-
1
-
-
0037380723
-
Comparative genomics: Genome-wide analysis in metazoan eukaryotes
-
10.1038/nrg1043 12671656
-
Ureta-Vidal A Ettwiller L Birney E Comparative genomics: Genome-wide analysis in metazoan eukaryotes Nat Rev Genet 2003, 4(4):251-262. 10.1038/nrg1043 12671656
-
(2003)
Nat Rev Genet
, vol.4
, Issue.4
, pp. 251-262
-
-
Ureta-Vidal, A.1
Ettwiller, L.2
Birney, E.3
-
2
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
10.1038/nature01644 12748633
-
Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423(6937):241-254. 10.1038/nature01644 12748633
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
3
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
10.1126/science.1084337 12775844
-
Cliften P Sudarsanam P Desikan A Fulton L Fulton B Majors J Waterston R Cohen BA Johnston M Finding functional features in Saccharomyces genomes by phylogenetic footprinting Science 2003, 301(5629):71-76. 10.1126/ science.1084337 12775844
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
4
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
10.1038/nature03441 15735639
-
Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals Nature 2005, 434(7031):338-345. 10.1038/nature03441 15735639
-
(2005)
Nature
, vol.434
, Issue.7031
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
5
-
-
3242888285
-
rVISTA 2.0: Evolutionary analysis of transcription factor binding sites
-
(Web server issue) 10.1093/nar/gkh383 15215384 441521
-
Loots GG Ovcharenko I rVISTA 2.0: Evolutionary analysis of transcription factor binding sites Nucleic Acids Res 2004, 32(Web server issue):W217-21. 10.1093/nar/gkh383 15215384 441521
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Loots, G.G.1
Ovcharenko, I.2
-
6
-
-
0345874725
-
CONREAL: Conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting
-
314294 14672977 10.1101/gr.1642804
-
Berezikov E Guryev V Plasterk RH Cuppen E CONREAL: Conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting Genome Res 2004, 14(1):170-178. 314294 14672977 10.1101/gr.1642804
-
(2004)
Genome Res
, vol.14
, Issue.1
, pp. 170-178
-
-
Berezikov, E.1
Guryev, V.2
Plasterk, R.H.3
Cuppen, E.4
-
7
-
-
3242891274
-
ConSite: Web-based prediction of regulatory elements using cross-species comparison
-
(Web server issue). 10.1093/nar/gkh372 15215389 441510
-
Sandelin A Wasserman WW Lenhard B ConSite: Web-based prediction of regulatory elements using cross-species comparison Nucleic Acids Res 2004, 32(Web server issue):W249-52. 10.1093/nar/gkh372 15215389 441510
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Sandelin, A.1
Wasserman, W.W.2
Lenhard, B.3
-
8
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
430961 12529312 10.1101/gr.809403
-
Schwartz S Kent WJ Smit A Zhang Z Baertsch R Hardison RC Haussler D Miller W Human-mouse alignments with BLASTZ Genome Res 2003, 13(1):103-107. 430961 12529312 10.1101/gr.809403
-
(2003)
Genome Res
, vol.13
, Issue.1
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
9
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
-
430158 12654723 10.1101/gr.926603
-
Brudno M Do CB Cooper GM Kim MF Davydov E NISC Comparative Sequencing Program Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Genome Research 2003, 13(4):721-731. 430158 12654723 10.1101/gr.926603
-
(2003)
Genome Research
, vol.13
, Issue.4
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
Kim, M.F.4
Davydov, E.5
Green, E.D.6
Sidow, A.7
Batzoglou, S.8
-
10
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
383315 15060012 10.1101/gr.1960404
-
Bray N Pachter L MAVID: Constrained ancestral alignment of multiple sequences Genome Res 2004, 14(4):693-699. 383315 15060012 10.1101/ gr.1960404
-
(2004)
Genome Res
, vol.14
, Issue.4
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
11
-
-
33748526495
-
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
-
1557810 16899447 10.1093/nar/gkl525
-
Johnson R Gamblin RJ Ooi L Bruce AW Donaldson IJ Westhead DR Wood IC Jackson RM Buckley NJ Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication Nucleic Acids Res 2006, 34(14):3862-3877. 1557810 16899447 10.1093/nar/gkl525
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.14
, pp. 3862-3877
-
-
Johnson, R.1
Gamblin, R.J.2
Ooi, L.3
Bruce, A.W.4
Donaldson, I.J.5
Westhead, D.R.6
Wood, I.C.7
Jackson, R.M.8
Buckley, N.J.9
-
12
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
10.1038/nature04696 16625209
-
Bejerano G Lowe CB Ahituv N King B Siepel A Salama SR Rubin EM Kent WJ Haussler D A distal enhancer and an ultraconserved exon are derived from a novel retroposon Nature 2006, 441(7089):87-90. 10.1038/nature04696 16625209
-
(2006)
Nature
, vol.441
, Issue.7089
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.B.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.R.6
Rubin, E.M.7
Kent, W.J.8
Haussler, D.9
-
13
-
-
0037301560
-
Origin of a substantial fraction of human regulatory sequences from transposable elements
-
10.1016/S0168-9525(02)00006-9 12547512
-
Jordan IK Rogozin IB Glazko GV Koonin EV Origin of a substantial fraction of human regulatory sequences from transposable elements Trends Genet 2003, 19(2):68-72. 10.1016/S0168-9525(02)00006-9 12547512
-
(2003)
Trends Genet
, vol.19
, Issue.2
, pp. 68-72
-
-
Jordan, I.K.1
Rogozin, I.B.2
Glazko, G.V.3
Koonin, E.V.4
-
14
-
-
0037270315
-
AVID: A global alignment program
