-
1
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Alexa, A., Rahnenfuhrer, J., and Lengauer, T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607.
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
2
-
-
65349085291
-
Global networks of functional coupling in eukaryotes from comprehensive data integration
-
Alexeyenko, A., and Sonnhammer, E. L. 2009. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res. 19: 1107-1116.
-
(2009)
Genome Res
, vol.19
, pp. 1107-1116
-
-
Alexeyenko, A.1
Sonnhammer, E.L.2
-
3
-
-
74049088856
-
Lost in translation: an assessment and perspective for computational microRNA target identification
-
Alexiou, P., Maragkakis, M., Papadopoulos, G. L., Reczko, M., and Hatzigeorgiou, A. G. 2009. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049-3055.
-
(2009)
Bioinformatics
, vol.25
, pp. 3049-3055
-
-
Alexiou, P.1
Maragkakis, M.2
Papadopoulos, G.L.3
Reczko, M.4
Hatzigeorgiou, A.G.5
-
4
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The gene ontology consortium
-
Ashburner, M., et al. 2000. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25: 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
5
-
-
33846064113
-
NCBI GEO: mining tens of millions of expression profiles-database and tools update
-
(Database issue)
-
Barrett, T., et al. 2007. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acid Res. 35 (Database issue): D760-D765.
-
(2007)
Nucleic Acid Res
, vol.35
-
-
Barrett, T.1
-
6
-
-
48249136251
-
Bgee: Integrating and comparing heterogeneous transcriptome data among species
-
Bastian, F., Parmentier, G., Roux, J., Moretti, S., Laudet, V., and Robinson-Rechavi, M. 2008. Bgee: Integrating and comparing heterogeneous transcriptome data among species. Lect. Notes in Comput. Sc. 5109: 124-131.
-
(2008)
Lect. Notes in Comput. Sc.
, vol.5109
, pp. 124-131
-
-
Bastian, F.1
Parmentier, G.2
Roux, J.3
Moretti, S.4
Laudet, V.5
Robinson-Rechavi, M.6
-
7
-
-
51249119826
-
Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence in Drosophila
-
Cruickshank, T., and Wade, M. J. 2008. Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence in Drosophila. Evol. Dev. 10: 583-590.
-
(2008)
Evol. Dev.
, vol.10
, pp. 583-590
-
-
Cruickshank, T.1
Wade, M.J.2
-
8
-
-
21244484614
-
Protein evolution in the context of Drosophila development
-
Davis, J. C., Brandman, O., and Petrov, D. A. 2005. Protein evolution in the context of Drosophila development. J. Mol. Evol. 60: 774-785.
-
(2005)
J. Mol. Evol.
, vol.60
, pp. 774-785
-
-
Davis, J.C.1
Brandman, O.2
Petrov, D.A.3
-
9
-
-
0028605603
-
Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony
-
Duboule, D. 1994. Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony. Development (suppl.): 135-142.
-
(1994)
Development
, Issue.SUPPL.
, pp. 135-142
-
-
Duboule, D.1
-
10
-
-
33750177351
-
Centrality in social networks: conceptual clarification
-
Freeman, L. C. 1978/79. Centrality in social networks: conceptual clarification. Social Networks 1: 215-239.
-
(1978)
Social Networks
, vol.1
, pp. 215-239
-
-
Freeman, L.C.1
-
11
-
-
39749150362
-
Calcium dynamics integrated into signalling pathways that influence vertebrate axial patterning
-
Freisinger, C. M., Schneider, I., Westfall, T. A., and Slusarski, D. C. 2008. Calcium dynamics integrated into signalling pathways that influence vertebrate axial patterning. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363: 1377-1385.
-
(2008)
Philos. Trans. R. Soc. Lond. B Biol. Sci.
, vol.363
, pp. 1377-1385
-
-
Freisinger, C.M.1
Schneider, I.2
Westfall, T.A.3
Slusarski, D.C.4
-
12
-
-
22544432531
-
Noise-robust soft clustering of gene expression time-course data
-
Futschik, M. E., and Carlisle, B. 2005. Noise-robust soft clustering of gene expression time-course data. J. Bioinform. Comput. Biol. 3: 965-988.
