-
1
-
-
23744454242
-
A cluster algorithm for graphs
-
Technical Report INS-R0010
-
Van Dongen,S. (2000) A cluster algorithm for graphs. Technical Report INS-R0010.
-
(2000)
-
-
Van Dongen, S.1
-
2
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright,A.J., Van Dongen,S. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
3
-
-
0347432399
-
PlantGDB, plant genome database and analysis tools
-
Dong,Q., Schlueter,S.D. and Brendel,V. (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res., 32, D354-D359.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Dong, Q.1
Schlueter, S.D.2
Brendel, V.3
-
4
-
-
13444293288
-
openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections
-
Rudd,S. (2005) openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res. 33, D622-D627.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Rudd, S.1
-
5
-
-
33344478092
-
Phytome: A platform for plant comparative genomics
-
Hartmann,S., Lu,D., Phillips,J. and Vision,TJ. (2006) Phytome: A platform for plant comparative genomics. Nucleic Acids Res., 34 D724-D730.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Hartmann, S.1
Lu, D.2
Phillips, J.3
Vision, T.J.4
-
6
-
-
33846059234
-
The TIGR Plant Transcript Assemblies database
-
Childs,K.L., Hamilton,J.P., Zhu,W., Ly,E., Cheung,F., Wu,H., Rabinowicz,P.D., Town,C.D., BuelI,C.R. et al. (2007) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res., 35 D846-D851.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Childs, K.L.1
Hamilton, J.P.2
Zhu, W.3
Ly, E.4
Cheung, F.5
Wu, H.6
Rabinowicz, P.D.7
Town, C.D.8
BuelI, C.R.9
-
7
-
-
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
-
8
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S. 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
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
-
9
-
-
0036087630
-
CDD: A database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer,A., Panchenko,A.R., Shoemaker,B.A., Thicssen,P.A., Geer,L.Y. and Bryant,S.H. (2002) CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 281-283
-
-
Marchler-Bauer, A.1
Panchenko, A.R.2
Shoemaker, B.A.3
Thicssen, P.A.4
Geer, L.Y.5
Bryant, S.H.6
-
10
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
11
-
-
11144358140
-
PRAP - computation of Bremer support for large data sets
-
Müller,K.F. (2004) PRAP - computation of Bremer support for large data sets. Mol. Phylogenet. Evol., 31, 780-782.
-
(2004)
Mol. Phylogenet. Evol
, vol.31
, pp. 780-782
-
-
Müller, K.F.1
-
12
-
-
38549170917
-
-
Swofford,D.L, 2002) PAUP*. Phylogenetic Analysis Using Parsimony *and Other Methods, Version 4
-
Swofford,D.L. (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.
-
-
-
-
13
-
-
0033504552
-
The Parsimony Ratchet, a new method for rapid parsimony analysis
-
Nixon,K.C. (1999) The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407-414.
-
(1999)
Cladistics
, vol.15
, pp. 407-414
-
-
Nixon, K.C.1
-
15
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood based inference of large phylogenetic trees
-
Stamatakis,A., Ludwig,T. and Meier,H. (2005) RAxML-III: A fast program for maximum likelihood based inference of large phylogenetic trees. Bioinformatics, 21, 456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
16
-
-
9644287776
-
TreeGraph: Automated drawing of complex tree figures using an extensible tree description format
-
Müller,J. and Müller,K. (2004) TreeGraph: Automated drawing of complex tree figures using an extensible tree description format. Mol. Ecol. Notes, 4, 786-788.
