-
1
-
-
67749113808
-
Transcriptional regulatory circuits: predicting numbers from alphabets
-
2745280, 19628860
-
Kim HD, Shay T, O'Shea EK, Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science 2009, 325(5939):429-432. 2745280, 19628860.
-
(2009)
Science
, vol.325
, Issue.5939
, pp. 429-432
-
-
Kim, H.D.1
Shay, T.2
O'Shea, E.K.3
Regev, A.4
-
2
-
-
31144435316
-
Towards multidimensional genome annotation
-
10.1038/nrg1769, 16418748
-
Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7(2):130-141. 10.1038/nrg1769, 16418748.
-
(2006)
Nat Rev Genet
, vol.7
, Issue.2
, pp. 130-141
-
-
Reed, J.L.1
Famili, I.2
Thiele, I.3
Palsson, B.O.4
-
3
-
-
33746835021
-
Computational identification of transcriptional regulatory elements in DNA sequence
-
10.1093/nar/gkl372, 1524905, 16855295
-
GuhaThakurta D. Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res 2006, 34(12):3585-3598. 10.1093/nar/gkl372, 1524905, 16855295.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.12
, pp. 3585-3598
-
-
GuhaThakurta, D.1
-
4
-
-
0037443976
-
Toucan: deciphering the cis-regulatory logic of coregulated genes
-
10.1093/nar/gkg268, 152870, 12626717
-
Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, De Moor B. Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res 2003, 31(6):1753-1764. 10.1093/nar/gkg268, 152870, 12626717.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.6
, pp. 1753-1764
-
-
Aerts, S.1
Thijs, G.2
Coessens, B.3
Staes, M.4
Moreau, Y.5
De Moor, B.6
-
5
-
-
0033374594
-
Recognition of regulatory sites by genomic comparison
-
10.1016/S0923-2508(99)00117-5, 10673013
-
Gelfand MS. Recognition of regulatory sites by genomic comparison. Res Microbiol 1999, 150:755-771. 10.1016/S0923-2508(99)00117-5, 10673013.
-
(1999)
Res Microbiol
, vol.150
, pp. 755-771
-
-
Gelfand, M.S.1
-
6
-
-
38549144819
-
A survey of DNA motif finding algorithms
-
10.1186/1471-2105-8-S7-S21, 2099490, 18047721
-
Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21. 10.1186/1471-2105-8-S7-S21, 2099490, 18047721.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 7
-
-
Das, M.K.1
Dai, H.K.2
-
7
-
-
34247579156
-
A survey of motif discovery methods in an integrated framework
-
10.1186/1745-6150-1-11, 1479319, 16600018
-
Sandve GK, Drablos F. A survey of motif discovery methods in an integrated framework. Biol Direct 2006, 1:11. 10.1186/1745-6150-1-11, 1479319, 16600018.
-
(2006)
Biol Direct
, vol.1
, pp. 11
-
-
Sandve, G.K.1
Drablos, F.2
-
8
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
10.1371/journal.pcbi.0020036, 1447654, 16683017
-
MacIsaac KD, Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol 2006, 2(4):e36. 10.1371/journal.pcbi.0020036, 1447654, 16683017.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.4
-
-
MacIsaac, K.D.1
Fraenkel, E.2
-
9
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu XS, Brutlag DL, Liu JS. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20(8):835-839.
-
(2002)
Nat Biotechnol
, vol.20
, Issue.8
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
10
-
-
33747829925
-
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
-
1538899, 16845071
-
Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res 2006, 34(Web Server issue):W566-570. 1538899, 16845071.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Pavesi, G.1
Mereghetti, P.2
Zambelli, F.3
Stefani, M.4
Mauri, G.5
Pesole, G.6
-
11
-
-
0034565285
-
Combinatorial approaches to finding subtle signals in DNA sequences
-
Pevzner PA, Sze SH. Combinatorial approaches to finding subtle signals in DNA sequences. Proc Int Conf Intell Syst Mol Biol 2000, 8:269-278.
