69 related articles for article (PubMed ID: 26105820)
1. Transcription Factor Binding Site Mapping Using ChIP-Seq.
Jaini S; Lyubetskaya A; Gomes A; Peterson M; Tae Park S; Raman S; Schoolnik G; Galagan J
Microbiol Spectr; 2014 Apr; 2(2):. PubMed ID: 26105820
[TBL] [Abstract][Full Text] [Related]
2. Mapping genome-wide transcription-factor binding sites using DAP-seq.
Bartlett A; O'Malley RC; Huang SC; Galli M; Nery JR; Gallavotti A; Ecker JR
Nat Protoc; 2017 Aug; 12(8):1659-1672. PubMed ID: 28726847
[TBL] [Abstract][Full Text] [Related]
3. UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
Puig RR; Boddie P; Khan A; Castro-Mondragon JA; Mathelier A
BMC Genomics; 2021 Jun; 22(1):482. PubMed ID: 34174819
[TBL] [Abstract][Full Text] [Related]
4. Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data.
Levitsky V; Oshchepkov D; Zemlyanskaya E; Merkulova T
Int J Mol Sci; 2020 Aug; 21(17):. PubMed ID: 32825662
[TBL] [Abstract][Full Text] [Related]
5. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
Decker KT; Gao Y; Rychel K; Al Bulushi T; Chauhan SM; Kim D; Cho BK; Palsson BO
Nucleic Acids Res; 2022 Jan; 50(D1):D1077-D1084. PubMed ID: 34791440
[TBL] [Abstract][Full Text] [Related]
6. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.
Sherwood RI; Hashimoto T; O'Donnell CW; Lewis S; Barkal AA; van Hoff JP; Karun V; Jaakkola T; Gifford DK
Nat Biotechnol; 2014 Feb; 32(2):171-178. PubMed ID: 24441470
[TBL] [Abstract][Full Text] [Related]
7. BayesPeak: Bayesian analysis of ChIP-seq data.
Spyrou C; Stark R; Lynch AG; Tavaré S
BMC Bioinformatics; 2009 Sep; 10():299. PubMed ID: 19772557
[TBL] [Abstract][Full Text] [Related]
8. Anchor: trans-cell type prediction of transcription factor binding sites.
Li H; Quang D; Guan Y
Genome Res; 2019 Feb; 29(2):281-292. PubMed ID: 30567711
[TBL] [Abstract][Full Text] [Related]
9. Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq.
Hutin S; Blanc-Mathieu R; Rieu P; Parcy F; Lai X; Zubieta C
Methods Mol Biol; 2023; 2698():119-145. PubMed ID: 37682473
[TBL] [Abstract][Full Text] [Related]
10. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.
Garber M; Yosef N; Goren A; Raychowdhury R; Thielke A; Guttman M; Robinson J; Minie B; Chevrier N; Itzhaki Z; Blecher-Gonen R; Bornstein C; Amann-Zalcenstein D; Weiner A; Friedrich D; Meldrim J; Ram O; Cheng C; Gnirke A; Fisher S; Friedman N; Wong B; Bernstein BE; Nusbaum C; Hacohen N; Regev A; Amit I
Mol Cell; 2012 Sep; 47(5):810-22. PubMed ID: 22940246
[TBL] [Abstract][Full Text] [Related]
11. ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mapping
VanBelzen J; Duan C; Brickner DG; Brickner JH
bioRxiv; 2023 Oct; ():. PubMed ID: 37905156
[TBL] [Abstract][Full Text] [Related]
12. Protocol to capture transcription factor-mediated 3D chromatin interactions using affinity tag-based BL-HiChIP.
Ren R; Hua Y; Wang H
STAR Protoc; 2023 Dec; 4(4):102589. PubMed ID: 37738118
[TBL] [Abstract][Full Text] [Related]
13. ChEC-seq2: an improved chromatin endogenous cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions.
VanBelzen J; Duan C; Brickner DG; Brickner JH
NAR Genom Bioinform; 2024 Mar; 6(1):lqae012. PubMed ID: 38327869
[TBL] [Abstract][Full Text] [Related]
14. Improved models for transcription factor binding site identification using nonindependent interactions.
Zhao Y; Ruan S; Pandey M; Stormo GD
Genetics; 2012 Jul; 191(3):781-90. PubMed ID: 22505627
[TBL] [Abstract][Full Text] [Related]
15. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.
Moudgil A; Wilkinson MN; Chen X; He J; Cammack AJ; Vasek MJ; Lagunas T; Qi Z; Lalli MA; Guo C; Morris SA; Dougherty JD; Mitra RD
Cell; 2020 Aug; 182(4):992-1008.e21. PubMed ID: 32710817
[TBL] [Abstract][Full Text] [Related]
16. Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data.
Guo J; Zhang W; Chen X; Yen A; Chen L; Shively CA; Li D; Wang T; Dougherty JD; Mitra RD
Bioinformatics; 2024 Feb; 40(2):. PubMed ID: 38323623
[TBL] [Abstract][Full Text] [Related]
17. High-Resolution Chromatin Profiling Using CUT&RUN.
Hainer SJ; Fazzio TG
Curr Protoc Mol Biol; 2019 Apr; 126(1):e85. PubMed ID: 30688406
[TBL] [Abstract][Full Text] [Related]
18. cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.
Reiss DJ; Plaisier CL; Wu WJ; Baliga NS
Nucleic Acids Res; 2015 Jul; 43(13):e87. PubMed ID: 25873626
[TBL] [Abstract][Full Text] [Related]
19. Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.
Wade JT
Adv Exp Med Biol; 2015; 883():119-34. PubMed ID: 26621465
[TBL] [Abstract][Full Text] [Related]
20. ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks.
Pavesi G
Adv Biochem Eng Biotechnol; 2017; 160():1-14. PubMed ID: 28070596
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
