-
1
-
-
0035172256
-
The TRANSFAC system on gene expression regulation
-
Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., OhnhaÌuser,R. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 281-283
-
-
Wingender, E.1
Chen, X.2
Fricke, E.3
Geffers, R.4
Hehl, R.5
Liebich, I.6
Krull, M.7
Matys, V.8
Michael, H.9
OhnhaÌuser, R.10
-
2
-
-
0036089483
-
The Eukaryotic Promoter Database, EPD: New entry types and links to gene expression data
-
Praz,V., Perier,R., Bonnard,C. and Bucher,P. (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res., 30, 322-324.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 322-324
-
-
Praz, V.1
Perier, R.2
Bonnard, C.3
Bucher, P.4
-
3
-
-
0035998754
-
TRANSCompel: A database on composite regulatory elements in eukaryotic genes
-
Kel-Margoulis,O.V., Kel,A.E., Reuter,I., Deineko,I.V. and Wingender,E. (2002) TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res., 30, 332-334.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 332-334
-
-
Kel-Margoulis, O.V.1
Kel, A.E.2
Reuter, I.3
Deineko, I.V.4
Wingender, E.5
-
4
-
-
18444387984
-
Transcription Regulatory Regions Database (TRRD): Its status in 2002
-
Kolchanov,N.A., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Stepanenko,I.L., Merkulova,T.I., Pozdnyakov,M.A., Podkolodny,N.L., Naumochkin,A.N. and Romashchenko,A.G. (2002) Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res., 30, 312-317.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 312-317
-
-
Kolchanov, N.A.1
Ignatieva, E.V.2
Ananko, E.A.3
Podkolodnaya, O.A.4
Stepanenko, I.L.5
Merkulova, T.I.6
Pozdnyakov, M.A.7
Podkolodny, N.L.8
Naumochkin, A.N.9
Romashchenko, A.G.10
-
5
-
-
0028971143
-
Matind and MatInspector - New fast and versatile tools for detection of consensus matches in nucleotide-sequence data
-
Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) Matind and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide-sequence data. Nucleic Acids Res., 23, 4878-4884.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 4878-4884
-
-
Quandt, K.1
Frech, K.2
Karas, H.3
Wingender, E.4
Werner, T.5
-
6
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice,P., Longden,I. and Bleasby,A.J. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 6, 276-277.
-
(2000)
Trends Genet.
, vol.6
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.J.3
-
7
-
-
0032803439
-
Isolation and characterisation of the retinoic acid receptor-alpha gene in the Japanese pufferfish, F.rubripes
-
Wentworth,J.M., Schoenfeld,V., Meek,S., Elgar,G., Brenner,S. and Chattejee,V.K. (1999) Isolation and characterisation of the retinoic acid receptor-alpha gene in the Japanese pufferfish, F.rubripes. Gene, 236, 315-323.
-
(1999)
Gene
, vol.236
, pp. 315-323
-
-
Wentworth, J.M.1
Schoenfeld, V.2
Meek, S.3
Elgar, G.4
Brenner, S.5
Chattejee, V.K.6
-
8
-
-
0034284481
-
Conserved noncoding sequences are reliable guides to regulatory elements
-
Hardison,R.C. (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet., 16, 369-372.
-
(2000)
Trends Genet.
, vol.16
, pp. 369-372
-
-
Hardison, R.C.1
-
9
-
-
0035934254
-
Cloning and characterization of murine p53 upstream sequences reveals additional positive transcriptional regulatory elements
-
Reisman,D., Eaton,E., McMillin,D., Doudican,N.A. and Boggs,K. (2001) Cloning and characterization of murine p53 upstream sequences reveals additional positive transcriptional regulatory elements. Gene, 274, 129-137.
-
(2001)
Gene
, vol.274
, pp. 129-137
-
-
Reisman, D.1
Eaton, E.2
McMillin, D.3
Doudican, N.A.4
Boggs, K.5
-
10
-
-
0034919602
-
Identifying functional elements by comparative DNA sequence analysis
-
Tompa,M. (2001) Identifying functional elements by comparative DNA sequence analysis. Genome Res., 11, 1143-1144.
-
(2001)
Genome Res.
