-
1
-
-
66649093842
-
Integrative analysis of cyclin protein levels identiWes cyclin b1 as a classiWer and predictor of outcomes in breast cancer
-
Agarwal R, Gonzalez-Angulo AM, Myhre S, Carey M, Lee JS, Overgaard J, Alsner J, Stemke-Hale K, Lluch A, Neve RM, Kuo WL, Sorlie T, Sahin A, Valero V, Keyomarsi K, Gray JW, Borresen-Dale AL, Mills GB, Hennessy BT (2009) Integrative analysis of cyclin protein levels identiWes cyclin b1 as a classiWer and predictor of outcomes in breast cancer. Clin Cancer Res 15:3654-3662
-
(2009)
Clin Cancer Res
, vol.15
, pp. 3654-3662
-
-
Agarwal, R.1
Gonzalez-Angulo, A.M.2
Myhre, S.3
Carey, M.4
Lee, J.S.5
Overgaard, J.6
Alsner, J.7
Stemke-Hale, K.8
Lluch, A.9
Neve, R.M.10
Kuo, W.L.11
Sorlie, T.12
Sahin, A.13
Valero, V.14
Keyomarsi, K.15
Gray, J.W.16
Borresen-Dale, A.L.17
Mills, G.B.18
Hennessy, B.T.19
-
2
-
-
31544460919
-
Topological and functional discovery in a gene coexpression meta-network of gastric cancer
-
DOI 10.1158/0008-5472.CAN-05-2232
-
Aggarwal A, Guo DL, Hoshida Y, Yuen ST, Chu KM, So S, Boussioutas A, Chen X, Bowtell D, Aburatani H, Leung SY, Tan P (2006) Topological and functional discovery in a gene coexpression meta-network of gastric cancer. Cancer Res 66:232-241 (Pubitemid 43166029)
-
(2006)
Cancer Research
, vol.66
, Issue.1
, pp. 232-241
-
-
Aggarwal, A.1
Guo, D.L.2
Hoshida, Y.3
Yuen, S.T.4
Chu, K.-M.5
So, S.6
Boussioutas, A.7
Chen, X.8
Bowtell, D.9
Aburatani, H.10
Leung, S.Y.11
Tan, P.12
-
3
-
-
51049121625
-
Text mining for biology-The way forward: Opinions from leading scientists
-
Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A (2008) Text mining for biology-the way forward: Opinions from leading scientists. Genome Biol 9(Suppl 2):S7
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 2
-
-
Altman, R.B.1
Bergman, C.M.2
Blake, J.3
Blaschke, C.4
Cohen, A.5
Gannon, F.6
Grivell, L.7
Hahn, U.8
Hersh, W.9
Hirschman, L.10
Jensen, L.J.11
Krallinger, M.12
Mons, B.13
O'Donoghue, S.I.14
Peitsch, M.C.15
Rebholz-Schuhmann, D.16
Shatkay, H.17
Valencia, A.18
-
4
-
-
43749096790
-
Predicting cancer involvement of genes from heterogeneous data
-
Aragues R, Sander C, Oliva B (2008) Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics 9:172
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 172
-
-
Aragues, R.1
Sander, C.2
Oliva, B.3
-
5
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: Tool for the uniWcation of biology. The Gene Ontology Consortium. Nat Genet 25:25-29 (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, 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..
-
6
-
-
77953397764
-
Systems medicine: The future of medical genomics and healthcare
-
AuVray C, Chen Z, Hood L (2009) Systems medicine: The future of medical genomics and healthcare. Genome Med 1:2
-
(2009)
Genome Med
, vol.1
, pp. 2
-
-
AuVray, C.1
Chen, Z.2
Hood, L.3
-
7
-
-
18044400410
-
Information technology to the rescue!
-
Augen J (2001) Information technology to the rescue! Nat Biotechnol 19 Suppl: BE39-40
-
(2001)
Nat Biotechnol
, vol.19
, Issue.SUPPL.
-
-
Augen, J.1
-
8
-
-
77957106949
-
Avoiding pitfalls in the statistical analysis of heterogeneous tumors
-
Axelrod DE, Miller N, Chapman JA (2009) Avoiding pitfalls in the statistical analysis of heterogeneous tumors. Biomed Inform Insights 2:11-18
-
(2009)
Biomed Inform Insights
, vol.2
, pp. 11-18
-
-
Axelrod, D.E.1
Miller, N.2
Chapman, J.A.3
-
9
-
-
33750352288
-
Gene expression profiling in cervical cancer: An exploration of intratumor heterogeneity
-
DOI 10.1158/1078-0432.CCR-06-0357
-
Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF (2006) Gene expression proWling in cervical cancer: An exploration of intratumor heterogeneity. Clin Cancer Res 12:5632-5640 (Pubitemid 44629589)
-
(2006)
Clinical Cancer Research
, vol.12
, Issue.19
, pp. 5632-5640
-
-
Bachtiary, B.1
Boutros, P.C.2
Pintilie, M.3
Shi, W.4
Bastianutto, C.5
Li, J.-H.6
Schwock, J.7
Zhang, W.8
Penn, L.Z.9
Jurisica, I.10
Fyles, A.11
Liu, F.-F.12
-
10
-
-
0037245913
-
BIND: The biomolecular interaction network database
-
DOI 10.1093/nar/gkg056
-
Bader GD, Betel D, Hogue CW (2003) BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res 31:248-250 (Pubitemid 36150376)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.V.3
-
11
-
-
77951163222
-
Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
-
Baggerly KA, Coombes KR (2009) Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat 3:1309-1334
-
(2009)
Ann Appl Stat
, vol.3
, pp. 1309-1334
-
-
Baggerly, K.A.1
Coombes, K.R.2
-
12
-
-
3843084078
-
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website
-
Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 91:355-358 (Pubitemid 39037083)
-
(2004)
British Journal of Cancer
, vol.91
, Issue.2
, pp. 355-358
-
-
Bamford, S.1
Dawson, E.2
Forbes, S.3
Clements, J.4
Pettett, R.5
Dogan, A.6
Flanagan, A.7
Teague, J.8
Futreal, P.A.9
Stratton, M.R.10
Wooster, R.11
-
13
-
-
27144486151
-
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
-
DOI 10.1093/nar/gki890
-
Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P (2005) Experimental comparison and cross-validation of the AVymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33:5914-5923 (Pubitemid 41742611)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.18
, pp. 5914-5923
-
-
Barnes, M.1
Freudenberg, J.2
Thompson, S.3
Aronow, B.4
Pavlidis, P.5
-
14
-
-
13444304325
-
NCBI GEO: Mining millions of expression profiles - Database and tools
-
DOI 10.1093/nar/gki022
-
Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R (2005) NCBI GEO: Mining millions of expression proWles-database and tools. Nucleic Acids Res 33:D562-D566 (Pubitemid 40207937)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Barrett, T.1
Suzek, T.O.2
Troup, D.B.3
Wilhite, S.E.4
Ngau, W.-C.5
Ledoux, P.6
Rudnev, D.7
Lash, A.E.8
Fujibuchi, W.9
Edgar, R.10
-
15
-
-
67349196123
-
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
-
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ (2009) A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 6:423-430
-
(2009)
Nat Methods
, vol.6
, pp. 423-430
-
-
Bell, A.W.1
Deutsch, E.W.2
Au, C.E.3
Kearney, R.E.4
Beavis, R.5
Sechi, S.6
Nilsson, T.7
Bergeron, J.J.8
-
16
-
-
11144263678
-
Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection
-
DOI 10.1593/neo.04301
-
Blackhall FH, Pintilie M, Wigle D, Jurisica I, Liu N, Radulovitch N, Keshavjee S, Johnston M, Shepherd FA, Tsao M-S (2004) Stability and heterogeneity of expression proWles in lung cancer specimens harvested following surgical resection. Neoplasia 6:761-767 (Pubitemid 40041494)
-
(2004)
Neoplasia
, vol.6
, Issue.6
, pp. 761-767
-
-
Blackhall, F.H.1
Pintilie, M.2
Wigle, D.A.3
Jurisica, I.4
Liu, N.5
Radulovich, N.6
Johnston, M.R.7
Keshavjee, S.8
Tsao, M.-S.9
-
17
-
-
62449271525
-
Prognostic gene signatures for nonsmall-cell lung cancer
-
Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I (2009) Prognostic gene signatures for nonsmall-cell lung cancer. Proc Natl Acad Sci USA 106:2824-2828
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 2824-2828
-
-
Boutros, P.C.1
Lau, S.K.2
Pintilie, M.3
Liu, N.4
Shepherd, F.A.5
Der, S.D.6
Tsao, M.S.7
Penn, L.Z.8
Jurisica, I.9
-
18
-
-
58149242456
-
An experimentally derived conWdence score for binary protein-protein interactions
-
Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M (2009) An experimentally derived conWdence score for binary protein-protein interactions. Nat Methods 6:91-97
-
(2009)
Nat Methods
, vol.6
, pp. 91-97
-
-
Braun, P.1
Tasan, M.2
Dreze, M.3
Barrios-Rodiles, M.4
Lemmens, I.5
Yu, H.6
Sahalie, J.M.7
Murray, R.R.8
Roncari, L.9
De Smet, A.S.10
Venkatesan, K.11
Rual, J.F.12
Vandenhaute, J.13
Cusick, M.E.14
Pawson, T.15
Hill, D.E.16
Tavernier, J.17
Wrana, J.L.18
Roth, F.P.19
Vidal, M.20
more..
