-
1
-
-
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
-
2
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
10.1038/nbt1053, 15637633
-
Tompa M, Li N, Bailey TL, Church GM, Moor BD, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, R'egnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23:137-144. 10.1038/nbt1053, 15637633.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
Moor, B.D.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
Makeev, V.J.11
Mironov, A.A.12
Noble, W.S.13
Pavesi, G.14
Pesole, G.15
R'egnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
van Helden, J.20
Vandenbogaert, M.21
Weng, Z.22
Workman, C.23
Ye, C.24
Zhu, Z.25
more..
-
3
-
-
33846510838
-
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
-
10.1371/journal.pcbi.0030007, 1779301,1779301, 17238282
-
Down TA, Bergman CM, Su J, Hubbard TJP. Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster. PLoS Comput Biol 2007, 3:e7. 10.1371/journal.pcbi.0030007, 1779301,1779301, 17238282.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Down, T.A.1
Bergman, C.M.2
Su, J.3
Hubbard, T.J.P.4
-
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
-
-
34249848791
-
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
-
10.1073/pnas.0701811104, 1852749, 17442748
-
Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci USA 2007, 104(17):7145-50. 10.1073/pnas.0701811104, 1852749, 17442748.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.17
, pp. 7145-7150
-
-
Xie, X.1
Mikkelsen, T.S.2
Gnirke, A.3
Lindblad-Toh, K.4
Kellis, M.5
Lander, E.S.6
-
6
-
-
42649103655
-
W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data
-
10.1093/bioinformatics/btn088, 18325926
-
Chen X, Guo L, Fan Z, Jiang T. W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics 2008, 24(9):1121-8. 10.1093/bioinformatics/btn088, 18325926.
-
(2008)
Bioinformatics
, vol.24
, Issue.9
, pp. 1121-1128
-
-
Chen, X.1
Guo, L.2
Fan, Z.3
Jiang, T.4
-
7
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
10.1038/84792, 11175784
-
Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nat Genet 2001, 27(2):167-71. 10.1038/84792, 11175784.
-
(2001)
Nat Genet
, vol.27
, Issue.2
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
8
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu X, Brutlag D, Liu J. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature biotechnology 2002, 20(8):835-839.
-
(2002)
Nature biotechnology
, vol.20
, Issue.8
, pp. 835-839
-
-
Liu, X.1
Brutlag, D.2
Liu, J.3
-
9
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
10.1073/pnas.0630591100, 152294, 12626739
-
Conlon EM, Liu XS, Lieb JD, Liu JS. Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA 2003, 100(6):3339-44. 10.1073/pnas.0630591100, 152294, 12626739.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.6
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
10
-
-
77949916244
-
On the detection and refinement of transcription factor binding sites using ChIP-Seq data
-
10.1093/nar/gkp1180, 2853110, 20056654
-
Hu M, Yu J, Taylor JMG, Chinnaiyan AM, Qin ZS. On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Research 2010, 38(7):2154-67. 10.1093/nar/gkp1180, 2853110, 20056654.
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.7
, pp. 2154-2167
-
-
Hu, M.1
Yu, J.2
Taylor, J.M.G.3
Chinnaiyan, A.M.4
Qin, Z.S.5
-
11
-
-
77349120278
-
Genome-wide prediction of transcription factor binding sites using an integrated model
-
10.1186/gb-2010-11-1-r7, 2847719, 20096096
-
Won KJ, Ren B, Wang W. Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol 2010, 11:R7. 10.1186/gb-2010-11-1-r7, 2847719, 20096096.
-
(2010)
Genome Biol
, vol.11
-
-
Won, K.J.1
Ren, B.2
Wang, W.3
-
12
-
-
34250661506
-
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system
-
Meng X, Wolfe SA. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Methods 2006, 1:30-45.
-
(2006)
Nat Methods
, vol.1
, pp. 30-45
-
-
Meng, X.1
Wolfe, S.A.2
-
13
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcriptionfactor binding site specificities
-
10.1038/nbt1246, 16998473
-
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcriptionfactor binding site specificities. Nat Biotechnol 2006, 24(11):1429-35. 10.1038/nbt1246, 16998473.
-
(2006)
Nat Biotechnol
, vol.24
, Issue.11
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep, P.W.5
Bulyk, M.L.6
-
14
-
-
0020480251
-
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli
-
10.1093/nar/10.9.2997, 320670, 7048259
-
Stormo GD, Schneider TD, Gold L, Ehrenfeucht A. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Research 1982, 10(9):2997-3011. 10.1093/nar/10.9.2997, 320670, 7048259.
