173 related articles for article (PubMed ID: 38014229)
1. SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes.
Bhogale S; Seward C; Stubbs L; Sinha S
bioRxiv; 2023 Nov; ():. PubMed ID: 38014229
[TBL] [Abstract][Full Text] [Related]
2. Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.
Kim SG; Theera-Ampornpunt N; Fang CH; Harwani M; Grama A; Chaterji S
BMC Syst Biol; 2016 Aug; 10 Suppl 2(Suppl 2):54. PubMed ID: 27490187
[TBL] [Abstract][Full Text] [Related]
3. Information content differentiates enhancers from silencers in mouse photoreceptors.
Friedman RZ; Granas DM; Myers CA; Corbo JC; Cohen BA; White MA
Elife; 2021 Sep; 10():. PubMed ID: 34486522
[TBL] [Abstract][Full Text] [Related]
4. Characterization of sequence determinants of enhancer function using natural genetic variation.
Yang MG; Ling E; Cowley CJ; Greenberg ME; Vierbuchen T
Elife; 2022 Aug; 11():. PubMed ID: 36043696
[TBL] [Abstract][Full Text] [Related]
5. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.
Mateo JL; van den Berg DL; Haeussler M; Drechsel D; Gaber ZB; Castro DS; Robson P; Lu QR; Crawford GE; Flicek P; Ettwiller L; Wittbrodt J; Guillemot F; Martynoga B
Genome Res; 2015 Jan; 25(1):41-56. PubMed ID: 25294244
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers.
Ross J; Kuzin A; Brody T; Odenwald WF
BMC Genomics; 2015 Sep; 16(1):700. PubMed ID: 26377945
[TBL] [Abstract][Full Text] [Related]
8. Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework.
Wang Y; Hou Z; Yang Y; Wong KC; Li X
PLoS Comput Biol; 2022 Dec; 18(12):e1010779. PubMed ID: 36520922
[TBL] [Abstract][Full Text] [Related]
9. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.
Yáñez-Cuna JO; Arnold CD; Stampfel G; Boryń LM; Gerlach D; Rath M; Stark A
Genome Res; 2014 Jul; 24(7):1147-56. PubMed ID: 24714811
[TBL] [Abstract][Full Text] [Related]
10. Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network.
Zeng W; Wang Y; Jiang R
Bioinformatics; 2020 Jan; 36(2):496-503. PubMed ID: 31318408
[TBL] [Abstract][Full Text] [Related]
11. Epigenomic landscape of enhancer elements during Hydra head organizer formation.
Reddy PC; Gungi A; Ubhe S; Galande S
Epigenetics Chromatin; 2020 Oct; 13(1):43. PubMed ID: 33046126
[TBL] [Abstract][Full Text] [Related]
12. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.
Chen CY; Morris Q; Mitchell JA
BMC Genomics; 2012 Apr; 13():152. PubMed ID: 22537144
[TBL] [Abstract][Full Text] [Related]
13. Deciphering transcription factors and their corresponding regulatory elements during inhibitory interneuron differentiation using deep neural networks.
Alatawneh R; Salomon Y; Eshel R; Orenstein Y; Birnbaum RY
Front Cell Dev Biol; 2023; 11():1034604. PubMed ID: 36891511
[TBL] [Abstract][Full Text] [Related]
14. Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.
Busser BW; Haimovich J; Huang D; Ovcharenko I; Michelson AM
Nucleic Acids Res; 2015 Feb; 43(3):1726-39. PubMed ID: 25609699
[TBL] [Abstract][Full Text] [Related]
15. Enhancer prediction with histone modification marks using a hybrid neural network model.
Lim A; Lim S; Kim S
Methods; 2019 Aug; 166():48-56. PubMed ID: 30905748
[TBL] [Abstract][Full Text] [Related]
16. Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.
Busser BW; Huang D; Rogacki KR; Lane EA; Shokri L; Ni T; Gamble CE; Gisselbrecht SS; Zhu J; Bulyk ML; Ovcharenko I; Michelson AM
Proc Natl Acad Sci U S A; 2012 Dec; 109(50):20768-73. PubMed ID: 23184988
[TBL] [Abstract][Full Text] [Related]
17. Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data.
Panchy NL; Lloyd JP; Shiu SH
BMC Genomics; 2020 Feb; 21(1):159. PubMed ID: 32054475
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Enhancers display constrained sequence flexibility and context-specific modulation of motif function.
Reiter F; de Almeida BP; Stark A
Genome Res; 2023 Mar; 33(3):346-358. PubMed ID: 36941077
[TBL] [Abstract][Full Text] [Related]
20. Short DNA sequence patterns accurately identify broadly active human enhancers.
Colbran LL; Chen L; Capra JA
BMC Genomics; 2017 Jul; 18(1):536. PubMed ID: 28716036
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
