-
1
-
-
84863643651
-
KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
-
N. Alcaraz H. Kucuk J. Weile A. Wipat J. Baumbach KeyPathwayMiner - detecting case-specific biological pathways by using expression data Internet Math. 2011 7 4 299 313
-
(2011)
Internet Math.
, vol.7
, Issue.4
, pp. 299-313
-
-
Alcaraz, N.1
Kucuk, H.2
Weile, J.3
Wipat, A.4
Baumbach, J.5
-
2
-
-
79959846617
-
PSICQUIC and PSISCORE: Accessing and scoring molecular interactions
-
B. Aranda H. Blankenburg S. Kerrien F. S. L. Brinkman A. Ceol E. Chautard J. M. Dana J. De Las Rivas M. Dumousseau E. Galeota A. Gaulton J. Goll R. E. W. Hancock R. Isserlin R. C. Jimenez J. Kerssemakers J. Khadake D. J. Lynn M. Michaut G. O'Kelly K. Ono S. Orchard C. Prieto S. Razick O. Rigina L. Salwinski M. Simonovic S. Velankar A. Winter G. Wu G. D. Bader G. Cesareni I. M. Donaldson D. Eisenberg G. J. Kleywegt J. Overington S. Ricard-Blum M. Tyers M. Albrecht H. Hermjakob PSICQUIC and PSISCORE: accessing and scoring molecular interactions Nat. Methods 2011 8 7 528 529
-
(2011)
Nat. Methods
, vol.8
, Issue.7
, pp. 528-529
-
-
Aranda, B.1
Blankenburg, H.2
Kerrien, S.3
Brinkman, F.S.L.4
Ceol, A.5
Chautard, E.6
Dana, J.M.7
De Las Rivas, J.8
Dumousseau, M.9
Galeota, E.10
Gaulton, A.11
Goll, J.12
Hancock, R.E.W.13
Isserlin, R.14
Jimenez, R.C.15
Kerssemakers, J.16
Khadake, J.17
Lynn, D.J.18
Michaut, M.19
O'Kelly, G.20
Ono, K.21
Orchard, S.22
Prieto, C.23
Razick, S.24
Rigina, O.25
Salwinski, L.26
Simonovic, M.27
Velankar, S.28
Winter, A.29
Wu, G.30
Bader, G.D.31
Cesareni, G.32
Donaldson, I.M.33
Eisenberg, D.34
Kleywegt, G.J.35
Overington, J.36
Ricard-Blum, S.37
Tyers, M.38
Albrecht, M.39
Hermjakob, H.40
more..
-
4
-
-
33745242506
-
Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
-
S. Balaji L. M. Iyer L. Aravind M. Madan Babu Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks J. Mol. Biol. 2006 360 1 204 212
-
(2006)
J. Mol. Biol.
, vol.360
, Issue.1
, pp. 204-212
-
-
Balaji, S.1
Iyer, L.M.2
Aravind, L.3
Madan Babu, M.4
-
5
-
-
78650497790
-
On the power and limits of evolutionary conservation - Unraveling bacterial gene regulatory networks
-
J. Baumbach On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks Nucleic Acids Res. 2010 38 22 7877 7884
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.22
, pp. 7877-7884
-
-
Baumbach, J.1
-
6
-
-
43249091569
-
Linking cytoscape and the corynebacterial reference database coryneregnet
-
J. Baumbach L. Apeltsin Linking cytoscape and the corynebacterial reference database coryneregnet BMC Genomics 2008 9 184
-
(2008)
BMC Genomics
, vol.9
, pp. 184
-
-
Baumbach, J.1
Apeltsin, L.2
-
7
-
-
60749118619
-
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
-
J. Baumbach A. Tauch S. Rahmann Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks Briefings Bioinf. 2009 10 1 75 83
-
(2009)
Briefings Bioinf.
, vol.10
, Issue.1
, pp. 75-83
-
-
Baumbach, J.1
Tauch, A.2
Rahmann, S.3
-
8
-
-
13244253770
-
Graph-based iterative group analysis enhances microarray interpretation
-
R. Breitling A. Amtmann P. Herzyk Graph-based iterative group analysis enhances microarray interpretation BMC Bioinf. 2004 5 1 100
-
(2004)
BMC Bioinf.
