-
1
-
-
77955393112
-
Uncovering the complexity of transcriptomes with RNA-Seq
-
Costa V, Angelini C, De Feis I, Ciccodicola A. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010, 2010:1-19.
-
(2010)
J Biomed Biotechnol
, vol.2010
, pp. 1-19
-
-
Costa, V.1
Angelini, C.2
De Feis, I.3
Ciccodicola, A.4
-
2
-
-
84875590756
-
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
-
3603212, 22517426
-
Zambelli F, Pesole G, Pavesi G. Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Brief Bioinform 2012, 14:225-237. 3603212, 22517426.
-
(2012)
Brief Bioinform
, vol.14
, pp. 225-237
-
-
Zambelli, F.1
Pesole, G.2
Pavesi, G.3
-
3
-
-
84883587895
-
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
-
10.1093/nar/gkt448, 3692095, 23748563
-
Zambelli F, Pesole G, Pavesi G. PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res 2013, 41:W535-W543. 10.1093/nar/gkt448, 3692095, 23748563.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Zambelli, F.1
Pesole, G.2
Pavesi, G.3
-
4
-
-
33747823564
-
MEME: discovering and analyzing DNA and protein sequence motifs
-
10.1093/nar/gkl198, 1538909, 16845028
-
Bailey T, Williams N, Misleh C, Li W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34:W369-W373. 10.1093/nar/gkl198, 1538909, 16845028.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Bailey, T.1
Williams, N.2
Misleh, C.3
Li, W.4
-
5
-
-
44949239504
-
Discovering sequence motifs with arbitrary insertions and deletions
-
10.1371/journal.pcbi.1000071, 2323616, 18437229
-
Frith M, Saunders N, Kobe B, Bailey T. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol 2008, 4:e1000071. 10.1371/journal.pcbi.1000071, 2323616, 18437229.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Frith, M.1
Saunders, N.2
Kobe, B.3
Bailey, T.4
-
6
-
-
74949138014
-
Exhaustive search for over-represented DNA sequence motifs with CisFinder
-
10.1093/dnares/dsp014, 2762409, 19740934
-
Sharov A, Ko M. Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res 2009, 16:261-273. 10.1093/dnares/dsp014, 2762409, 19740934.
-
(2009)
DNA Res
, vol.16
, pp. 261-273
-
-
Sharov, A.1
Ko, M.2
-
7
-
-
75949114262
-
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data
-
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics 2006, 25:3191-3193.
-
(2006)
Bioinformatics
, vol.25
, pp. 3191-3193
-
-
Jin, V.X.1
Apostolos, J.2
Nagisetty, N.S.3
Farnham, P.J.4
-
8
-
-
79951974373
-
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
-
10.1093/bioinformatics/btq707, 3105477, 21183585
-
Kuttippurathu L, Hsing M, Liu Y. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics 2011, 27:715-717. 10.1093/bioinformatics/btq707, 3105477, 21183585.
-
(2011)
Bioinformatics
, vol.27
, pp. 715-717
-
-
Kuttippurathu, L.1
Hsing, M.2
Liu, Y.3
-
9
-
-
79958090979
-
DREME: motif discovery in transcription factor ChIP-seq data
-
10.1093/bioinformatics/btr261, 3106199, 21543442
-
Bailey T. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011, 27:1653-1659. 10.1093/bioinformatics/btr261, 3106199, 21543442.
-
(2011)
Bioinformatics
, vol.27
, pp. 1653-1659
-
-
Bailey, T.1
-
10
-
-
79958117256
-
MEME-ChIP: motif analysis of large DNA datasets
-
10.1093/bioinformatics/btr189, 3106185, 21486936
-
Machanick P, Bailey T. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 2011, 27:1696-1697. 10.1093/bioinformatics/btr189, 3106185, 21486936.
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.2
-
11
-
-
84857859359
-
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
-
10.1093/nar/gkr1104, 3287167, 22156162
-
Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 2012, 40:e31. 10.1093/nar/gkr1104, 3287167, 22156162.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Thomas-Chollier, M.1
Herrmann, C.2
Defrance, M.3
Sand, O.4
Thieffry, D.5
van Helden, J.6
-
12
-
-
36248974151
-
Fast and practical algorithms for planted (l, d) motif search
-
Davila J, Balla S, Rajasekaran S. Fast and practical algorithms for planted (l, d) motif search. IEEE/ACM Trans Comp Biol Bioinfo 2007, 4:544-552.