-
19
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data
-
DOI 10.1038/ng1201-365
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371 (Pubitemid 34326681)
-
(2001)
Nature Genetics
, vol.29
, Issue.4
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
Gaasterland, T.11
Glenisson, P.12
Holstege, F.C.P.13
Kim, I.F.14
Markowitz, V.15
Matese, J.C.16
Parkinson, H.17
Robinson, A.18
Sarkans, U.19
Schulze-Kremer, S.20
Stewart, J.21
Taylor, R.22
Vilo, J.23
Vingron, M.24
more..
-
22
-
-
18744376914
-
Online predicted human interaction database
-
DOI 10.1093/bioinformatics/bti273
-
Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21:2076-2082 (Pubitemid 40668047)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2076-2082
-
-
Brown, K.R.1
Jurisica, I.2
-
23
-
-
34548855730
-
Unequal evolutionary conservation of human protein interactions in interologous networks
-
Brown KR, Jurisica I (2007) Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 8:R95
-
(2007)
Genome Biol
, vol.8
-
-
Brown, K.R.1
Jurisica, I.2
-
24
-
-
75249086155
-
NAViGaTOR: Network analysis, visualization and graphing toronto
-
Brown KR, Otasek D, Ali M, McGuYn M, Xie W, Devani B, van Toch IL, Jurisica I (2009) NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics 25:3327-3329
-
(2009)
Bioinformatics
, vol.25
, pp. 3327-3329
-
-
Brown, K.R.1
Otasek, D.2
Ali, M.3
McGuYn, M.4
Xie, W.5
Devani, B.6
Van Toch, I.L.7
Jurisica, I.8
-
25
-
-
33748693297
-
Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer
-
DOI 10.1093/jnci/djj329
-
Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris A, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, Piccart MJ (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98: 1183-92 (Pubitemid 44390989)
-
(2006)
Journal of the National Cancer Institute
, vol.98
, Issue.17
, pp. 1183-1192
-
-
Buyse, M.1
Loi, S.2
Van't Veer, L.3
Viale, G.4
Delorenzi, M.5
Glas, A.M.6
D'Assignies, M.S.7
Bergh, J.8
Lidereau, R.9
Ellis, P.10
Harris, A.11
Bogaerts, J.12
Therasse, P.13
Floore, A.14
Amakrane, M.15
Piette, F.16
Rutgers, E.17
Sotiriou, C.18
Cardoso, F.19
Piccart, M.J.20
Decker, N.21
Straehle, C.22
more..
-
26
-
-
79955763421
-
Reproducible research concepts and tools for cancer bioinformatics
-
Ochs MF, Cassagrande JT, Davuluri RV (eds) Springer, US
-
Carey VJ, Stodden V (2010) Reproducible research concepts and tools for cancer bioinformatics. In: Ochs MF, Cassagrande JT, Davuluri RV (eds) Biomedical informatics for cancer research. Springer, US, pp 149-175
-
(2010)
Biomedical informatics for cancer research.
, pp. 149-175
-
-
Carey, V.J.1
Stodden, V.2
-
27
-
-
25444515422
-
RedeWnition of AVymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
-
Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z (2005) RedeWnition of AVymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6:107
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 107
-
-
Carter, S.L.1
Eklund, A.C.2
Mecham, B.H.3
Kohane, I.S.4
Szallasi, Z.5
-
28
-
-
78651332286
-
Pathway Commons a web resource for biological pathway data
-
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 39: D685-D690
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
Rodchenkov, I.4
Babur, O.5
Anwar, N.6
Schultz, N.7
Bader, G.D.8
Sander, C.9
-
29
-
-
70450179727
-
IdentiWcation of a microRNA signature associated with progression of leukoplakia to oral carcinoma
-
Cervigne NK, Reis PP, Machado J, Sadikovic B, Bradley G, Galloni NN, Pintilie M, Jurisica I, Perez-Ordonez B, Gilbert R, Gullane P, Irish J, Kamel-Reid S (2009) IdentiWcation of a microRNA signature associated with progression of leukoplakia to oral carcinoma. Hum Mol Genet 18:4818-4829
-
(2009)
Hum Mol Genet
, vol.18
, pp. 4818-4829
-
-
Cervigne, N.K.1
Reis, P.P.2
Machado, J.3
Sadikovic, B.4
Bradley, G.5
Galloni, N.N.6
Pintilie, M.7
Jurisica, I.8
Perez-Ordonez, B.9
Gilbert, R.10
Gullane, P.11
Irish, J.12
Kamel-Reid, S.13
-
30
-
-
26844467247
-
DiVerences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors
-
Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J (2005) DiVerences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer 5:45
-
(2005)
BMC Cancer
, vol.5
, pp. 45
-
-
Chandran, U.R.1
Dhir, R.2
Ma, C.3
Michalopoulos, G.4
Becich, M.5
Gilbertson, J.6
-
31
-
-
28944444652
-
Differential coexpression analysis using microarray data and its application to human cancer
-
DOI 10.1093/bioinformatics/bti722
-
Choi JK, Yu U, Yoo OJ, Kim S (2005) DiVerential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21:4348-4355 (Pubitemid 41782924)
-
(2005)
Bioinformatics
, vol.21
, Issue.24
, pp. 4348-4355
-
-
Choi, J.K.1
Yu, U.2
Yoo, O.J.3
Kim, S.4
-
32
-
-
35348891430
-
Network-based classiWcation of breast cancer metastasis
-
Chuang HY, Lee E, Liu YT, Lee D, Ideker T (2007) Network-based classiWcation of breast cancer metastasis. Mol Syst Biol 3:140
-
(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
-
33
-
-
37648999313
-
Distinguishing protein-coding and noncoding genes in the human genome
-
Clamp M, Fry B, Kamal M, Xie X, CuV J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 104:19428-19433
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 19428-19433
-
-
Clamp, M.1
Fry, B.2
Kamal, M.3
Xie, X.4
CuV, J.5
Lin, M.F.6
Kellis, M.7
Lindblad-Toh, K.8
Lander, E.S.9
-
34
-
-
33745445353
-
The eVect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis
-
Cleator SJ, Powles TJ, Dexter T, Fulford L, Mackay A, Smith IE, Valgeirsson H, Ashworth A, Dowsett M (2006) The eVect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis. Breast Cancer Res 8:R32
-
(2006)
Breast Cancer Res
, vol.8
-
-
Cleator, S.J.1
Powles, T.J.2
Dexter, T.3
Fulford, L.4
Mackay, A.5
Smith, I.E.6
Valgeirsson, H.7
Ashworth, A.8
Dowsett, M.9
-
36
-
-
48049120399
-
Cancer survival in Wve continents: A worldwide population-based study (CONCORD
-
Coleman MP, Quaresma M, Berrino F, Lutz JM, De Angelis R, Capocaccia R, Baili P, Rachet B, Gatta G, Hakulinen T, Micheli A, Sant M, Weir HK, Elwood JM, Tsukuma H, Koifman S, ES GA, Francisci S, Santaquilani M, Verdecchia A, Storm HH, Young JL (2008) Cancer survival in Wve continents: A worldwide population-based study (CONCORD). Lancet Oncol 9:730-756
-
(2008)
Lancet Oncol
, vol.9
, pp. 730-756
-
-
Coleman, M.P.1
Quaresma, M.2
Berrino, F.3
Lutz, J.M.4
De Angelis, R.5
Capocaccia, R.6
Baili, P.7
Rachet, B.8
Gatta, G.9
Hakulinen, T.10
Micheli, A.11
Sant, M.12
Weir, H.K.13
Elwood, J.M.14
Tsukuma, H.15
Koifman, S.16
Es, G.A.17
Francisci, S.18
Santaquilani, M.19
Verdecchia, A.20
Storm, H.H.21
Young, J.L.22
more..
-
37
-
-
75549084555
-
GeneSigDB - A curated database of gene expression signatures
-
Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J (2010) GeneSigDB-a curated database of gene expression signatures. Nucleic Acids Res 38:D716-D725
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Culhane, A.C.1
Schwarzl, T.2
Sultana, R.3
Picard, K.C.4
Picard, S.C.5
Lu, T.H.6
Franklin, K.R.7
French, S.J.8
Papenhausen, G.9
Correll, M.10
Quackenbush, J.11
-
38
-
-
73449095762
-
The pitfalls of platform comparison: DNA copy number array technologies assessed
-
Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, HadWeld J, Chin SF, Brenton JD, Tavare S, Caldas C (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10:588
-
(2009)
BMC Genomics
, vol.10
, pp. 588
-
-
Curtis, C.1
Lynch, A.G.2
Dunning, M.J.3
Spiteri, I.4
Marioni, J.C.5
HadWeld, J.6
Chin, S.F.7
Brenton, J.D.8
Tavare, S.9
Caldas, C.10
-
40
-
-
0035939903
-
Delineation of prognostic biomarkers in prostate cancer
-
DOI 10.1038/35090585
-
Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM (2001) Delineation of prognostic biomarkers in prostate cancer. Nature 412:822-826 (Pubitemid 32801464)
-
(2001)
Nature
, vol.412
, Issue.6849
, pp. 822-826
-
-
Dhanasekaran, S.M.1
Barrette, T.R.2
Ghosh, D.3
Shah, R.4
Varambally, S.5
Kurachi, K.6
Pienta, K.J.7
Rubin, M.A.8
Chinnaiyan, A.M.9
-
41
-
-
77957833984
-
Cancer biomarkers: Can we turn recent failures into success?
