-
1
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative.
-
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000;408:796-815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
2
-
-
85029465873
-
-
http://open-bio.org/.
-
-
-
-
3
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
J.E. Stajich, D. Block, K. Boulez, S.E. Brenner, S.A. Chervitz, and C. Dagdigian The Bioperl toolkit: Perl modules for the life sciences Genome Res 12 2002 1611 1618
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
-
4
-
-
9244247410
-
The BioMOBY project explores open-source, simple, extensible protocols for enabling biological database interoperability
-
M.D. Wilkinson, D. Gessler, A. Farmer, and L. Stein The BioMOBY project explores open-source, simple, extensible protocols for enabling biological database interoperability Proc Virt Conf Genom Bioinform 3 2003 16 26
-
(2003)
Proc Virt Conf Genom Bioinform
, vol.3
, pp. 16-26
-
-
Wilkinson, M.D.1
Gessler, D.2
Farmer, A.3
Stein, L.4
-
5
-
-
85029465571
-
-
http://www.eurogrid.org/wp1.html.
-
-
-
-
6
-
-
85029464071
-
-
http://www.ncbiogrid.org/.
-
-
-
-
8
-
-
85029465118
-
-
http://www.ncbi.nih.gov/genomes/PLANTS/PlantList.html.
-
-
-
-
9
-
-
0037252739
-
GénoPlante-Info (GPI): A collection of databases and bioinformatics reassures for plant genomics
-
D. Samson, F. Legeai, E. Karesenty, S. Reboux, J.B. Veyrieras, and J. Just GénoPlante-Info (GPI): a collection of databases and bioinformatics reassures for plant genomics Nucleic Acids Res 31 2003 179 182
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 179-182
-
-
Samson, D.1
Legeai, F.2
Karesenty, E.3
Reboux, S.4
Veyrieras, J.B.5
Just, J.6
-
10
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
B.J. Haas, A.L. Delcher, S.M. Mount, J.R. Wortman, R.K. Smith, and L.I. Hannick Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res 31 19 2003 5654 5666
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.19
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith, R.K.5
Hannick, L.I.6
-
11
-
-
0038797803
-
Annotation of the Arabidopsis genome
-
J.R. Wortman, B.J. Haas, L.I. Hannick, R.K. Smith, R. Maiti, and C.M. Ronning Annotation of the Arabidopsis genome Plant Physiol 132 2 2003 461 468
-
(2003)
Plant Physiol
, vol.132
, Issue.2
, pp. 461-468
-
-
Wortman, J.R.1
Haas, B.J.2
Hannick, L.I.3
Smith, R.K.4
Maiti, R.5
Ronning, C.M.6
-
12
-
-
0036084355
-
MIPS Arabidopsis thaliana Database (MAtDB): An integrated biological knowledge resource based on the first complete plant genome
-
H. Schoof, P. Zaccaria, H. Gundlach, K. Lemcke, S. Rudd, and G. Kolesov MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome Nucleic Acids Res 30 2002 91 93
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 91-93
-
-
Schoof, H.1
Zaccaria, P.2
Gundlach, H.3
Lemcke, K.4
Rudd, S.5
Kolesov, G.6
-
13
-
-
85029466127
-
-
The CATMA Consortium
-
The CATMA Consortium, http://www.catma.org/.
-
-
-
-
14
-
-
0037783258
-
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping
-
W. Zhu, S.D. Schlueter, and V. Brendel Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping Plant Physiol 132 2003 469 484
-
(2003)
Plant Physiol
, vol.132
, pp. 469-484
-
-
Zhu, W.1
Schlueter, S.D.2
Brendel, V.3
-
15
-
-
85029463800
-
-
http://www.nal.usda.gov/pgdic/.
-
-
-
-
16
-
-
85029466526
-
-
http://www.bioperl.org/.