-
(2007)
IEEE/ACM Trans Comp Biol Bioinfo
, vol.4
, pp. 544-552
-
-
Davila, J.1
Balla, S.2
Rajasekaran, S.3
-
13
-
-
37549019305
-
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
-
10.1093/bioinformatics/btm543, 18024972
-
Liang K, Wang X, Anastassiou D. A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. Bioinformatics 2008, 24:46-55. 10.1093/bioinformatics/btm543, 18024972.
-
(2008)
Bioinformatics
, vol.24
, pp. 46-55
-
-
Liang, K.1
Wang, X.2
Anastassiou, D.3
-
15
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey T, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Second Int Conf Intell Syst Mol Biol 1994, 2:28-36.
-
(1994)
Proc Second Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.1
Elkan, C.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(5131):208-214. 10.1126/science.8211139, 8211139.
-
(1993)
Science
, vol.262
, Issue.5131
, 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
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
10.1038/nbt1098-939, 9788350
-
Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 1998, 16:939-945. 10.1038/nbt1098-939, 9788350.
-
(1998)
Nat Biotechnol
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
18
-
-
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
-
19
-
-
6344236416
-
Statistical models for biological sequence motif discovery
-
Liu J, Gupta M, Liu X, Mayerhofere L, Lawrence CE. Statistical models for biological sequence motif discovery. Case Stud Bayesian Stat 2002, 6(167):4-24.
-
(2002)
Case Stud Bayesian Stat
, vol.6
, Issue.167
, pp. 4-24
-
-
Liu, J.1
Gupta, M.2
Liu, X.3
Mayerhofere, L.4
Lawrence, C.E.5
-
20
-
-
0034565285
-
Combinatorial approaches to finding subtle signals in DNA sequences
-
Pevzner P, Sze S. Combinatorial approaches to finding subtle signals in DNA sequences. Proc Eighth Int Conf Intell Syst Mol Biol 2000, 8:269-278.
-
(2000)
Proc Eighth Int Conf Intell Syst Mol Biol
, vol.8
, pp. 269-278
-
-
Pevzner, P.1
Sze, S.2
-
21
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
10.1093/bioinformatics/15.7.563, 10487864
-
Hertz G, Stormo G. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577. 10.1093/bioinformatics/15.7.563, 10487864.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.1
Stormo, G.2
-
22
-
-
2342476143
-
Finding subtle motifs by branching from sample strings
-
10.1093/bioinformatics/19.1.149, 14534184
-
Price A, Ramabhadran S, Pevzner P. Finding subtle motifs by branching from sample strings. Bioinformatics 2003, 19:ii149-ii155. 10.1093/bioinformatics/19.1.149, 14534184.
-
(2003)
Bioinformatics
, vol.19
-
-
Price, A.1
Ramabhadran, S.2
Pevzner, P.3
-
23
-
-
0036110853
-
Finding motifs using random projections
-
10.1089/10665270252935430, 12015879
-
Buhler J, Tompa M. Finding motifs using random projections. J Comput Biol 2002, 9:225-242. 10.1089/10665270252935430, 12015879.
-
(2002)
J Comput Biol
, vol.9
, pp. 225-242
-
-
Buhler, J.1
Tompa, M.2
-
24
-
-
10944244607
-
A uniform projection method for motif discovery in DNA sequences
-
Raphael B, Liu L, Varghese G. A uniform projection method for motif discovery in DNA sequences. IEEE Trans Comp Biol Bioinfo 2004, 1:91-94.
-
(2004)
IEEE Trans Comp Biol Bioinfo
, vol.1
, pp. 91-94
-
-
Raphael, B.1
Liu, L.2
Varghese, G.3
-
25
-
-
79959259983
-
MotifClick: prediction of cis-regulatory binding sites via merging cliques
-
Zhang S, Li S, Niu M, Pham PT, Su Z. MotifClick: prediction of cis-regulatory binding sites via merging cliques. BMC Bioinforma 2011, 12:238.
