299 related articles for article (PubMed ID: 35681170)
1. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.
Karimzadeh M; Hoffman MM
Genome Biol; 2022 Jun; 23(1):126. PubMed ID: 35681170
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J; Zhuang J; Iyer S; Lin X; Whitfield TW; Greven MC; Pierce BG; Dong X; Kundaje A; Cheng Y; Rando OJ; Birney E; Myers RM; Noble WS; Snyder M; Weng Z
Genome Res; 2012 Sep; 22(9):1798-812. PubMed ID: 22955990
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.
Chen X; Yu B; Carriero N; Silva C; Bonneau R
Nucleic Acids Res; 2017 May; 45(8):4315-4329. PubMed ID: 28334916
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Base-resolution prediction of transcription factor binding signals by a deep learning framework.
Zhang Q; He Y; Wang S; Chen Z; Guo Z; Cui Z; Liu Q; Huang DS
PLoS Comput Biol; 2022 Mar; 18(3):e1009941. PubMed ID: 35263332
[TBL] [Abstract][Full Text] [Related]
8. BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.
Kähärä J; Lähdesmäki H
Bioinformatics; 2015 Sep; 31(17):2852-9. PubMed ID: 25957350
[TBL] [Abstract][Full Text] [Related]
9. Anchor: trans-cell type prediction of transcription factor binding sites.
Li H; Quang D; Guan Y
Genome Res; 2019 Feb; 29(2):281-292. PubMed ID: 30567711
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
Puig RR; Boddie P; Khan A; Castro-Mondragon JA; Mathelier A
BMC Genomics; 2021 Jun; 22(1):482. PubMed ID: 34174819
[TBL] [Abstract][Full Text] [Related]
12. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
Agius P; Arvey A; Chang W; Noble WS; Leslie C
PLoS Comput Biol; 2010 Sep; 6(9):. PubMed ID: 20838582
[TBL] [Abstract][Full Text] [Related]
13. An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.
Cheng CY; Chu CH; Hsu HW; Hsu FR; Tang CY; Wang WC; Kung HJ; Chang PC
BMC Genomics; 2014; 15 Suppl 1(Suppl 1):S1. PubMed ID: 24564277
[TBL] [Abstract][Full Text] [Related]
14. 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]
15. Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.
Yu CP; Kuo CH; Nelson CW; Chen CA; Soh ZT; Lin JJ; Hsiao RX; Chang CY; Li WH
Proc Natl Acad Sci U S A; 2021 May; 118(20):. PubMed ID: 33975951
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Learning Useful Representations of DNA Sequences From ChIP-Seq Datasets for Exploring Transcription Factor Binding Specificities.
Quan L; Sun X; Wu J; Mei J; Huang L; He R; Nie L; Chen Y; Lyu Q
IEEE/ACM Trans Comput Biol Bioinform; 2022; 19(2):998-1008. PubMed ID: 32976105
[TBL] [Abstract][Full Text] [Related]
18. An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency.
Guo WL; Huang DS
Mol Biosyst; 2017 Aug; 13(9):1827-1837. PubMed ID: 28718849
[TBL] [Abstract][Full Text] [Related]
19. Cooperative binding of transcription factors in the human genome.
Nie Y; Shu C; Sun X
Genomics; 2020 Sep; 112(5):3427-3434. PubMed ID: 32574834
[TBL] [Abstract][Full Text] [Related]
20. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Arvey A; Agius P; Noble WS; Leslie C
Genome Res; 2012 Sep; 22(9):1723-34. PubMed ID: 22955984
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
