-
1
-
-
51549120104
-
The purple sea urchin genome
-
The Sea Urchin Sequencing Consortium
-
The Sea Urchin Sequencing Consortium (2006) The purple sea urchin genome. Science, 314, 941-952.
-
(2006)
Science
, vol.314
, pp. 941-952
-
-
-
2
-
-
34547624884
-
A missing link in the sea urchin embryo gene regulatory network: HesC and the double-negative specification of micromeres
-
Revilla-i-Domingo,R., Oliveri,P. and Davidson,E.H. (2007) A missing link in the sea urchin embryo gene regulatory network: HesC and the double-negative specification of micromeres. Proc. Natl Acad. Sci. USA, 104, 12383-12388.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 12383-12388
-
-
Revilla-i-Domingo, R.1
Oliveri, P.2
Davidson, E.H.3
-
3
-
-
33751538623
-
Shedding genetic light on Aristotle's lantern
-
Sodergren,E., Shen,Y., Song,X., Zhang,L., Gibbs,R. and Weinstock,G. (2006) Shedding genetic light on Aristotle's lantern. Dev. Biol., 300, 2-8.
-
(2006)
Dev. Biol
, vol.300
, pp. 2-8
-
-
Sodergren, E.1
Shen, Y.2
Song, X.3
Zhang, L.4
Gibbs, R.5
Weinstock, G.6
-
4
-
-
0028967345
-
Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer
-
Springer,M.S., Tusneem,N.A., Davidson,E.H. and Britten,R.J. (1995) Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Mol. Biol. Evol., 12, 219-230.
-
(1995)
Mol. Biol. Evol
, vol.12
, pp. 219-230
-
-
Springer, M.S.1
Tusneem, N.A.2
Davidson, E.H.3
Britten, R.J.4
-
5
-
-
0033048228
-
Evolution of Sea Urchin Retroviral-Like (SURL) elements: Evidence from 40 Echinoid species
-
Gonzalez,P. and Lessios,H.A. (1999) Evolution of Sea Urchin Retroviral-Like (SURL) elements: Evidence from 40 Echinoid species. Mol. Biol. Evol., 16, 938-952.
-
(1999)
Mol. Biol. Evol
, vol.16
, pp. 938-952
-
-
Gonzalez, P.1
Lessios, H.A.2
-
6
-
-
0029654308
-
A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)
-
Littlewood,D.T.J. and Smith,A.B. (1995) A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata). Phil. Trans. R. Soc. Lond. B, 347, 213-234.
-
(1995)
Phil. Trans. R. Soc. Lond. B
, vol.347
, pp. 213-234
-
-
Littlewood, D.T.J.1
Smith, A.B.2
-
8
-
-
12944270583
-
A sea urchin genome project: Sequence scan, virtual map, and additional resources
-
Cameron,R.A., Mahairas,G., Rast,J.P., Martinez,P., Biondi,T.R., Swartzell,S., Wallace,J.C., Poustka,A.J., Livingston,B.T., Wray,G.A. et al. (2000) A sea urchin genome project: Sequence scan, virtual map, and additional resources. Proc. Natl Acad. Sci. USA, 97 9514-9518.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 9514-9518
-
-
Cameron, R.A.1
Mahairas, G.2
Rast, J.P.3
Martinez, P.4
Biondi, T.R.5
Swartzell, S.6
Wallace, J.C.7
Poustka, A.J.8
Livingston, B.T.9
Wray, G.A.10
-
9
-
-
1842717960
-
The atlas genome assembly system
-
Havlak,P., Chen,R., Durbin,K.J., Egan,A., Ren,Y., Song,X-Z., Weinstock,G.M. and Gibbs,R.A. (2004) The atlas genome assembly system. Genome Res., 14, 721-732.
-
(2004)
Genome Res
, vol.14
, pp. 721-732
-
-
Havlak, P.1
Chen, R.2
Durbin, K.J.3
Egan, A.4
Ren, Y.5
Song, X.-Z.6
Weinstock, G.M.7
Gibbs, R.A.8
-
10
-
-
1842684068
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
-
Gibbs,R.A., Weinstock,G.M., Metzker,M.L., Muzny,D.M., Sodergren,E.J., Scherer,S., Scott,G., Steffen,D., Worley,K.C., Burch,P.E. et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428, 493-521.
