-
1
-
-
67149098194
-
Current-generation high-throughputsequencing: Deepening insights intomammalian transcriptomes
-
Blencowe BJ, Ahmad S, Lee LJ. 2009. Current-generation high-throughputsequencing: Deepening insights intomammalian transcriptomes. GenesDev 23: 1379-1386.
-
(2009)
GenesDev
, vol.23
, pp. 1379-1386
-
-
Blencowe, B.J.1
Ahmad, S.2
Lee, L.J.3
-
2
-
-
0042424655
-
Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics
-
DOI 10.1073/pnas.1533293100
-
Bolouri H, Davidson EH. 2003. Transcriptional regulatory cascades indevelopment: Initial rates, not steady state, determine network kinetics.Proc Natl Acad Sci 100: 9371-9376. (Pubitemid 37033935)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.16
, pp. 9371-9376
-
-
Bolouri, H.1
Davidson, E.H.2
-
3
-
-
51849126044
-
Longer first introns are a general property ofeukaryotic gene structure
-
doi: 10.1371/journal.pone.0003093
-
Bradnam KR, Korf I. 2008. Longer first introns are a general property ofeukaryotic gene structure. PLoS ONE 3: e3093. doi: 10.1371/journal.pone. 0003093.
-
(2008)
PLoS ONE
, vol.3
-
-
Bradnam, K.R.1
Korf, I.2
-
4
-
-
58149199570
-
SpBase: The seaurchin genome database and web site
-
Cameron RA, Samanta M, Yuan A, He D, Davidson EH. 2009. SpBase: The seaurchin genome database and web site. Nucleic Acids Res 37: D750-D754.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cameron, R.A.1
Samanta, M.2
Yuan, A.3
He, D.4
Davidson, E.H.5
-
6
-
-
45549089420
-
High-throughputfunctional annotation and data mining with the Blast2GO suite
-
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ,Robles M, Talón M, Dopazo J, Conesa A. 2008. High-throughputfunctional annotation and data mining with the Blast2GO suite. NucleicAcids Res 36: 3420-3435.
-
(2008)
NucleicAcids Res
, vol.36
, pp. 3420-3435
-
-
Götz, S.1
García-Gómez, J.M.2
Terol, J.3
Williams, T.D.4
Nagaraj, S.H.5
Nueda, M.J.6
Robles, M.7
Talón, M.8
Dopazo, J.9
Conesa, A.10
-
7
-
-
79960264362
-
Full-lengthtranscriptome assembly from RNA-Seq data without a referencegenome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, AdiconisX, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Full-lengthtranscriptome assembly from RNA-Seq data without a referencegenome. Nat Biotechnol 29: 644-652.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
-
8
-
-
15244363004
-
SL trans-splicing: Easy come or easy go?
-
DOI 10.1016/j.tig.2005.02.005
-
Hastings KEM. 2005. SL trans-splicing: Easy come or easy go? Trends Genet21: 240-247. (Pubitemid 40387902)
-
(2005)
Trends in Genetics
, vol.21
, Issue.4
, pp. 240-247
-
-
Hastings, K.E.M.1
-
9
-
-
33751549306
-
The immune gene repertoire encoded in the purple sea urchin genome
-
DOI 10.1016/j.ydbio.2006.08.065, PII S0012160606011572, Sea Urchin Genome: Implications and Insights
-
Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP,Buckley KM, Brockton V, Nair SV, Berney K, et al. 2006. The immunegene repertoire encoded in the purple sea urchin genome. Dev Biol 300:349-365. (Pubitemid 44834388)
-
(2006)
Developmental Biology
, vol.300
, Issue.1
, pp. 349-365
-
-
Hibino, T.1
Loza-Coll, M.2
Messier, C.3
Majeske, A.J.4
Cohen, A.H.5
Terwilliger, D.P.6
Buckley, K.M.7
Brockton, V.8
Nair, S.V.9
Berney, K.10
Fugmann, S.D.11
Anderson, M.K.12
Pancer, Z.13
Cameron, R.A.14
Smith, L.C.15
Rast, J.P.16
-
10
-
-
34547634659
-
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution
-
DOI 10.1016/j.ydbio.2006.10.016, PII S0012160606013091, Sea Urchin Genome: Implications and Insights
-
Howard-Ashby ML, Materna SC, Brown CT, Tu Q, Oliveri P, Cameron RA,Davidson EH. 2006. High regulatory gene use in sea urchinembryogenesis: Implications for bilaterian development and evolution.Dev Biol 300: 27-34. (Pubitemid 44827007)
-
(2006)
Developmental Biology
, vol.300
, Issue.1
, 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
-
11
-
-
77949601825
-
CD-HIT Suite: A web server forclustering and comparing biological sequences
-
Huang Y, Niu B, Gao Y, Fu L, Li W. 2010. CD-HIT Suite: A web server forclustering and comparing biological sequences. Bioinformatics 26: 680-682.