-
(1982)
Nucleic Acids Research
, vol.10
, Issue.9
, pp. 2997-3011
-
-
Stormo, G.D.1
Schneider, T.D.2
Gold, L.3
Ehrenfeucht, A.4
-
15
-
-
2942558697
-
On the power of profiles for transcription factor binding site detection
-
Rahmann S, Müller T, Vingron M. On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol 2003, 2:Article7.
-
(2003)
Stat Appl Genet Mol Biol
, vol.2
-
-
Rahmann, S.1
Müller, T.2
Vingron, M.3
-
16
-
-
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
-
17
-
-
0036493201
-
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
-
10.1093/nar/30.5.1255, 101241, 11861919
-
Bulyk ML, Johnson PLF, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 2002, 30(5):1255-1261. 10.1093/nar/30.5.1255, 101241, 11861919.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.5
, pp. 1255-1261
-
-
Bulyk, M.L.1
Johnson, P.L.F.2
Church, G.M.3
-
18
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
10.1126/science.1162327, 19443739
-
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML. Diversity and complexity in DNA recognition by transcription factors. Science 2009, 324(5935):1720-3. 10.1126/science.1162327, 19443739.
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
Kuznetsov, H.11
Wang, C.F.12
Coburn, D.13
Newburger, D.E.14
Morris, Q.15
Hughes, T.R.16
Bulyk, M.L.17
-
19
-
-
50449102853
-
Energydependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites
-
10.1073/pnas.0805909105, 2527919, 18723669
-
Mustonen V, Kinney J, Callan CG, Lässig M. Energydependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci USA 2008, 105(34):12376-81. 10.1073/pnas.0805909105, 2527919, 18723669.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.34
, pp. 12376-12381
-
-
Mustonen, V.1
Kinney, J.2
Callan, C.G.3
Lässig, M.4
-
20
-
-
20744440509
-
Identification of transcription factor binding sites with variable-order Bayesian networks
-
10.1093/bioinformatics/bti410, 15797905
-
Ben-Gal I, Shani A, Gohr A, Grau J, Arviv S, Shmilovici A, Posch S, Grosse I. Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics 2005, 21(11):2657-66. 10.1093/bioinformatics/bti410, 15797905.
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2657-2666
-
-
Ben-Gal, I.1
Shani, A.2
Gohr, A.3
Grau, J.4
Arviv, S.5
Shmilovici, A.6
Posch, S.7
Grosse, I.8
-
22
-
-
50949097456
-
A Feature-Based Approach to Modeling Protein-DNA Interactions
-
10.1371/journal.pcbi.1000154, 2516605, 18725950
-
Sharon E, Lubliner S, Segal E, Stormo G. A Feature-Based Approach to Modeling Protein-DNA Interactions. PLoS Comput Biol 2008, 4(8):e1000154. 10.1371/journal.pcbi.1000154, 2516605, 18725950.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.8
-
-
Sharon, E.1
Lubliner, S.2
Segal, E.3
Stormo, G.4
-
23
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
10.1126/science.1131007, 17218526
-
Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science 2007, 315(5809):233-7. 10.1126/science.1131007, 17218526.
-
(2007)
Science
, vol.315
, Issue.5809
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
24
-
-
0025008168
-
Sequence logos: a new way to display consensus sequences
-
10.1093/nar/18.20.6097, 332411, 2172928
-
Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Research 1990, 18(20):6097-100. 10.1093/nar/18.20.6097, 332411, 2172928.
-
(1990)
Nucleic Acids Research
, vol.18
, Issue.20
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
25
-
-
12344291347
-
Comparative analysis of methods for representing and searching for transcription factor binding sites
-
10.1093/bioinformatics/bth438, 15297295
-
Osada R, Zaslavsky E, Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics 2004, 20(18):3516-25. 10.1093/bioinformatics/bth438, 15297295.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3516-3525
-
-
Osada, R.1
Zaslavsky, E.2
Singh, M.3
-
26
-
-
1842505125
-
Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
-
10.1016/j.jmb.2004.02.048, 15066426
-
Sandelin A, Wasserman WW. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol Biol 2004, 338(2):207-215. 10.1016/j.jmb.2004.02.048, 15066426.