-
(2011)
BMC Bioinforma
, vol.12
, pp. 238
-
-
Zhang, S.1
Li, S.2
Niu, M.3
Pham, P.T.4
Su, Z.5
-
26
-
-
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:e150-e157. 10.1093/bioinformatics/btl243, 16873465.
-
(2006)
Bioinformatics
, vol.22
-
-
Fratkin, E.1
Naughton, B.T.2
Brutlag, D.L.3
Batzoglou, S.4
-
27
-
-
79951535158
-
SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model
-
Lee N, Wang D. SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model. BMC Bioinforma 2011, 12(Suppl 1):S16.
-
(2011)
BMC Bioinforma
, vol.12
, Issue.SUPPL. 1
-
-
Lee, N.1
Wang, D.2
-
28
-
-
18744388326
-
Transcription factor binding site identification using the self-organizing map
-
10.1093/bioinformatics/bti256, 15647296
-
Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS. Transcription factor binding site identification using the self-organizing map. Bioinformatics 2005, 21:1807-1814. 10.1093/bioinformatics/bti256, 15647296.
-
(2005)
Bioinformatics
, vol.21
, pp. 1807-1814
-
-
Mahony, S.1
Hendrix, D.2
Golden, A.3
Smith, T.J.4
Rokhsar, D.S.5
-
30
-
-
0347125328
-
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
-
10.1093/nar/gkh012, 308747, 14681366
-
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, 32:D91-D94. 10.1093/nar/gkh012, 308747, 14681366.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
31
-
-
0037208166
-
TRANSFAC®: transcriptional regulation, from patterns to profiles
-
10.1093/nar/gkg108, 165555, 12520026
-
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch 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):374-378. 10.1093/nar/gkg108, 165555, 12520026.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, 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
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
32
-
-
33750048444
-
CisView: a browser and database of cis-regulatory modules predicted in the mouse genome
-
10.1093/dnares/dsl005, 16980320
-
Sharov A, Dudekula D, Ko M. CisView: a browser and database of cis-regulatory modules predicted in the mouse genome. DNA Res 2006, 13:123-134. 10.1093/dnares/dsl005, 16980320.
-
(2006)
DNA Res
, vol.13
, pp. 123-134
-
-
Sharov, A.1
Dudekula, D.2
Ko, M.3
-
33
-
-
58149200952
-
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
-
10.1093/nar/gkn660, 2686578, 18842628
-
Newburger N, Bulyk M. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 2009, 37:D77-D82. 10.1093/nar/gkn660, 2686578, 18842628.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Newburger, N.1
Bulyk, M.2
-
34
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
10.1093/nar/gkp335, 2703892, 19458158
-
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-W208. 10.1093/nar/gkp335, 2703892, 19458158.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
35
-
-
0030763957
-
Recent enhancements to the blocks database servers
-
10.1093/nar/25.1.222, 146414, 9016540
-
Henikoff J, Pietrokovski S, Henikoff S. Recent enhancements to the blocks database servers. Nucleic Acids Res 1997, 25:222-225. 10.1093/nar/25.1.222, 146414, 9016540.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 222-225
-
-
Henikoff, J.1
Pietrokovski, S.2
Henikoff, S.3
-
36
-
-
34447506667
-
Quantifying similarity between motifs
-
10.1186/gb-2007-8-2-r24, 1852410, 17324271
-
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol 2007, 8:R24. 10.1186/gb-2007-8-2-r24, 1852410, 17324271.
-
(2007)
Genome Biol
, vol.8
-
-
Gupta, S.1
Stamatoyannopoulos, J.A.2
Bailey, T.L.3
Noble, W.S.4
-
37
-
-
0031877016
-
Combining evidence using p-values: application to sequence homology searches
-
10.1093/bioinformatics/14.1.48, 9520501
-
Bailey T, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998, 14:48-54. 10.1093/bioinformatics/14.1.48, 9520501.
-
(1998)
Bioinformatics
, vol.14
, pp. 48-54
-
-
Bailey, T.1
Gribskov, M.2
-
38
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
-
Bailey T, Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach Learn 1995, 21:51-80.