-
Diamandis EP (2010) Cancer biomarkers: Can we turn recent failures into success? J Natl Cancer Inst 102:1462-1467
-
(2010)
J Natl Cancer Inst
, vol.102
, pp. 1462-1467
-
-
Diamandis, E.P.1
-
42
-
-
40749107034
-
How large a training set is needed to develop a classifier for microarray data?
-
DOI 10.1158/1078-0432.CCR-07-0443
-
Dobbin KK, Zhao Y, Simon RM (2008) How large a training set is needed to develop a classiWer for microarray data? Clin Cancer Res 14:108-114 (Pubitemid 351377984)
-
(2008)
Clinical Cancer Research
, vol.14
, Issue.1
, pp. 108-114
-
-
Dobbin, K.K.1
Zhao, Y.2
Simon, R.M.3
-
43
-
-
33846978784
-
Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
-
Dupuy A, Simon RM (2007) Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 99:147-157
-
(2007)
J Natl Cancer Inst
, vol.99
, pp. 147-157
-
-
Dupuy, A.1
Simon, R.M.2
-
44
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210 (Pubitemid 34679544)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.1
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
45
-
-
67650730222
-
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
-
Eggle D, Debey-Pascher S, Beyer M, Schultze JL (2009) The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays. BMC Bioinformatics 10:186
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 186
-
-
Eggle, D.1
Debey-Pascher, S.2
Beyer, M.3
Schultze, J.L.4
-
46
-
-
13444282534
-
Outcome signature genes in breast cancer: Is there a unique set?
-
DOI 10.1093/bioinformatics/bth469
-
Ein-Dor L, Kela I, Getz G, Givol D, Domany E (2005) Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics 21:171-178 (Pubitemid 40202018)
-
(2005)
Bioinformatics
, vol.21
, Issue.2
, pp. 171-178
-
-
Ein-Dor, L.1
Kela, I.2
Getz, G.3
Givol, D.4
Domany, E.5
-
47
-
-
33645825183
-
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
-
Ein-Dor L, Zuk O, Domany E (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103:5923-5928
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5923-5928
-
-
Ein-Dor, L.1
Zuk, O.2
Domany, E.3
-
48
-
-
24044513966
-
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
-
DOI 10.1038/nmeth785
-
Elias JE, Haas W, Faherty BK, Gygi SP (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2:667-675 (Pubitemid 41223093)
-
(2005)
Nature Methods
, vol.2
, Issue.9
, pp. 667-675
-
-
Elias, J.E.1
Haas, W.2
Faherty, B.K.3
Gygi, S.P.4
-
49
-
-
31344436621
-
Integrating probe-level expression changes across generations of affymetrix arrays
-
DOI 10.1093/nar/gni193
-
Elo LL, Lahti L, Skottman H, Kylaniemi M, Lahesmaa R, Aittokallio T (2005) Integrating probe-level expression changes across generations of AVymetrix arrays. Nucleic Acids Res 33:e193 (Pubitemid 43135686)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.22
-
-
Elo, L.L.1
Lahti, L.2
Skottman, H.3
Kylaniemi, M.4
Lahesmaa, R.5
Aittokallio, T.6
-
50
-
-
77950789262
-
Standards aVecting the consistency of gene expression arrays in clinical applications
-
Enkemann SA (2010) Standards aVecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev 19:1000-1003
-
(2010)
Cancer Epidemiol Biomarkers Prev
, vol.19
, pp. 1000-1003
-
-
Enkemann, S.A.1
-
51
-
-
33847008688
-
A network biology approach to prostate cancer
-
Ergun A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ (2007) A network biology approach to prostate cancer. Mol Syst Biol 3:82
-
(2007)
Mol Syst Biol
, vol.3
, pp. 82
-
-
Ergun, A.1
Lawrence, C.A.2
Kohanski, M.A.3
Brennan, T.A.4
Collins, J.J.5
-
52
-
-
0033816482
-
Laser capture microdissection in pathology
-
Fend F, RaVeld M (2000) Laser capture microdissection in pathology. J Clin Pathol 53:666-672
-
(2000)
J Clin Pathol
, vol.53
, pp. 666-672
-
-
Fend, F.1
RaVeld, M.2
-
53
-
-
66049144026
-
Meta analysis of gene expression data within and across species
-
Fierro AC, Vandenbussche F, Engelen K, Van de Peer Y, Marchal K (2008) Meta analysis of gene expression data within and across species. Curr Genomics 9:525-534
-
(2008)
Curr Genomics
, vol.9
, pp. 525-534
-
-
Fierro, A.C.1
Vandenbussche, F.2
Engelen, K.3
Van De Peer, Y.4
Marchal, K.5
-
54
-
-
77953194530
-
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
-
Fortney K, Kotlyar M, Jurisica I (2010) Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol 11:R13
-
(2010)
Genome Biol
, vol.11
-
-
Fortney, K.1
Kotlyar, M.2
Jurisica, I.3
-
55
-
-
58749098785
-
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
-
Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S (2008) Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Syst Biol 2:106
-
(2008)
BMC Syst Biol
, vol.2
, pp. 106
-
-
Fujita, A.1
Gomes, L.R.2
Sato, J.R.3
Yamaguchi, R.4
Thomaz, C.E.5
Sogayar, M.C.6
Miyano, S.7
-
56
-
-
1542515338
-
A census of human cancer genes
-
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR (2004) A census of human cancer genes. Nat Rev Cancer 4:177-183 (Pubitemid 38337497)
-
(2004)
Nature Reviews Cancer
, vol.4
, Issue.3
, pp. 177-183
-
-
Futreal, P.A.1
Coin, L.2
Marshall, M.3
Down, T.4
Hubbard, T.5
Wooster, R.6
Rahman, N.7
Stratton, M.R.8
-
59
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
DOI 10.1038/415141a
-
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, RuVner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147 (Pubitemid 34059510)
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 141-147
-
-
Gavin, A.-C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.-M.9
Cruciat, C.-M.10
Remor, M.11
Hofert, C.12
Schelder, M.13
Brajenovic, M.14
Ruffner, H.15
Merino, A.16
Klein, K.17
Hudak, M.18
Dickson, D.19
Rudi, T.20
Gnau, V.21
Bauch, A.22
Bastuck, S.23
Huhse, B.24
Leutwein, C.25
Heurtier, M.-A.26
Copley, R.R.27
Edelmann, A.28
Querfurth, E.29
Rybin, V.30
Drewes, G.31
Raida, M.32
Bouwmeester, T.33
Bork, P.34
Seraphin, B.35
Kuster, B.36
Neubauer, G.37
Superti-Furga, G.38
more..
-
60
-
-
34547140875
-
The human disease network
-
DOI 10.1073/pnas.0701361104
-
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL (2007) The human disease network. Proc Natl Acad Sci USA 104:8685-8690 (Pubitemid 47175372)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.21
, pp. 8685-8690
-
-
Goh, K.-I.1
Cusick, M.E.2
Valle, D.3
Childs, B.4
Vidal, M.5
Barabasi, A.-L.6
-
61
-
-
38649104431
-
A proteome resource of ovarian cancer ascites: Integrated proteomic and bioinformatic analyses to identify putative biomarkers
-
DOI 10.1021/pr0703223
-
Gortzak-Uzan L, Ignatchenko A, Evangelou AI, Agochiya M, Brown KA, St Onge P, Kireeva I, Schmitt-Ulms G, Brown TJ, Murphy J, Rosen B, Shaw P, Jurisica I, Kislinger T (2008) A proteome resource of ovarian cancer ascites: Integrated proteomic and bioinformatic analyses to identify putative biomarkers. J Proteome Res 7:339-351 (Pubitemid 351171148)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 339-351
-
-
Gortzak-Uzan, L.1
Ignatchenko, A.2
Evangelou, A.I.3
Agochiya, M.4
Brown, K.A.5
St.Onge, P.6
Kireeva, I.7
Schmitt-Ulms, G.8
Brown, T.J.9
Murphy, J.10
Rosen, B.11
Shaw, P.12
Jurisica, I.13
Kislinger, T.14
-
62
-
-
68949206409
-
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
-
Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10:617-627
-
(2009)
Nat Rev Genet
, vol.10
, pp. 617-627
-
-
Gstaiger, M.1
Aebersold, R.2
-
63
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
DOI 10.1093/molbev/msi072
-
Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22:803-806 (Pubitemid 40471393)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.4
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
64
-
-
13444266370
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
DOI 10.1093/nar/gki033
-
Hamosh A, Scott A, Amberger J, Bocchini C, McKusick V (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514-D517 (Pubitemid 40207927)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
McKusick, V.A.5
-
65
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
DOI 10.1038/nature02555
-
Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93 (Pubitemid 38915230)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 88-93
-
-
Han, J.-D.J.1
Berlin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
66
-
-
9144248312
-
IntAct: An open source molecular interaction database
-
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, RoepstorV P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R (2004) IntAct: An open source molecular interaction database. Nucleic Acids Res 32:D452-D455 (Pubitemid 38081697)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Lewington, C.3
Mudali, S.4
Kerrien, S.5
Orchard, S.6
Vingron, M.7
Roechert, B.8
Roepstorff, P.9
Valencia, A.10
Margalit, H.11
Armstrong, J.12
Bairoch, A.13
Cesareni, G.14
Sherman, D.15
Apweiler, R.16
-
67
-
-
27544448536
-
Implementing the iHOP concept for navigation of biomedical literature
-
DOI 10.1093/bioinformatics/bti1142
-
HoVmann R, Valencia A (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 Suppl 2: Ii252-ii258 (Pubitemid 41535458)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Hoffmann, R.1
Valencia, A.2
-
68
-
-
27744543196
-
Text mining for metabolic pathways, signaling cascades, and protein networks
-
HoVmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A (2005) Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE 2005(283):pe21
-
(2005)
Sci STKE
, vol.2005
, Issue.283
-
-
HoVmann, R.1
Krallinger, M.2
Andres, E.3
Tamames, J.4
Blaschke, C.5
Valencia, A.6
-
69
-
-
2942598149
-
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
-
DOI 10.1002/pmic.200300772
-
Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4:1551-1561 (Pubitemid 38738314)
-
(2004)
Proteomics
, vol.4
, Issue.6
, pp. 1551-1561
-
-
Hornbeck, P.V.1
Chabra, I.2
Kornhauser, J.M.3
Skrzypek, E.4
Zhang, B.5
-
70
-
-
32044451325
-
Cancer: A Systems Biology disease
-
DOI 10.1016/j.biosystems.2005.05.014, PII S0303264705001176
-
Hornberg JJ, Bruggeman FJ, WesterhoV HV, Lankelma J (2006) Cancer: A systems biology disease. Biosystems 83:81-90 (Pubitemid 43199809)
-
(2006)
BioSystems
, vol.83
, Issue.2-3 SPEC. ISS.
