303 related articles for article (PubMed ID: 35410163)
1. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.
Kaplow IM; Schäffer DE; Wirthlin ME; Lawler AJ; Brown AR; Kleyman M; Pfenning AR
BMC Genomics; 2022 Apr; 23(1):291. PubMed ID: 35410163
[TBL] [Abstract][Full Text] [Related]
2. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.
Chen L; Fish AE; Capra JA
PLoS Comput Biol; 2018 Oct; 14(10):e1006484. PubMed ID: 30286077
[TBL] [Abstract][Full Text] [Related]
3. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.
Kheradpour P; Ernst J; Melnikov A; Rogov P; Wang L; Zhang X; Alston J; Mikkelsen TS; Kellis M
Genome Res; 2013 May; 23(5):800-11. PubMed ID: 23512712
[TBL] [Abstract][Full Text] [Related]
4. Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity.
Fish A; Chen L; Capra JA
Genome Biol Evol; 2017 Oct; 9(10):2615-2625. PubMed ID: 28985297
[TBL] [Abstract][Full Text] [Related]
5. Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.
Madgwick A; Magri MS; Dantec C; Gailly D; Fiuza UM; Guignard L; Hettinger S; Gomez-Skarmeta JL; Lemaire P
Dev Biol; 2019 Apr; 448(2):71-87. PubMed ID: 30661644
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Functional tests of enhancer conservation between distantly related species.
Ruvinsky I; Ruvkun G
Development; 2003 Nov; 130(21):5133-42. PubMed ID: 12944426
[TBL] [Abstract][Full Text] [Related]
8. Integrating diverse datasets improves developmental enhancer prediction.
Erwin GD; Oksenberg N; Truty RM; Kostka D; Murphy KK; Ahituv N; Pollard KS; Capra JA
PLoS Comput Biol; 2014 Jun; 10(6):e1003677. PubMed ID: 24967590
[TBL] [Abstract][Full Text] [Related]
9. Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns.
Osmala M; Lähdesmäki H
BMC Bioinformatics; 2020 Jul; 21(1):317. PubMed ID: 32689977
[TBL] [Abstract][Full Text] [Related]
10. Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.
Glinsky GV
Chromosome Res; 2018 Mar; 26(1-2):61-84. PubMed ID: 29335803
[TBL] [Abstract][Full Text] [Related]
11. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling.
Davie K; Jacobs J; Atkins M; Potier D; Christiaens V; Halder G; Aerts S
PLoS Genet; 2015 Feb; 11(2):e1004994. PubMed ID: 25679813
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species.
Hujoel MLA; Gazal S; Hormozdiari F; van de Geijn B; Price AL
Am J Hum Genet; 2019 Apr; 104(4):611-624. PubMed ID: 30905396
[TBL] [Abstract][Full Text] [Related]
14. Predicting enhancers in mammalian genomes using supervised hidden Markov models.
Zehnder T; Benner P; Vingron M
BMC Bioinformatics; 2019 Mar; 20(1):157. PubMed ID: 30917778
[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. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.
Pérez-Rico YA; Boeva V; Mallory AC; Bitetti A; Majello S; Barillot E; Shkumatava A
Genome Res; 2017 Feb; 27(2):259-268. PubMed ID: 27965291
[TBL] [Abstract][Full Text] [Related]
17. Many human accelerated regions are developmental enhancers.
Capra JA; Erwin GD; McKinsey G; Rubenstein JL; Pollard KS
Philos Trans R Soc Lond B Biol Sci; 2013 Dec; 368(1632):20130025. PubMed ID: 24218637
[TBL] [Abstract][Full Text] [Related]
18. Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data.
Podsiadło A; Wrzesień M; Paja W; Rudnicki W; Wilczyński B
BMC Syst Biol; 2013; 7 Suppl 6(Suppl 6):S16. PubMed ID: 24565409
[TBL] [Abstract][Full Text] [Related]
19. An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Arunachalam M; Jayasurya K; Tomancak P; Ohler U
Bioinformatics; 2010 Sep; 26(17):2109-15. PubMed ID: 20624780
[TBL] [Abstract][Full Text] [Related]
20. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues.
Halstead MM; Kern C; Saelao P; Wang Y; Chanthavixay G; Medrano JF; Van Eenennaam AL; Korf I; Tuggle CK; Ernst CW; Zhou H; Ross PJ
BMC Genomics; 2020 Oct; 21(1):698. PubMed ID: 33028202
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