-
(1995)
Mach Learn
, vol.21
, pp. 51-80
-
-
Bailey, T.1
Elkan, C.2
-
39
-
-
45749129367
-
Detection of subtle variations as consensus motifs
-
Comin M, Parida L. Detection of subtle variations as consensus motifs. Theor Comput Sci 2008, 395:158-170.
-
(2008)
Theor Comput Sci
, vol.395
, pp. 158-170
-
-
Comin, M.1
Parida, L.2
-
40
-
-
84875404794
-
The UCSC genome browser database: extensions and updates 2013
-
10.1093/nar/gks1048, 3531082, 23155063
-
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res 2013, 41:D64-D69. 10.1093/nar/gks1048, 3531082, 23155063.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
Raney, B.J.11
Pohl, A.12
Malladi, V.S.13
Li, C.H.14
Lee, B.T.15
Learned, K.16
Kirkup, V.17
Hsu, F.18
Heitner, S.19
Harte, R.A.20
Haeussler, M.21
Guruvadoo, L.22
Goldman, M.23
Giardine, B.M.24
Fujita, P.A.25
Dreszer, T.R.26
Diekhans, M.27
Cline, M.S.28
Clawson, H.29
Barber, G.P.30
Haussler, D.31
Kent, W.J.32
more..
-
41
-
-
33847664259
-
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
-
Pavesi G, Zambelli F, Pesole G. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinforma 2007, 8:46.
-
(2007)
BMC Bioinforma
, vol.8
, pp. 46
-
-
Pavesi, G.1
Zambelli, F.2
Pesole, G.3
-
42
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
10.1006/jmbi.1998.1947, 9719638
-
van Helden J, Andre B, Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 1998, 281:827-842. 10.1006/jmbi.1998.1947, 9719638.
-
(1998)
J Mol Biol
, vol.281
, pp. 827-842
-
-
van Helden, J.1
Andre, B.2
Collado-Vides, J.3
-
43
-
-
34547569191
-
STAMP: a web tool for exploring DNA-binding motif similarities
-
10.1093/nar/gkm272, 1933206, 17478497
-
Mahony S, Benos P. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, 35:W253-W258. 10.1093/nar/gkm272, 1933206, 17478497.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Mahony, S.1
Benos, P.2
-
44
-
-
33646158909
-
A deterministic motif finding algorithm with application to the human genome
-
10.1093/bioinformatics/btl037, 16455748
-
Hon L, Jain A. A deterministic motif finding algorithm with application to the human genome. Bioinformatics 2006, 22:1047-1054. 10.1093/bioinformatics/btl037, 16455748.
-
(2006)
Bioinformatics
, vol.22
, pp. 1047-1054
-
-
Hon, L.1
Jain, A.2
-
45
-
-
3242884167
-
Weeder web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
-
10.1093/nar/gkh465, 441603, 15215380
-
Pavesi G, Mereghetti P, Mauri G, Graziano P. Weeder web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res 2004, 32:W199-W203. 10.1093/nar/gkh465, 441603, 15215380.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Pavesi, G.1
Mereghetti, P.2
Mauri, G.3
Graziano, P.4
-
46
-
-
14944363825
-
NestedMICA: sensitive inference of overrepresented motifs in nucleic acid sequence
-
10.1093/nar/gki282, 1064142, 15760844
-
Down T, Hubbard T. NestedMICA: sensitive inference of overrepresented motifs in nucleic acid sequence. Nucleic Acids Res 2005, 33:1445-1453. 10.1093/nar/gki282, 1064142, 15760844.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1445-1453
-
-
Down, T.1
Hubbard, T.2
-
47
-
-
84866937220
-
Inferring direct DNA binding from ChIP-seq
-
10.1093/nar/gks433, 3458523, 22610855
-
Bailey T, Machanick P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 2012, 40:e128. 10.1093/nar/gks433, 3458523, 22610855.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Bailey, T.1
Machanick, P.2
-
48
-
-
77950529946
-
Motif enrichment analysis: a unified framework and an evaluation on ChIP data
-
McLeay R, Bailey T. Motif enrichment analysis: a unified framework and an evaluation on ChIP data. BMC Bioinforma 2010, 11:165.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 165
-
-
McLeay, R.1
Bailey, T.2
-
49
-
-
77951956867
-
Assigning roles to DNA regulatory motifs using comparative genomics
-
10.1093/bioinformatics/btq049, 2844991, 20147307
-
Buske FA, Boden M, Bauer DC, Bailey TL. Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics 2010, 26:860-866. 10.1093/bioinformatics/btq049, 2844991, 20147307.