-
(2004)
J Mol Biol
, vol.338
, Issue.2
, pp. 207-215
-
-
Sandelin, A.1
Wasserman, W.W.2
-
27
-
-
38549096565
-
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
-
2238834, 18006571, Database
-
Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 2008, (36 Database):D102-6. 2238834, 18006571.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.H.E.3
Marstrand, T.4
Winther, O.5
da Piedade, I.6
Krogh, A.7
Lenhard, B.8
Sandelin, A.9
-
28
-
-
27644499659
-
Measuring similarities between transcription factor binding sites
-
10.1186/1471-2105-6-237, 1261160, 16191190
-
Kielbasa SM, Gonze D, Herzel H. Measuring similarities between transcription factor binding sites. BMC Bioinformatics 2005, 6:237. 10.1186/1471-2105-6-237, 1261160, 16191190.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 237
-
-
Kielbasa, S.M.1
Gonze, D.2
Herzel, H.3
-
29
-
-
34047192976
-
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
-
10.1371/journal.pcbi.0030061, 1848003, 17397256
-
Mahony S, Auron PE, Benos PV. DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput Biol 2007, 3(3):e61. 10.1371/journal.pcbi.0030061, 1848003, 17397256.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.3
-
-
Mahony, S.1
Auron, P.E.2
Benos, P.V.3
-
30
-
-
38849122853
-
Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering
-
10.1093/bioinformatics/btm610, 18174183
-
Pape UJ, Rahmann S, Vingron M. Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering. Bioinformatics 2008, 24(3):350-7. 10.1093/bioinformatics/btm610, 18174183.
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 350-357
-
-
Pape, U.J.1
Rahmann, S.2
Vingron, M.3
-
31
-
-
40149105450
-
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
-
10.1371/journal.pcbi.1000010, 2265534, 18463706
-
Habib N, Kaplan T, Margalit H, Friedman N, Fraenkel E. A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval. PLoS Computational Biology 2008, 4(2):e1000010. 10.1371/journal.pcbi.1000010, 2265534, 18463706.
-
(2008)
PLoS Computational Biology
, vol.4
, Issue.2
-
-
Habib, N.1
Kaplan, T.2
Margalit, H.3
Friedman, N.4
Fraenkel, E.5
-
32
-
-
68949147686
-
FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral
-
10.1186/1471-2105-10-224, 2722654, 19615102
-
Garcia F, Lopez FJ, Cano C, Blanco A. FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral. BMC bioinformatics 2009, 10:224. 10.1186/1471-2105-10-224, 2722654, 19615102.
-
(2009)
BMC bioinformatics
, vol.10
, pp. 224
-
-
Garcia, F.1
Lopez, F.J.2
Cano, C.3
Blanco, A.4
-
33
-
-
29144465554
-
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
-
10.1093/bioinformatics/bti1025, 15961468
-
Mahony S, Golden A, Smith TJ, Benos PV. Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics 2005, 21(Suppl 1):i283-i291. 10.1093/bioinformatics/bti1025, 15961468.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL 1
-
-
Mahony, S.1
Golden, A.2
Smith, T.J.3
Benos, P.V.4
-
34
-
-
32144452542
-
Sequence features of DNA binding sites reveal structural class of associated transcription factor
-
10.1093/bioinformatics/bti731, 16267080
-
Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics 2006, 22(2):157-163. 10.1093/bioinformatics/bti731, 16267080.
-
(2006)
Bioinformatics
, vol.22
, Issue.2
, pp. 157-163
-
-
Narlikar, L.1
Hartemink, A.J.2
-
35
-
-
33747879675
-
Informative priors based on transcription factor structural class improve de novo motif discovery
-
10.1093/bioinformatics/btl251, 16873497
-
Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics 2006, 22(14):e384-e392. 10.1093/bioinformatics/btl251, 16873497.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Narlikar, L.1
Gordân, R.2
Ohler, U.3
Hartemink, A.J.4
-
36
-
-
3242662380
-
MotifPrototyper: a Bayesian profile model for motif families
-
10.1073/pnas.0403564101, 489970, 15252200
-
Xing EP, Karp RM. MotifPrototyper: a Bayesian profile model for motif families. Proc Natl Acad Sci USA 2004, 101(29):10523-10528. 10.1073/pnas.0403564101, 489970, 15252200.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.29
, pp. 10523-10528
-
-
Xing, E.P.1
Karp, R.M.2
-
37
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
-
10.1093/nar/gkj143, 1347505, 16381825, Database
-
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 Database):D108-D110. 10.1093/nar/gkj143, 1347505, 16381825.
