253 related articles for article (PubMed ID: 34255854)
1. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.
Mitra S; Zhong J; Tran TQ; MacAlpine DM; Hartemink AJ
Nucleic Acids Res; 2021 Aug; 49(14):7925-7938. PubMed ID: 34255854
[TBL] [Abstract][Full Text] [Related]
2. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.
Mitra S; Zhong J; MacAlpine DM; Hartemink AJ
Res Comput Mol Biol; 2020 May; 12074():136-151. PubMed ID: 34386808
[TBL] [Abstract][Full Text] [Related]
3. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.
Gossett AJ; Lieb JD
PLoS Genet; 2012; 8(6):e1002771. PubMed ID: 22737086
[TBL] [Abstract][Full Text] [Related]
4. Mapping nucleosome positions using DNase-seq.
Zhong J; Luo K; Winter PS; Crawford GE; Iversen ES; Hartemink AJ
Genome Res; 2016 Mar; 26(3):351-64. PubMed ID: 26772197
[TBL] [Abstract][Full Text] [Related]
5. Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.
de Jonge WJ; Brok M; Lijnzaad P; Kemmeren P; Holstege FC
Mol Syst Biol; 2020 Oct; 16(10):e9885. PubMed ID: 33280256
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data.
Cesur MF; Çakır T; Pir P
mSystems; 2022 Jun; 7(3):e0134721. PubMed ID: 35695574
[TBL] [Abstract][Full Text] [Related]
8. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
Kumar S; Bucher P
BMC Bioinformatics; 2016 Jan; 17 Suppl 1(Suppl 1):4. PubMed ID: 26818008
[TBL] [Abstract][Full Text] [Related]
9. Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis.
Pajoro A; Muiño JM; Angenent GC; Kaufmann K
Methods Mol Biol; 2018; 1675():167-181. PubMed ID: 29052192
[TBL] [Abstract][Full Text] [Related]
10. Mapping Chromatin Accessibility in Human Naïve Pluripotent Stem Cells Using ATAC-Seq.
Cinkornpumin JK; Hossain I; Pastor WA
Methods Mol Biol; 2022; 2416():201-211. PubMed ID: 34870838
[TBL] [Abstract][Full Text] [Related]
11. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.
Chabbert CD; Adjalley SH; Steinmetz LM; Pelechano V
Methods Mol Biol; 2018; 1689():177-194. PubMed ID: 29027175
[TBL] [Abstract][Full Text] [Related]
12. Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation.
Henikoff S; Henikoff JG; Kaya-Okur HS; Ahmad K
Elife; 2020 Nov; 9():. PubMed ID: 33191916
[TBL] [Abstract][Full Text] [Related]
13. Measuring Chromatin Accessibility: ATAC-Seq.
Sahu SK; Basu A; Tiwari VK
Methods Mol Biol; 2021; 2351():105-121. PubMed ID: 34382186
[TBL] [Abstract][Full Text] [Related]
14. Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.
Levo M; Avnit-Sagi T; Lotan-Pompan M; Kalma Y; Weinberger A; Yakhini Z; Segal E
Mol Cell; 2017 Feb; 65(4):604-617.e6. PubMed ID: 28212748
[TBL] [Abstract][Full Text] [Related]
15. Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq).
Hoeijmakers WAM; Bártfai R
Methods Mol Biol; 2018; 1689():83-101. PubMed ID: 29027167
[TBL] [Abstract][Full Text] [Related]
16. NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.
Vainshtein Y; Rippe K; Teif VB
BMC Genomics; 2017 Feb; 18(1):158. PubMed ID: 28196481
[TBL] [Abstract][Full Text] [Related]
17. Absolute nucleosome occupancy map for the
Oberbeckmann E; Wolff M; Krietenstein N; Heron M; Ellins JL; Schmid A; Krebs S; Blum H; Gerland U; Korber P
Genome Res; 2019 Dec; 29(12):1996-2009. PubMed ID: 31694866
[TBL] [Abstract][Full Text] [Related]
18. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.
Goh WS; Orlov Y; Li J; Clarke ND
PLoS Comput Biol; 2010 Jan; 6(1):e1000649. PubMed ID: 20098497
[TBL] [Abstract][Full Text] [Related]
19. Analyses of Promoter , Enhancer, and Nucleosome Organization in Mammalian Cells by MNase-Seq.
Esnault C; Magat T; García-Oliver E; Andrau JC
Methods Mol Biol; 2021; 2351():93-104. PubMed ID: 34382185
[TBL] [Abstract][Full Text] [Related]
20. Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae.
Zawadzki KA; Morozov AV; Broach JR
Mol Biol Cell; 2009 Aug; 20(15):3503-13. PubMed ID: 19494041
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