-
(2000)
Proc Int Conf Intell Syst Mol Biol
, vol.8
, pp. 269-278
-
-
Pevzner, P.A.1
Sze, S.H.2
-
12
-
-
0345614410
-
CUBIC: identification of regulatory binding sites through data clustering
-
10.1142/S0219720003000162, 15290780
-
Olman V, Xu D, Xu Y. CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol 2003, 1(1):21-40. 10.1142/S0219720003000162, 15290780.
-
(2003)
J Bioinform Comput Biol
, vol.1
, Issue.1
, pp. 21-40
-
-
Olman, V.1
Xu, D.2
Xu, Y.3
-
13
-
-
3242888795
-
CWINNOWER algorithm for finding fuzzy dna motifs
-
10.1142/S0219720004000466, 15272432
-
Liang S, Samanta MP, Biegel BA. cWINNOWER algorithm for finding fuzzy dna motifs. J Bioinform Comput Biol 2004, 2(1):47-60. 10.1142/S0219720004000466, 15272432.
-
(2004)
J Bioinform Comput Biol
, vol.2
, Issue.1
, pp. 47-60
-
-
Liang, S.1
Samanta, M.P.2
Biegel, B.A.3
-
14
-
-
33747893656
-
MotifCut: regulatory motifs finding with maximum density subgraphs
-
10.1093/bioinformatics/btl243, 16873465
-
Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. MotifCut: regulatory motifs finding with maximum density subgraphs. Bioinformatics 2006, 22(14):e150-157. 10.1093/bioinformatics/btl243, 16873465.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Fratkin, E.1
Naughton, B.T.2
Brutlag, D.L.3
Batzoglou, S.4
-
15
-
-
66349110658
-
Efficient exact motif discovery
-
10.1093/bioinformatics/btp188, 2687942, 19478010
-
Marschall T, Rahmann S. Efficient exact motif discovery. Bioinformatics 2009, 25(12):i356-364. 10.1093/bioinformatics/btp188, 2687942, 19478010.
-
(2009)
Bioinformatics
, vol.25
, Issue.12
-
-
Marschall, T.1
Rahmann, S.2
-
16
-
-
0027912333
-
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
-
10.1126/science.8211139, 8211139
-
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214. 10.1126/science.8211139, 8211139.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
17
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
10.1006/jmbi.2000.3519, 10698627
-
Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296(5):1205-1214. 10.1006/jmbi.2000.3519, 10698627.
-
(2000)
J Mol Biol
, vol.296
, Issue.5
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
18
-
-
0036137323
-
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
10.1093/bioinformatics/17.12.1113, 11751219
-
Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouze P, Moreau Y. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113-1122. 10.1093/bioinformatics/17.12.1113, 11751219.
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1113-1122
-
-
Thijs, G.1
Lescot, M.2
Marchal, K.3
Rombauts, S.4
De Moor, B.5
Rouze, P.6
Moreau, Y.7
-
19
-
-
0035228215
-
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. PacSympBiocomput: 2001 2001, 127-138.
-
(2001)
PacSympBiocomput: 2001
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
20
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
21
-
-
38049141180
-
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
-
10.1186/1471-2105-8-385, 2194741, 17937785
-
Redhead E, Bailey TL. Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics 2007, 8:385. 10.1186/1471-2105-8-385, 2194741, 17937785.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 385
-
-
Redhead, E.1
Bailey, T.L.2
-
22
-
-
53749093398
-
Seeder: discriminative seeding DNA motif discovery
-
10.1093/bioinformatics/btn444, 2562012, 18718942
-
Fauteux F, Blanchette M, Stromvik MV. Seeder: discriminative seeding DNA motif discovery. Bioinformatics 2008, 24(20):2303-2307. 10.1093/bioinformatics/btn444, 2562012, 18718942.
