148 related articles for article (PubMed ID: 38565260)
1. EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery.
Schmitz JE; Aggarwal N; Laufer L; Walter J; Salhab A; Rahmann S
Bioinformatics; 2024 Mar; 40(4):. PubMed ID: 38565260
[TBL] [Abstract][Full Text] [Related]
2. Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome.
Mammana A; Chung HR
Genome Biol; 2015 Jul; 16(1):151. PubMed ID: 26206277
[TBL] [Abstract][Full Text] [Related]
3. Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell-Part 1: Epigenomics Assays.
Cheng K; McCarrey JR
Methods Mol Biol; 2023; 2656():71-108. PubMed ID: 37249867
[TBL] [Abstract][Full Text] [Related]
4. Probabilistic partitioning methods to find significant patterns in ChIP-Seq data.
Nair NU; Kumar S; Moret BM; Bucher P
Bioinformatics; 2014 Sep; 30(17):2406-13. PubMed ID: 24812341
[TBL] [Abstract][Full Text] [Related]
5. Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell: Part 2-Computational Analysis of Epigenomics Data.
Cheng K; McCarrey JR
Methods Mol Biol; 2023; 2656():109-125. PubMed ID: 37249868
[TBL] [Abstract][Full Text] [Related]
6. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Qin Q; Mei S; Wu Q; Sun H; Li L; Taing L; Chen S; Li F; Liu T; Zang C; Xu H; Chen Y; Meyer CA; Zhang Y; Brown M; Long HW; Liu XS
BMC Bioinformatics; 2016 Oct; 17(1):404. PubMed ID: 27716038
[TBL] [Abstract][Full Text] [Related]
7. Quantitative Comparison of Multiple Chromatin Immunoprecipitation-Sequencing (ChIP-seq) Experiments with spikChIP.
Blanco E; Ballaré C; Di Croce L; Aranda S
Methods Mol Biol; 2023; 2624():55-72. PubMed ID: 36723809
[TBL] [Abstract][Full Text] [Related]
8. Creating 2D Occupancy Plots Using plot2DO.
Beati P; Chereji RV
Methods Mol Biol; 2020; 2117():93-108. PubMed ID: 31960374
[TBL] [Abstract][Full Text] [Related]
9. A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Chen L; Wang C; Qin ZS; Wu H
Bioinformatics; 2015 Jun; 31(12):1889-96. PubMed ID: 25682068
[TBL] [Abstract][Full Text] [Related]
10. Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.
Nakato R; Shirahige K
Bioinformatics; 2018 Jul; 34(14):2356-2363. PubMed ID: 29528371
[TBL] [Abstract][Full Text] [Related]
11. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.
Fanelli M; Amatori S; Barozzi I; Minucci S
Nat Protoc; 2011 Nov; 6(12):1905-19. PubMed ID: 22082985
[TBL] [Abstract][Full Text] [Related]
12. Software for rapid time dependent ChIP-sequencing analysis (TDCA).
Myschyshyn M; Farren-Dai M; Chuang TJ; Vocadlo D
BMC Bioinformatics; 2017 Nov; 18(1):521. PubMed ID: 29178831
[TBL] [Abstract][Full Text] [Related]
13. Denoising genome-wide histone ChIP-seq with convolutional neural networks.
Koh PW; Pierson E; Kundaje A
Bioinformatics; 2017 Jul; 33(14):i225-i233. PubMed ID: 28881977
[TBL] [Abstract][Full Text] [Related]
14. A High-Throughput Chromatin Immunoprecipitation Sequencing Approach to Study the Role of MYC on the Epigenetic Landscape.
Fagnocchi L; Zippo A
Methods Mol Biol; 2021; 2318():187-208. PubMed ID: 34019291
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Discovering and mapping chromatin states using a tree hidden Markov model.
Biesinger J; Wang Y; Xie X
BMC Bioinformatics; 2013; 14 Suppl 5(Suppl 5):S4. PubMed ID: 23734743
[TBL] [Abstract][Full Text] [Related]
17. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications.
Zhu B; Hsieh YP; Murphy TW; Zhang Q; Naler LB; Lu C
Nat Protoc; 2019 Dec; 14(12):3366-3394. PubMed ID: 31666743
[TBL] [Abstract][Full Text] [Related]
18. DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.
Chen Y; Chen S; Lei EP
Bioinformatics; 2022 Sep; 38(17):4062-4069. PubMed ID: 35809062
[TBL] [Abstract][Full Text] [Related]
19. Universal count correction for high-throughput sequencing.
Hashimoto TB; Edwards MD; Gifford DK
PLoS Comput Biol; 2014 Mar; 10(3):e1003494. PubMed ID: 24603409
[TBL] [Abstract][Full Text] [Related]
20. Chromatin-state discovery and genome annotation with ChromHMM.
Ernst J; Kellis M
Nat Protoc; 2017 Dec; 12(12):2478-2492. PubMed ID: 29120462
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