, pp. 81-90
-
-
Hornberg, J.J.1
Bruggeman, F.J.2
Westerhoff, H.V.3
Lankelma, J.4
-
71
-
-
33751208636
-
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target
-
DOI 10.1073/pnas.0608396103
-
Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, Lee Y, Scheck AC, Liau LM, Wu H, Geschwind DH, Febbo PG, Kornblum HI, Cloughesy TF, Nelson SF, Mischel PS (2006) Analysis of oncogenic signaling networks in glioblastoma identiWes ASPM as a molecular target. Proc Natl Acad Sci USA 103:17402-17407 (Pubitemid 44788981)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.46
, pp. 17402-17407
-
-
Horvath, S.1
Zhang, B.2
Carlson, M.3
Lu, K.V.4
Zhu, S.5
Felciano, R.M.6
Laurence, M.F.7
Zhao, W.8
Qi, S.9
Chen, Z.10
Lee, Y.11
Schecks, A.C.12
Liau, L.M.13
Wu, H.14
Geschwind, D.H.15
Febbo, P.G.16
Kornblum, H.I.17
Cloughesy, T.F.18
Nelson, S.F.19
Mischel, P.S.20
more..
-
72
-
-
33845864703
-
Computational prediction of cancer-gene function
-
DOI 10.1038/nrc2036, PII NRC2036
-
Hu P, Bader G, Wigle DA, Emili A (2007) Computational prediction of cancer-gene function. Nat Rev Cancer 7:23-34 (Pubitemid 46023413)
-
(2007)
Nature Reviews Cancer
, vol.7
, Issue.1
, pp. 23-34
-
-
Hu, P.1
Bader, G.2
Wigle, D.A.3
Emili, A.4
-
73
-
-
58149185123
-
-
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P (2009) Ensembl 2009. Nucleic Acids Res 37:D690-D697
-
(2009)
Ensembl 2009. Nucleic Acids Res
, vol.37
-
-
Hubbard, T.J.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
Bragin, E.6
Brent, S.7
Chen, Y.8
Clapham, P.9
Clarke, L.10
Coates, G.11
Fairley, S.12
Fitzgerald, S.13
Fernandez-Banet, J.14
Gordon, L.15
Graf, S.16
Haider, S.17
Hammond, M.18
Holland, R.19
Howe, K.20
Jenkinson, A.21
Johnson, N.22
Kahari, A.23
Keefe, D.24
Keenan, S.25
Kinsella, R.26
Kokocinski, F.27
Kulesha, E.28
Lawson, D.29
Longden, I.30
Megy, K.31
Meidl, P.32
Overduin, B.33
Parker, A.34
Pritchard, B.35
Rios, D.36
Schuster, M.37
Slater, G.38
Smedley, D.39
Spooner, W.40
Spudich, G.41
Trevanion, S.42
Vilella, A.43
Vogel, J.44
White, S.45
Wilder, S.46
Zadissa, A.47
Birney, E.48
Cunningham, F.49
Curwen, V.50
Durbin, R.51
Fernandez-Suarez, X.M.52
Herrero, J.53
Kasprzyk, A.54
Proctor, G.55
Smith, J.56
Searle, S.57
Flicek, P.58
more..
-
74
-
-
77951115122
-
International network of cancer genome projects
-
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabe RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolas P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clement B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, van de Vijver M, Futreal PA, Aburatani H, Bayes M, Botwell DD, Campbell PJ, Estivill X, Grimmond SM, Gut I, Hirst M, Lopez-Otin C, Majumder P, Marra M, McPherson JD, Ning Z, Puente XS, Ruan Y, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Flicek P, Getz G, Guigo R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T et al (2010) International network of cancer genome projects. Nature 464:993-998
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
Hudson, T.J.1
Anderson, W.2
Artez, A.3
Barker, A.D.4
Bell, C.5
Bernabe, R.R.6
Bhan, M.K.7
Calvo, F.8
Eerola, I.9
Gerhard, D.S.10
Guttmacher, A.11
Guyer, M.12
Hemsley, F.M.13
Jennings, J.L.14
Kerr, D.15
Klatt, P.16
Kolar, P.17
Kusada, J.18
Lane, D.P.19
Laplace, F.20
Youyong, L.21
Nettekoven, G.22
Ozenberger, B.23
Peterson, J.24
Rao, T.S.25
Remacle, J.26
Schafer, A.J.27
Shibata, T.28
Stratton, M.R.29
Vockley, J.G.30
Watanabe, K.31
Yang, H.32
Yuen, M.M.33
Knoppers, B.M.34
Bobrow, M.35
Cambon-Thomsen, A.36
Dressler, L.G.37
Dyke, S.O.38
Joly, Y.39
Kato, K.40
Kennedy, K.L.41
Nicolas, P.42
Parker, M.J.43
Rial-Sebbag, E.44
Romeo-Casabona, C.M.45
Shaw, K.M.46
Wallace, S.47
Wiesner, G.L.48
Zeps, N.49
Lichter, P.50
Biankin, A.V.51
Chabannon, C.52
Chin, L.53
Clement, B.54
De Alava, E.55
Degos, F.56
Ferguson, M.L.57
Geary, P.58
Hayes, D.N.59
Johns, A.L.60
Kasprzyk, A.61
Nakagawa, H.62
Penny, R.63
Piris, M.A.64
Sarin, R.65
Scarpa, A.66
Van De Vijver, M.67
Futreal, P.A.68
Aburatani, H.69
Bayes, M.70
Botwell, D.D.71
Campbell, P.J.72
Estivill, X.73
Grimmond, S.M.74
more..