-
430967 12529311 10.1101/gr.789803
-
Bray N Dubchak I Pachter L AVID: A global alignment program Genome Res 2003, 13(1):97-102. 430967 12529311 10.1101/gr.789803
-
(2003)
Genome Res
, vol.13
, Issue.1
, pp. 97-102
-
-
Bray, N.1
Dubchak, I.2
Pachter, L.3
-
15
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
(DB)10.1093/nar/gkj143 16381825 1347505
-
Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A Reuter I Chekmenev D Krull M Hornischer K Voss N Stegmaier P Lewicki-Potapov B Saxel H Kel AE Wingender E TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res 2006, 34(DB):D108-110. 10.1093/nar/gkj143 16381825 1347505
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
Voss, N.11
Stegmaier, P.12
Lewicki-Potapov, B.13
Saxel, H.14
Kel, A.E.15
Wingender, E.16
-
16
-
-
84886756307
-
-
TRANSFAC® http://www.gene-regulation.com/pub/databases.html#transfac
-
TRANSFAC®
-
-
-
17
-
-
0041853625
-
MATCH: A tool for searching transcription factor binding sites in DNA sequences
-
169193 12824369 10.1093/nar/gkg585
-
Kel AE Gossling E Reuter I Cheremushkin E Kel-Margoulis OV Wingender E MATCH: A tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res 2003, 31(13):3576-3579. 169193 12824369 10.1093/nar/gkg585
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3576-3579
-
-
Kel, A.E.1
Gossling, E.2
Reuter, I.3
Cheremushkin, E.4
Kel-Margoulis, O.V.5
Wingender, E.6
-
18
-
-
84886767503
-
-
Match™ http://www.gene-regulation.com/cgi-bin/pub/programs/match/ bin/match.cgi
-
Match™
-
-
-
20
-
-
10344251533
-
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network
-
534610 15572454 10.1073/pnas.0407670101
-
Iwama H Gojobori T Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network Proc Natl Acad Sci USA 2004, 101(49):17156-17161. 534610 15572454 10.1073/ pnas.0407670101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.49
, pp. 17156-17161
-
-
Iwama, H.1
Gojobori, T.2
-
21
-
-
84886754567
-
-
ReAlignerV http://genet.med.kagawa-u.ac.jp
-
ReAlignerV
-
-
-
22
-
-
0032964297
-
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
-
10.1111/j.1574-6968.1999.tb13575.x 10339815
-
Tatusova TA Madden TL BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences FEMS Microbiol Lett 1999, 174(2):247-50. 10.1111/j.1574-6968.1999.tb13575.x 10339815
-
(1999)
FEMS Microbiol Lett
, vol.174
, Issue.2
, pp. 247-250
-
-
Tatusova, T.A.1
Madden, T.L.2
-
23
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
539979 15608248
-
Pruitt KD Tatusova T Maglott DR NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2005, 33(1):D501-D504. 539979 15608248
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.1
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
25
-
-
84886758005
-
-
Entrez GENE via FTP ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
-
Entrez GENE Via FTP
-
-
-
26
-
-
0036206069
-
Guidelines for Human Gene Nomenclature
-
10.1006/geno.2002.6748 11944974
-
Wain HM Lovering RC Bruford EA Lush MJ Wright MW Povey S Guidelines for Human Gene Nomenclature Genomics 2002, 79(4):464-470. 10.1006/ geno.2002.6748 11944974
-
(2002)
Genomics
, vol.79
, Issue.4
, pp. 464-470
-
-
Wain, H.M.1
Lovering, R.C.2
Bruford, E.A.3
Lush, M.J.4
Wright, M.W.5
Povey, S.6
-
30
-
-
84886754547
-
-
mavid-package-2.0.4 http://bio.math.berkeley.edu/mavid/download/
-
Mavid-package-2.0.4
-
-
-
31
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
308517 7984417 10.1093/nar/22.22.4673
-
Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680. 308517 7984417 10.1093/nar/22.22.4673
-
(1994)
Nucleic Acids Res
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
32
-
-
84874646997
-
-
ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
-
clustalw1.83 ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
-
Clustalw1.83
-
-
-
33
-
-
0027957393
-
fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
-
8193955
-
Olsen GJ Matsuda H Hagstrom R Overbeek R fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood Comput Appl Biosci 1994, 10(1):41-8. 8193955
-
(1994)
Comput Appl Biosci
, vol.10
, Issue.1
, pp. 41-48
-
-
Olsen, G.J.1
Matsuda, H.2
Hagstrom, R.3
Overbeek, R.4
-
34
-
-
84886755021
-
-
fastDNAml_1.2.2 http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
-
FastDNAml_1.2.2
-
-
-
37
-
-
2942516151
-
Correction: Benchmarking tools for the alignment of functional noncoding DNA
-
446183 15186509 10.1186/1471-2105-5-73
-
Pollard DA Bergman CM Stoye J Celniker SE Eisen MB Correction: Benchmarking tools for the alignment of functional noncoding DNA BMC Bioinformatics 2004, 5:73. 446183 15186509 10.1186/1471-2105-5-73
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 73
-
-
Pollard, D.A.1
Bergman, C.M.2
Stoye, J.3
Celniker, S.E.4
Eisen, M.B.5
-
38
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
165555 12520026 10.1093/nar/gkg108
-
Matys V Fricke E Geffers R Gössling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV Kloos DU Land S Lewicki-Potapov B Michael H Münch R Reuter I Rotert S Saxel H Scheer M Thiele S Wingender E TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31(1):374-8. 165555 12520026 10.1093/ nar/gkg108
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gössling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Münch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
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