171 related articles for article (PubMed ID: 35659235)
1. Modeling binding specificities of transcription factor pairs with random forests.
Antikainen AA; Heinonen M; Lähdesmäki H
BMC Bioinformatics; 2022 Jun; 23(1):212. PubMed ID: 35659235
[TBL] [Abstract][Full Text] [Related]
2. abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.
Ali O; Farooq A; Yang M; Jin VX; Bjørås M; Wang J
BMC Bioinformatics; 2022 Mar; 23(1):83. PubMed ID: 35240993
[TBL] [Abstract][Full Text] [Related]
3. A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites.
Santolini M; Mora T; Hakim V
PLoS One; 2014; 9(6):e99015. PubMed ID: 24926895
[TBL] [Abstract][Full Text] [Related]
4. DNA-dependent formation of transcription factor pairs alters their binding specificity.
Jolma A; Yin Y; Nitta KR; Dave K; Popov A; Taipale M; Enge M; Kivioja T; Morgunova E; Taipale J
Nature; 2015 Nov; 527(7578):384-8. PubMed ID: 26550823
[TBL] [Abstract][Full Text] [Related]
5. The next generation of transcription factor binding site prediction.
Mathelier A; Wasserman WW
PLoS Comput Biol; 2013; 9(9):e1003214. PubMed ID: 24039567
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. 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]
8. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.
Omidi S; Zavolan M; Pachkov M; Breda J; Berger S; van Nimwegen E
PLoS Comput Biol; 2017 Jul; 13(7):e1005176. PubMed ID: 28753602
[TBL] [Abstract][Full Text] [Related]
9. Flanking sequence context-dependent transcription factor binding in early Drosophila development.
Stringham JL; Brown AS; Drewell RA; Dresch JM
BMC Bioinformatics; 2013 Oct; 14():298. PubMed ID: 24093548
[TBL] [Abstract][Full Text] [Related]
10. Comparison of discriminative motif optimization using matrix and DNA shape-based models.
Ruan S; Stormo GD
BMC Bioinformatics; 2018 Mar; 19(1):86. PubMed ID: 29510689
[TBL] [Abstract][Full Text] [Related]
11. A flexible integrative approach based on random forest improves prediction of transcription factor binding sites.
Hooghe B; Broos S; van Roy F; De Bleser P
Nucleic Acids Res; 2012 Aug; 40(14):e106. PubMed ID: 22492513
[TBL] [Abstract][Full Text] [Related]
12. A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J; Ramsey SA
Bioinformatics; 2015 Nov; 31(21):3445-50. PubMed ID: 26130577
[TBL] [Abstract][Full Text] [Related]
13. BEESEM: estimation of binding energy models using HT-SELEX data.
Ruan S; Swamidass SJ; Stormo GD
Bioinformatics; 2017 Aug; 33(15):2288-2295. PubMed ID: 28379348
[TBL] [Abstract][Full Text] [Related]
14. Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.
Oh YM; Kim JK; Choi S; Yoo JY
Nucleic Acids Res; 2012 Mar; 40(5):e38. PubMed ID: 22187154
[TBL] [Abstract][Full Text] [Related]
15. Enhancing the interpretability of transcription factor binding site prediction using attention mechanism.
Park S; Koh Y; Jeon H; Kim H; Yeo Y; Kang J
Sci Rep; 2020 Aug; 10(1):13413. PubMed ID: 32770026
[TBL] [Abstract][Full Text] [Related]
16. Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome.
Morozov VY; Ioshikhes IP
PLoS One; 2013; 8(8):e68712. PubMed ID: 23936309
[TBL] [Abstract][Full Text] [Related]
17. A structural-based strategy for recognition of transcription factor binding sites.
Xu B; Schones DE; Wang Y; Liang H; Li G
PLoS One; 2013; 8(1):e52460. PubMed ID: 23320072
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. 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]
20. Increasing coverage of transcription factor position weight matrices through domain-level homology.
Bernard B; Thorsson V; Rovira H; Shmulevich I
PLoS One; 2012; 7(8):e42779. PubMed ID: 22952610
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