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
Gibbs, R.A.1
Weinstock, G.M.2
Metzker, M.L.3
Muzny, D.M.4
Sodergren, E.J.5
Scherer, S.6
Scott, G.7
Steffen, D.8
Worley, K.C.9
Burch, P.E.10
-
11
-
-
0034760329
-
A clonearray pooled shotgun strategy for sequencing large genomes
-
Cai,W.W., Chen,R., Gibbs,R.A. and Bradley,A. (2001) A clonearray pooled shotgun strategy for sequencing large genomes. Genome Res., 11 1619-1623.
-
(2001)
Genome Res
, vol.11
, pp. 1619-1623
-
-
Cai, W.W.1
Chen, R.2
Gibbs, R.A.3
Bradley, A.4
-
12
-
-
10744232510
-
Generation, annotation, evolutionary analysis and database integration of 20,000 unique sea urchin EST clusters
-
Poustka,A.J., Groth,D., Hennig,S., Thamm,S., Cameron,R.A., Beck,A., Reinhardt,R., Herwig,R., Panopoulou,G. and Lehrach,H. (2003) Generation, annotation, evolutionary analysis and database integration of 20,000 unique sea urchin EST clusters. Genome Res., 13, 2736-2746.
-
(2003)
Genome Res
, vol.13
, pp. 2736-2746
-
-
Poustka, A.J.1
Groth, D.2
Hennig, S.3
Thamm, S.4
Cameron, R.A.5
Beck, A.6
Reinhardt, R.7
Herwig, R.8
Panopoulou, G.9
Lehrach, H.10
-
13
-
-
58149182285
-
-
Souvorov,A., Tatusova,T. and Lipman,D.J. (2004) Genome annotation with Gnomon - A multi-step combined gene prediction tool. National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/projects/genome/ guide/gnomon.shtml (30 October 2008, date last accessed).
-
Souvorov,A., Tatusova,T. and Lipman,D.J. (2004) Genome annotation with Gnomon - A multi-step combined gene prediction tool. National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/projects/genome/ guide/gnomon.shtml (30 October 2008, date last accessed).
-
-
-
-
14
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
Salamov,A.A. and Solovyev,V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res., 10, 516-522.
-
(2000)
Genome Res
, vol.10
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
15
-
-
0012190262
-
Statistical approaches in eukaryotic gene prediction
-
Balding,D.E.A, ed, John Wiley and Sons, Ltd, Chichester, New York, pp
-
Solovyev,V.V. (2001) Statistical approaches in eukaryotic gene prediction. In Balding,D.E.A. (ed.), Handbook of Statistical Genetics John Wiley and Sons, Ltd, Chichester, New York, pp. 83-127.
-
(2001)
Handbook of Statistical Genetics
, pp. 83-127
-
-
Solovyev, V.V.1
-
16
-
-
34248200124
-
A database of mRNA expression patterns for the sea urchin embryo
-
Wei,Z., Angerer,R.C. and Angerer,L.M. (2006) A database of mRNA expression patterns for the sea urchin embryo. Dev. Biol., 300 476-484.
-
(2006)
Dev. Biol
, vol.300
, pp. 476-484
-
-
Wei, Z.1
Angerer, R.C.2
Angerer, L.M.3
-
17
-
-
2442707676
-
The Ensembl automatic gene annotation system
-
Curwen,V., Eyras,E., Andrews,T.D., Clarke,L., Mongin,E., Searle,S.M.J. and Clamp,M. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
-
(2004)
Genome Res
, vol.14
, pp. 942-950
-
-
Curwen, V.1
Eyras, E.2
Andrews, T.D.3
Clarke, L.4
Mongin, E.5
Searle, S.M.J.6
Clamp, M.7
-
18
-
-
33750504034
-
Community annotation: Procedures, protocols, and supporting tools
-
Elsik,C.G., Worley,K.C., Zhang,L., Milshina,N.V., Jiang,H., Reese,J.T., Childs,K.L., Venkatraman,A., Dickens,C.M., Weinstock,G.M. et al. (2006) Community annotation: Procedures, protocols, and supporting tools. Genome Res., 16, 1329-1333.