-
(2010)
Bioinformatics
, vol.26
, pp. 860-866
-
-
Buske, F.A.1
Boden, M.2
Bauer, D.C.3
Bailey, T.L.4
-
50
-
-
77957818564
-
Deep and wide digging for binding motifs in ChIP-Seq data
-
10.1093/bioinformatics/btq488, 20736340
-
Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ. Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics 2010, 26:2622-2623. 10.1093/bioinformatics/btq488, 20736340.
-
(2010)
Bioinformatics
, vol.26
, pp. 2622-2623
-
-
Kulakovskiy, I.V.1
Boeva, V.A.2
Favorov, A.V.3
Makeev, V.J.4
-
51
-
-
0034656326
-
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
-
10.1093/nar/28.8.1808, 102821, 10734201
-
van Helden J, Rios A, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 2000, 28:1808-1818. 10.1093/nar/28.8.1808, 102821, 10734201.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1808-1818
-
-
van Helden, J.1
Rios, A.2
Collado-Vides, J.3
-
52
-
-
79959954386
-
RSAT 2011: regulatory sequence analysis tools
-
Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J. RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res 2011, 29:W86-W91.
-
(2011)
Nucleic Acids Res
, vol.29
-
-
Thomas-Chollier, M.1
Defrance, M.2
Medina-Rivera, A.3
Sand, O.4
Herrmann, C.5
Thieffry, D.6
van Helden, J.7
-
53
-
-
52749097035
-
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
-
10.1038/nprot.2008.97, 18802439
-
Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 2008, 3:1578-1588. 10.1038/nprot.2008.97, 18802439.
-
(2008)
Nat Protoc
, vol.3
, pp. 1578-1588
-
-
Turatsinze, J.V.1
Thomas-Chollier, M.2
Defrance, M.3
van Helden, J.4
-
54
-
-
79951980115
-
BayesPeak-an R package for analysing ChIP-seq data
-
10.1093/bioinformatics/btq685, 3042177, 21245054
-
Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG, Tavare S. BayesPeak-an R package for analysing ChIP-seq data. Bioinformatics 2011, 27:713-714. 10.1093/bioinformatics/btq685, 3042177, 21245054.
-
(2011)
Bioinformatics
, vol.27
, pp. 713-714
-
-
Cairns, J.1
Spyrou, C.2
Stark, R.3
Smith, M.L.4
Lynch, A.G.5
Tavare, S.6
-
55
-
-
84874308615
-
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
-
10.1093/bioinformatics/bts722, 23300134
-
Wang J, Lunyak V, Jordan I. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. Bioinformatics 2013, 29:492-493. 10.1093/bioinformatics/bts722, 23300134.
-
(2013)
Bioinformatics
, vol.29
, pp. 492-493
-
-
Wang, J.1
Lunyak, V.2
Jordan, I.3
-
56
-
-
55749094855
-
An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data
-
10.1038/nbt.1505, 2596672, 18978777
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26(11):1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.11
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
57
-
-
84879412369
-
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data
-
10.1111/gtc.12058, 3738949, 23672187
-
Nakato R, Itoh T, Shirahige K. DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes to Cells 2013, 18:589-601. 10.1111/gtc.12058, 3738949, 23672187.
-
(2013)
Genes to Cells
, vol.18
, pp. 589-601
-
-
Nakato, R.1
Itoh, T.2
Shirahige, K.3
-
58
-
-
54949147307
-
F-Seq: a feature density estimator for high-throughput sequence tags
-
10.1093/bioinformatics/btn480, 2732284, 18784119
-
Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24:2537-2538. 10.1093/bioinformatics/btn480, 2732284, 18784119.