-
(2005)
J. Bioinform. Comput. Biol.
, vol.3
, pp. 965-988
-
-
Futschik, M.E.1
Carlisle, B.2
-
13
-
-
34347398567
-
Inference of miRNA targets using evolutionary conservation and pathway analysis
-
Gaidatzis, D., van Nimwegen, E., Hausser, J., and Zavolan, M. 2007. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinform. 8: 69.
-
(2007)
BMC Bioinform
, vol.8
, pp. 69
-
-
Gaidatzis, D.1
van Nimwegen, E.2
Hausser, J.3
Zavolan, M.4
-
14
-
-
0035881381
-
Testing the vulnerability of the phylotypic stage: on modularity and evolutionary conservation
-
Galis, F., and Metz, J. A. 2001. Testing the vulnerability of the phylotypic stage: on modularity and evolutionary conservation. J. Exp. Zool. 291: 195-204.
-
(2001)
J. Exp. Zool.
, vol.291
, pp. 195-204
-
-
Galis, F.1
Metz, J.A.2
-
15
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman, R. C., et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
-
16
-
-
38549150275
-
miRBase: tools for microRNA genomics
-
(Database issue)
-
Griffiths-Jones, S., Saini, H. K., van Dongen, S., and Enright, A. J. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (Database issue): D154-D158.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Griffiths-Jones, S.1
Saini, H.K.2
van Dongen, S.3
Enright, A.J.4
-
17
-
-
17844409075
-
In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law
-
Hazkani-Covo, E., Wool, D., and Graur, D. 2005. In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law. J. Exp. Zool. B Mol. Dev. Evol. 304: 150-158.
-
(2005)
J. Exp. Zool. B Mol. Dev. Evol.
, vol.304
, pp. 150-158
-
-
Hazkani-Covo, E.1
Wool, D.2
Graur, D.3
-
18
-
-
9144248312
-
IntAct: an open source molecular interaction database
-
(Database issue)
-
Hermjakob, H., et al. 2004. IntAct: an open source molecular interaction database. Nucleic Acids Res. 32 (Database issue): D452-D455.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Hermjakob, H.1
-
19
-
-
33846039019
-
Ensembl 2007
-
(Database issue)
-
Hubbard, T. J., et al. 2007. Ensembl 2007. Nucleic Acids Res. 35 (Database issue): D610-D617.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Hubbard, T.J.1
-
20
-
-
33846900737
-
The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information
-
Irie, N., and Sehara-Fujisawa, A. 2007. The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information. BMC Biol. 5: 1.
-
(2007)
BMC Biol
, vol.5
, pp. 1
-
-
Irie, N.1
Sehara-Fujisawa, A.2
-
21
-
-
7244225022
-
Developmental variability during early embryonic development of zebra fish, Danio rerio
-
Irmler, I., Schmidt, K., and Starck, J. M. 2004. Developmental variability during early embryonic development of zebra fish, Danio rerio. J. Exp. Zool. B Mol. Dev. Evol. 302: 446-457.
-
(2004)
J. Exp. Zool. B Mol. Dev. Evol.
, vol.302
, pp. 446-457
-
-
Irmler, I.1
Schmidt, K.2
Starck, J.M.3
-
22
-
-
9144269670
-
EnsMart: a generic system for fast and flexible access to biological data
-
Kasprzyk, A., et al. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 14: 160-169.
-
(2004)
Genome Res
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
-
23
-
-
70349969940
-
Functional compensation by duplicated genes in mouse
-
Liang, H., and Li, W.-H. 2009. Functional compensation by duplicated genes in mouse. Trend. Genet. 25: 441-442.
-
(2009)
Trend. Genet.
, vol.25
, pp. 441-442
-
-
Liang, H.1
Li, W.-H.2
-
24
-
-
33644877439
-
Human protein reference database-2006 update
-
(Database issue)
-
Mishra, G. R., et al. 2006. Human protein reference database-2006 update. Nucleic Acids Res. 34 (Database issue): D411-D414.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Mishra, G.R.1
-
25
-
-
33646182934
-
An integrated view of protein evolution
-
Pal, C., Papp, B., and Lercher, M. J. 2006. An integrated view of protein evolution. Nat. Rev. Genet. 7: 337-348.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
26
-
-
33846039701
-
ArrayExpressFa public database of microarray experiments and gene expression profiles
-
(Database issue)
-
Parkinson, H., et al. 2007. ArrayExpressFa public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35 (Database issue): D747-D750.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Parkinson, H.1
-
27
-
-
35748932852
-
-
R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team. 2007. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2007)
R: A Language and Environment for Statistical Computing
-
-
-
29
-
-
0029618678
-
Heterochrony and the phylotypic period
-
Richardson, M. K. 1995. Heterochrony and the phylotypic period. Dev. Biol. 172: 412-421.
