255 related articles for article (PubMed ID: 38256085)
1. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.
Vishnevsky OV; Bocharnikov AV; Ignatieva EV
Int J Mol Sci; 2024 Jan; 25(2):. PubMed ID: 38256085
[TBL] [Abstract][Full Text] [Related]
2. Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.
Vishnevsky OV; Bocharnikov AV; Kolchanov NA
J Bioinform Comput Biol; 2018 Feb; 16(1):1740012. PubMed ID: 29281953
[TBL] [Abstract][Full Text] [Related]
3. Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data.
Levitsky VG; Mukhin AM; Oshchepkov DY; Zemlyanskaya EV; Lashin SA
Int J Mol Sci; 2022 Aug; 23(16):. PubMed ID: 36012247
[TBL] [Abstract][Full Text] [Related]
4. Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.
Berger S; Pachkov M; Arnold P; Omidi S; Kelley N; Salatino S; van Nimwegen E
Genome Res; 2019 Jul; 29(7):1164-1177. PubMed ID: 31138617
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.
Levitsky V; Zemlyanskaya E; Oshchepkov D; Podkolodnaya O; Ignatieva E; Grosse I; Mironova V; Merkulova T
Nucleic Acids Res; 2019 Dec; 47(21):e139. PubMed ID: 31750523
[TBL] [Abstract][Full Text] [Related]
7. SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
Ding J; Hu H; Li X
Nucleic Acids Res; 2014 Mar; 42(5):e35. PubMed ID: 24322294
[TBL] [Abstract][Full Text] [Related]
8. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Robertson G; Hirst M; Bainbridge M; Bilenky M; Zhao Y; Zeng T; Euskirchen G; Bernier B; Varhol R; Delaney A; Thiessen N; Griffith OL; He A; Marra M; Snyder M; Jones S
Nat Methods; 2007 Aug; 4(8):651-7. PubMed ID: 17558387
[TBL] [Abstract][Full Text] [Related]
9. Cell-type specificity of ChIP-predicted transcription factor binding sites.
Håndstad T; Rye M; Močnik R; Drabløs F; Sætrom P
BMC Genomics; 2012 Aug; 13():372. PubMed ID: 22863112
[TBL] [Abstract][Full Text] [Related]
10. ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates.
Newell R; Pienaar R; Balderson B; Piper M; Essebier A; Bodén M
Genomics; 2021 Jul; 113(4):1855-1866. PubMed ID: 33878366
[TBL] [Abstract][Full Text] [Related]
11. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.
Chung D; Kuan PF; Li B; Sanalkumar R; Liang K; Bresnick EH; Dewey C; Keleş S
PLoS Comput Biol; 2011 Jul; 7(7):e1002111. PubMed ID: 21779159
[TBL] [Abstract][Full Text] [Related]
12. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.
Mundade R; Ozer HG; Wei H; Prabhu L; Lu T
Cell Cycle; 2014; 13(18):2847-52. PubMed ID: 25486472
[TBL] [Abstract][Full Text] [Related]
13. From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
Kulakovskiy I; Levitsky V; Oshchepkov D; Bryzgalov L; Vorontsov I; Makeev V
J Bioinform Comput Biol; 2013 Feb; 11(1):1340004. PubMed ID: 23427986
[TBL] [Abstract][Full Text] [Related]
14. NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling.
Menzel M; Hurka S; Glasenhardt S; Gogol-Döring A
Bioinformatics; 2021 May; 37(5):596-602. PubMed ID: 32991679
[TBL] [Abstract][Full Text] [Related]
15. A map of direct TF-DNA interactions in the human genome.
Gheorghe M; Sandve GK; Khan A; Chèneby J; Ballester B; Mathelier A
Nucleic Acids Res; 2019 Feb; 47(4):e21. PubMed ID: 30517703
[TBL] [Abstract][Full Text] [Related]
16. Differential motif enrichment analysis of paired ChIP-seq experiments.
Lesluyes T; Johnson J; Machanick P; Bailey TL
BMC Genomics; 2014 Sep; 15(1):752. PubMed ID: 25179504
[TBL] [Abstract][Full Text] [Related]
17. High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.
Chumsakul O; Nakamura K; Kurata T; Sakamoto T; Hobman JL; Ogasawara N; Oshima T; Ishikawa S
DNA Res; 2013 Aug; 20(4):325-38. PubMed ID: 23580539
[TBL] [Abstract][Full Text] [Related]
18. Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA.
Nagy G; Czipa E; Steiner L; Nagy T; Pongor S; Nagy L; Barta E
BMC Genomics; 2016 Aug; 17(1):637. PubMed ID: 27526722
[TBL] [Abstract][Full Text] [Related]
19. Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.
Yu CP; Kuo CH; Nelson CW; Chen CA; Soh ZT; Lin JJ; Hsiao RX; Chang CY; Li WH
Proc Natl Acad Sci U S A; 2021 May; 118(20):. PubMed ID: 33975951
[TBL] [Abstract][Full Text] [Related]
20. Using CisGenome to analyze ChIP-chip and ChIP-seq data.
Ji H; Jiang H; Ma W; Wong WH
Curr Protoc Bioinformatics; 2011 Mar; Chapter 2():Unit2.13. PubMed ID: 21400695
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