-
(2008)
Bioinformatics
, vol.24
, Issue.20
, pp. 2303-2307
-
-
Fauteux, F.1
Blanchette, M.2
Stromvik, M.V.3
-
23
-
-
73449094886
-
Discovery of regulatory elements is improved by a discriminatory approach
-
10.1371/journal.pcbi.1000562, 2770120, 19911049
-
Valen E, Sandelin A, Winther O, Krogh A. Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol 2009, 5(11):e1000562. 10.1371/journal.pcbi.1000562, 2770120, 19911049.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.11
-
-
Valen, E.1
Sandelin, A.2
Winther, O.3
Krogh, A.4
-
24
-
-
0242690451
-
Discriminative motifs
-
10.1089/10665270360688219, 12935347
-
Sinha S. Discriminative motifs. J Comput Biol 2003, 10(3-4):599-615. 10.1089/10665270360688219, 12935347.
-
(2003)
J Comput Biol
, vol.10
, Issue.3-4
, pp. 599-615
-
-
Sinha, S.1
-
25
-
-
0037109192
-
Additivity in protein-DNA interactions: how good an approximation is it?
-
10.1093/nar/gkf578, 137142, 12384591
-
Benos PV, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic Acids Res 2002, 30(20):4442-4451. 10.1093/nar/gkf578, 137142, 12384591.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.20
, pp. 4442-4451
-
-
Benos, P.V.1
Bulyk, M.L.2
Stormo, G.D.3
-
26
-
-
67249157808
-
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
-
10.1093/nar/gkp248, 2691844, 19383880
-
Zhang S, Xu M, Li S, Su Z. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res 2009, 37(10):e72. 10.1093/nar/gkp248, 2691844, 19383880.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.10
-
-
Zhang, S.1
Xu, M.2
Li, S.3
Su, Z.4
-
27
-
-
75549087626
-
Saccharomyces Genome Database provides mutant phenotype data
-
2808950, 19906697
-
Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, et al. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res 2010, 38(Database issue):D433-436. 2808950, 19906697.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Engel, S.R.1
Balakrishnan, R.2
Binkley, G.3
Christie, K.R.4
Costanzo, M.C.5
Dwight, S.S.6
Fisk, D.G.7
Hirschman, J.E.8
Hitz, B.C.9
Hong, E.L.10
-
28
-
-
38549140094
-
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
2238961, 18158297
-
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2008, 36(Database issue):D120-124. 2238961, 18158297.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gama-Castro, S.1
Jimenez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Penaloza-Spinola, M.I.5
Contreras-Moreira, B.6
Segura-Salazar, J.7
Muniz-Rascado, L.8
Martinez-Flores, I.9
Salgado, H.10
-
29
-
-
38549162091
-
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
-
2247474, 17962296
-
Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008, 36(Database issue):D93-96. 2247474, 17962296.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Sierro, N.1
Makita, Y.2
de Hoon, M.3
Nakai, K.4
-
30
-
-
38549105493
-
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
-
2238825, 18039705
-
Halfon MS, Gallo SM, Bergman CM. REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res 2008, 36(Database issue):D594-598. 2238825, 18039705.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Halfon, M.S.1
Gallo, S.M.2
Bergman, C.M.3
-
31
-
-
75549083247
-
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38(Database):D105-110.
-
Nucleic Acids Res
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
32
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
10.1038/nbt1053, 15637633
-
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23(1):137-144. 10.1038/nbt1053, 15637633.
-
(2005)
Nat Biotechnol
, vol.23
, Issue.1
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
-
33
-
-
26444584579
-
Limitations and potentials of current motif discovery algorithms
-
10.1093/nar/gki791, 1199555, 16284194
-
Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913. 10.1093/nar/gki791, 1199555, 16284194.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.15
, pp. 4899-4913
-
-
Hu, J.1
Li, B.2
Kihara, D.3
-
34
-
-
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
-
35
-
-
0000133199
-
Identifying protein-binding sites from unaligned DNA fragments
-
10.1073/pnas.86.4.1183, 286650, 2919167
-
Stormo GD, Hartzell GW. Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA 1989, 86(4):1183-1187. 10.1073/pnas.86.4.1183, 286650, 2919167.