-
(2004)
Mol. Ecol. Notes
, vol.4
, pp. 786-788
-
-
Müller, J.1
Müller, K.2
-
17
-
-
30744464824
-
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
-
Duarte,J.M., Cui,L.Y., Wall,P.K., Zhang,Q., Zhang,X.H., Leebens-Mack,J., Ma,H, Altman,N. and dePamphilis,C.W. (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 23, 469-478.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 469-478
-
-
Duarte, J.M.1
Cui, L.Y.2
Wall, P.K.3
Zhang, Q.4
Zhang, X.H.5
Leebens-Mack, J.6
Ma, H.7
Altman, N.8
dePamphilis, C.W.9
-
18
-
-
13444312020
-
BarleyBase - an expression profiling database for plant genomics
-
Shen,L., Gong,J., Caldo,R.A., Nettleton,D., Cook,D., Wise,R.P. and Dickerson,J.A. (2005) BarleyBase - an expression profiling database for plant genomics. Nucleic Acids Res., 33, D614-D618.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Shen, L.1
Gong, J.2
Caldo, R.A.3
Nettleton, D.4
Cook, D.5
Wise, R.P.6
Dickerson, J.A.7
-
19
-
-
0347968038
-
NASCArrays: A repository for microarray data generated by NASC's transcriptomics service
-
Craigon,D.J., Jamcs,N., Okycre,J., Higgins,J., Jotham,J. and May,S. (2004) NASCArrays: A repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res., 32, D575-D577.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Craigon, D.J.1
Jamcs, N.2
Okycre, J.3
Higgins, J.4
Jotham, J.5
May, S.6
-
20
-
-
1842426839
-
Towards a comprehensive integration of morphological and genetic studies of floral development
-
Buzgo,M., Soltis,D.E., Soltis,P.S. and Ma,H. (2004) Towards a comprehensive integration of morphological and genetic studies of floral development. Trends Plant Sci., 9, 164-173.
-
(2004)
Trends Plant Sci
, vol.9
, pp. 164-173
-
-
Buzgo, M.1
Soltis, D.E.2
Soltis, P.S.3
Ma, H.4
-
21
-
-
34247192074
-
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
-
Ilic,K., Kcllogg, E.A., Jaiswal,P., Zapata,F., Stevens, P.F., Vincent,L.P., Avraham,S., Reiser,L., Pujar,A. et al. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol., 143, 587-599.
-
(2007)
Plant Physiol
, vol.143
, pp. 587-599
-
-
Ilic, K.1
Kcllogg, E.A.2
Jaiswal, P.3
Zapata, F.4
Stevens, P.F.5
Vincent, L.P.6
Avraham, S.7
Reiser, L.8
Pujar, A.9
-
22
-
-
33750079855
-
Whole-plant growth stage ontology for angiosperms and its application in plant biology
-
Pujar,A, Jaiswal,P., Kellogg,E.A., Ilic,K., Vincent,L., Avraham,S., Stevens,P., Zapata,F., Reiser, L. et al. (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol., 142, 414-428.
-
(2006)
Plant Physiol
, vol.142
, pp. 414-428
-
-
Pujar, A.1
Jaiswal, P.2
Kellogg, E.A.3
Ilic, K.4
Vincent, L.5
Avraham, S.6
Stevens, P.7
Zapata, F.8
Reiser, L.9
-
23
-
-
33748760611
-
The genom of black cottonwood, Populus trichocarpa (Torr. & Gray)
-
Tuskan,G.A., Difazio,S., Jansson,S., Bohlmann,J., Grigoriev,I., Hellsten,U., Putnam,N., Ralph,S., Rombauts,S. et al. (2006) The genom of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596-1604.
-
(2006)
Science
, vol.313
, pp. 1596-1604
-
-
Tuskan, G.A.1
Difazio, S.2
Jansson, S.3
Bohlmann, J.4
Grigoriev, I.5
Hellsten, U.6
Putnam, N.7
Ralph, S.8
Rombauts, S.9
-
24
-
-
0036156680
-
Missing links: The genetic architecture of flowers [correction of flower] and floral diversification
-
Soltis,D.E., Soltis,P.S., Albert,V.A., Oppenheimer,D.G., dePamphilis,C.W., Ma,H., Froldich,M.W. and Theisaen,G. (2002) Missing links: The genetic architecture of flowers [correction of flower] and floral diversification. Trends Plant Sci., 7, 22-31dicussion 31-24.
-
(2002)
Trends Plant Sci
, vol.7
-
-
Soltis, D.E.1
Soltis, P.S.2
Albert, V.A.3
Oppenheimer, D.G.4
dePamphilis, C.W.5
Ma, H.6
Froldich, M.W.7
Theisaen, G.8
-
25
-
-
18844427708
-
Floral gene resources from basal angiosperms for comparative genomics research
-
Albert,V.A., Soltis,D.E., Carlson,J.E., Farmerie,W.G., Wall,P.K., Ilut,D.C., Solow,T.M., Mueller,L.A., Landherr,L.L. et al. (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol., 5, 5.
