231 related articles for article (PubMed ID: 30791920)
1. Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
Karabacak Calviello A; Hirsekorn A; Wurmus R; Yusuf D; Ohler U
Genome Biol; 2019 Feb; 20(1):42. PubMed ID: 30791920
[TBL] [Abstract][Full Text] [Related]
2. XL-DNase-seq: improved footprinting of dynamic transcription factors.
Oh KS; Ha J; Baek S; Sung MH
Epigenetics Chromatin; 2019 Jun; 12(1):30. PubMed ID: 31164146
[TBL] [Abstract][Full Text] [Related]
3. Identification of transcription factor binding sites using ATAC-seq.
Li Z; Schulz MH; Look T; Begemann M; Zenke M; Costa IG
Genome Biol; 2019 Feb; 20(1):45. PubMed ID: 30808370
[TBL] [Abstract][Full Text] [Related]
4. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı GG; Frank CL; Crawford GE; Ohler U
Nucleic Acids Res; 2014 Oct; 42(19):11865-78. PubMed ID: 25294828
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. Analysis of computational footprinting methods for DNase sequencing experiments.
Gusmao EG; Allhoff M; Zenke M; Costa IG
Nat Methods; 2016 Apr; 13(4):303-9. PubMed ID: 26901649
[TBL] [Abstract][Full Text] [Related]
8. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
Ouyang N; Boyle AP
Genome Res; 2020 Jul; 30(7):1040-1046. PubMed ID: 32660981
[TBL] [Abstract][Full Text] [Related]
9. Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity.
Baek S; Goldstein I; Hager GL
Cell Rep; 2017 May; 19(8):1710-1722. PubMed ID: 28538187
[TBL] [Abstract][Full Text] [Related]
10. ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference.
Pranzatelli TJF; Michael DG; Chiorini JA
BMC Genomics; 2018 Jul; 19(1):563. PubMed ID: 30064353
[TBL] [Abstract][Full Text] [Related]
11. ATAC-seq with unique molecular identifiers improves quantification and footprinting.
Zhu T; Liao K; Zhou R; Xia C; Xie W
Commun Biol; 2020 Nov; 3(1):675. PubMed ID: 33188264
[TBL] [Abstract][Full Text] [Related]
12. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.
Moyano TC; Gutiérrez RA; Alvarez JM
Methods Mol Biol; 2021; 2328():25-46. PubMed ID: 34251618
[TBL] [Abstract][Full Text] [Related]
13. Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.
Hu SS; Liu L; Li Q; Ma W; Guertin MJ; Meyer CA; Deng K; Zhang T; Zang C
Nat Commun; 2022 Sep; 13(1):5533. PubMed ID: 36130957
[TBL] [Abstract][Full Text] [Related]
14. Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain.
Handel AE; Gallone G; Zameel Cader M; Ponting CP
Hum Mol Genet; 2017 Jan; 26(1):79-89. PubMed ID: 27798116
[TBL] [Abstract][Full Text] [Related]
15. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
Piper J; Elze MC; Cauchy P; Cockerill PN; Bonifer C; Ott S
Nucleic Acids Res; 2013 Nov; 41(21):e201. PubMed ID: 24071585
[TBL] [Abstract][Full Text] [Related]
16. Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.
Baek S; Sung MH
Methods Mol Biol; 2016; 1418():225-40. PubMed ID: 27008018
[TBL] [Abstract][Full Text] [Related]
17. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.
Funk CC; Casella AM; Jung S; Richards MA; Rodriguez A; Shannon P; Donovan-Maiye R; Heavner B; Chard K; Xiao Y; Glusman G; Ertekin-Taner N; Golde TE; Toga A; Hood L; Van Horn JD; Kesselman C; Foster I; Madduri R; Price ND; Ament SA
Cell Rep; 2020 Aug; 32(7):108029. PubMed ID: 32814038
[TBL] [Abstract][Full Text] [Related]
18. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes.
Lu Z; Hofmeister BT; Vollmers C; DuBois RM; Schmitz RJ
Nucleic Acids Res; 2017 Apr; 45(6):e41. PubMed ID: 27903897
[TBL] [Abstract][Full Text] [Related]
19. The native cistrome and sequence motif families of the maize ear.
Savadel SD; Hartwig T; Turpin ZM; Vera DL; Lung PY; Sui X; Blank M; Frommer WB; Dennis JH; Zhang J; Bass HW
PLoS Genet; 2021 Aug; 17(8):e1009689. PubMed ID: 34383745
[TBL] [Abstract][Full Text] [Related]
20. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.
He HH; Meyer CA; Hu SS; Chen MW; Zang C; Liu Y; Rao PK; Fei T; Xu H; Long H; Liu XS; Brown M
Nat Methods; 2014 Jan; 11(1):73-78. PubMed ID: 24317252
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