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, Issue.4
, pp. 1183-1187
-
-
Stormo, G.D.1
Hartzell, G.W.2
-
36
-
-
0034919548
-
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
-
10.1101/gr.182901, 11435399
-
Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 2001, 11(7):1175-1186. 10.1101/gr.182901, 11435399.
-
(2001)
Genome Res
, vol.11
, Issue.7
, 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
-
37
-
-
0035253676
-
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
-
10.1093/nar/29.3.774, 30389, 11160901
-
McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 2001, 29(3):774-782. 10.1093/nar/29.3.774, 30389, 11160901.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.3
, pp. 774-782
-
-
McCue, L.1
Thompson, W.2
Carmack, C.3
Ryan, M.P.4
Liu, J.S.5
Derbyshire, V.6
Lawrence, C.E.7
-
38
-
-
3543068251
-
Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus
-
10.1101/gr.2242604, 442153, 15231752
-
Alkema WB, Lenhard B, Wasserman WW. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res 2004, 14(7):1362-1373. 10.1101/gr.2242604, 442153, 15231752.
-
(2004)
Genome Res
, vol.14
, Issue.7
, pp. 1362-1373
-
-
Alkema, W.B.1
Lenhard, B.2
Wasserman, W.W.3
-
39
-
-
33645832957
-
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups
-
10.1093/nar/gkl138, 1435977, 16614445
-
Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res 2006, 34(7):1947-1958. 10.1093/nar/gkl138, 1435977, 16614445.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.7
, pp. 1947-1958
-
-
Wels, M.1
Francke, C.2
Kerkhoven, R.3
Kleerebezem, M.4
Siezen, R.J.5
-
40
-
-
28444484981
-
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
-
10.1073/pnas.0505147102, 1297658, 16301543
-
Wang T, Stormo GD. Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci USA 2005, 102(48):17400-17405. 10.1073/pnas.0505147102, 1297658, 16301543.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.48
, pp. 17400-17405
-
-
Wang, T.1
Stormo, G.D.2
-
41
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
10.1101/gr.6902, 186562, 11997340
-
Blanchette M, Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 2002, 12:739-748. 10.1101/gr.6902, 186562, 11997340.
-
(2002)
Genome Res
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
42
-
-
0041589546
-
FootPrinter: A program designed for phylogenetic footprinting
-
10.1093/nar/gkg606, 169012, 12824433
-
Blanchette M, Tompa M. FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res 2003, 31(13):3840-3842. 10.1093/nar/gkg606, 169012, 12824433.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3840-3842
-
-
Blanchette, M.1
Tompa, M.2
-
43
-
-
33847664259
-
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
-
10.1186/1471-2105-8-46, 1803799, 17286865
-
Pavesi G, Zambelli F, Pesole G. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 2007, 8:46. 10.1186/1471-2105-8-46, 1803799, 17286865.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 46
-
-
Pavesi, G.1
Zambelli, F.2
Pesole, G.3
-
44
-
-
34547876110
-
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
-
10.1093/bioinformatics/btm241, 2268014, 17488758
-
Newberg LA, Thompson WA, Conlan S, Smith TM, McCue LA, Lawrence CE. A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction. Bioinformatics 2007, 23(14):1718-1727. 10.1093/bioinformatics/btm241, 2268014, 17488758.
-
(2007)
Bioinformatics
, vol.23
, Issue.14
, pp. 1718-1727
-
-
Newberg, L.A.1
Thompson, W.A.2
Conlan, S.3
Smith, T.M.4
McCue, L.A.5
Lawrence, C.E.6
-
45
-
-
33750218960
-
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
-
10.1371/journal.pcbi.0010067, 1309704, 16477324
-
Siddharthan R, Siggia ED, van Nimwegen E. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 2005, 1(7):e67. 10.1371/journal.pcbi.0010067, 1309704, 16477324.