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
59
-
-
48249140621
-
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
10.1093/bioinformatics/btn305, 2638869, 18599518
-
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24:1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
Jones, S.J.6
-
60
-
-
84866086842
-
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
-
10.1371/journal.pcbi.1002638, 3415389, 22912568
-
Guo Y, Mahony S, Gifford D. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol 2012, 8:e1002638. 10.1371/journal.pcbi.1002638, 3415389, 22912568.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Guo, Y.1
Mahony, S.2
Gifford, D.3
-
61
-
-
73049112582
-
Extracting transcription factor targets from ChIP-Seq data
-
10.1093/nar/gkp536, 2761252, 19553195
-
Tuteja G, White P, Schug J, Kaestner KH. Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res 2009, 37:e113. 10.1093/nar/gkp536, 2761252, 19553195.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Tuteja, G.1
White, P.2
Schug, J.3
Kaestner, K.H.4
-
62
-
-
84862570727
-
A generalized linear model for peak calling in ChIP-Seq data
-
10.1089/cmb.2012.0023, 3375645, 22533622
-
Xu J, Zhang Y. A generalized linear model for peak calling in ChIP-Seq data. J Comput Biol 2012, 19:826-838. 10.1089/cmb.2012.0023, 3375645, 22533622.
-
(2012)
J Comput Biol
, vol.19
, pp. 826-838
-
-
Xu, J.1
Zhang, Y.2
-
63
-
-
77954041808
-
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
-
Qin J, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinforma 2010, 11:369.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 369
-
-
Qin, J.1
Yu, J.2
Shen, J.3
Maher, C.A.4
Hu, M.5
Kalyana-Sundaram, S.6
Yu, J.7
Chinnaiyan, A.M.8
-
64
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
65
-
-
84878008923
-
NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data
-
Kim N, Jayatillake R, Spouge J. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Bioinforma 2013, 14:349.
-
(2013)
BMC Bioinforma
, vol.14
, pp. 349
-
-
Kim, N.1
Jayatillake, R.2
Spouge, J.3
-
66
-
-
79955676390
-
PeakRanger: a cloud-enabled peak caller for ChIP-seq data
-
Feng X, Grossman R, Stein L. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinforma 2011, 12:139.
-
(2011)
BMC Bioinforma
, vol.12
, pp. 139
-
-
Feng, X.1
Grossman, R.2
Stein, L.3
-
67
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 2009, 27:1.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 1
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
68
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
10.1038/nmeth.1246, 2917543, 19160518
-
Valouev A, Johnson D, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008, 5(9):829-834. 10.1038/nmeth.1246, 2917543, 19160518.
-
(2008)
Nat Methods
, vol.5
, Issue.9
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.2
Sundquist, A.3
Medina, C.4
Anton, E.5
Batzoglou, S.6
Myers, R.M.7
Sidow, A.8
-
69
-
-
84870369023
-
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite
-
Wang X, Zhang X. Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol 2011, 5(Suppl 2):S3.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.SUPPL. 2
-
-
Wang, X.1
Zhang, X.2
-
70
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
10.1093/bioinformatics/btp340, 2732366, 19505939
-
Zang C, Schones D, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25:1952-1958. 10.1093/bioinformatics/btp340, 2732366, 19505939.
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.2
Zeng, C.3
Cui, K.4
Zhao, K.5
Peng, W.6
-
71
-
-
77949532153
-
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
-
Wang C, Xu J, Zhang D, Wilson ZA, Zhang D. An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. BMC Bioinforma 2010, 11:81.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 81
-
-
Wang, C.1
Xu, J.2
Zhang, D.3
Wilson, Z.A.4
Zhang, D.5
-
72
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
10.1093/nar/gkn488, 2532738, 18684996
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36:5221-5231. 10.1093/nar/gkn488, 2532738, 18684996.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
73
-
-
77951230100
-
Sole-search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
-
10.1093/nar/gkp1012, 2817454, 19906703
-
McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludascher B, Korf I, Farnham PJ. Sole-search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 2010, 38:e13. 10.1093/nar/gkp1012, 2817454, 19906703.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
McPhillips, T.1
Xu, X.2
Cao, A.R.3
Iyengar, S.4
Nicolet, C.M.5
Ludascher, B.6
Korf, I.7
Farnham, P.J.8
-
74
-
-
78651257371
-
Shape-based peak identification for ChIP-Seq
-
Hower V, Evans S, Pachter L. Shape-based peak identification for ChIP-Seq. BMC Bioinforma 2011, 12:15.
