. 656-660
-
-
Tammela, T.1
Zarkada, G.2
Wallgard, E.3
Murtomaki, A.4
Suchting, S.5
Wirzenius, M.6
Waltari, M.7
Hellstrom, M.8
Schomber, T.9
Peltonen, R.10
-
57
-
-
33847607880
-
The Notch ligand Delta-like 4 negatively regulates endothelial tip cell formation and vessel branching
-
10.1073/pnas.0611177104, 1805603, 17296941
-
Suchting S, Freitas C, le Noble F, Benedito R, Breant C, Duarte A, Eichmann A. The Notch ligand Delta-like 4 negatively regulates endothelial tip cell formation and vessel branching. Proc Natl Acad Sci USA 2007, 104:3225-3230. 10.1073/pnas.0611177104, 1805603, 17296941.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 3225-3230
-
-
Suchting, S.1
Freitas, C.2
le Noble, F.3
Benedito, R.4
Breant, C.5
Duarte, A.6
Eichmann, A.7
-
58
-
-
33846107777
-
TRED: a transcriptional regulatory element database, new entries and other development
-
10.1093/nar/gkl1041, 1899102, 17202159
-
Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 2007, 35:D137-140. 10.1093/nar/gkl1041, 1899102, 17202159.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Jiang, C.1
Xuan, Z.2
Zhao, F.3
Zhang, M.Q.4
-
59
-
-
13444305306
-
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
-
10.1093/nar/gki004, 539958, 15608156
-
Zhao F, Xuan Z, Liu L, Zhang MQ. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res 2005, 33:D103-107. 10.1093/nar/gki004, 539958, 15608156.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Zhao, F.1
Xuan, Z.2
Liu, L.3
Zhang, M.Q.4
-
60
-
-
33846064113
-
NCBI GEO: mining tens of millions of expression profiles--database and tools update
-
10.1093/nar/gkl887, 1669752, 17099226
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res 2007, 35:D760-765. 10.1093/nar/gkl887, 1669752, 17099226.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Edgar, R.10
-
61
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
10.1093/nar/30.1.207, 99122, 11752295
-
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210. 10.1093/nar/30.1.207, 99122, 11752295.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
62
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
-
10.1073/pnas.011404098, 14539, 11134512
-
Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98:31-36. 10.1073/pnas.011404098, 14539, 11134512.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
63
-
-
77953362167
-
An implementation of Yen's algorithm
-
An implementation of Yen's algorithm. , http://code.google.com/p/k-shortest-paths/
-
-
-
-
64
-
-
33846892994
-
IDconverter and IDClight: conversion and annotation of gene and protein IDs
-
10.1186/1471-2105-8-9, 1779800, 17214880
-
Alibes A, Yankilevich P, Canada A, Diaz-Uriarte R. IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC Bioinformatics 2007, 8:9. 10.1186/1471-2105-8-9, 1779800, 17214880.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 9
-
-
Alibes, A.1
Yankilevich, P.2
Canada, A.3
Diaz-Uriarte, R.4
-
65
-
-
77953357727
-
NetPath
-
NetPath. , http://www.netpath.org/
-
-
-
-
66
-
-
34147102165
-
BioCarta Pathways
-
BioCarta Pathways. , http://www.biocarta.com/genes/index.asp
-
-
-
-
67
-
-
84874019016
-
Pathway Interaction Database
-
Pathway Interaction Database. , http://pid.nci.nih.gov/
-
-
-
-
68
-
-
77953363327
-
Reactome
-
Reactome. , http://www.reactome.org/
-
-
-
-
69
-
-
32544433476
-
EDGE: extraction and analysis of differential gene expression
-
10.1093/bioinformatics/btk005, 16357033
-
Leek JT, Monsen E, Dabney AR, Storey JD. EDGE: extraction and analysis of differential gene expression. Bioinformatics 2006, 22:507-508. 10.1093/bioinformatics/btk005, 16357033.
-
(2006)
Bioinformatics
, vol.22
, pp. 507-508
-
-
Leek, J.T.1
Monsen, E.2
Dabney, A.R.3
Storey, J.D.4
-
70
-
-
34547555796
-
Global and local architecture of the mammalian microRNA-transcription factor regulatory network
-
10.1371/journal.pcbi.0030131, 1914371,1914371, 17630826
-
Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol 2007, 3:e131. 10.1371/journal.pcbi.0030131, 1914371,1914371, 17630826.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shalgi, R.1
Lieber, D.2
Oren, M.3
Pilpel, Y.4
|