-
75
-
-
72949094885
-
Predicting essential genes based on network and sequence analysis
-
Hwang YC, Lin CC, Chang JY, Mori H, Juan HF, Huang HC (2009) Predicting essential genes based on network and sequence analysis. Mol Biosyst 5:1672-1678
-
(2009)
Mol Biosyst
, vol.5
, pp. 1672-1678
-
-
Hwang, Y.C.1
Lin, C.C.2
Chang, J.Y.3
Mori, H.4
Juan, H.F.5
Huang, H.C.6
-
76
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18(Suppl 1):S233-S240 (Pubitemid 41185658)
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
77
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, GriYn C, Hilmer SC, HoVman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345-350
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.8
Geoghegan, J.9
Germino, G.10
GriYn, C.11
Hilmer, S.C.12
HoVman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martinez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
78
-
-
31144432293
-
Literature mining for the biologist: From information retrieval to biological discovery
-
DOI 10.1038/nrg1768, PII NRG1768
-
Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: From information retrieval to biological discovery. Nat Rev Genet 7:119-129 (Pubitemid 43128897)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.2
, pp. 119-129
-
-
Jensen, L.J.1
Saric, J.2
Bork, P.3
-
79
-
-
0035799707
-
Lethality and centrality in protein networks
-
DOI 10.1038/35075138
-
Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42 (Pubitemid 32428180)
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.-L.3
Oltvai, Z.N.4
-
80
-
-
33644875983
-
PRIDE: A public repository of protein and peptide identiWcations for the proteomics community
-
Jones P, Cote RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R (2006) PRIDE: A public repository of protein and peptide identiWcations for the proteomics community. Nucleic Acids Res 34:D659-D663
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Jones, P.1
Cote, R.G.2
Martens, L.3
Quinn, A.F.4
Taylor, C.F.5
Derache, W.6
Hermjakob, H.7
Apweiler, R.8
-
81
-
-
33748706765
-
Global topological features of cancer proteins in the human interactome
-
DOI 10.1093/bioinformatics/btl390
-
Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22:2291-2297 (Pubitemid 44390886)
-
(2006)
Bioinformatics
, vol.22
, Issue.18
, pp. 2291-2297
-
-
Jonsson, P.F.1
Bates, P.A.2
-
82
-
-
77952107920
-
Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis
-
Jubb AM, BuVa FM, Harris AL (2010) Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis. J Cell Mol Med 14:18-29
-
(2010)
J Cell Mol Med
, vol.14
, pp. 18-29
-
-
Jubb, A.M.1
BuVa, F.M.2
Harris, A.L.3
-
83
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
DOI 10.1093/nar/gkm882
-
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480-D484 (Pubitemid 351149770)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
84
-
-
10244264813
-
Protein complex prediction via cost-based clustering
-
DOI 10.1093/bioinformatics/bth351
-
King AD, Przulj N, Jurisica I (2004) Protein complex prediction via cost-based clustering. Bioinformatics 20:3013-3020 (Pubitemid 39619193)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3013-3020
-
-
King, A.D.1
Przulj, N.2
Jurisica, I.3
-
85
-
-
19344375343
-
The meaning of systems biology
-
DOI 10.1016/j.cell.2005.05.005, PII S0092867405004472
-
Kirschner MW (2005) The meaning of systems biology. Cell 121:503-504 (Pubitemid 40720002)
-
(2005)
Cell
, vol.121
, Issue.4
, pp. 503-504
-
-
Kirschner, M.W.1
-
86
-
-
14344260140
-
Multidimensional protein identification technology: Current status and future prospects
-
DOI 10.1586/14789450.2.1.27
-
Kislinger T, Emili A (2005) Multidimensional protein identiWcation technology: Current status and future prospects. Expert Rev Proteomics 2:27-39 (Pubitemid 40292577)
-
(2005)
Expert Review of Proteomics
, vol.2
, Issue.1
, pp. 27-39
-
-
Kislinger, T.1
Emili, A.2
-
87
-
-
33645993265
-
Global survey of organ and organelle protein expression in mouse: Combined proteomic and transcriptomic proWling
-
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A (2006) Global survey of organ and organelle protein expression in mouse: Combined proteomic and transcriptomic proWling. Cell 125:173-186
-
(2006)
Cell
, vol.125
, pp. 173-186
-
-
Kislinger, T.1
Cox, B.2
Kannan, A.3
Chung, C.4
Hu, P.5
Ignatchenko, A.6
Scott, M.S.7
Gramolini, A.O.8
Morris, Q.9
Hallett, M.T.10
Rossant, J.11
Hughes, T.R.12
Frey, B.13
Emili, A.14
-
88
-
-
33144466926
-
Predicting protein-protein interactions by association mining
-
DOI 10.1007/s10796-005-6102-8
-
Kotlyar M, Jurisica I (2006) Predicting protein-protein interactions by association mining. Inf Syst Frontiers 8:37-47 (Pubitemid 43269399)
-
(2006)
Information Systems Frontiers
, vol.8
, Issue.1
, pp. 37-47
-
-
Kotlyar, M.1
Jurisica, I.2
-
89
-
-
80054848807
-
-
(in preparation
-
Kotlyar M, Niu Y, Ponzielli R, Ding Z, Mills GB, Penn LZ, Jurisica I (2011) Predicting human protein-protein interactions using nonindependent features (in preparation)
-
(2011)
Predicting Human Protein-Protein Interactions using Nonindependent Features
-
-
Kotlyar, M.1
Niu, Y.2
Ponzielli, R.3
Ding, Z.4
Mills, G.B.5
Penn, L.Z.6
Jurisica, I.7
-
90
-
-
75549087827
-
STITCH 2: An interaction network database for small molecules and proteins
-
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P (2010) STITCH 2: An interaction network database for small molecules and proteins. Nucleic Acids Res 38:D552-D556
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Kuhn, M.1
Szklarczyk, D.2
Franceschini, A.3
Campillos, M.4
Von Mering, C.5
Jensen, L.J.6
Beyer, A.7
Bork, P.8
-
91
-
-
37649004550
-
Three-gene prognostic classiWer for early-stage non small-cell lung cancer
-
Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica I, Der SD, Tsao MS (2007) Three-gene prognostic classiWer for early-stage non small-cell lung cancer. J Clin Oncol 25:5562-5569
-
(2007)
J Clin Oncol
, vol.25
, pp. 5562-5569
-
-
Lau, S.K.1
Boutros, P.C.2
Pintilie, M.3
Blackhall, F.H.4
Zhu, C.Q.5
Strumpf, D.6
Johnston, M.R.7
Darling, G.8
Keshavjee, S.9
Waddell, T.K.10
Liu, N.11
Lau, D.12
Penn, L.Z.13
Shepherd, F.A.14
Jurisica, I.15
Der, S.D.16
Tsao, M.S.17
-
92
-
-
77951094805
-
Big science: The cancer genome challenge
-
Ledford H (2010) Big science: The cancer genome challenge. Nature 464:972-974
-
(2010)
Nature
, vol.464
, pp. 972-974
-
-
Ledford, H.1
-
93
-
-
70350674928
-
Discovering cancer genes by integrating network and functional properties
-
Li L, Zhang K, Lee J, Cordes S, Davis DP, Tang Z (2009) Discovering cancer genes by integrating network and functional properties. BMC Med Genomics 2:61
-
(2009)
BMC Med Genomics
, vol.2
, pp. 61
-
-
Li, L.1
Zhang, K.2
Lee, J.3
Cordes, S.4
Davis, D.P.5
Tang, Z.6
-
95
-
-
51049113607
-
InnateDB: Facilitating systems-level analyses of the mammalian innate immune response
-
Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS (2008) InnateDB: Facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 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.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.22
Brinkman, F.S.23
more..
-
96
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
DOI 10.1126/science.1065103
-
Maslov S, Sneppen K (2002) SpeciWcity and stability in topology of protein networks. Science 296:910-913 (Pubitemid 34464896)
-
(2002)
Science
, vol.296
, Issue.5569
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
97
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619-D622
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
Croft, D.5
De Bono, B.6
Garapati, P.7
Hemish, J.8
Hermjakob, H.9
Jassal, B.10
Kanapin, A.11
Lewis, S.12
Mahajan, S.13
May, B.14
Schmidt, E.15
Vastrik, I.16
Wu, G.17
Birney, E.18
Stein, L.19
D'Eustachio, P.20
more..
-
98
-
-
70350638951
-
Interaction techniques for selecting and manipulating subgraphs in network visualizations
-
McGuYn M, Jurisica I (2009) Interaction techniques for selecting and manipulating subgraphs in network visualizations. IEEE Trans Vis Comput Graph 15(6):937-944
-
(2009)
IEEE Trans Vis Comput Graph
, vol.15
, Issue.6
, pp. 937-944
-
-
McGuYn, M.1
Jurisica, I.2
-
100
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
DOI 10.1126/science.298.5594.824
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827 (Pubitemid 35231534)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
101
-
-
78649524955
-
In silico ascription of gene expression diVerences to tumor and stromal cells in a model to study impact on breast cancer outcome
-
Myhre S, Mohammed H, Tramm T, Alsner J, Finak G, Park M, Overgaard J, Borresen-Dale AL, Frigessi A, Sorlie T (2010) In silico ascription of gene expression diVerences to tumor and stromal cells in a model to study impact on breast cancer outcome. PLoS One 5:e14002
-
(2010)
PLoS One
, vol.5
-
-
Myhre, S.1
Mohammed, H.2
Tramm, T.3
Alsner, J.4
Finak, G.5
Park, M.6
Overgaard, J.7
Borresen-Dale, A.L.8
Frigessi, A.9
Sorlie, T.10
-
102
-
-
34248593385
-
Gene expression network analysis and applications to immunology
-
DOI 10.1093/bioinformatics/btm019
-
Nacu S, Critchley-Thorne R, Lee P, Holmes S (2007) Gene expression network analysis and applications to immunology. Bioinformatics 23:850-858 (Pubitemid 47049919)
-
(2007)
Bioinformatics
, vol.23
, Issue.7
, pp. 850-858
-
-
Nacu, S.1
Critchley-Thorne, R.2
Lee, P.3
Holmes, S.4
-
104
-
-
66149156998
-
Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer
-
Nibbe RK, Markowitz S, MyeroV L, Ewing R, Chance MR (2009) Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics 8:827-845
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 827-845
-
-
Nibbe, R.K.1
Markowitz, S.2
MyeroV, L.3
Ewing, R.4
Chance, M.R.5
-
105
-
-
76749148657
-
An integrative-omics approach to identify functional sub-networks in human colorectal cancer
-
Nibbe RK, Koyuturk M, Chance MR (2010) An integrative-omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol 6:e1000639
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Nibbe, R.K.1
Koyuturk, M.2
Chance, M.R.3
-
106
-
-
75249101080
-
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D
-
Niu Y, Otasek D, Jurisica I (2010) Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics 26:111-119
-
(2010)
Bioinformatics
, vol.26
, pp. 111-119
-
-
Niu, Y.1
Otasek, D.2
Jurisica, I.3
-
107
-
-
41649106470
-
Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition
-
DOI 10.1002/pmic.200700286
-
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H (2007) Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition. Proteomics 7(Suppl 1):28-34 (Pubitemid 351547767)
-
(2007)
Proteomics - Practical Proteomics
, vol.2
, Issue.1
, pp. 28-34
-
-
Orchard, S.1
Kerrien, S.2
Jones, P.3
Ceol, A.4
Chatr-Aryamontri, A.5
Salwinski, L.6
Nerothin, J.7
Hermjakob, H.8
-
108
-
-
77952351989
-
Implementing data standards: A report on the HUPOPSI workshop September2009, Toronto
-
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H (2010) Implementing data standards: A report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics 10:1895-1898
-
(2010)
Canada. Proteomics
, vol.10
, pp. 1895-1898
-
-
Orchard, S.1
Albar, J.P.2
Deutsch, E.W.3
Eisenacher, M.4
Binz, P.A.5
Hermjakob, H.6
-
109
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
DOI 10.1038/nature03607
-
Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818 (Pubitemid 40839731)
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Derenyi, I.2
Farkas, I.3
Vicsek, T.4
-
110
-
-
0031903646
-
Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185(HER2/neu) monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment
-
Pegram MD, Lipton A, Hayes DF, Weber BL, Baselga JM, Tripathy D, Baly D, Baughman SA, Twaddell T, Glaspy JA, Slamon DJ (1998) Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185HER2/neu monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment. J Clin Oncol 16:2659-2671 (Pubitemid 28363029)
-
(1998)
Journal of Clinical Oncology
, vol.16
, Issue.8
, pp. 2659-2671
-
-
Pegram, M.D.1
Lipton, A.2
Hayes, D.F.3
Weber, B.L.4
Baselga, J.M.5
Tripathy, D.6
Baly, D.7
Baughman, S.A.8
Twaddell, T.9
Glaspy, J.A.10
Slamon, D.J.11
-
111
-
-
47549116997
-
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
-
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 9(Suppl 1): S2
-
(2008)
Genome Biol
, vol.9
, Issue.SUPPL. 1
-
-
Pena-Castillo, L.1
Tasan, M.2
Myers, C.L.3
Lee, H.4
Joshi, T.5
Zhang, C.6
Guan, Y.7
Leone, M.8
Pagnani, A.9
Kim, W.K.10
Krumpelman, C.11
Tian, W.12
Obozinski, G.13
Qi, Y.14
Mostafavi, S.15
Lin, G.N.16
Berriz, G.F.17
Gibbons, F.D.18
Lanckriet, G.19
Qiu, J.20
Grant, C.21
Barutcuoglu, Z.22
Hill, D.P.23
Warde-Farley, D.24
Grouios, C.25
Ray, D.26
Blake, J.A.27
Deng, M.28
Jordan, M.I.29
Noble, W.S.30
Morris, Q.31
Klein-Seetharaman, J.32
Bar-Joseph, Z.33
Chen, T.34
Sun, F.35
Troyanskaya, O.G.36
Marcotte, E.M.37
Xu, D.38
Hughes, T.R.39
Roth, F.P.40
more..