, vol.5
, Issue.1
, pp. 100
-
-
Breitling, R.1
Amtmann, A.2
Herzyk, P.3
-
9
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
M. S. Cline M. Smoot E. Cerami A. Kuchinsky N. Landys C. Workman R. Christmas I. Avila-Campilo M. Creech B. Gross K. Hanspers R. Isserlin R. Kelley S. Killcoyne S. Lotia S. Maere J. Morris K. Ono V. Pavlovic A. R. Pico A. Vailaya P.-L. Wang A. Adler B. R. Conklin L. Hood M. Kuiper C. Sander I. Schmulevich B. Schwikowski G. J. Warner T. Ideker G. D. Bader Integration of biological networks and gene expression data using Cytoscape Nat. Protoc. 2007 2 10 2366 2382
-
(2007)
Nat. Protoc.
, vol.2
, Issue.10
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
Workman, C.6
Christmas, R.7
Avila-Campilo, I.8
Creech, M.9
Gross, B.10
Hanspers, K.11
Isserlin, R.12
Kelley, R.13
Killcoyne, S.14
Lotia, S.15
Maere, S.16
Morris, J.17
Ono, K.18
Pavlovic, V.19
Pico, A.R.20
Vailaya, A.21
Wang, P.-L.22
Adler, A.23
Conklin, B.R.24
Hood, L.25
Kuiper, M.26
Sander, C.27
Schmulevich, I.28
Schwikowski, B.29
Warner, G.J.30
Ideker, T.31
Bader, G.D.32
more..
-
10
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
R. Edgar M. Domrachev A. E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 2002 30 1 207 210
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.1
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
11
-
-
10744229448
-
DNA damage induced by polyglutamine-expanded proteins
-
P. Giuliano T. De Cristofaro A. Affaitati G. M. Pizzulo A. Feliciello C. Criscuolo G. De Michele A. Filla E. V. Avvedimento S. Varrone DNA damage induced by polyglutamine-expanded proteins Hum. Mol. Genet. 2003 12 18 2301 2309
-
(2003)
Hum. Mol. Genet.
, vol.12
, Issue.18
, pp. 2301-2309
-
-
Giuliano, P.1
De Cristofaro, T.2
Affaitati, A.3
Pizzulo, G.M.4
Feliciello, A.5
Criscuolo, C.6
De Michele, G.7
Filla, A.8
Avvedimento, E.V.9
Varrone, S.10
-
12
-
-
78149486261
-
HiNO: An approach for inferring hierarchical organization from regulatory networks
-
M. L. Hartsperger R. Strache V. Stümpflen HiNO: an approach for inferring hierarchical organization from regulatory networks PLoS One 2010 5 11 e13698
-
(2010)
PLoS One
, vol.5
, Issue.11
, pp. 13698
-
-
Hartsperger, M.L.1
Strache, R.2
Stümpflen, V.3
-
13
-
-
84856549042
-
Genome-scale analysis of aberrant DNA methylation in colorectal cancer
-
T. Hinoue D. J. Weisenberger C. P. E. Lange H. Shen H.-M. Byun D. Van Den Berg S. Malik F. Pan H. Noushmehr C. M. van Dijk R. A. E. M. Tollenaar P. W. Laird Genome-scale analysis of aberrant DNA methylation in colorectal cancer Genome Res. 2011 22 271 282
-
(2011)
Genome Res.