-
-
-
-
17
-
-
0037246585
-
Ensembl 2002: Accommodating comparative genomics
-
M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, and Y. Chen Ensembl 2002: accommodating comparative genomics Nucleic Acids Res 31 2003 38 42
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 38-42
-
-
Clamp, M.1
Andrews, D.2
Barker, D.3
Bevan, P.4
Cameron, G.5
Chen, Y.6
-
18
-
-
18644378331
-
The generic genome browser: A building block for a model organism
-
L.D. Stein, C. Mungall, S. Shu, M. Caudy, M. Mangone, and A. Day The generic genome browser: a building block for a model organism Syst Database Genome Res 12 2002 1599 1610
-
(2002)
Syst Database 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
-
19
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
S.Y. Rhee, W. Beavis, T.Z. Berardini, G. Chen, D. Dixon, and A. Doyle The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community Nucleic Acids Res 31 2003 224 228
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 224-228
-
-
Rhee, S.Y.1
Beavis, W.2
Berardini, T.Z.3
Chen, G.4
Dixon, D.5
Doyle, A.6
-
20
-
-
0347269087
-
MIPS Arabidopsis thaliana Database (MAtDB): An integrated biological knowledge resource for plant genomics
-
H. Schoof, R. Ernst, V. Nazarov, L. Pfeifer, H.-W. Mewes, and K.F.X. Mayer MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics Nucleic Acids Res 32 2004 D377 D382
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Schoof, H.1
Ernst, R.2
Nazarov, V.3
Pfeifer, L.4
Mewes, H.-W.5
Mayer, K.F.X.6
-
21
-
-
85029464897
-
-
http://www.arabidopsis.info/.
-
-
-
-
22
-
-
85029465855
-
-
http://www.agrikola.org/.
-
-
-
-
23
-
-
0141502037
-
European consortia building integrated resources for Arabidopsis functional genomics
-
P. Hilson, I. Small, and M.T. Kuiper European consortia building integrated resources for Arabidopsis functional genomics Curr Opin Plant Biol 6 2003 426 429
-
(2003)
Curr Opin Plant Biol
, vol.6
, pp. 426-429
-
-
Hilson, P.1
Small, I.2
Kuiper, M.T.3
-
24
-
-
12244283747
-
Gramene, a tool for grass genomics
-
D.H. Ware, P. Jaiswal, J. Ni, I.V. Yap, X. Pan, and K.Y. Clark Gramene, a tool for grass genomics Plant Physiol 130 2002 1606 1613
-
(2002)
Plant Physiol
, vol.130
, pp. 1606-1613
-
-
Ware, D.H.1
Jaiswal, P.2
Ni, J.3
Yap, I.V.4
Pan, X.5
Clark, K.Y.6
-
25
-
-
0348062817
-
MaizeGDB, the community database for maize genetics and genomics
-
C.J. Lawrence, Q. Dong, M.L. Polacco, T.E. Seigfried, and V. Brendel MaizeGDB, the community database for maize genetics and genomics Nucleic Acids Res 32 2004 D398 D400
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Lawrence, C.J.1
Dong, Q.2
Polacco, M.L.3
Seigfried, T.E.4
Brendel, V.5
-
26
-
-
0037271322
-
Cross-species sequence comparisons: A review of methods and available resources
-
K.A. Frazer, L. Elnitski, D.M. Church, I. Dubchak, and R.C. Hardison Cross-species sequence comparisons: a review of methods and available resources Genome Res 13 1 2003 1 12
-
(2003)
Genome Res
, vol.13
, Issue.1
, pp. 1-12
-
-
Frazer, K.A.1
Elnitski, L.2
Church, D.M.3
Dubchak, I.4
Hardison, R.C.5
-
27
-
-
2942516151
-
Benchmarking tools for the alignment of functional noncoding DNA
-
D.A. Pollard, C.M. Bergman, J. Stoye, S.E. Celniker, and M.B. Eisen Benchmarking tools for the alignment of functional noncoding DNA BMC Bioinform 5 2004 6
-
(2004)
BMC Bioinform
, vol.5
, pp. 6
-
-
Pollard, D.A.1
Bergman, C.M.2
Stoye, J.3
Celniker, S.E.4
Eisen, M.B.5
-
28
-
-
0037767267
-
LineUp: Statistical detection of chromosomal homology with application to plant comparative genomics
-
S. Hampson, A. McLysaght, B. Gaut, and P. Baldi LineUp: statistical detection of chromosomal homology with application to plant comparative genomics Genome Res 5 2003 753 763
-
(2003)
Genome Res
, vol.5
, pp. 753-763
-
-
Hampson, S.1