-
(2010)
Bioinformatics
, vol.26
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
Gao, Y.3
Fu, L.4
Li, W.5
-
12
-
-
79953064734
-
Evolution of exon-intron structure and alternative splicing
-
doi: 10.1371/journal.pone.0018055
-
Koralewski TE, Krutovsky KV. 2011. Evolution of exon-intron structure and alternative splicing. PLoS ONE 6: e18055. doi: 10.1371/journal.pone.0018055.
-
(2011)
PLoS ONE
, vol.6
-
-
Koralewski, T.E.1
Krutovsky, K.V.2
-
13
-
-
62349130698
-
Ultrafast and memory-efficientalignment of short DNA sequences to the human genome
-
doi: 10.1186/gb-2009-10-3-r25
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficientalignment of short DNA sequences to the human genome.Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
14
-
-
33745685200
-
Expression and function of blimp1/krox, analternatively transcribed regulatory gene of the sea urchinendomesoderm network
-
Livi CB, Davidson EH. 2006. Expression and function of blimp1/krox, analternatively transcribed regulatory gene of the sea urchinendomesoderm network. Dev Biol 293: 513-525.
-
(2006)
Dev Biol
, vol.293
, pp. 513-525
-
-
Livi, C.B.1
Davidson, E.H.2
-
15
-
-
0002237356
-
The organization of eukaryotic genes
-
Maroni G. 1996. The organization of eukaryotic genes. Evol Biol 29: 1-19.
-
(1996)
Evol Biol
, vol.29
, pp. 1-19
-
-
Maroni, G.1
-
16
-
-
77956628617
-
High accuracy, high-resolutionprevalence measurement for the majority of locally expressedregulatory genes in early sea urchin development
-
Materna SC, Nam J, Davidson EH. 2010. High accuracy, high- resolutionprevalence measurement for the majority of locally expressedregulatory genes in early sea urchin development. Gene Expr Patterns10: 177-184.
-
(2010)
Gene Expr Patterns
, vol.10
, pp. 177-184
-
-
Materna, S.C.1
Nam, J.2
Davidson, E.H.3
-
17
-
-
77949273867
-
Highly diversified innatereceptor systems and new forms of animal immunity
-
Messier-Solek C, Buckley KM, Rast JP. 2010. Highly diversified innatereceptor systems and new forms of animal immunity. Semin Immunol22: 39-47.
-
(2010)
Semin Immunol
, vol.22
, pp. 39-47
-
-
Messier-Solek, C.1
Buckley, K.M.2
Rast, J.P.3
-
18
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
DOI 10.1038/nmeth.1226, PII NMETH.1226
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mappingand quantifying mammalian transcriptomes by RNA-Seq. Nat Methods5: 621-628. (Pubitemid 351911867)
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
20
-
-
4344633763
-
SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis
-
DOI 10.1016/j.ydbio.2004.05.033, PII S0012160604004129
-
Otim O, Amore G, Minokawa T, McClay DR, Davidson EH. 2004. SpHnf6,a transcription factor that executes multiple functions in sea urchinembryogenesis. Dev Biol 273: 226-243. (Pubitemid 39140900)
-
(2004)
Developmental Biology
, vol.273
, Issue.2
, pp. 226-243
-
-
Otim, O.1
Amore, G.2
Minokawa, T.3
McClay, D.R.4
Davidson, E.H.5
-
21
-
-
71149103484
-
Modularity and design principles in the seaurchin embryo gene regulatory network
-
Peter IS, Davidson EH. 2009. Modularity and design principles in the seaurchin embryo gene regulatory network. FEBS Lett 583: 3948-3958.
-
(2009)
FEBS Lett
, vol.583
, pp. 3948-3958
-
-
Peter, I.S.1
Davidson, E.H.2
-
22
-
-
79959853681
-
A gene regulatory network controlling theembryonic specification of endoderm
-
Peter IS, Davidson EH. 2011. A gene regulatory network controlling theembryonic specification of endoderm. Nature 474: 635-639.
-
(2011)
Nature
, vol.474
, pp. 635-639
-
-
Peter, I.S.1
Davidson, E.H.2
-
23
-
-
45749086679
-
The amphioxus genome and the evolution of the chordate karyotype
-
DOI 10.1038/nature06967, PII NATURE06967
-
Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T,Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, et al. 2008. Theamphioxus genome and the evolution of the chordate karyotype. Nature453: 1064-1071. (Pubitemid 351888243)
-
(2008)
Nature
, vol.453
, Issue.7198
, pp. 1064-1071
-
-
Putnam, N.H.1
Butts, T.2
Ferrier, D.E.K.3
Furlong, R.F.4
Hellsten, U.5
Kawashima, T.6
Robinson-Rechavi, M.7
Shoguchi, E.8
Terry, A.9
Yu Jr., K.10
Benito-Gutierrez, E.11
Dubchak, I.12
Garcia-Fernandez, J.13
Gibson-Brown, J.J.14
Grigoriev, I.V.15
Horton, A.C.16
De Jong, P.J.17
Jurka, J.18
Kapitonov, V.V.19
Kohara, Y.20
Kuroki, Y.21
Lindquist, E.22
Lucas, S.23
Osoegawa, K.24
Pennacchio, L.A.25
Salamov, A.A.26
Satou, Y.27
Sauka-Spengler, T.28
Schmutz, J.29
Shin-I, T.30
Toyoda, A.31
Bronner-Fraser, M.32
Fujiyama, A.33
Holland, L.Z.34
Holland, P.W.H.35
Satoh, N.36
Rokhsar, D.S.37
more..