, vol.22
, pp. 271-282
-
-
Hinoue, T.1
Weisenberger, D.J.2
Lange, C.P.E.3
Shen, H.4
Byun, H.-M.5
Van Den Berg, D.6
Malik, S.7
Pan, F.8
Noushmehr, H.9
Van Dijk, C.M.10
Tollenaar, R.A.E.M.11
Laird, P.W.12
-
14
-
-
33644783812
-
Regional and cellular gene expression changes in human Huntington's disease brain
-
A. Hodges A. D. Strand A. K. Aragaki A. Kuhn T. Sengstag G. Hughes L. A. Elliston C. Hartog D. R. Goldstein D. Thu Z. R. Hollingsworth F. Collin B. Synek P. A. Holmans A. B. Young N. S. Wexler M. Delorenzi C. Kooperberg S. J. Augood R. L. Faull J. M. Olson L. Jones R. Luthi-Carter Regional and cellular gene expression changes in human Huntington's disease brain Hum. Mol. Genet. 2006 15 6 965 977
-
(2006)
Hum. Mol. Genet.
, vol.15
, Issue.6
, pp. 965-977
-
-
Hodges, A.1
Strand, A.D.2
Aragaki, A.K.3
Kuhn, A.4
Sengstag, T.5
Hughes, G.6
Elliston, L.A.7
Hartog, C.8
Goldstein, D.R.9
Thu, D.10
Hollingsworth, Z.R.11
Collin, F.12
Synek, B.13
Holmans, P.A.14
Young, A.B.15
Wexler, N.S.16
Delorenzi, M.17
Kooperberg, C.18
Augood, S.J.19
Faull, R.L.20
Olson, J.M.21
Jones, L.22
Luthi-Carter, R.23
more..
-
15
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
T. Ideker O. Ozier B. Schwikowski A. F. Siegel Discovering regulatory and signalling circuits in molecular interaction networks Bioinformatics 2002 18 Suppl 1 S233 S240
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
16
-
-
69049104258
-
From Corynebacterium glutamicum to Mycobacterium tuberculosis - Towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet
-
J. Krawczyk T. A. Kohl A. Goesmann J. Kalinowski J. Baumbach From Corynebacterium glutamicum to Mycobacterium tuberculosis - towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet Nucleic Acids Res. 2009 37 14 e97
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.14
, pp. 97
-
-
Krawczyk, J.1
Kohl, T.A.2
Goesmann, A.3
Kalinowski, J.4
Baumbach, J.5
-
17
-
-
79961207218
-
RhizoRegNet - A database of rhizobial transcription factors and regulatory networks
-
E. Krol J. Blom J. Winnebald A. Berhörster M. J. Barnett A. Goesmann J. Baumbach A. Becker RhizoRegNet - a database of rhizobial transcription factors and regulatory networks J. Biotechnol. 2011 155 1 127 134
-
(2011)
J. Biotechnol.
, vol.155
, Issue.1
, pp. 127-134
-
-
Krol, E.1
Blom, J.2
Winnebald, J.3
Berhörster, A.4
Barnett, M.J.5
Goesmann, A.6
Baumbach, J.7
Becker, A.8
-
18
-
-
60149110378
-
Analysis of different MMAS ACO algorithms on unimodal functions and plateaus
-
F. Neumann D. Sudholt C. Witt Analysis of different MMAS ACO algorithms on unimodal functions and plateaus Swarm Intell. 2009 3 1 35 68
-
(2009)
Swarm Intell.
, vol.3
, Issue.1
, pp. 35-68
-
-
Neumann, F.1
Sudholt, D.2
Witt, C.3
-
19
-
-
84862195656
-
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
-
J. Pauling R. Röttger A. Tauch V. Azevedo J. Baumbach CoryneRegNet 6.0 - updated database content, new analysis methods and novel features focusing on community demands Nucleic Acids Res. 2012 40 D1 D610 D614
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.D1
-
-
Pauling, J.1
Röttger, R.2
Tauch, A.3
Azevedo, V.4
Baumbach, J.5
-
20
-
-
75549085083
-
Human protein reference database and human proteinpedia as discovery tools for systems biology
-
T. S. Keshava Prasad K. Kandasamy A. Pandey Human protein reference database and human proteinpedia as discovery tools for systems biology Methods Mol. Biol. 2009 577 67-79
-
(2009)
Methods Mol. Biol.