-
(2011)
BMC Bioinforma
, vol.12
, pp. 15
-
-
Hower, V.1
Evans, S.2
Pachter, L.3
-
75
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
-
Nix D, Courdy S, Boucher K. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinforma 2008, 9:523.
-
(2008)
BMC Bioinforma
, vol.9
, pp. 523
-
-
Nix, D.1
Courdy, S.2
Boucher, K.3
-
76
-
-
79551590211
-
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
-
10.1093/bioinformatics/btq669, 3031039, 21138948
-
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX. W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics 2011, 27:428-430. 10.1093/bioinformatics/btq669, 3031039, 21138948.
-
(2011)
Bioinformatics
, vol.27
, pp. 428-430
-
-
Lan, X.1
Bonneville, R.2
Apostolos, J.3
Wu, W.4
Jin, V.X.5
-
77
-
-
79960614727
-
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
-
10.1186/gb-2011-12-7-r67, 3218829, 21787385
-
Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol 2011, 12:R67. 10.1186/gb-2011-12-7-r67, 3218829, 21787385.
-
(2011)
Genome Biol
, vol.12
-
-
Rashid, N.U.1
Giresi, P.G.2
Ibrahim, J.G.3
Sun, W.4
Lieb, J.D.5
-
78
-
-
79955838994
-
A short survey of computational analysis methods in analysing ChIP-seq data
-
10.1186/1479-7364-5-2-117, 3525234, 21296745
-
Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan AC. A short survey of computational analysis methods in analysing ChIP-seq data. Human Genomics 2011, 5:117-123. 10.1186/1479-7364-5-2-117, 3525234, 21296745.
-
(2011)
Human Genomics
, vol.5
, pp. 117-123
-
-
Kim, H.1
Kim, J.2
Selby, H.3
Gao, D.4
Tong, T.5
Phang, T.L.6
Tan, A.C.7
-
79
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
10.1038/nmeth.1371, 19844228
-
Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32. 10.1038/nmeth.1371, 19844228.
-
(2009)
Nat Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
80
-
-
84855279817
-
Optimized detection of transcription factor-binding sites in ChIP-seq experiments
-
10.1093/nar/gkr839, 3245948, 22009681
-
Elo L, Kallio A, Laajala T, Hawkins TD, Hawkins RD, Korpelainen E, Aittokallio T. Optimized detection of transcription factor-binding sites in ChIP-seq experiments. Nucleic Acids Res 2012, 40:e1. 10.1093/nar/gkr839, 3245948, 22009681.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Elo, L.1
Kallio, A.2
Laajala, T.3
Hawkins, T.D.4
Hawkins, R.D.5
Korpelainen, E.6
Aittokallio, T.7
-
81
-
-
84878771050
-
Combining multiple ChIP-seq peak detection systems using combinatorial fusion
-
Schweikert C, Brown S, Tang Z, Smith PR, Hsu DF. Combining multiple ChIP-seq peak detection systems using combinatorial fusion. BMC Genomics 2012, 13(Suppl 8):S12.
-
(2012)
BMC Genomics
, vol.13
, Issue.SUPPL. 8
-
-
Schweikert, C.1
Brown, S.2
Tang, Z.3
Smith, P.R.4
Hsu, D.F.5
-
82
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
10.1038/nature11243, 22763441
-
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature 2012, 488:116-120. 10.1038/nature11243, 22763441.
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
Yue, F.2
McCleary, D.F.3
Ye, Z.4
Edsall, L.5
Kuan, S.6
Wagner, U.7
Dixon, J.8
Lee, L.9
Lobanenkov, V.V.10
Ren, B.11
-
83
-
-
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, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier 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
De Moor, B.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
Regnier, 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..
-
84
-
-
84899479619
-
STAMP Help
-
STAMP Help. http://www.benoslab.pitt.edu/stamp/help.html#input.
-
-
-
|