-
112
-
-
9144236198
-
Human protein reference database as a discovery resource for proteomics
-
Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32:D497-D501 (Pubitemid 38094227)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Peri, S.1
Navarro, J.D.2
Kristiansen, T.Z.3
Amanchy, R.4
Surendranath, V.5
Muthusamy, B.6
Gandhi, T.K.B.7
Chandrika, K.N.8
Deshpande, N.9
Suresh, S.10
Rashmi, B.P.11
Shanker, K.12
Padma, N.13
Niranjan, V.14
Harsha, H.C.15
Talreja, N.16
Vrushabendra, B.M.17
Ramya, M.A.18
Yatish, A.J.19
Joy, M.20
Shivashankar, H.N.21
Kavitha, M.P.22
Menezes, M.23
Choudhury, D.R.24
Ghosh, N.25
Saravana, R.26
Chandran, S.27
Mohan, S.28
Jonnalagadda, C.K.29
Prasad, C.K.30
Kumar-Sinha, C.31
Deshpande, K.S.32
Pandey, A.33
more..
-
113
-
-
68549130871
-
An active registry for bioinformatics web services
-
Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D, Vriend G (2009) An active registry for bioinformatics web services. Bioinformatics 25:2090-2091
-
(2009)
Bioinformatics
, vol.25
, pp. 2090-2091
-
-
Pettifer, S.1
Thorne, D.2
McDermott, P.3
Attwood, T.4
Baran, J.5
Bryne, J.C.6
Hupponen, T.7
Mowbray, D.8
Vriend, G.9
-
114
-
-
48349105261
-
WikiPathways: Pathway editing for the people
-
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C (2008) WikiPathways: Pathway editing for the people. PLoS Biol 6:e184
-
(2008)
PLoS Biol
, vol.6
-
-
Pico, A.R.1
Kelder, T.2
Van Iersel, M.P.3
Hanspers, K.4
Conklin, B.R.5
Evelo, C.6
-
115
-
-
57149089456
-
Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies
-
Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, Penn LZ (2008) Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res 36:e144
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Ponzielli, R.1
Boutros, P.C.2
Katz, S.3
Stojanova, A.4
Hanley, A.P.5
Khosravi, F.6
Bros, C.7
Jurisica, I.8
Penn, L.Z.9
-
116
-
-
33846672214
-
Biological network comparison using graphlet degree distribution
-
DOI 10.1093/bioinformatics/btl301
-
Przulj N (2007) Biological network comparison using graphlet degree distribution. Bioinformatics 23:e177-e183 (Pubitemid 46189654)
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Przulj, N.1
-
117
-
-
33645803834
-
EYcient estimation of graphlet frequency distributions in protein-protein interaction networks
-
Przulj N, Corneil DG, Jurisica I (2006) EYcient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics 22:974-980
-
(2006)
Bioinformatics
, vol.22
, pp. 974-980
-
-
Przulj, N.1
Corneil, D.G.2
Jurisica, I.3
-
118
-
-
77349095037
-
DiVerential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma
-
Radulovich N, Pham NA, Strumpf D, Leung L, Xie W, Jurisica I, Tsao MS (2010) DiVerential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma. Mol Cancer 9:24
-
(2010)
Mol Cancer
, vol.9
, pp. 24
-
-
Radulovich, N.1
Pham, N.A.2
Strumpf, D.3
Leung, L.4
Xie, W.5
Jurisica, I.6
Tsao, M.S.7
-
119
-
-
49849100187
-
Low duplicability and network fragility of cancer genes
-
Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD (2008) Low duplicability and network fragility of cancer genes. Trends Genet 24:427-430
-
(2008)
Trends Genet
, vol.24
, pp. 427-430
-
-
Rambaldi, D.1
Giorgi, F.M.2
Capuani, F.3
Ciliberto, A.4
Ciccarelli, F.D.5
-
120
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
DOI 10.1126/science.1073374
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555 (Pubitemid 34971002)
-
(2002)
Science
, vol.297
, Issue.5586
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.-L.5
-
121
-
-
0031114483
-
GeneCards: Integrating information about genes, proteins and diseases
-
PII S0168952597011037
-
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D (1997) GeneCards: Integrating information about genes, proteins and diseases. Trends Genet 13:163 (Pubitemid 127739947)
-
(1997)
Trends in Genetics
, vol.13
, Issue.4
, pp. 163
-
-
Rebhan, M.1
Chalifa-Caspi, V.2
Prilusky, J.3
Lancet, D.4
-
122
-
-
77956453805
-
Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma
-
Reis PP, Tomenson M, Cervigne NK, Machado J, Jurisica I, Pintilie M, Sukhai MA, Perez-Ordonez B, Grenman R, Gilbert RW, Gullane PJ, Irish JC, Kamel-Reid S (2010) Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma. Mol Cancer 9:238
-
(2010)
Mol Cancer
, vol.9
, pp. 238
-
-
Reis, P.P.1
Tomenson, M.2
Cervigne, N.K.3
Machado, J.4
Jurisica, I.5
Pintilie, M.6
Sukhai, M.A.7
Perez-Ordonez, B.8
Grenman, R.9
Gilbert, R.W.10
Gullane, P.J.11
Irish, J.C.12
Kamel-Reid, S.13
-
123
-
-
20044396570
-
Integrative analysis of the cancer transcriptome
-
DOI 10.1038/ng1570
-
Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37 Suppl: S31-37 (Pubitemid 40770401)
-
(2005)
Nature Genetics
, vol.37
, Issue.6 SUPPL.
-
-
Rhodes, D.R.1
Chinnaiyan, A.M.2
-
124
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
DOI 10.1038/nbt1103
-
Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 23:951-959 (Pubitemid 41114028)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.8
, pp. 951-959
-
-
Rhodes, D.R.1
Tomlins, S.A.2
Varambally, S.3
Mahavisno, V.4
Barrette, T.5
Kalyana-Sundaram, S.6
Ghosh, D.7
Pandey, A.8
Chinnaiyan, A.M.9
-
125
-
-
33847246805
-
Oncomine 3.0: Genes, pathways, and networks in a collection of 18, 000 cancer gene expression proWles
-
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM (2007) Oncomine 3.0: Genes, pathways, and networks in a collection of 18, 000 cancer gene expression proWles. Neoplasia 9:166-180
-
(2007)
Neoplasia
, vol.9
, pp. 166-180
-
-
Rhodes, D.R.1
Kalyana-Sundaram, S.2
Mahavisno, V.3
Varambally, R.4
Yu, J.5
Briggs, B.B.6
Barrette, T.R.7
Anstet, M.J.8
Kincead-Beal, C.9
Kulkarni, P.10
Varambally, S.11
Ghosh, D.12
Chinnaiyan, A.M.13
-
127
-
-
34248591612
-
Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer
-
DOI 10.1038/sj.onc.1210422, PII 1210422
-
Roberts PJ, Der CJ (2007) Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene 26:3291-3310 (Pubitemid 46763022)
-
(2007)
Oncogene
, vol.26
, Issue.22
, pp. 3291-3310
-
-
Roberts, P.J.1
Der, C.J.2
-
128
-
-
74549117176
-
Biomedical text mining and its applications
-
Rodriguez-Esteban R (2009) Biomedical text mining and its applications. PLoS Comput Biol 5:e1000597
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Rodriguez-Esteban, R.1
-
129
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
DOI 10.1038/nature04209, PII N04209
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-1178 (Pubitemid 41509356)
-
(2005)
Nature
, vol.437
, Issue.7062
, pp. 1173-1178
-
-
Rual, J.-F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
Klitgord, N.11
Simon, C.12
Boxem, M.13
Milstein, S.14
Rosenberg, J.15
Goldberg, D.S.16
Zhang, L.V.17
Wong, S.L.18
Franklin, G.19
Li, S.20
Albala, J.S.21
Lim, J.22
Fraughton, C.23
Llamosas, E.24
Cevik, S.25
Bex, C.26
Lamesch, P.27
Sikorski, R.S.28
Vandenhaute, J.29
Zoghbi, H.Y.30
Smolyar, A.31
Bosak, S.32
Sequerra, R.33
Doucette-Stamm, L.34
Cusick, M.E.35
Hill, D.E.36
Roth, F.P.37
Vidal, M.38
more..