-
(2006)
Nucleic Acids Res
, Issue.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
-
38
-
-
75549083247
-
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
-
10.1093/nar/gkp950, 2808906, 19906716 Database
-
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 Research 2010, (38 Database):D105-D110. 10.1093/nar/gkp950, 2808906, 19906716.
-
(2010)
Nucleic Acids Research
, Issue.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
-
39
-
-
58149200952
-
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
-
10.1093/nar/gkn660, 2686578, 18842628, Database
-
Newburger DE, Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Research 2009, (37 Database):D77-D82. 10.1093/nar/gkn660, 2686578, 18842628.
-
(2009)
Nucleic Acids Research
, Issue.37
-
-
Newburger, D.E.1
Bulyk, M.L.2
-
40
-
-
0026538243
-
Molecular characterization of helixloop-helix peptides
-
10.1126/science.1312255, 1312255
-
Anthony-Cahill SJ, Benfield PA, Fairman R, Wasserman ZR, Brenner SL, Stafford WF, Altenbach C, Hubbell WL, DeGrado WF. Molecular characterization of helixloop-helix peptides. Science 1992, 255(5047):979-83. 10.1126/science.1312255, 1312255.
-
(1992)
Science
, vol.255
, Issue.5047
, pp. 979-983
-
-
Anthony-Cahill, S.J.1
Benfield, P.A.2
Fairman, R.3
Wasserman, Z.R.4
Brenner, S.L.5
Stafford, W.F.6
Altenbach, C.7
Hubbell, W.L.8
DeGrado, W.F.9
-
41
-
-
0027960541
-
Selection of new HSF1 and HSF2 DNA-binding sites reveals difference in trimer cooperativity
-
359295, 7935474
-
Kroeger PE, Morimoto RI. Selection of new HSF1 and HSF2 DNA-binding sites reveals difference in trimer cooperativity. Mol Cell Biol 1994, 14(11):7592-603. 359295, 7935474.
-
(1994)
Mol Cell Biol
, vol.14
, Issue.11
, pp. 7592-7603
-
-
Kroeger, P.E.1
Morimoto, R.I.2
-
42
-
-
0141596527
-
Estimating a Dirichlet distribution
-
Minka TP. Estimating a Dirichlet distribution. 2003, http://research.microsoft.com/en-us/um/people/minka/papers/dirichlet/minka-dirichlet.pdf
-
(2003)
-
-
Minka, T.P.1
-
43
-
-
41149162675
-
NestedMICA as an ab initio protein motif discovery tool
-
10.1186/1471-2105-9-19, 2267705, 18194537
-
Dogruel M, Down T, Hubbard T. NestedMICA as an ab initio protein motif discovery tool. BMC Bioinformatics 2008, 9:19. 10.1186/1471-2105-9-19, 2267705, 18194537.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 19
-
-
Dogruel, M.1
Down, T.2
Hubbard, T.3
-
44
-
-
34249662161
-
Nested Sampling for General Bayesian Computation
-
2447321, 18629038
-
Skilling J. Nested Sampling for General Bayesian Computation. 2004, 2447321, 18629038.
-
(2004)
-
-
Skilling, J.1
-
45
-
-
34547569191
-
STAMP: a web tool for exploring DNA-binding motif similarities
-
10.1093/nar/gkm272, 1933206, 17478497, Web Server
-
Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, (35 Web Server):W253-W258. 10.1093/nar/gkm272, 1933206, 17478497.
-
(2007)
Nucleic Acids Res
, Issue.35
-
-
Mahony, S.1
Benos, P.V.2
-
46
-
-
14944363825
-
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
-
10.1093/nar/gki282, 1064142, 15760844
-
Down TA, Hubbard TJP. NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 2005, 33(5):1445-1453. 10.1093/nar/gki282, 1064142, 15760844.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.5
, pp. 1445-1453
-
-
Down, T.A.1
Hubbard, T.J.P.2
-
47
-
-
57149113149
-
BayesMD: Flexible Biological Modeling for Motif Discovery
-
10.1089/cmb.2007.0176, 19040368
-
Tang MHE, Krogh A, Winther O. BayesMD: Flexible Biological Modeling for Motif Discovery. Journal of Computational Biology 2008, 15(10):1347-1363. 10.1089/cmb.2007.0176, 19040368.
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.10
, pp. 1347-1363
-
-
Tang, M.H.E.1
Krogh, A.2
Winther, O.3
-
48
-
-
38549176691
-
Ensembl 2008
-
2238821, 18000006, Database
-
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJP, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. Ensembl 2008. Nucleic Acids Res 2008, (36 Database):D707-14. 2238821, 18000006.