, vol.577
, pp. 67-79
-
-
Keshava Prasad, T.S.1
Kandasamy, K.2
Pandey, A.3
-
21
-
-
78651310799
-
Database resources of the national center for biotechnology information
-
E. W. Sayers T. Barrett D. A. Benson E. Bolton S. H. Bryant K. Canese V. Chetvernin D. M. Church M. DiCuccio S. Federhen M. Feolo I. M. Fingerman L. Y. Geer W. Helmberg Y. Kapustin D. Landsman D. J. Lipman Z. Lu T. L. Madden T. Madej D. R. Maglott A. Marchler-Bauer V. Miller I. Mizrachi J. Ostell A. Panchenko L. Phan K. D. Pruitt G. D. Schuler E. Sequeira S. T. Sherry M. Shumway K. Sirotkin D. Slotta A. Souvorov G. Starchenko T. A. Tatusova L. Wagner Y. Wang W. John Wilbur E. Yaschenko J. Ye Database resources of the national center for biotechnology information Nucleic Acids Res. 2011 39 Database issue D38 D51
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.DATABASE ISSUE
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
Canese, K.6
Chetvernin, V.7
Church, D.M.8
Dicuccio, M.9
Federhen, S.10
Feolo, M.11
Fingerman, I.M.12
Geer, L.Y.13
Helmberg, W.14
Kapustin, Y.15
Landsman, D.16
Lipman, D.J.17
Lu, Z.18
Madden, T.L.19
Madej, T.20
Maglott, D.R.21
Marchler-Bauer, A.22
Miller, V.23
Mizrachi, I.24
Ostell, J.25
Panchenko, A.26
Phan, L.27
Pruitt, K.D.28
Schuler, G.D.29
Sequeira, E.30
Sherry, S.T.31
Shumway, M.32
Sirotkin, K.33
Slotta, D.34
Souvorov, A.35
Starchenko, G.36
Tatusova, T.A.37
Wagner, L.38
Wang, Y.39
John Wilbur, W.40
Yaschenko, E.41
Ye, J.42
more..
-
22
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
P. Shannon A. Markiel O. Ozier N. S. Baliga J. T. Wang D. Ramage N. Amin B. Schwikowski T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 2003 13 11 2498 2504
-
(2003)
Genome Res.
, 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
-
24
-
-
47249120912
-
Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles
-
I. Ulitsky R. Karp R. Shamir Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles Proc. RECOMB, Res. Comput. Mol. Biol. 2008 4955 347 359
-
(2008)
Proc. RECOMB, Res. Comput. Mol. Biol.
, vol.4955
, pp. 347-359
-
-
Ulitsky, I.1
Karp, R.2
Shamir, R.3
-
25
-
-
77952983494
-
Partitioning biological data with transitivity clustering
-
T. Wittkop D. Emig S. Lange S. Rahmann M. Albrecht J. H. Morris S. Böcker J. Stoye J. Baumbach Partitioning biological data with transitivity clustering Nat. Methods 2010 7 6 419 420
-
(2010)
Nat. Methods
, vol.7
, Issue.6
, pp. 419-420
-
-
Wittkop, T.1
Emig, D.2
Lange, S.3
Rahmann, S.4
Albrecht, M.5
Morris, J.H.6
Böcker, S.7
Stoye, J.8
Baumbach, J.9
-
26
-
-
84863682471
-
Extension and robustness of transitivity clustering for protein-protein interaction network analysis
-
T. Wittkop S. Rahmann R. Röttger S. Böcker J. Baumbach Extension and robustness of transitivity clustering for protein-protein interaction network analysis Internet Math. 2011 7 255 273
-
(2011)
Internet Math.
, vol.7
, pp. 255-273
-
-
Wittkop, T.1
Rahmann, S.2
Röttger, R.3
Böcker, S.4
Baumbach, J.5
-
27
-
-
70349853066
-
Runtime analysis of an ant colony optimization algorithm for TSP instances
-
Y. Zhou Runtime analysis of an ant colony optimization algorithm for TSP instances IEEE Trans. Evol. Comput. 2009 13 5 1083 1092
-
(2009)
IEEE Trans. Evol. Comput.
, vol.13
, Issue.5
, pp. 1083-1092
-
-
Zhou, Y.1
|