, vol.11
, pp. 1143-1144
-
-
Tompa, M.1
-
11
-
-
0034919548
-
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
-
Cliften,P.F., Hillier,L.W., Fulton,L., Graves,T., Miner,T., Gish,W.R., Waterston,R.H. and Johnston,M. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res., 11, 1175-1186.
-
(2001)
Genome Res.
, vol.11
, pp. 1175-1186
-
-
Cliften, P.F.1
Hillier, L.W.2
Fulton, L.3
Graves, T.4
Miner, T.5
Gish, W.R.6
Waterston, R.H.7
Johnston, M.8
-
12
-
-
0029445204
-
Studies of DNA methylation in animals
-
Bird,A., Tate,P., Xinsheng,N., Campoy,J., Meehan,R., Cross,S., Tweedie,S., Charlton,J. and Macleod,D. (1995) Studies of DNA methylation in animals. J. Cell Sci., Suppl., 19, 37-39.
-
(1995)
J. Cell Sci. Suppl.
, vol.19
, pp. 37-39
-
-
Bird, A.1
Tate, P.2
Xinsheng, N.3
Campoy, J.4
Meehan, R.5
Cross, S.6
Tweedie, S.7
Charlton, J.8
Macleod, D.9
-
13
-
-
0030801002
-
Gapped BLAST and PSI-BLAST, a new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST, a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
14
-
-
0033957834
-
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 2000
-
Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
15
-
-
0000241874
-
GENEMARK - Parallel gene recognition for both DNA strands
-
Borodovosky,M. and McIninch,J. (1993) GENEMARK - parallel gene recognition for both DNA strands. Comput. Chem., 17, 123-133.
-
(1993)
Comput. Chem.
, vol.17
, pp. 123-133
-
-
Borodovosky, M.1
McIninch, J.2
-
16
-
-
0029976603
-
Using Clustalw for multiple sequence alignments
-
Higgins,D.G., Thompson,J.D. and Gibson,T.J. (1996) Using Clustalw for multiple sequence alignments. Meth. Enzymol., 266, 383-402.
-
(1996)
Meth. Enzymol.
, vol.266
, pp. 383-402
-
-
Higgins, D.G.1
Thompson, J.D.2
Gibson, T.J.3
-
17
-
-
0004207406
-
-
2nd Edn. O'Reilly and Associates, Inc., Sabastopol, CA
-
Wall,L., Christiansen,T. and Schwartz,R. (1996) Programming Perl, 2nd Edn. O'Reilly and Associates, Inc., Sabastopol, CA.
-
(1996)
Programming Perl.
-
-
Wall, L.1
Christiansen, T.2
Schwartz, R.3
-
19
-
-
0344376588
-
The LAGAN Server
-
Brudno,M., Kim,M.F., Do,C. and Batzoglou,S. (2002) The LAGAN Server, http://lagan.stanford.edu.
-
(2002)
-
-
Brudno, M.1
Kim, M.F.2
Do, C.3
Batzoglou, S.4
-
21
-
-
18444410747
-
The EMBL Nucleotide Sequence Database
-
Stoesser,G., Baker,W., van den Broek,A., Camon,E., Garcia-Pastor,M., Kanz,C., Kulikova,T., Leinonen,R., Lin,Q., Lombard,V. et al. (2002) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 30, 21-26.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 21-26
-
-
Stoesser, G.1
Baker, W.2
van den Broek, A.3
Camon, E.4
Garcia-Pastor, M.5
Kanz, C.6
Kulikova, T.7
Leinonen, R.8
Lin, Q.9
Lombard, V.10
-
22
-
-
0034726961
-
Additive effect between NF-kappaB subunits and p53 protein for transcriptional activation of human p53 promoter
-
Benoit,V., Hellin,A.C., Huygen,S., Gielen,J., Bours,V. and Merville,M.P. (2000) Additive effect between NF-kappaB subunits and p53 protein for transcriptional activation of human p53 promoter. Oncogene, 19, 4787-4794.