McLysaght, A.2
Gaut, B.3
Baldi, P.4
-
29
-
-
0036852286
-
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
-
K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice Genome Res 12 2002 1792 1801
-
(2002)
Genome Res
, vol.12
, pp. 1792-1801
-
-
Vandepoele, K.1
Saeys, Y.2
Simillion, C.3
Raes, J.4
Van De Peer, Y.5
-
30
-
-
0042024907
-
Comparative DNA sequence analysis of wheat and rice genomes
-
M.E. Sorrells, M. La Rota, C.E. Bermudez-Kandianis, R.A. Greene, R. Kantety, and J.D. Munkvold Comparative DNA sequence analysis of wheat and rice genomes Genome Res 13 2003 1818 1827
-
(2003)
Genome Res
, vol.13
, pp. 1818-1827
-
-
Sorrells, M.E.1
La Rota, M.2
Bermudez-Kandianis, C.E.3
Greene, R.A.4
Kantety, R.5
Munkvold, J.D.6
-
31
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, and C. Antonescu Versatile and open software for comparing large genomes Genome Biol 5 2004 R12
-
(2004)
Genome Biol
, vol.5
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
-
32
-
-
0035890910
-
REPuter: The manifold applications of repeat analysis on a genomic scale
-
S. Kurtz, J.V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich REPuter: the manifold applications of repeat analysis on a genomic scale Nucleic Acids Res 29 2001 4633 4642
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 4633-4642
-
-
Kurtz, S.1
Choudhuri, J.V.2
Ohlebusch, E.3
Schleiermacher, C.4
Stoye, J.5
Giegerich, R.6
-
33
-
-
0037433046
-
FORRepeats: Detects repeats on entire chromosomes and between genomes
-
A. Lefebvre, T. Lecroq, H. Dauchel, and J. Alexandre FORRepeats: detects repeats on entire chromosomes and between genomes Bioinformatics 19 2003 319 326
-
(2003)
Bioinformatics
, vol.19
, pp. 319-326
-
-
Lefebvre, A.1
Lecroq, T.2
Dauchel, H.3
Alexandre, J.4
-
34
-
-
0043026711
-
Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana
-
S.I. Wright, N. Agrawal, and T.E. Bureau Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana Genome Res 2003 1897 1903
-
(2003)
Genome Res
, pp. 1897-1903
-
-
Wright, S.I.1
Agrawal, N.2
Bureau, T.E.3
-
35
-
-
0346494835
-
The TIGR plant repeat databases: A collective resource for the identification of repetitive sequences in plants
-
S. Ouyang, and C.R. Buell The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants Nucleic Acids Res 2004 D360 D363
-
(2004)
Nucleic Acids Res
-
-
Ouyang, S.1
Buell, C.R.2
-
36
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
S. Schwartz, W.J. Kent, A. Smit, Z. Zhang, R. Baertsch, and R.C. Hardison Human-mouse alignments with BLASTZ Genome Res 13 2003 103 107
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
-
38
-
-
85029462485
-
-
http://www.sanger.ac.uk/Software/ACT/.
-
-
-
-
39
-
-
0034020416
-
PipMaker - A web server for aligning two genomic DNA sequences
-
S. Schwartz, Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, and J. Bouck PipMaker - a web server for aligning two genomic DNA sequences Genome Res 10 2000 577 586
-
(2000)
Genome Res
, vol.10
, pp. 577-586
-
-
Schwartz, S.1
Zhang, Z.2
Frazer, K.A.3
Smit, A.4
Riemer, C.5
Bouck, J.6
-
40
-
-
0642309748
-
SeqVISTA: A graphical tool for sequence feature visualization and comparison
-
Z. Hu, M. Frith, T. Niu, and Y. Weng SeqVISTA: a graphical tool for sequence feature visualization and comparison BMC Bioinform 4 2003 1
-
(2003)
BMC Bioinform
, vol.4
, pp. 1
-
-
Hu, Z.1
Frith, M.2
Niu, T.3
Weng, Y.4
-
41
-
-
0036190876
-
GenomePixelizer - A visualization program for comparative genomics within and between species
-
A. Kozik, E. Kochetkova, and R. Michelmore GenomePixelizer - a visualization program for comparative genomics within and between species Bioinformatics 18 2002 335 336
-
(2002)
Bioinformatics
, vol.18
, pp. 335-336
-
-
Kozik, A.1
Kochetkova, E.2
Michelmore, R.3
-
42
-
-
85029465471
-
-
http://tcl.activestate.com/.