-
130
-
-
33847679625
-
Improved precision and accuracy for microarrays using updated probe set deWnitions
-
Sandberg R, Larsson O (2007) Improved precision and accuracy for microarrays using updated probe set deWnitions. BMC Bioinformatics 8:48
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 48
-
-
Sandberg, R.1
Larsson, O.2
-
131
-
-
68249142895
-
A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research
-
Savas S, Geraci J, Jurisica I, Liu G (2009) A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research. Int J Cancer 125:1257-1265
-
(2009)
Int J Cancer
, vol.125
, pp. 1257-1265
-
-
Savas, S.1
Geraci, J.2
Jurisica, I.3
Liu, G.4
-
132
-
-
0034625260
-
Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity
-
Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, Dixon JE, Zipursky SL (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101:671-684
-
(2000)
Cell
, vol.101
, pp. 671-684
-
-
Schmucker, D.1
Clemens, J.C.2
Shu, H.3
Worby, C.A.4
Xiao, J.5
Muda, M.6
Dixon, J.E.7
Zipursky, S.L.8
-
133
-
-
10344258041
-
Targeting the mitogen-activated protein kinase cascade to treat cancer
-
DOI 10.1038/nrc1503
-
Sebolt-Leopold JS, Herrera R (2004) Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer 4:937-947 (Pubitemid 39626217)
-
(2004)
Nature Reviews Cancer
, vol.4
, Issue.12
, pp. 937-947
-
-
Sebolt-Leopold, J.S.1
Herrera, R.2
-
134
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504 (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, 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
-
135
-
-
49149129916
-
Gene expression-based survival prediction in lung adenocarcinoma: A multi-site, blinded validation study
-
Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG (2008) Gene expression-based survival prediction in lung adenocarcinoma: A multi-site, blinded validation study. Nat Med 14:822-827
-
(2008)
Nat Med
, vol.14
, pp. 822-827
-
-
Shedden, K.1
Taylor, J.M.2
Enkemann, S.A.3
Tsao, M.S.4
Yeatman, T.J.5
Gerald, W.L.6
Eschrich, S.7
Jurisica, I.8
Giordano, T.J.9
Misek, D.E.10
Chang, A.C.11
Zhu, C.Q.12
Strumpf, D.13
Hanash, S.14
Shepherd, F.A.15
Ding, K.16
Seymour, L.17
Naoki, K.18
Pennell, N.19
Weir, B.20
Verhaak, R.21
Ladd-Acosta, C.22
Golub, T.23
Gruidl, M.24
Sharma, A.25
Szoke, J.26
Zakowski, M.27
Rusch, V.28
Kris, M.29
Viale, A.30
Motoi, N.31
Travis, W.32
Conley, B.33
Seshan, V.E.34
Meyerson, M.35
Kuick, R.36
Dobbin, K.K.37
Lively, T.38
Jacobson, J.W.39
Beer, D.G.40
more..
-
136
-
-
79952146521
-
NAViGaTing the microNome-using multiple microRNA prediction databases to identify signaling pathway-associated microRNA
-
Shirdel EA, Xie W, Mak TW, Jurisica I (2011) NAViGaTing the microNome-using multiple microRNA prediction databases to identify signaling pathway-associated microRNA. PLoS One 6(2):e17429
-
(2011)
PLoS One
, vol.6
, Issue.2
-
-
Shirdel, E.A.1
Xie, W.2
Mak, T.W.3
Jurisica, I.4
-
137
-
-
65549112480
-
Alterations in the TOP2A and HER2 genes: Association with adjuvant anthracycline sensitivity in human breast cancers
-
Slamon DJ, Press MF (2009) Alterations in the TOP2A and HER2 genes: Association with adjuvant anthracycline sensitivity in human breast cancers. J Natl Cancer Inst 101:615-618
-
(2009)
J Natl Cancer Inst
, vol.101
, pp. 615-618
-
-
Slamon, D.J.1
Press, M.F.2
-
138
-
-
45749106371
-
Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)
-
DOI 10.1039/b717542f
-
Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T (2008) IdentiWcation of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identiWcation technology (Mud-PIT). Mol Biosyst 4:762-773 (Pubitemid 351871749)
-
(2008)
Molecular BioSystems
, vol.4
, Issue.7
, pp. 762-773
-
-
Sodek, K.L.1
Evangelou, A.I.2
Ignatchenko, A.3
Agochiya, M.4
Brown, T.J.5
Ringuette, M.J.6
Jurisica, I.7
Kislinger, T.8
-
139
-
-
12344267687
-
Gene expression signature with independent prognostic signiWcance in epithelial ovarian cancer
-
Spentzos D, Levine DA, Ramoni MF, Joseph M, Gu X, Boyd J, Libermann TA, Cannistra SA (2004) Gene expression signature with independent prognostic signiWcance in epithelial ovarian cancer. J Clin Oncol 22:4700-4710
-
(2004)
J Clin Oncol
, vol.22
, pp. 4700-4710
-
-
Spentzos, D.1
Levine, D.A.2
Ramoni, M.F.3
Joseph, M.4
Gu, X.5
Boyd, J.6
Libermann, T.A.7
Cannistra, S.A.8
-
141
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34:D535-D539
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
142
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
DOI 10.1016/j.cell.2005.08.029, PII S0092867405008664
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H,
-
(2005)
Cell
, vol.122
, Issue.6
, 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
Timm, J.11
Mintzlaff, S.12
Abraham, C.13
Bock, N.14
Kietzmann, S.15
Goedde, A.16
Toksoz, E.17
Droege, A.18
Krobitsch, S.19
Korn, B.20
Birchmeier, W.21
Lehrach, H.22
Wanker, E.E.23
more..
-
144
-
-
44349113144
-
Estimating the size of the human interactome
-
DOI 10.1073/pnas.0708078105
-
Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C (2008) Estimating the size of the human interactome. Proc Natl Acad Sci USA 105:6959-6964 (Pubitemid 351754512)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.19
, pp. 6959-6964
-
-
Stumpf, M.P.H.1
Thorne, T.2
De Silva, E.3
Stewart, R.4
Hyeong, J.A.5
Lappe, M.6
Wiuf, C.7
-
145
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
DOI 10.1073/pnas.0506580102
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression proWles. Proc Natl Acad Sci USA 102:15545-15550 (Pubitemid 41528093)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
146
-
-
75549089911
-
Network of Cancer Genes: A web resource to analyze duplicability, orthology and network properties of cancer genes
-
Syed AS, D'Antonio M, Ciccarelli FD (2010) Network of Cancer Genes: A web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res 38:D670-D675
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Syed, A.S.1
D'Antonio, M.2
Ciccarelli, F.D.3
-
147
-
-
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 LJ, von Mering C (2011) The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 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
-
148
-
-
0141905890
-
Evaluation of gene expression measurements from commercial microarray platforms
-
DOI 10.1093/nar/gkg763
-
Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676-5684 (Pubitemid 37441938)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.19
, pp. 5676-5684
-
-
Tan, P.K.1
Downey, T.J.2
Spitznagel Jr., E.L.3
Xu, P.4
Fu, D.5
Dimitrov, D.S.6
Lempicki, R.A.7
Raaka, B.M.8
Cam, M.C.9
-
149
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
DOI 10.1073/pnas.0506577102
-
Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ (2005) Discovering statistically signiWcant pathways in expression proWling studies. Proc Natl Acad Sci USA 102:13544-13549 (Pubitemid 41420885)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.38
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
Kohane, I.S.5
Park, P.J.6
-
150
-
-
53549134949
-
TAp73 knockout shows genomic instability with infertility and tumor suppressor functions
-
Tomasini R, Tsuchihara K, Wilhelm M, Fujitani M, RuWni A, Cheung CC, Khan F, Itie-Youten A, Wakeham A, Tsao MS, Iovanna JL, Squire J, Jurisica I, Kaplan D, Melino G, Jurisicova A, Mak TW (2008) TAp73 knockout shows genomic instability with infertility and tumor suppressor functions. Genes Dev 22:2677-2691
-
(2008)
Genes Dev
, vol.22
, pp. 2677-2691
-
-
Tomasini, R.1
Tsuchihara, K.2
Wilhelm, M.3
Fujitani, M.4
RuWni, A.5
Cheung, C.C.6
Khan, F.7
Itie-Youten, A.8
Wakeham, A.9
Tsao, M.S.10
Iovanna, J.L.11
Squire, J.12
Jurisica, I.13
Kaplan, D.14
Melino, G.15
Jurisicova, A.16
Mak, T.W.17
-
151
-
-
50849109505
-
Pooling breast cancer datasets has a synergetic eVect on classiWcation performance and improves signature stability