-
(2000)
Oncogene
, vol.19
, pp. 4787-4794
-
-
Benoit, V.1
Hellin, A.C.2
Huygen, S.3
Gielen, J.4
Bours, V.5
Merville, M.P.6
-
23
-
-
0022290594
-
The 5� region of the p53 gene: Evolutionary conservation and evidence for a negative regulatory element
-
Bienz-Tadmor,B., Zakut-Houri,R., Libresco,S., Givol,D. and Oren,M. (1985) The 5� region of the p53 gene: evolutionary conservation and evidence for a negative regulatory element. EMBO J., 4, 3209-3213.
-
(1985)
EMBO J.
, vol.4
, pp. 3209-3213
-
-
Bienz-Tadmor, B.1
Zakut-Houri, R.2
Libresco, S.3
Givol, D.4
Oren, M.5
-
24
-
-
0028077155
-
Cloning of the Syrian hamster p53 gene: Structural and functional characterization of the upstream promoter region
-
Albor,A., Laborda,J. and Notario,V. (1994) Cloning of the Syrian hamster p53 gene: structural and functional characterization of the upstream promoter region. Mol. Carcin., 11, 176-183.
-
(1994)
Mol. Carcin.
, vol.11
, pp. 176-183
-
-
Albor, A.1
Laborda, J.2
Notario, V.3
-
25
-
-
0032697205
-
Generation and analysis of 25 Mb of genomic DNA from the puffer fish Fugu rubripes by sequence scanning
-
Elgar,G., Clark,M.S., Meek,S., Smith,S., Warner,S., Edwards,Y.J.K., Bouchireb,N., Cottage,A., Yeo,G.S., Umrania,Y. et al. (1999) Generation and analysis of 25 Mb of genomic DNA from the puffer fish Fugu rubripes by sequence scanning. Genome Res., 9, 960-971.
-
(1999)
Genome Res.
, vol.9
, pp. 960-971
-
-
Elgar, G.1
Clark, M.S.2
Meek, S.3
Smith, S.4
Warner, S.5
Edwards, Y.J.K.6
Bouchireb, N.7
Cottage, A.8
Yeo, G.S.9
Umrania, Y.10
-
26
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
Aparicio,S., Chapman,J., Stupka,E., Putnam,N., Chia,J.M., Dehal,P., Christoffels,A., Rash,S., Hoon,S. et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297, 1301-1310.
-
(2002)
Science
, vol.297
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
Putnam, N.4
Chia, J.M.5
Dehal, P.6
Christoffels, A.7
Rash, S.8
Hoon, S.9
-
27
-
-
0033860203
-
Characterization and repeat analysis of the compact genome of the freshwater puffer fish Tetraodon nigroviridis
-
Crollius,H.R., Jaillon,O., Dasilva,C., Ozouf-Costaz,C., Fizames,C., Fischer,C., Bouneau,L., Billault,A., Quetier,F., Saurin,W. et al. (2000) Characterization and repeat analysis of the compact genome of the freshwater puffer fish Tetraodon nigroviridis. Genome Res., 10, 939-949.
-
(2000)
Genome Res.
, vol.10
, pp. 939-949
-
-
Crollius, H.R.1
Jaillon, O.2
Dasilva, C.3
Ozouf-Costaz, C.4
Fizames, C.5
Fischer, C.6
Bouneau, L.7
Billault, A.8
Quetier, F.9
Saurin, W.10
-
28
-
-
0027412196
-
ALSCRIPT - A tool to format multiple sequence alignments
-
Barton,G.J. (1993) ALSCRIPT - A tool to format multiple sequence alignments. Protein Eng., 6, 37-40.
-
(1993)
Protein Eng.
, vol.6
, pp. 37-40
-
-
Barton, G.J.1
-
29
-
-
0032500897
-
Cinema - A novel colour interactive editor for multiple alignments
-
Parry-Smith,D.J., Payne,A.W.R., Michie,A.D. and Attwood,T.K. (1998) Cinema - a novel colour interactive editor for multiple alignments. Gene, 221, GC57-GC63.
-
(1998)
Gene
, vol.221
, pp. GC57-GC63
-
-
Parry-Smith, D.J.1
Payne, A.W.R.2
Michie, A.D.3
Attwood, T.K.4
-
30
-
-
0033828267
-
Alfresco - A workbench for comparative genomic sequence analysis
-
Jareborg,N. and Durbin,R. (2000) Alfresco - a workbench for comparative genomic sequence analysis. Genome Res., 10, 1148-1157.