-
-
-
-
43
-
-
0035165672
-
Mendel-GFDb and Mendel-ESTS: Databases of plant gene families and ESTs annotated with gene family numbers and gene family names
-
D. Lonsdale, M. Crowe, B. Arnold, and B.C. Arnold Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names Nucleic Acids Res 29 2001 120 122
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 120-122
-
-
Lonsdale, D.1
Crowe, M.2
Arnold, B.3
Arnold, B.C.4
-
44
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, and E.V. Koonin The COG database: an updated version includes eukaryotes BMC Bioinform 4 2003 41
-
(2003)
BMC Bioinform
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
-
45
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet 2000;25:25-9.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
-
47
-
-
0034887203
-
Creating the gene ontology resource: Design and implementation
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium Creating the gene ontology resource: design and implementation Genome Res 11 2001 1425 1433
-
(2001)
Genome Res
, vol.11
, pp. 1425-1433
-
-
-
48
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Gene Ontology Consortium R.
-
M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource Nucleic Acids Res 32 2004 D258 D261
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
Lomax, J.4
Ashburner, M.5
Foulger6
-
49
-
-
85029463708
-
-
http://www.geneontology.org/.
-
-
-
-
50
-
-
9144252016
-
The Gene Ontology Annotation (GOA) Database: Sharing knowledge in uniprot with gene ontology
-
E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, and J. Maslen The Gene Ontology Annotation (GOA) Database: sharing knowledge in uniprot with gene ontology Nucleic Acids Res 32 2004 D262 D266
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Camon, E.1
Magrane, M.2
Barrell, D.3
Lee, V.4
Dimmer, E.5
Maslen, J.6
-
51
-
-
85029462459
-
-
http://www.plantontology.org/.
-
-
-
-
52
-
-
0037390933
-
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
-
B.C. Meyers, A. Kozik, A. Griego, H. Kuang, and R.W. Michelmore Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis Plant Cell 15 4 2003 809 834 (Erratum in: Plant Cell 2003;15:1683)
-
(2003)
Plant Cell
, vol.15
, Issue.4
, pp. 809-834
-
-
Meyers, B.C.1
Kozik, A.2
Griego, A.3
Kuang, H.4
Michelmore, R.W.5
-
53
-
-
0037460985
-
TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST datasets
-
G. Pertea, X.Q. Huang, F. Liang, V. Antonescu, R. Sultana, and S. Karamycheva TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets Bioinformatics 19 2003 651 652
-
(2003)
Bioinformatics
, vol.19
, pp. 651-652
-
-
Pertea, G.1
Huang, X.Q.2
Liang, F.3
Antonescu, V.4
Sultana, R.5
Karamycheva, S.6
-
54
-
-
85029464771
-
-
http://www.tigr.org/tdb/tgi/plant.shtml.
-
-
-
-
55
-
-
9244230702
-
Applied computational tools for crop genome research
-
C.G. Love, J. Batley, and D. Edwards Applied computational tools for crop genome research J Plant Biotechnol 5 2003 193 195
-
(2003)
J Plant Biotechnol
, vol.5
, pp. 193-195
-
-
Love, C.G.1
Batley, J.2
Edwards, D.3
-
58
-
-
0142035247
-
Genome-wide characterization of the lignification toolbox in Arabidopsis
-
J. Raes, A. Rohde, J.H. Christensen, Y. Van de Peer, and W. Boerjan Genome-wide characterization of the lignification toolbox in Arabidopsis Plant Physiol 133 2003 1051 1071
-
(2003)
Plant Physiol
, vol.133
, pp. 1051-1071
-
-
Raes, J.1
Rohde, A.2
Christensen, J.H.3
Van De Peer, Y.4
Boerjan, W.5
-
60
-
-
0034954896
-
Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana
-
J.M. Ward Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana Bioinformatics 17 2001 560 563
-
(2001)
Bioinformatics
, vol.17
, pp. 560-563
-
-
Ward, J.M.1
-
61
-
-
0037986744
-
Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis
-
G. Breton, J. Danyluk, J.B.F. Charron, and F. Sarhan Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis Plant Physiol 132 2003 64 74
-
(2003)
Plant Physiol
, vol.132
, pp. 64-74
-
-
Breton, G.1
Danyluk, J.2
Charron, J.B.F.3
Sarhan, F.4
-
62
-
-
0036010770
-
Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat
-
R.V. Kantety, M. La Rota, D.E. Matthews, and M.E. Sorrells Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat Plant Mol Biol 48 2002 501 510
-
(2002)
Plant Mol Biol
, vol.48
, pp. 501-510
-
-
Kantety, R.V.1
La Rota, M.2
Matthews, D.E.3
Sorrells, M.E.4
-
63
-
-
85029465977
-
-
http://hornbill.cspp.latrobe.edu.au/cgi-binpub/index.pl.
