90 related articles for article (PubMed ID: 27574199)
21. Memes: A motif analysis environment in R using tools from the MEME Suite.
Nystrom SL; McKay DJ
PLoS Comput Biol; 2021 Sep; 17(9):e1008991. PubMed ID: 34570758
[TBL] [Abstract][Full Text] [Related]
22. Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences.
Siebert M; Söding J
Nucleic Acids Res; 2016 Jul; 44(13):6055-69. PubMed ID: 27288444
[TBL] [Abstract][Full Text] [Related]
23. Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS.
Ding J; Dhillon V; Li X; Hu H
Methods; 2015 Jun; 79-80():47-51. PubMed ID: 25171961
[TBL] [Abstract][Full Text] [Related]
24. PRECISE: software for prediction of cis-acting regulatory elements.
Trindade LM; van Berloo R; Fiers M; Visser RG
J Hered; 2005; 96(5):618-22. PubMed ID: 16135709
[TBL] [Abstract][Full Text] [Related]
25. CEAS: cis-regulatory element annotation system.
Shin H; Liu T; Manrai AK; Liu XS
Bioinformatics; 2009 Oct; 25(19):2605-6. PubMed ID: 19689956
[TBL] [Abstract][Full Text] [Related]
26. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.
Zhang S; Chen Y
PLoS One; 2016; 11(8):e0160435. PubMed ID: 27487245
[TBL] [Abstract][Full Text] [Related]
27. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Vlieghe D; Sandelin A; De Bleser PJ; Vleminckx K; Wasserman WW; van Roy F; Lenhard B
Nucleic Acids Res; 2006 Jan; 34(Database issue):D95-7. PubMed ID: 16381983
[TBL] [Abstract][Full Text] [Related]
28. Discovering novel sequence motifs with MEME.
Bailey TL
Curr Protoc Bioinformatics; 2002 Nov; Chapter 2():Unit 2.4. PubMed ID: 18792935
[TBL] [Abstract][Full Text] [Related]
29. Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.
Sand O; Thomas-Chollier M; Vervisch E; van Helden J
Nat Protoc; 2008; 3(10):1604-15. PubMed ID: 18802441
[TBL] [Abstract][Full Text] [Related]
30. GAME: detecting cis-regulatory elements using a genetic algorithm.
Wei Z; Jensen ST
Bioinformatics; 2006 Jul; 22(13):1577-84. PubMed ID: 16632495
[TBL] [Abstract][Full Text] [Related]
31. Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding).
Hung JH; Weng Z
Cold Spring Harb Protoc; 2017 Feb; 2017(2):. PubMed ID: 27574193
[TBL] [Abstract][Full Text] [Related]
32. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.
Oliver P; Peralta-Gil M; Tabche ML; Merino E
BMC Genomics; 2016 Aug; 17(1):686. PubMed ID: 27567672
[TBL] [Abstract][Full Text] [Related]
33. Systematic identification of mammalian regulatory motifs' target genes and functions.
Warner JB; Philippakis AA; Jaeger SA; He FS; Lin J; Bulyk ML
Nat Methods; 2008 Apr; 5(4):347-53. PubMed ID: 18311145
[TBL] [Abstract][Full Text] [Related]
34. Discovering sequence motifs.
Bailey TL
Methods Mol Biol; 2007; 395():271-92. PubMed ID: 17993680
[TBL] [Abstract][Full Text] [Related]
35. Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.
Wang X; Lin P; Ho JWK
BMC Genomics; 2018 Jan; 19(Suppl 1):929. PubMed ID: 29363433
[TBL] [Abstract][Full Text] [Related]
36. RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A; Defrance M; Sand O; Herrmann C; Castro-Mondragon JA; Delerce J; Jaeger S; Blanchet C; Vincens P; Caron C; Staines DM; Contreras-Moreira B; Artufel M; Charbonnier-Khamvongsa L; Hernandez C; Thieffry D; Thomas-Chollier M; van Helden J
Nucleic Acids Res; 2015 Jul; 43(W1):W50-6. PubMed ID: 25904632
[TBL] [Abstract][Full Text] [Related]
37. Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.
Suzuki M; Ketterling MG; McCarty DR
Plant Physiol; 2005 Sep; 139(1):437-47. PubMed ID: 16113229
[TBL] [Abstract][Full Text] [Related]
38. MCAT: Motif Combining and Association Tool.
Yang Y; Robertson JA; Guo Z; Martinez J; Coghlan C; Heath LS
J Comput Biol; 2019 Jan; 26(1):1-15. PubMed ID: 30418034
[TBL] [Abstract][Full Text] [Related]
39. An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Ji H; Jiang H; Ma W; Johnson DS; Myers RM; Wong WH
Nat Biotechnol; 2008 Nov; 26(11):1293-300. PubMed ID: 18978777
[TBL] [Abstract][Full Text] [Related]
40. Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.
Defrance M; Janky R; Sand O; van Helden J
Nat Protoc; 2008; 3(10):1589-603. PubMed ID: 18802440
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]