These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

276 related articles for article (PubMed ID: 34099725)

  • 1. HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.
    Sahin M; Wong W; Zhan Y; Van Deynze K; Koche R; Leslie CS
    Nat Commun; 2021 Jun; 12(1):3366. PubMed ID: 34099725
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Identification of significant chromatin contacts from HiChIP data by FitHiChIP.
    Bhattacharyya S; Chandra V; Vijayanand P; Ay F
    Nat Commun; 2019 Sep; 10(1):4221. PubMed ID: 31530818
    [TBL] [Abstract][Full Text] [Related]  

  • 3. An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.
    Carty M; Zamparo L; Sahin M; González A; Pelossof R; Elemento O; Leslie CS
    Nat Commun; 2017 May; 8():15454. PubMed ID: 28513628
    [TBL] [Abstract][Full Text] [Related]  

  • 4. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking.
    Lazaris C; Kelly S; Ntziachristos P; Aifantis I; Tsirigos A
    BMC Genomics; 2017 Jan; 18(1):22. PubMed ID: 28056762
    [TBL] [Abstract][Full Text] [Related]  

  • 5. HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test.
    Lagler TM; Abnousi A; Hu M; Yang Y; Li Y
    Am J Hum Genet; 2021 Feb; 108(2):257-268. PubMed ID: 33545029
    [TBL] [Abstract][Full Text] [Related]  

  • 6. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
    Juric I; Yu M; Abnousi A; Raviram R; Fang R; Zhao Y; Zhang Y; Qiu Y; Yang Y; Li Y; Ren B; Hu M
    PLoS Comput Biol; 2019 Apr; 15(4):e1006982. PubMed ID: 30986246
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Machine and Deep Learning Methods for Predicting 3D Genome Organization.
    Wall BPG; Nguyen M; Harrell JC; Dozmorov MG
    Methods Mol Biol; 2025; 2856():357-400. PubMed ID: 39283464
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture.
    Cubeñas-Potts C; Rowley MJ; Lyu X; Li G; Lei EP; Corces VG
    Nucleic Acids Res; 2017 Feb; 45(4):1714-1730. PubMed ID: 27899590
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.
    Fu S; Wang Q; Moore JE; Purcaro MJ; Pratt HE; Fan K; Gu C; Jiang C; Zhu R; Kundaje A; Lu A; Weng Z
    Nucleic Acids Res; 2018 Nov; 46(21):11184-11201. PubMed ID: 30137428
    [TBL] [Abstract][Full Text] [Related]  

  • 10. In silico prediction of high-resolution Hi-C interaction matrices.
    Zhang S; Chasman D; Knaack S; Roy S
    Nat Commun; 2019 Dec; 10(1):5449. PubMed ID: 31811132
    [TBL] [Abstract][Full Text] [Related]  

  • 11. A comparison of topologically associating domain callers over mammals at high resolution.
    Sefer E
    BMC Bioinformatics; 2022 Apr; 23(1):127. PubMed ID: 35413815
    [TBL] [Abstract][Full Text] [Related]  

  • 12. HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.
    Rosen J; Lee L; Abnousi A; Chen J; Wen J; Hu M; Li Y
    Comput Struct Biotechnol J; 2023; 21():931-939. PubMed ID: 38213897
    [TBL] [Abstract][Full Text] [Related]  

  • 13. ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.
    Oluwadare O; Cheng J
    BMC Bioinformatics; 2017 Nov; 18(1):480. PubMed ID: 29137603
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.
    Salviato E; Djordjilović V; Hariprakash JM; Tagliaferri I; Pal K; Ferrari F
    Nucleic Acids Res; 2021 Sep; 49(17):e97. PubMed ID: 34197622
    [TBL] [Abstract][Full Text] [Related]  

  • 15. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps.
    Ye Y; Gao L; Zhang S
    Nucleic Acids Res; 2019 Jun; 47(11):e65. PubMed ID: 30941409
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases.
    Lu L; Liu X; Huang WK; Giusti-Rodríguez P; Cui J; Zhang S; Xu W; Wen Z; Ma S; Rosen JD; Xu Z; Bartels CF; Kawaguchi R; Hu M; Scacheri PC; Rong Z; Li Y; Sullivan PF; Song H; Ming GL; Li Y; Jin F
    Mol Cell; 2020 Aug; 79(3):521-534.e15. PubMed ID: 32592681
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.
    Rubin AJ; Barajas BC; Furlan-Magaril M; Lopez-Pajares V; Mumbach MR; Howard I; Kim DS; Boxer LD; Cairns J; Spivakov M; Wingett SW; Shi M; Zhao Z; Greenleaf WJ; Kundaje A; Snyder M; Chang HY; Fraser P; Khavari PA
    Nat Genet; 2017 Oct; 49(10):1522-1528. PubMed ID: 28805829
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.
    Roayaei Ardakany A; Gezer HT; Lonardi S; Ay F
    Genome Biol; 2020 Sep; 21(1):256. PubMed ID: 32998764
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Functional genomic assays to annotate enhancer-promoter interactions genome wide.
    Leung AK; Yao L; Yu H
    Hum Mol Genet; 2022 Oct; 31(R1):R97-R104. PubMed ID: 36018818
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Methods for the Analysis of Topologically Associating Domains (TADs).
    Zufferey M; Tavernari D; Ciriello G
    Methods Mol Biol; 2022; 2301():39-59. PubMed ID: 34415530
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 14.