-
-
-
-
64
-
-
0037348718
-
Large-scale identification of single-feature polymorphisms in complex genomes
-
J.O. Borevitz, D. Liang, D. Plouffe, H.S. Chang, T. Zhu, and D. Weigel Large-scale identification of single-feature polymorphisms in complex genomes Genome Res 13 2003 513 523
-
(2003)
Genome Res
, vol.13
, pp. 513-523
-
-
Borevitz, J.O.1
Liang, D.2
Plouffe, D.3
Chang, H.S.4
Zhu, T.5
Weigel, D.6
-
65
-
-
0038376923
-
Computational approaches to identify promoters and cis-regulatory elements in plant genomes
-
S. Rombauts, K. Florquin, M. Lescot, K. Marchal, P. Rouzé, and Y. Van de Peer Computational approaches to identify promoters and cis-regulatory elements in plant genomes Plant Physiol 132 2003 1162 1176
-
(2003)
Plant Physiol
, vol.132
, pp. 1162-1176
-
-
Rombauts, S.1
Florquin, K.2
Lescot, M.3
Marchal, K.4
Rouzé, P.5
Van De Peer, Y.6
-
66
-
-
85029462707
-
-
http://www.athamap.de.
-
-
-
-
67
-
-
0345863918
-
AthaMap: An online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
-
N.O. Steffens, C. Galuschka, M. Schindler, L. Bülow, and R. Hehl AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome Nucleic Acids Res 32 2004 D368 D372
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Steffens, N.O.1
Galuschka, C.2
Schindler, M.3
Bülow, L.4
Hehl, R.5
-
68
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
G.Z. Hertz, and G.D. Stormo Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 15 1999 563 577
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
69
-
-
0242574990
-
A biophysical approach to transcription factor binding site discovery
-
M. Djordjevic, A.M. Sengupta, and B.I. Shraiman A biophysical approach to transcription factor binding site discovery Genome Res 13 2003 2381 2390
-
(2003)
Genome Res
, vol.13
, pp. 2381-2390
-
-
Djordjevic, M.1
Sengupta, A.M.2
Shraiman, B.I.3
-
70
-
-
0036137323
-
Higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, and P. Rouze Higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling Bioinformatics 17 2001 1113 1122
-
(2001)
Bioinformatics
, vol.17
, pp. 1113-1122
-
-
Thijs, G.1
Lescot, M.2
Marchal, K.3
Rombauts, S.4
De Moor, B.5
Rouze, P.6
-
71
-
-
0036090123
-
Genome wide distribution and potential regulatory functions of AtATE, a novel miniature inverted-repeat transposable element that is present in the promoter region of one of the Arginine Decarboxylase genes in Arabidopsis thaliana
-
A. Elamrani, L. Marie, A. Aïnouche, J. Nicolas, and I. Couée Genome wide distribution and potential regulatory functions of AtATE, a novel miniature inverted-repeat transposable element that is present in the promoter region of one of the Arginine Decarboxylase genes in Arabidopsis thaliana Mol Gen Genomics 267 2002 459 471
-
(2002)
Mol Gen Genomics
, vol.267
, pp. 459-471
-
-
Elamrani, A.1
Marie, L.2
Aïnouche, A.3
Nicolas, J.4
Couée, I.5
-
72
-
-
0038817772
-
Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana
-
K.J. Schmid, T.R. Sorensen, R. Stracke, O. Torjek, T. Altmann, and T. Mitchell-Olds Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana Genome Res 13 2003 1250 1257
-
(2003)
Genome Res
, vol.13
, pp. 1250-1257
-
-
Schmid, K.J.1
Sorensen, T.R.2
Stracke, R.3
Torjek, O.4
Altmann, T.5
Mitchell-Olds, T.6
-
73
-
-
0347135946
-
Whole-genome discovery of transcription factor binding sites by network-level conservation