-
24
-
-
33750980112
-
Genomic insights into the immune system of the sea urchin
-
DOI 10.1126/science.1134301
-
Rast JP, Smith LC, Loza-Coll M, Hibino T, Litman GW. 2006. Genomicinsights into the immune system of the sea urchin. Science 314: 952-956. (Pubitemid 44749931)
-
(2006)
Science
, vol.314
, Issue.5801
, pp. 952-956
-
-
Rast, J.P.1
Smith, L.C.2
Loza-Coll, M.3
Hibino, T.4
Litman, G.W.5
-
25
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES,Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol29: 24-26.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdóttir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
26
-
-
33750995860
-
The genome of the seaurchin Strongylocentrotus purpuratus
-
Sea Urchin Genome Sequencing Consortium
-
Sea Urchin Genome Sequencing Consortium. 2006. The genome of the seaurchin Strongylocentrotus purpuratus. Science 314: 941-952.
-
(2006)
Science
, vol.314
, pp. 941-952
-
-
-
27
-
-
48049106734
-
The larval stagesof the sea urchin, Strongylocentrotus purpuratus
-
Smith MM, Cruz Smith L, Cameron RA, Urry LA. 2008. The larval stagesof the sea urchin, Strongylocentrotus purpuratus . J Morphol 269:713-733.
-
(2008)
J Morphol
, vol.269
, pp. 713-733
-
-
Smith, M.M.1
Cruz, S.L.2
Cameron, R.A.3
Urry, L.A.4
-
28
-
-
33751538623
-
Shedding genomic light on Aristotle's lantern
-
DOI 10.1016/j.ydbio.2006.10.005, PII S0012160606012954, Sea Urchin Genome: Implications and Insights
-
Sodergren E, Shen Y, Song X, Zhang L, Gibbs RA, Weinstock GM. 2006.Shedding genomic light on Aristotle's lantern. Dev Biol 300: 2-8. (Pubitemid 44834391)
-
(2006)
Developmental Biology
, vol.300
, Issue.1
, pp. 2-8
-
-
Sodergren, E.1
Shen, Y.2
Song, X.3
Zhang, L.4
Gibbs, R.A.5
Weinstock, G.M.6
-
29
-
-
83055192078
-
Differentialexpression in RNA-seq: A matter of depth
-
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differentialexpression in RNA-seq: A matter of depth. Genome Res 21: 2213-2223.
-
(2011)
Genome Res
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
García-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
31
-
-
65449136284
-
TopHat: Discovering splicejunctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splicejunctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
32
-
-
77952123055
-
Transcript assembly andquantification by RNA-Seq reveals unannotated transcripts and isoformswitching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ,Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly andquantification by RNA-Seq reveals unannotated transcripts and isoformswitching during cell differentiation. Nat Biotechnol 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
33
-
-
57749195712
-
RNA-Seq: A revolutionary tool fortranscriptomics
-
Wang Z, Gerstein MB, Snyder M. 2009. RNA-Seq: A revolutionary tool fortranscriptomics. Nat Rev Genet 10: 57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.B.2
Snyder, M.3
-
34
-
-
16644384900
-
Culture of echinoderm larvae throughmetamorphosis
-
Development of sea urchins, ascidians, and otherinvertebrate deuterostomes: Experimental approaches ed. CA Ettensohnet al., Academic Press, Amsterdam
-
Wray GA, Kitazawa C, Miner B. 2004. Culture of echinoderm larvae throughmetamorphosis. In Development of sea urchins, ascidians, and otherinvertebrate deuterostomes: Experimental approaches (ed. CA Ettensohnet al.), Method in Cell Biology, Vol. 74. Academic Press, Amsterdam.
-
(2004)
Method in Cell Biology
, vol.74
-
-
Wray, G.A.1
Kitazawa, C.2
Miner, B.3
-
35
-
-
60549105899
-
Patterns of exon-intron architecture variation of genes in eukaryotic genomes
-
doi: 10.1186/1471-2164-10-47
-
Zhu L, Zhang Y, Zhang W, Yang S, Chen J-Q, Tian D. 2009. Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMCGenomics 10: 47. doi: 10.1186/1471-2164-10-47.
-
(2009)
BMCGenomics
, vol.10
, pp. 47
-
-
Zhu, L.1
Zhang, Y.2
Zhang, W.3
Yang, S.4
Chen, J.-Q.5
Tian, D.6
|