-
(2006)
Genome Res
, vol.16
, pp. 1329-1333
-
-
Elsik, C.G.1
Worley, K.C.2
Zhang, L.3
Milshina, N.V.4
Jiang, H.5
Reese, J.T.6
Childs, K.L.7
Venkatraman, A.8
Dickens, C.M.9
Weinstock, G.M.10
-
19
-
-
33751011601
-
The transcriptome of the sea urchin embryo
-
Samanta,M.P., Tongprasit,W., Istrail,S., Cameron,R.A., Tu,Q., Davidson,E.H. and Stolc,V. (2006) The transcriptome of the sea urchin embryo. Science, 314, 960-962.
-
(2006)
Science
, vol.314
, pp. 960-962
-
-
Samanta, M.P.1
Tongprasit, W.2
Istrail, S.3
Cameron, R.A.4
Tu, Q.5
Davidson, E.H.6
Stolc, V.7
-
20
-
-
34547634659
-
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution
-
Howard-Ashby,M., Materna,S.C., Brown,C.T., Tu,Q., Oliveri,P., Cameron,R.A. and Davidson,E.H. (2006) High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Dev. Biol., 300, 27-34.
-
(2006)
Dev. Biol
, vol.300
, pp. 27-34
-
-
Howard-Ashby, M.1
Materna, S.C.2
Brown, C.T.3
Tu, Q.4
Oliveri, P.5
Cameron, R.A.6
Davidson, E.H.7
-
21
-
-
34547844136
-
A Chado case study: An ontology-based modular schema for representing genome-associated biological information
-
Mungall,C.J. and Emmert,D.B. (2007) A Chado case study: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, I337-I346.
-
(2007)
Bioinformatics
, vol.23
-
-
Mungall, C.J.1
Emmert, D.B.2
-
22
-
-
51349115095
-
The future of biocuration
-
Howe,D., Costanzo,M., Fey,P., Gojobori,T., Hannick,L., Hide,W., Hill,D.P., Kania,R., Schaeffer,M., St Pierre,S. et al. (2008) The future of biocuration. Nature, 455, 47-50.
-
(2008)
Nature
, vol.455
, pp. 47-50
-
-
Howe, D.1
Costanzo, M.2
Fey, P.3
Gojobori, T.4
Hannick, L.5
Hide, W.6
Hill, D.P.7
Kania, R.8
Schaeffer, M.9
St Pierre, S.10
-
23
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
24
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
-
(2002)
Genome Res
, vol.12
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.3
Caudy, M.4
Mangone, M.5
Day, A.6
Nickerson, E.7
Stajich, J.E.8
Harris, T.W.9
Arva, A.10
-
25
-
-
0036607698
-
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
-
Davidson,E.H., Rast,J.P., Oliveri,P., Ransick,A., Calestani,C., Yuh,C.-H., Minokawa,T., Amore,G., Hinman,V., Arenas-Mena,C. et al. (2002) A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol., 246, 162-190.
-
(2002)
Dev. Biol
, vol.246
, pp. 162-190
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.-H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
-
26
-
-
0036500609
-
A genomic regulatory network for development
-
Davidson,E.H., Rast,J.P., Oliveri,P., Ransick,A., Calestani,C., Yuh,C.-H., Minokawa,T., Amore,G., Hinman,V., Arenas-Mena,C. et al. (2002) A genomic regulatory network for development. Science, 295, 1669-1678.
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.-H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
-
27
-
-
33947396707
-
Built to run, not fail
-
Oliveri,P. and Davidson,E.H. (2007) Built to run, not fail. Science 315, 1510-1511.
-
(2007)
Science
, vol.315
, pp. 1510-1511
-
-
Oliveri, P.1
Davidson, E.H.2
-
28
-
-
14044254746
-
Textpresso: An ontology-based information retrieval and extraction system for biological literature
-
Epub ahead of print 21 September
-
Müller,H.M., Kenny,E.E. and Sternberg,P.W. (2004) Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biol., 2, e309 [Epub ahead of print 21 September 2004].
-
(2004)
PLoS Biol
, vol.2
-
-
Müller, H.M.1
Kenny, E.E.2
Sternberg, P.W.3
|