-
M. Pritsker, Y.C. Liu, M.A. Beer, and S. Tavazoie Whole-genome discovery of transcription factor binding sites by network-level conservation Genome Res 14 2004 99 108
-
(2004)
Genome Res
, vol.14
, pp. 99-108
-
-
Pritsker, M.1
Liu, Y.C.2
Beer, M.A.3
Tavazoie, S.4
-
74
-
-
0347513219
-
Characterizing gene sets with FuncAssociate
-
G.F. Berriz, O.D. King, B. Bryant, C. Sander, and F.P. Roth Characterizing gene sets with FuncAssociate Bioinformatics 19 2003 2502 2504
-
(2003)
Bioinformatics
, vol.19
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
Sander, C.4
Roth, F.P.5
-
75
-
-
0346494829
-
SGMD: The soybean genomics and microarray database
-
N.W. Alkharouf, and B.F. Matthews SGMD: the soybean genomics and microarray database Nucleic Acids Res 32 2004 D398 D400
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Alkharouf, N.W.1
Matthews, B.F.2
-
76
-
-
0036739499
-
VIZARD: Analysis of Affymetrix Arabidopsis GeneChip (R) data
-
N. Moseyko, and L.J. Feldman VIZARD: analysis of Affymetrix Arabidopsis GeneChip (R) data Bioinformatics 18 2002 1264 1265
-
(2002)
Bioinformatics
, vol.18
, pp. 1264-1265
-
-
Moseyko, N.1
Feldman, L.J.2
-
77
-
-
0347755545
-
-
S. Komatsu, K. Kojima, K. Suzuki, K. Ozaki, and K. Higo Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003 32 2004 D388 D392
-
(2004)
Rice Proteome Database Based on Two-dimensional Polyacrylamide Gel Electrophoresis: Its Status in 2003
, vol.32
-
-
Komatsu, S.1
Kojima, K.2
Suzuki, K.3
Ozaki, K.4
Higo, K.5
-
78
-
-
0033757963
-
Metabolite profiling for plant functional genomics
-
O. Fiehn, J. Kopka, P. Dormann, T. Altmann, R.N. Trethewey, and L. Willmitzer Metabolite profiling for plant functional genomics Nat Biotechnol 11 2000 1157 1161 (Erratum in Nat Biotechnol 2000, February;19(2):173)
-
(2000)
Nat Biotechnol
, vol.11
, pp. 1157-1161
-
-
Fiehn, O.1
Kopka, J.2
Dormann, P.3
Altmann, T.4
Trethewey, R.N.5
Willmitzer, L.6
-
80
-
-
0345270397
-
Plant metabolomics: Large-scale phytochemistry in the functional genomics era
-
L.W. Sumner, P. Mendes, and R.A. Dixon Plant metabolomics: large-scale phytochemistry in the functional genomics era Phytochemistry 62 2003 817 836
-
(2003)
Phytochemistry
, vol.62
, pp. 817-836
-
-
Sumner, L.W.1
Mendes, P.2
Dixon, R.A.3
-
81
-
-
9244239299
-
Functional genomics from a plant biochemist's perspective
-
J. Ohlrogge, S. Ruuska, S. Mekhedov, T. Girke, and C. Benning Functional genomics from a plant biochemist's perspective Acta Agric Scand 53 2003 41 50
-
(2003)
Acta Agric Scand
, vol.53
, pp. 41-50
-
-
Ohlrogge, J.1
Ruuska, S.2
Mekhedov, S.3
Girke, T.4
Benning, C.5
-
82
-
-
0035105106
-
Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems
-
U. Roessner, A. Luedemann, D. Brust, O. Fiehn, T. Linke, and L. Willmitzer Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems Plant Cell 13 2001 11 29
-
(2001)
Plant Cell
, vol.13
, pp. 11-29
-
-
Roessner, U.1
Luedemann, A.2
Brust, D.3
Fiehn, O.4
Linke, T.5
Willmitzer, L.6
-
83
-
-
0033757963
-
Metabolite profiling for plant functional genomics
-
O. Fiehn, J. Kopka, P. Dormann, T. Altmann, R.N. Trethewey, and L. Willmitzer Metabolite profiling for plant functional genomics Nat Biotechnol 18 2000 1157 1161
-
(2000)
Nat Biotechnol
, vol.18
, pp. 1157-1161
-
-
Fiehn, O.1
Kopka, J.2
Dormann, P.3