-
(2005)
BMC Plant Biol
, vol.5
, pp. 5
-
-
Albert, V.A.1
Soltis, D.E.2
Carlson, J.E.3
Farmerie, W.G.4
Wall, P.K.5
Ilut, D.C.6
Solow, T.M.7
Mueller, L.A.8
Landherr, L.L.9
-
26
-
-
34547505064
-
The floral genome: An evolutionary history of gene duplication and shifting patterns of gene expression
-
Soltis,D.E., Ma,H., Frohlich,M.W., Soltis,P.S., Albert,V.A., Oppenheimer,D.G., Altman,N.S., Depamphilis,C. and Leebens-Mack,J. (2007) The floral genome: An evolutionary history of gene duplication and shifting patterns of gene expression. Trends Plant Sci., 12, 358-367.
-
(2007)
Trends Plant Sci
, vol.12
, pp. 358-367
-
-
Soltis, D.E.1
Ma, H.2
Frohlich, M.W.3
Soltis, P.S.4
Albert, V.A.5
Oppenheimer, D.G.6
Altman, N.S.7
Depamphilis, C.8
Leebens-Mack, J.9
-
27
-
-
33749033318
-
EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot
-
Carlson,J.E., Leebens-Mack,J.H., Wall,P.K., Zahn,L.M., Mueller,L.A., Landherr,L.L., Hu,Y., Ilut,D.C., Arrington,J.M. et al. (2006) EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot. Plant Mol. Biol., 62, 351-369.
-
(2006)
Plant Mol. Biol
, vol.62
, pp. 351-369
-
-
Carlson, J.E.1
Leebens-Mack, J.H.2
Wall, P.K.3
Zahn, L.M.4
Mueller, L.A.5
Landherr, L.L.6
Hu, Y.7
Ilut, D.C.8
Arrington, J.M.9
-
28
-
-
28944435369
-
Phylogeny and domain evolution in the APETALA2-like gene family
-
Kim,S., Soltis,P.S., Wall,K. and Soltis,D.E. (2006) Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol., 23, 107-120.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 107-120
-
-
Kim, S.1
Soltis, P.S.2
Wall, K.3
Soltis, D.E.4
-
29
-
-
46749093968
-
Utility of Amborella trichopoda and Nuphar advena ESTs for phylogeny and comparative sequence analysis
-
in press
-
Duarte,J.M., Wall,P.K., Zahn,L.M., Leebeens-Mack,J.H. and dePamphilis,C.W. Utility of Amborella trichopoda and Nuphar advena ESTs for phylogeny and comparative sequence analysis. Taxon (in press).
-
Taxon
-
-
Duarte, J.M.1
Wall, P.K.2
Zahn, L.M.3
Leebeens-Mack, J.H.4
dePamphilis, C.W.5
-
30
-
-
38549116579
-
-
Elsevier Limited, London
-
Leebens-Mack,J.H., Wall,K., Zheng,Z., Oppenheimer,D. and dePampbilis,C.W. (2006) Developmental Genetics of the Flower. Elsevier Limited, London.
-
(2006)
Developmental Genetics of the Flower
-
-
Leebens-Mack, J.H.1
Wall, K.2
Zheng, Z.3
Oppenheimer, D.4
dePampbilis, C.W.5
-
31
-
-
33744822985
-
Widespread genome duplications throughout the history of flowering plants
-
Cui,L., Wall,P.K., Leebens-Mack,J.H., Lindsay,B.G., Soltis,D.E., Doyle,J.J., Soltis,P.S., Carlson,J.E., Arumuganathan,K. et al. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res., 16, 738-749.
-
(2006)
Genome Res
, vol.16
, pp. 738-749
-
-
Cui, L.1
Wall, P.K.2
Leebens-Mack, J.H.3
Lindsay, B.G.4
Soltis, D.E.5
Doyle, J.J.6
Soltis, P.S.7
Carlson, J.E.8
Arumuganathan, K.9
-
32
-
-
32944468574
-
Genome histories clarify evolution of the expansin superfamily: New insights from the poplar genome and pine ESTs
-
Sampedro,J., Carey,R.E. and Cosgrove,D.J. (2006) Genome histories clarify evolution of the expansin superfamily: New insights from the poplar genome and pine ESTs. J. Plant Res., 119, 11-21.
-
(2006)
J. Plant Res
, vol.119
, pp. 11-21
-
-
Sampedro, J.1
Carey, R.E.2
Cosgrove, D.J.3
-
33
-
-
0345255239
-
Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny
-
Martinez-Castilla,L.P. and Alvarez-Buylla,E.R. (2003) Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny. Proc. Natl Acad. Sci. USA, 100, 13407-13412.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13407-13412
-
-
Martinez-Castilla, L.P.1
Alvarez-Buylla, E.R.2
|