123 related articles for article (PubMed ID: 34524404)
21. Deep Learning of Sequence Patterns for CCCTC-Binding Factor-Mediated Chromatin Loop Formation.
Kuang S; Wang L
J Comput Biol; 2021 Feb; 28(2):133-145. PubMed ID: 33232622
[No Abstract] [Full Text] [Related]
22. A novel method to identify the DNA motifs recognized by a defined transcription factor.
Ji X; Wang L; Nie X; He L; Zang D; Liu Y; Zhang B; Wang Y
Plant Mol Biol; 2014 Nov; 86(4-5):367-80. PubMed ID: 25108460
[TBL] [Abstract][Full Text] [Related]
23. Improved linking of motifs to their TFs using domain information.
Baumgarten N; Schmidt F; Schulz MH
Bioinformatics; 2020 Mar; 36(6):1655-1662. PubMed ID: 31742324
[TBL] [Abstract][Full Text] [Related]
24. Modulation of DNA-protein Interactions by Proximal Genetic Elements as Uncovered by Interpretable Deep Learning.
Kalakoti Y; Peter SC; Gawande S; Sundar D
J Mol Biol; 2023 Jul; 435(13):168121. PubMed ID: 37100167
[TBL] [Abstract][Full Text] [Related]
25. 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]
26. 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]
27. 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]
28. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation.
Patra P; Gao YQ
J Phys Chem B; 2022 Nov; 126(45):9187-9206. PubMed ID: 36322688
[TBL] [Abstract][Full Text] [Related]
29. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.
Tsai ZT; Shiu SH; Tsai HK
PLoS Comput Biol; 2015 Aug; 11(8):e1004418. PubMed ID: 26291518
[TBL] [Abstract][Full Text] [Related]
30. MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences.
Wong KC
Bioinformatics; 2017 Oct; 33(19):3028-3035. PubMed ID: 28633280
[TBL] [Abstract][Full Text] [Related]
31. DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.
Quach B; Furey TS
Bioinformatics; 2017 Apr; 33(7):956-963. PubMed ID: 27993786
[TBL] [Abstract][Full Text] [Related]
32. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.
Kazemian M; Pham H; Wolfe SA; Brodsky MH; Sinha S
Nucleic Acids Res; 2013 Sep; 41(17):8237-52. PubMed ID: 23847101
[TBL] [Abstract][Full Text] [Related]
33. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
Gordân R; Murphy KF; McCord RP; Zhu C; Vedenko A; Bulyk ML
Genome Biol; 2011 Dec; 12(12):R125. PubMed ID: 22189060
[TBL] [Abstract][Full Text] [Related]
34. Multi-Scale Capsule Network for Predicting DNA-Protein Binding Sites.
Zhang Q; Yu W; Han K; Nandi AK; Huang DS
IEEE/ACM Trans Comput Biol Bioinform; 2021; 18(5):1793-1800. PubMed ID: 32960766
[TBL] [Abstract][Full Text] [Related]
35. Finding de novo methylated DNA motifs.
Ngo V; Wang M; Wang W
Bioinformatics; 2019 Sep; 35(18):3287-3293. PubMed ID: 30726880
[TBL] [Abstract][Full Text] [Related]
36. Identifying cooperative transcription factors in yeast using multiple data sources.
Lai FJ; Jhu MH; Chiu CC; Huang YM; Wu WS
BMC Syst Biol; 2014; 8 Suppl 5(Suppl 5):S2. PubMed ID: 25559499
[TBL] [Abstract][Full Text] [Related]
37. 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]
38. Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.
Schipper JL; Gordân RM
Cold Spring Harb Protoc; 2016 Nov; 2016(11):. PubMed ID: 27803259
[TBL] [Abstract][Full Text] [Related]
39. Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data.
Levitsky V; Oshchepkov D; Zemlyanskaya E; Merkulova T
Int J Mol Sci; 2020 Aug; 21(17):. PubMed ID: 32825662
[TBL] [Abstract][Full Text] [Related]
40. 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]
[Previous] [Next] [New Search]
