347 related articles for article (PubMed ID: 29363433)
1. 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]
2. COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.
Ha N; Polychronidou M; Lohmann I
PLoS One; 2012; 7(12):e52055. PubMed ID: 23272209
[TBL] [Abstract][Full Text] [Related]
3. Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans.
Tahara S; Tsuchiya T; Matsumoto H; Ozaki H
BMC Genomics; 2023 Oct; 24(1):597. PubMed ID: 37805453
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Probing transcription factor combinatorics in different promoter classes and in enhancers.
Vandel J; Cassan O; Lèbre S; Lecellier CH; Bréhélin L
BMC Genomics; 2019 Feb; 20(1):103. PubMed ID: 30709337
[TBL] [Abstract][Full Text] [Related]
6. RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
Castro-Mondragon JA; Rioualen C; Contreras-Moreira B; van Helden J
Methods Mol Biol; 2016; 1482():297-322. PubMed ID: 27557775
[TBL] [Abstract][Full Text] [Related]
7. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
Ozaki H; Iwasaki W
Comput Biol Chem; 2016 Aug; 63():62-72. PubMed ID: 26971251
[TBL] [Abstract][Full Text] [Related]
8. Analysis of Co-Associated Transcription Factors via Ordered Adjacency Differences on Motif Distribution.
Pan G; Tang J; Guo F
Sci Rep; 2017 Feb; 7():43597. PubMed ID: 28240320
[TBL] [Abstract][Full Text] [Related]
9. Predicting transcription factor binding using ensemble random forest models.
Behjati Ardakani F; Schmidt F; Schulz MH
F1000Res; 2018; 7():1603. PubMed ID: 31723409
[No Abstract] [Full Text] [Related]
10. 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]
11. FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.
Zhang S; Liang Y; Wang X; Su Z; Chen Y
DNA Res; 2019 Jun; 26(3):231-242. PubMed ID: 30957858
[TBL] [Abstract][Full Text] [Related]
12. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.
Liu S; Zibetti C; Wan J; Wang G; Blackshaw S; Qian J
BMC Bioinformatics; 2017 Jul; 18(1):355. PubMed ID: 28750606
[TBL] [Abstract][Full Text] [Related]
13. Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.
Ng FS; Schütte J; Ruau D; Diamanti E; Hannah R; Kinston SJ; Göttgens B
Nucleic Acids Res; 2014 Dec; 42(22):13513-24. PubMed ID: 25428352
[TBL] [Abstract][Full Text] [Related]
14. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
He X; Chen CC; Hong F; Fang F; Sinha S; Ng HH; Zhong S
PLoS One; 2009 Dec; 4(12):e8155. PubMed ID: 19956545
[TBL] [Abstract][Full Text] [Related]
15. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.
Yáñez-Cuna JO; Dinh HQ; Kvon EZ; Shlyueva D; Stark A
Genome Res; 2012 Oct; 22(10):2018-30. PubMed ID: 22534400
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. DREME: motif discovery in transcription factor ChIP-seq data.
Bailey TL
Bioinformatics; 2011 Jun; 27(12):1653-9. PubMed ID: 21543442
[TBL] [Abstract][Full Text] [Related]
18. Base-resolution methylation patterns accurately predict transcription factor bindings in vivo.
Xu T; Li B; Zhao M; Szulwach KE; Street RC; Lin L; Yao B; Zhang F; Jin P; Wu H; Qin ZS
Nucleic Acids Res; 2015 Mar; 43(5):2757-66. PubMed ID: 25722376
[TBL] [Abstract][Full Text] [Related]
19. Synthetic and genomic regulatory elements reveal aspects of
King DM; Hong CKY; Shepherdson JL; Granas DM; Maricque BB; Cohen BA
Elife; 2020 Feb; 9():. PubMed ID: 32043966
[TBL] [Abstract][Full Text] [Related]
20. Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.
Hutchins AP; Choo SH; Mistri TK; Rahmani M; Woon CT; Ng CK; Jauch R; Robson P
Stem Cells; 2013 Feb; 31(2):269-81. PubMed ID: 23169531
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]