-
(2008)
Nucleic Acids Res
, Issue.36
-
-
Flicek, P.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
Down, T.11
Dyer, S.C.12
Eyre, T.13
Fitzgerald, S.14
Fernandez-Banet, J.15
Gräf, S.16
Haider, S.17
Hammond, M.18
Holland, R.19
Howe, K.L.20
Howe, K.21
Johnson, N.22
Jenkinson, A.23
Kähäri, A.24
Keefe, D.25
Kokocinski, F.26
Kulesha, E.27
Lawson, D.28
Longden, I.29
Megy, K.30
Meidl, P.31
Overduin, B.32
Parker, A.33
Pritchard, B.34
Prlic, A.35
Rice, S.36
Rios, D.37
Schuster, M.38
Sealy, I.39
Slater, G.40
Smedley, D.41
Spudich, G.42
Trevanion, S.43
Vilella, A.J.44
Vogel, J.45
White, S.46
Wood, M.47
Birney, E.48
Cox, T.49
Curwen, V.50
Durbin, R.51
Fernandez-Suarez, X.M.52
Herrero, J.53
Hubbard, T.J.P.54
Kasprzyk, A.55
Proctor, G.56
Smith, J.57
Ureta-Vidal, A.58
Searle, S.59
more..
-
49
-
-
0035478854
-
Random Forests
-
Breiman L. Random Forests. Machine Learning 2001, 45:5-32.
-
(2001)
Machine Learning
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
50
-
-
0036513626
-
The snail superfamily of zinc-finger transcription factors
-
10.1038/nrm757, 11994736
-
Nieto MA. The snail superfamily of zinc-finger transcription factors. Nat Rev Mol Cell Biol 2002, 3(3):155-66. 10.1038/nrm757, 11994736.
-
(2002)
Nat Rev Mol Cell Biol
, vol.3
, Issue.3
, pp. 155-166
-
-
Nieto, M.A.1
-
51
-
-
45449115390
-
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
-
10.1016/j.cell.2008.05.024, 2531161, 18585359
-
Berger M, Badis G, Gehrke A, Talukder S, Philippakis A, Penacastillo L, Alleyne T, Mnaimneh S, Botvinnik O, Chan E. Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences. Cell 2008, 133(7):1266-1276. 10.1016/j.cell.2008.05.024, 2531161, 18585359.
-
(2008)
Cell
, vol.133
, Issue.7
, pp. 1266-1276
-
-
Berger, M.1
Badis, G.2
Gehrke, A.3
Talukder, S.4
Philippakis, A.5
Penacastillo, L.6
Alleyne, T.7
Mnaimneh, S.8
Botvinnik, O.9
Chan, E.10
-
52
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
10.1016/j.cell.2008.05.023, 2478728, 18585360
-
Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008, 133(7):1277-89. 10.1016/j.cell.2008.05.023, 2478728, 18585360.
-
(2008)
Cell
, vol.133
, Issue.7
, pp. 1277-1289
-
-
Noyes, M.B.1
Christensen, R.G.2
Wakabayashi, A.3
Stormo, G.D.4
Brodsky, M.H.5
Wolfe, S.A.6
-
53
-
-
77951944595
-
IMotifs: an integrated sequence motif visualization and analysis environment
-
Piipari M, Down TA, Saini H, Enright A, Hubbard TJ. iMotifs: an integrated sequence motif visualization and analysis environment. Bioinformatics 2010, btq026.
-
(2010)
Bioinformatics
-
-
Piipari, M.1
Down, T.A.2
Saini, H.3
Enright, A.4
Hubbard, T.J.5
-
55
-
-
32144436709
-
WindowMasker: window-based masker for sequenced genomes
-
10.1093/bioinformatics/bti774, 16287941
-
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics 2006, 22(2):134-41. 10.1093/bioinformatics/bti774, 16287941.
-
(2006)
Bioinformatics
, vol.22
, Issue.2
, pp. 134-141
-
-
Morgulis, A.1
Gertz, E.M.2
Schäffer, A.A.3
Agarwala, R.4
-
57
-
-
0345040873
-
Classification and Regression by randomForest
-
Liaw A, Wiener M. Classification and Regression by randomForest. R News 2002, 2(3):18-22.
-
(2002)
R News
, vol.2
, Issue.3
, pp. 18-22
-
-
Liaw, A.1
Wiener, M.2
|