652 related articles for article (PubMed ID: 31164146)
1. 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]
2. 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]
3. 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]
4. 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]
5. 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]
6. 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]
7. 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]
8. 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]
9. Genome-wide footprinting: ready for prime time?
Sung MH; Baek S; Hager GL
Nat Methods; 2016 Mar; 13(3):222-228. PubMed ID: 26914206
[TBL] [Abstract][Full Text] [Related]
10. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
Cazares TA; Rizvi FW; Iyer B; Chen X; Kotliar M; Bejjani AT; Wayman JA; Donmez O; Wronowski B; Parameswaran S; Kottyan LC; Barski A; Weirauch MT; Prasath VBS; Miraldi ER
PLoS Comput Biol; 2023 Jan; 19(1):e1010863. PubMed ID: 36719906
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. 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]
13. 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]
14. 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]
15. [Advances in assay for transposase-accessible chromatin with high-throughput sequencing].
Wu J; Quan JP; Ye Y; Wu ZF; Yang J; Yang M; Zheng EQ
Yi Chuan; 2020 Apr; 42(4):333-346. PubMed ID: 32312702
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. 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]
18. 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]
19. Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq.
Marinov GK; Shipony Z
Methods Mol Biol; 2021; 2243():183-226. PubMed ID: 33606259
[TBL] [Abstract][Full Text] [Related]
20. Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv.
Orchard P; Kyono Y; Hensley J; Kitzman JO; Parker SCJ
Cell Syst; 2020 Mar; 10(3):298-306.e4. PubMed ID: 32213349
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