-
van Vliet MH, Reyal F, Horlings HM, van de Vijver MJ, Reinders MJ, Wessels LF (2008) Pooling breast cancer datasets has a synergetic eVect on classiWcation performance and improves signature stability. BMC Genomics 9:375
-
(2008)
BMC Genomics
, vol.9
, pp. 375
-
-
Van Vliet, M.H.1
Reyal, F.2
Horlings, H.M.3
Van De Vijver, M.J.4
Reinders, M.J.5
Wessels, L.F.6
-
152
-
-
27644506613
-
Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression
-
DOI 10.1016/j.ccr.2005.10.001, PII S1535610805003053
-
Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM (2005) Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 8:393-406 (Pubitemid 41579834)
-
(2005)
Cancer Cell
, vol.8
, Issue.5
, pp. 393-406
-
-
Varambally, S.1
Yu, J.2
Laxman, B.3
Rhodes, D.R.4
Mehra, R.5
Tomlins, S.A.6
Shah, R.B.7
Chandran, U.8
Monzon, F.A.9
Becich, M.J.10
Wei, J.T.11
Pienta, K.J.12
Ghosh, D.13
Rubin, M.A.14
Chinnaiyan, A.M.15
-
153
-
-
78149255579
-
The Xowvizmenu and parallel scatterplot matrix: Hybrid multidimensional visualizations for network exploration
-
Viau C, McGuYn MJ, Chiricota Y, Jurisica I (2010) The Xowvizmenu and parallel scatterplot matrix: Hybrid multidimensional visualizations for network exploration. Vis Comput Graph IEEE Trans 16:1100-1108
-
(2010)
Vis Comput Graph IEEE Trans
, vol.16
, pp. 1100-1108
-
-
Viau, C.1
McGuYn, M.J.2
Chiricota, Y.3
Jurisica, I.4
-
154
-
-
78651321625
-
PROMISCUOUS: A database for networkbased drug-repositioning
-
von Eichborn J, Murgueitio MS, Dunkel M, Koerner S, Bourne PE, Preissner R (2011) PROMISCUOUS: A database for networkbased drug-repositioning. Nucleic Acids Res 39:D1060-D1066
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Von Eichborn, J.1
Murgueitio, M.S.2
Dunkel, M.3
Koerner, S.4
Bourne, P.E.5
Preissner, R.6
-
155
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
DOI 10.1038/nature07509, PII NATURE07509
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476 (Pubitemid 352759009)
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
156
-
-
73649135801
-
Gene networks and microRNAs implicated in aggressive prostate cancer
-
Wang L, Tang H, Thayanithy V, Subramanian S, Oberg AL, Cunningham JM, Cerhan JR, Steer CJ, Thibodeau SN (2009) Gene networks and microRNAs implicated in aggressive prostate cancer. Cancer Res 69:9490-9497
-
(2009)
Cancer Res
, vol.69
, pp. 9490-9497
-
-
Wang, L.1
Tang, H.2
Thayanithy, V.3
Subramanian, S.4
Oberg, A.L.5
Cunningham, J.M.6
Cerhan, J.R.7
Steer, C.J.8
Thibodeau, S.N.9
-
157
-
-
27844594381
-
Cross-platform analysis of cancer microarray data improves gene expression based classiWcation of phenotypes
-
Warnat P, Eils R, Brors B (2005) Cross-platform analysis of cancer microarray data improves gene expression based classiWcation of phenotypes. BMC Bioinformatics 6:265
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 265
-
-
Warnat, P.1
Eils, R.2
Brors, B.3
-
158
-
-
79951535612
-
Primary tumor xenografts of human lung adeno and squamous cell carcinoma express distinct proteomic signatures
-
Wei Y, Tong J, Taylor P, Strumpf D, Ignatchenko V, Pham NA, Yanagawa N, Liu G, Jurisica I, Shepherd FA, Tsao MS, Kislinger T, Moran MF (2011) Primary tumor xenografts of human lung adeno and squamous cell carcinoma express distinct proteomic signatures. J Proteome Res 10:161-174
-
(2011)
J Proteome Res
, vol.10
, pp. 161-174
-
-
Wei, Y.1
Tong, J.2
Taylor, P.3
Strumpf, D.4
Ignatchenko, V.5
Pham, N.A.6
Yanagawa, N.7
Liu, G.8
Jurisica, I.9
Shepherd, F.A.10
Tsao, M.S.11
Kislinger, T.12
Moran, M.F.13
-
159
-
-
33746647771
-
Topology and weights in a protein domain interaction network - A novel way to predict protein interactions
-
Wuchty S (2006) Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomics 7:122
-
(2006)
BMC Genomics
, vol.7
, pp. 122
-
-
Wuchty, S.1
-
160
-
-
0033971642
-
DIP: The database of interacting proteins
-
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D (2000) DIP: The database of interacting proteins. Nucleic Acids Res 28:289-291 (Pubitemid 30047782)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
161
-
-
33645319955
-
Predicting interactions in protein networks by completing defective cliques
-
Yu H, Paccanaro A, Trifonov V, Gerstein M (2006) Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7):823-829
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 823-829
-
-
Yu, H.1
Paccanaro, A.2
Trifonov, V.3
Gerstein, M.4
-
162
-
-
0037138406
-
MINT: A Molecular INTeraction database
-
DOI 10.1016/S0014-5793(01)03293-8, PII S0014579301032938
-
Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G (2002) MINT: A Molecular INTeraction database. FEBS Lett 513:135-140 (Pubitemid 34242991)
-
(2002)
FEBS Letters
, vol.513
, Issue.1
, pp. 135-140
-
-
Zanzoni, A.1
Montecchi-Palazzi, L.2
Quondam, M.3
Ausiello, G.4
Helmer-Citterich, M.5
Cesareni, G.6
-
163
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
(article17
-
Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4 (article17)
-
(2005)
Stat Appl Genet Mol Biol
, pp. 4
-
-
Zhang, B.1
Horvath, S.2
-
164
-
-
51749123784
-
Apparently low reproducibility of true diVerential expression discoveries in microarray studies
-
Zhang M, Yao C, Guo Z, Zou J, Zhang L, Xiao H, Wang D, Yang D, Gong X, Zhu J, Li Y, Li X (2008) Apparently low reproducibility of true diVerential expression discoveries in microarray studies. Bioinformatics 24:2057-2063
-
(2008)
Bioinformatics
, vol.24
, pp. 2057-2063
-
-
Zhang, M.1
Yao, C.2
Guo, Z.3
Zou, J.4
Zhang, L.5
Xiao, H.6
Wang, D.7
Yang, D.8
Gong, X.9
Zhu, J.10
Li, Y.11
Li, X.12
-
165
-
-
52049090365
-
Role of KRAS and EGFR as biomarkers of response to erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21
-
Zhu CQ, da Cunha Santos G, Ding K, Sakurada A, Cutz JC, Liu N, Zhang T, Marrano P, Whitehead M, Squire JA, Kamel-Reid S, Seymour L, Shepherd FA, Tsao MS (2008) Role of KRAS and EGFR as biomarkers of response to erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21. J Clin Oncol 26:4268-4275
-
(2008)
J Clin Oncol
, vol.26
, pp. 4268-4275
-
-
Zhu, C.Q.1
Da Cunha Santos, G.2
Ding, K.3
Sakurada, A.4
Cutz, J.C.5
Liu, N.6
Zhang, T.7
Marrano, P.8
Whitehead, M.9
Squire, J.A.10
Kamel-Reid, S.11
Seymour, L.12
Shepherd, F.A.13
Tsao, M.S.14
-
166
-
-
70349388721
-
Understanding prognostic gene expression signatures in lung cancer
-
Zhu CQ, Pintilie M, John T, Strumpf D, Shepherd FA, Der SD, Jurisica I, Tsao M-S (2009) Understanding prognostic gene expression signatures in lung cancer. Clin Lung Cancer 10(5):331-340
-
(2009)
Clin Lung Cancer
, vol.10
, Issue.5
, pp. 331-340
-
-
Zhu, C.Q.1
Pintilie, M.2
John, T.3
Strumpf, D.4
Shepherd, F.A.5
Der, S.D.6
Jurisica, I.7
Tsao, M.-S.8
-
167
-
-
78649680251
-
Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer
-
Zhu CQ, Ding K, Strumpf D, Weir BA, Meyerson M, Pennell N, Thomas RK, Naoki K, Ladd-Acosta C, Liu N, Pintilie M, Der S, Seymour L, Jurisica I, Shepherd FA, Tsao MS (2010a) Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer. J Clin Oncol 28:4417-4424
-
(2010)
J Clin Oncol
, vol.28
, pp. 4417-4424
-
-
Zhu, C.Q.1
Ding, K.2
Strumpf, D.3
Weir, B.A.4
Meyerson, M.5
Pennell, N.6
Thomas, R.K.7
Naoki, K.8
Ladd-Acosta, C.9
Liu, N.10
Pintilie, M.11
Der S Seymour, L.12
Jurisica, I.13
Shepherd, F.A.14
Tsao, M.S.15
-
168
-
-
77958023430
-
Prognostic gene expression signature for squamous cell carcinoma of lung
-
Zhu CQ, Strumpf D, Li CY, Li Q, Liu N, Der S, Shepherd FA, Tsao MS, Jurisica I (2010b) Prognostic gene expression signature for squamous cell carcinoma of lung. Clin Cancer Res 16:5038-5047
-
(2010)
Clin Cancer Res
, vol.16
, pp. 5038-5047
-
-
Zhu, C.Q.1
Strumpf, D.2
Li, C.Y.3
Li, Q.4
Liu, N.5
Der S Shepherd, F.A.6
Tsao, M.S.7
Jurisica, I.8
|