150 related articles for article (PubMed ID: 24974204)
1. Learning protein-DNA interaction landscapes by integrating experimental data through computational models.
Zhong J; Wasson T; Hartemink AJ
Bioinformatics; 2014 Oct; 30(20):2868-74. PubMed ID: 24974204
[TBL] [Abstract][Full Text] [Related]
2. Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.
Gao Z; Ruan J
Bioinformatics; 2017 Jul; 33(14):2097-2105. PubMed ID: 28334224
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding.
Kaplan T; Biggin MD
Methods Cell Biol; 2012; 110():263-83. PubMed ID: 22482953
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. Distinguishing direct versus indirect transcription factor-DNA interactions.
Gordân R; Hartemink AJ; Bulyk ML
Genome Res; 2009 Nov; 19(11):2090-100. PubMed ID: 19652015
[TBL] [Abstract][Full Text] [Related]
8. Efficient inference for sparse latent variable models of transcriptional regulation.
Dai Z; Iqbal M; Lawrence ND; Rattray M
Bioinformatics; 2017 Dec; 33(23):3776-3783. PubMed ID: 28961802
[TBL] [Abstract][Full Text] [Related]
9. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
Afek A; Cohen H; Barber-Zucker S; Gordân R; Lukatsky DB
PLoS Comput Biol; 2015 Aug; 11(8):e1004429. PubMed ID: 26285121
[TBL] [Abstract][Full Text] [Related]
10. SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles.
Wong KC; Li Y; Peng C; Zhang Z
Bioinformatics; 2015 Jan; 31(1):17-24. PubMed ID: 25192742
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. Incorporating nucleosomes into thermodynamic models of transcription regulation.
Raveh-Sadka T; Levo M; Segal E
Genome Res; 2009 Aug; 19(8):1480-96. PubMed ID: 19451592
[TBL] [Abstract][Full Text] [Related]
13. Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy.
Lubliner S; Segal E
Bioinformatics; 2009 Jun; 25(12):i348-55. PubMed ID: 19478009
[TBL] [Abstract][Full Text] [Related]
14. ChIPulate: A comprehensive ChIP-seq simulation pipeline.
Datta V; Hannenhalli S; Siddharthan R
PLoS Comput Biol; 2019 Mar; 15(3):e1006921. PubMed ID: 30897079
[TBL] [Abstract][Full Text] [Related]
15. Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.
Peng Y; Sun L; Jia Z; Li L; Alexov E
Bioinformatics; 2018 Mar; 34(5):779-786. PubMed ID: 29091991
[TBL] [Abstract][Full Text] [Related]
16. Transcriptional interaction-assisted identification of dynamic nucleosome positioning.
Dai Z; Dai X; Xiang Q; Feng J; Deng Y; Wang J; He C
BMC Bioinformatics; 2009 Jan; 10 Suppl 1(Suppl 1):S31. PubMed ID: 19208132
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Computational prediction and characterization of cell-type-specific and shared binding sites.
Zhang Q; Teng P; Wang S; He Y; Cui Z; Guo Z; Liu Y; Yuan C; Liu Q; Huang DS
Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36484687
[TBL] [Abstract][Full Text] [Related]
19. Identification of context-dependent motifs by contrasting ChIP binding data.
Mason MJ; Plath K; Zhou Q
Bioinformatics; 2010 Nov; 26(22):2826-32. PubMed ID: 20870645
[TBL] [Abstract][Full Text] [Related]
20. A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution.
Zhou X; Blocker AW; Airoldi EM; O'Shea EK
Elife; 2016 Sep; 5():. PubMed ID: 27623011
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