-
(1995)
Dev. Biol.
, vol.172
, pp. 412-421
-
-
Richardson, M.K.1
-
30
-
-
0033166286
-
Vertebrate evolution: the developmental origins of adult variation
-
Richardson, M. K. 1999.Vertebrate evolution: the developmental origins of adult variation. Bioessays 21: 604-613.
-
(1999)
Bioessays
, vol.21
, pp. 604-613
-
-
Richardson, M.K.1
-
31
-
-
58149149757
-
Developmental constraints on vertebrate genome evolution
-
Roux, J., and Robinson-Rechavi, M. 2008. Developmental constraints on vertebrate genome evolution. PLoS Genet 4: e1000311.
-
(2008)
PLoS Genet
, vol.4
-
-
Roux, J.1
Robinson-Rechavi, M.2
-
32
-
-
33845608152
-
The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint
-
Sempere, L. F., Cole, C. N., McPeek, M. A., and Peterson, K. J. 2006. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. B Mol. Dev. Evol. 306: 575-588.
-
(2006)
J. Exp. Zool. B Mol. Dev. Evol.
, vol.306
, pp. 575-588
-
-
Sempere, L.F.1
Cole, C.N.2
McPeek, M.A.3
Peterson, K.J.4
-
33
-
-
15744401970
-
Conserved patterns of cell movements during vertebrate gastrulation
-
Solnica-Krezel, L. 2005. Conserved patterns of cell movements during vertebrate gastrulation. Curr. Biol. 15: R213-R228.
-
(2005)
Curr. Biol.
, vol.15
-
-
Solnica-Krezel, L.1
-
34
-
-
33644876661
-
The zebrafish information network: the zebrafish model organism database
-
(Database issue)
-
Sprague, J., et al. 2006. The zebrafish information network: the zebrafish model organism database. Nucleic Acids Res. 34 (Database issue): D581-D585.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Sprague, J.1
-
35
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
(Database issue)
-
Stark, C., Breitkreutz, B. J., Reguly, T., Boucher, L., Breitkreutz, A., and Tyers, M. 2006. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34 (Database issue): 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
-
36
-
-
34548082532
-
MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways
-
Thatcher, E. J., Flynt, A. S., Li, N., Patton, J. R., and Patton, J. G. 2007. MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Dev. Dyn. 236: 2172-2180.
-
(2007)
Dev. Dyn.
, vol.236
, pp. 2172-2180
-
-
Thatcher, E.J.1
Flynt, A.S.2
Li, N.3
Patton, J.R.4
Patton, J.G.5
-
37
-
-
34447539857
-
2+ signalling and early embryonic patterning during zebrafish development
-
2+ signalling and early embryonic patterning during zebrafish development. Clin. Exp. Pharmacol. Physiol. 34: 897-904.
-
(2007)
Clin. Exp. Pharmacol. Physiol.
, vol.34
, pp. 897-904
-
-
Webb, S.E.1
Miller, A.L.2
-
38
-
-
33644834545
-
Calcium at fertilization and in early development
-
Whitaker, M. 2006. Calcium at fertilization and in early development. Physiol. Rev. 86: 25-88.
-
(2006)
Physiol. Rev.
, vol.86
, pp. 25-88
-
-
Whitaker, M.1
-
39
-
-
22044458072
-
MicroRNA expression in zebrafish embryonic development
-
Wienholds, E., et al. 2005. MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
-
(2005)
Science
, vol.309
, pp. 310-311
-
-
Wienholds, E.1
-
40
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu, Z., Irizarry, R. A., Gentleman, R., Martinez-Murillo, F., and Spencer, F. 2004. A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99: 909-917.
-
(2004)
J. Am. Stat. Assoc.
, vol.99
, pp. 909-917
-
-
Wu, Z.1
Irizarry, R.A.2
Gentleman, R.3
Martinez-Murillo, F.4
Spencer, F.5
|