Altmann, T.4
Trethewey, R.N.5
Willmitzer, L.6
-
84
-
-
0142033903
-
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)
-
A.L. Duran, J. Yang, L.J. Wang, and L.W. Sumner Metabolomics spectral formatting, alignment and conversion tools (MSFACTs) Bioinformatics 19 2003 2283 2293
-
(2003)
Bioinformatics
, vol.19
, pp. 2283-2293
-
-
Duran, A.L.1
Yang, J.2
Wang, L.J.3
Sumner, L.W.4
-
85
-
-
0037731046
-
Application of metabolomics to plant genotype discrimination using statistics and machine learning
-
J. Taylor, R.D. King, T. Altmann, and O. Fiehn Application of metabolomics to plant genotype discrimination using statistics and machine learning Bioinformatics 18 2002 S241 S248
-
(2002)
Bioinformatics
, vol.18
-
-
Taylor, J.1
King, R.D.2
Altmann, T.3
Fiehn, O.4
-
86
-
-
0037690801
-
MetNet: Software to build and model the biogenetic lattice of Arabidopsis
-
E.S. Wurtele, J. Li, L.X. Diao, H.L. Zhang, C.M. Foster, and B. Fatland MetNet: software to build and model the biogenetic lattice of Arabidopsis Comp Funct Genomics 4 2003 239 245
-
(2003)
Comp Funct Genomics
, vol.4
, pp. 239-245
-
-
Wurtele, E.S.1
Li, J.2
Diao, L.X.3
Zhang, H.L.4
Foster, C.M.5
Fatland, B.6
-
87
-
-
0038458655
-
Creating and modeling metabolic and regulatory networks using text mining and fuzzy expert systems
-
J.T.L. Wang C.H. Wu P.P. Wang World Scientific Publishing Singapore
-
J.A. Dickerson, D. Berleant, Z. Cox, W. Qi, D. Ashlock, and E.S. Wurtele Creating and modeling metabolic and regulatory networks using text mining and fuzzy expert systems J.T.L. Wang C.H. Wu P.P. Wang Computational biology and genome informatics 2003 World Scientific Publishing Singapore 207 238
-
(2003)
Computational Biology and Genome Informatics
, pp. 207-238
-
-
Dickerson, J.A.1
Berleant, D.2
Cox, Z.3
Qi, W.4
Ashlock, D.5
Wurtele, E.S.6
-
88
-
-
85029466206
-
-
http://www.ggobi.org/.
-
-
-
-
89
-
-
0030305457
-
A language for data analysis and graphics
-
R. Ihaka, and R. Gentleman A language for data analysis and graphics J Comput Graphic Stat 5 1996 299 314
-
(1996)
J Comput Graphic Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
90
-
-
85029462572
-
-
http://www.r-project.org/.
-
-
-
-
91
-
-
2942517980
-
PathMAPA: A tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
-
D. Pan, N. Sun, K.H. Cheung, Z. Guan, L. Ma, and M. Holford PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis BMC Bioinform 4 2003 56
-
(2003)
BMC Bioinform
, vol.4
, pp. 56
-
-
Pan, D.1
Sun, N.2
Cheung, K.H.3
Guan, Z.4
Ma, L.5
Holford, M.6
-
92
-
-
0042594466
-
GABI-Kat SimpleSearch: A flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana
-
Y. Li, M.G. Rosso, N. Strizhov, P. Viehoever, and B. Weisshaar GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana Bioinformatics 19 2003 1441 1442
-
(2003)
Bioinformatics
, vol.19
, pp. 1441-1442
-
-
Li, Y.1
Rosso, M.G.2
Strizhov, N.3
Viehoever, P.4
Weisshaar, B.5
-
93
-
-
0037440690
-
ATIDB: Arabidopsis thaliana insertion database
-
X.K. Pan, H. Liu, J. Clarke, J. Jones, M. Bevan, and L. Stein ATIDB: Arabidopsis thaliana insertion database Nucleic Acids Res 31 2003 1245 1251
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1245-1251
-
-
Pan, X.K.1
Liu, H.2
Clarke, J.3
Jones, J.4
Bevan, M.5
Stein, L.6
-
94
-
-
85029461739
-
-
http://arabidopsis.info/insertwatch/.
