These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
177 related articles for article (PubMed ID: 25505144)
21. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Pavesi G; Mereghetti P; Zambelli F; Stefani M; Mauri G; Pesole G Nucleic Acids Res; 2006 Jul; 34(Web Server issue):W566-70. PubMed ID: 16845071 [TBL] [Abstract][Full Text] [Related]
22. 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]
23. Stubb: a program for discovery and analysis of cis-regulatory modules. Sinha S; Liang Y; Siggia E Nucleic Acids Res; 2006 Jul; 34(Web Server issue):W555-9. PubMed ID: 16845069 [TBL] [Abstract][Full Text] [Related]
25. Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. Acevedo-Luna N; Mariño-Ramírez L; Halbert A; Hansen U; Landsman D; Spouge JL BMC Bioinformatics; 2016 Nov; 17(1):479. PubMed ID: 27871221 [TBL] [Abstract][Full Text] [Related]
26. A widespread role of the motif environment in transcription factor binding across diverse protein families. Dror I; Golan T; Levy C; Rohs R; Mandel-Gutfreund Y Genome Res; 2015 Sep; 25(9):1268-80. PubMed ID: 26160164 [TBL] [Abstract][Full Text] [Related]
27. A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. Levitsky V; Zemlyanskaya E; Oshchepkov D; Podkolodnaya O; Ignatieva E; Grosse I; Mironova V; Merkulova T Nucleic Acids Res; 2019 Dec; 47(21):e139. PubMed ID: 31750523 [TBL] [Abstract][Full Text] [Related]
29. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Yang L; Zhou T; Dror I; Mathelier A; Wasserman WW; Gordân R; Rohs R Nucleic Acids Res; 2014 Jan; 42(Database issue):D148-55. PubMed ID: 24214955 [TBL] [Abstract][Full Text] [Related]
30. A fast weak motif-finding algorithm based on community detection in graphs. Jia C; Carson MB; Yu J BMC Bioinformatics; 2013 Jul; 14():227. PubMed ID: 23865838 [TBL] [Abstract][Full Text] [Related]
31. MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Hu J; Hu H; Li X Nucleic Acids Res; 2008 Aug; 36(13):4488-97. PubMed ID: 18606616 [TBL] [Abstract][Full Text] [Related]
32. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. Müller-Molina AJ; Schöler HR; Araúzo-Bravo MJ PLoS One; 2012; 7(11):e49086. PubMed ID: 23209563 [TBL] [Abstract][Full Text] [Related]
33. A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. Samee MAH; Bruneau BG; Pollard KS Cell Syst; 2019 Jan; 8(1):27-42.e6. PubMed ID: 30660610 [TBL] [Abstract][Full Text] [Related]
35. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Wang J; Zhuang J; Iyer S; Lin XY; Greven MC; Kim BH; Moore J; Pierce BG; Dong X; Virgil D; Birney E; Hung JH; Weng Z Nucleic Acids Res; 2013 Jan; 41(Database issue):D171-6. PubMed ID: 23203885 [TBL] [Abstract][Full Text] [Related]
36. A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. Seitzer P; Wilbanks EG; Larsen DJ; Facciotti MT BMC Bioinformatics; 2012 Nov; 13():317. PubMed ID: 23181585 [TBL] [Abstract][Full Text] [Related]
37. GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif. Pei C; Wang SL; Fang J; Zhang W J Comput Biol; 2017 Dec; 24(12):1243-1253. PubMed ID: 29116820 [TBL] [Abstract][Full Text] [Related]
38. Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation. Chen N; Yu J; Liu Z; Meng L; Li X; Wong KC Nucleic Acids Res; 2024 May; 52(8):4137-4150. PubMed ID: 38572749 [TBL] [Abstract][Full Text] [Related]
39. De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. Niu M; Tabari ES; Su Z BMC Genomics; 2014 Dec; 15():1047. PubMed ID: 25442502 [TBL] [Abstract][Full Text] [Related]