-
(2005)
PLoS Comput Biol
, vol.1
, Issue.7
-
-
Siddharthan, R.1
Siggia, E.D.2
van Nimwegen, E.3
-
46
-
-
13244260826
-
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences
-
10.1186/1471-2105-5-170, 534098, 15511292
-
Sinha S, Blanchette M, Tompa M. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 2004, 5:170. 10.1186/1471-2105-5-170, 534098, 15511292.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 170
-
-
Sinha, S.1
Blanchette, M.2
Tompa, M.3
-
47
-
-
1542376789
-
Eukaryotic regulatory element conservation analysis and identification using comparative genomics
-
10.1101/gr.1327604, 353232, 14993210
-
Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 2004, 14(3):451-458. 10.1101/gr.1327604, 353232, 14993210.
-
(2004)
Genome Res
, vol.14
, Issue.3
, pp. 451-458
-
-
Liu, Y.1
Liu, X.S.2
Wei, L.3
Altman, R.B.4
Batzoglou, S.5
-
48
-
-
0344906814
-
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
-
10.1093/bioinformatics/btg329, 14668220
-
Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19(18):2369-2380. 10.1093/bioinformatics/btg329, 14668220.
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2369-2380
-
-
Wang, T.1
Stormo, G.D.2
-
49
-
-
77951266764
-
Finding regulatory DNA motifs using alignment-free evolutionary conservation information
-
Gordan R, Narlikar L, Hartemink AJ. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res 38(6):e90.
-
Nucleic Acids Res
, vol.38
, Issue.6
-
-
Gordan, R.1
Narlikar, L.2
Hartemink, A.J.3
-
50
-
-
34547568870
-
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches
-
10.1093/nar/gkm376, 1933171, 17584794
-
Romer KA, Kayombya GR, Fraenkel E. WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. Nucleic Acids Res 2007, 35(Web Server):W217-220. 10.1093/nar/gkm376, 1933171, 17584794.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Romer, K.A.1
Kayombya, G.R.2
Fraenkel, E.3
-
51
-
-
33847107996
-
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
-
10.1186/1471-2105-7-342, 1539026, 16839417
-
Hu J, Yang YD, Kihara D. EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinformatics 2006, 7:342. 10.1186/1471-2105-7-342, 1539026, 16839417.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 342
-
-
Hu, J.1
Yang, Y.D.2
Kihara, D.3
-
52
-
-
77954782940
-
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes
-
10.1186/1471-2105-11-397, 2920276, 20653963
-
Zhang S, Li S, Pham PT, Su Z. Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. BMC Bioinformatics 2010, 11:397. 10.1186/1471-2105-11-397, 2920276, 20653963.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 397
-
-
Zhang, S.1
Li, S.2
Pham, P.T.3
Su, Z.4
-
53
-
-
34347339593
-
Improved benchmarks for computational motif discovery
-
10.1186/1471-2105-8-193, 1903367, 17559676
-
Sandve GK, Abul O, Walseng V, Drablos F. Improved benchmarks for computational motif discovery. BMC Bioinformatics 2007, 8:193. 10.1186/1471-2105-8-193, 1903367, 17559676.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 193
-
-
Sandve, G.K.1
Abul, O.2
Walseng, V.3
Drablos, F.4
-
54
-
-
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
-
55
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. ProcNatlAcadSciUSA 1996, 93:10268-10273.
-
(1996)
ProcNatlAcadSciUSA
, vol.93
, pp. 10268-10273
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
56
-
-
0003037529
-
Reducibility Among Combinatorial Problems
-
New York: Plenum, R. E. Miller and J. W. Thatcher
-
Karp RM. Reducibility Among Combinatorial Problems. Complexity of Computer Computations 1972, 85-103. New York: Plenum, R. E. Miller and J. W. Thatcher.
-
(1972)
Complexity of Computer Computations
, pp. 85-103
-
-
Karp, R.M.1
|