-
-
-
-
95
-
-
0028949381
-
Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking
-
Y.-G. Liu, and R.F. Whittier Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking Genomics 25 1995 674 681
-
(1995)
Genomics
, vol.25
, pp. 674-681
-
-
Liu, Y.-G.1
Whittier, R.F.2
-
96
-
-
0037460949
-
Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome
-
G.G. Presting Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome Bioinformatics 19 2003 579 586
-
(2003)
Bioinformatics
, vol.19
, pp. 579-586
-
-
Presting, G.G.1
-
97
-
-
0037193707
-
Genomics and plant cells: Application of genomics strategies to Arabidopsis cell biology
-
M. Bevan Genomics and plant cells: application of genomics strategies to Arabidopsis cell biology Philos Trans R Soc Lond B Biol Sci 357 2002 731 736
-
(2002)
Philos Trans R Soc Lond B Biol Sci
, vol.357
, pp. 731-736
-
-
Bevan, M.1
-
98
-
-
0037303133
-
Agricultural genomics: An approach to plant protection
-
H. Koltai, and H. Volpin Agricultural genomics: an approach to plant protection Eur J Plant Pathol 109 2003 101 108
-
(2003)
Eur J Plant Pathol
, vol.109
, pp. 101-108
-
-
Koltai, H.1
Volpin, H.2
-
99
-
-
0036673480
-
Bioinformatic methods for allergenicity assessment using a comprehensive allergen database
-
R.E. Hileman, A. Silvanovich, R.E. Goodman, E.A. Rice, G. Holleschak, and J.D. Astwood Bioinformatic methods for allergenicity assessment using a comprehensive allergen database Int Arch Aller Immunol 128 2002 280 291
-
(2002)
Int Arch Aller Immunol
, vol.128
, pp. 280-291
-
-
Hileman, R.E.1
Silvanovich, A.2
Goodman, R.E.3
Rice, E.A.4
Holleschak, G.5
Astwood, J.D.6
-
100
-
-
0036963912
-
Genomics, bioinformatics and plant systematics
-
A. Liston Genomics, bioinformatics and plant systematics Israel J Plant Sci 50 2002 S-89 S-94
-
(2002)
Israel J Plant Sci
, vol.50
-
-
Liston, A.1
-
101
-
-
0346505465
-
A cross-genomic approach for systematic mapping of phenotypic traits to genes
-
K. Jim, K. Parmar, M. Singh, and S. Tavazoie A cross-genomic approach for systematic mapping of phenotypic traits to genes Genome Res 14 2004 109 115
-
(2004)
Genome Res
, vol.14
, pp. 109-115
-
-
Jim, K.1
Parmar, K.2
Singh, M.3
Tavazoie, S.4
-
102
-
-
0035736113
-
Bioinformatics and data knowledge: The new frontiers for nutrition and foods
-
F. Desiere, B. German, H. Watzke, A. Pfeifer, and S. Saguy Bioinformatics and data knowledge: the new frontiers for nutrition and foods Trends Food Sci Technol 12 2001 215 229
-
(2001)
Trends Food Sci Technol
, vol.12
, pp. 215-229
-
-
Desiere, F.1
German, B.2
Watzke, H.3
Pfeifer, A.4
Saguy, S.5
-
103
-
-
85029462542
-
-
http://www.gramene.org.
-
-
-
-
104
-
-
9144269670
-
EnsMart: A generic system for fast and flexible access to biological data
-
A. Kasprzyk, D. Keefe, D. Smedley, D. London, W. Spooner, and C. Melsopp EnsMart: a generic system for fast and flexible access to biological data Genome Res 14 2004 160 169
-
(2004)
Genome Res
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
|