-
(2000)
Genome Res.
, vol.10
, pp. 1148-1157
-
-
Jareborg, N.1
Durbin, R.2
-
31
-
-
0034518158
-
VISTA: Visualizing global DNA sequence alignments of arbitrary length
-
Mayor,C., Brudno,M., Schwartz,J.R., Poliakov,A., Rubin,E.M., Frazer,K.A., Pachter,L.S. and Dubchak,I. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16, 1046-1047.
-
(2000)
Bioinformatics
, vol.16
, pp. 1046-1047
-
-
Mayor, C.1
Brudno, M.2
Schwartz, J.R.3
Poliakov, A.4
Rubin, E.M.5
Frazer, K.A.6
Pachter, L.S.7
Dubchak, I.8
-
32
-
-
0034020416
-
PipMaker - A web server for aligning two genomic DNA sequences
-
Schwartz,S., Zhang,Z., Frazer,K.A., Smit,A., Riemer,C., Bouck,J., Gibbs,R., Hardison,R. and Miller,W. (2000) PipMaker - a web server for aligning two genomic DNA sequences. Genome Res., 10, 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
Gibbs, R.7
Hardison, R.8
Miller, W.9
-
33
-
-
0035154384
-
Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences
-
Gottgens,B., Gilbert,J.G., Barton,L.M., Grafham,D., Rogers,J., Bentley,D.R. and Green,A.R. (2001) Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res., 11, 87-97.
-
(2001)
Genome Res.
, vol.11
, pp. 87-97
-
-
Gottgens, B.1
Gilbert, J.G.2
Barton, L.M.3
Grafham, D.4
Rogers, J.5
Bentley, D.R.6
Green, A.R.7
-
34
-
-
0036381493
-
Fugu orthologues of human major histocompatibility complex genes: A genome survey
-
Sambrook,J.G., Russell,R., Umrania,Y., Edwards,Y.J.K., Campbell,R.D., Elgar,G. and Clark,M.S. (2002) Fugu orthologues of human major histocompatibility complex genes: a genome survey. Immunogenetics, 54, 367-380.
-
(2002)
Immunogenetics
, vol.54
, pp. 367-380
-
-
Sambrook, J.G.1
Russell, R.2
Umrania, Y.3
Edwards, Y.J.K.4
Campbell, R.D.5
Elgar, G.6
Clark, M.S.7
-
35
-
-
0036110294
-
Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q
-
Smith,S.F., Snell,P., Gruetzner,F., Bench,A.J., Haaf,T., Metcalfe,J.A., Green,A.R. and Elgar,G. (2002) Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q. Genome Res., 12, 776-784.
-
(2002)
Genome Res.
, vol.12
, pp. 776-784
-
-
Smith, S.F.1
Snell, P.2
Gruetzner, F.3
Bench, A.J.4
Haaf, T.5
Metcalfe, J.A.6
Green, A.R.7
Elgar, G.8
-
36
-
-
0032573059
-
Complete sequencing of the Fugu WAGR region from WT1 to PAX6: Dramatic compaction and conservation of synteny with human chromosome 11p13
-
Miles,C., Elgar,G., Coles,E., Kleinjan,D.J., van Heyningen,V. and Hastie,N. (1998) Complete sequencing of the Fugu WAGR region from WT1 to PAX6: dramatic compaction and conservation of synteny with human chromosome 11p13. Proc. Natl Acad. Sci. USA, 95, 13068-13072.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 13068-13072
-
-
Miles, C.1
Elgar, G.2
Coles, E.3
Kleinjan, D.J.4
van Heyningen, V.5
Hastie, N.6
-
37
-
-
0033828441
-
Genomic sequence analysis of Fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7
-
Davidson,H., Taylor,M.S., Doherty,A., Boyd,A.C. and Porteous,D.J. (2000) Genomic sequence analysis of Fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7. Genome Res., 10, 1194-1203.
-
(2000)
Genome Res.
, vol.10
, pp. 1194-1203
-
-
Davidson, H.1
Taylor, M.S.2
Doherty, A.3
Boyd, A.C.4
Porteous, D.J.5
|