BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

105 related articles for article (PubMed ID: 29800273)

  • 1. peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data.
    Geeven G; Teunissen H; de Laat W; de Wit E
    Nucleic Acids Res; 2018 Sep; 46(15):e91. PubMed ID: 29800273
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq.
    Miranda M; Noordermeer D; Moindrot B
    Methods Mol Biol; 2022; 2532():15-33. PubMed ID: 35867243
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Learning Micro-C from Hi-C with diffusion models.
    Liu T; Zhu H; Wang Z
    PLoS Comput Biol; 2024 May; 20(5):e1012136. PubMed ID: 38758956
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Analysis of Hi-C data using SIP effectively identifies loops in organisms from
    Rowley MJ; Poulet A; Nichols MH; Bixler BJ; Sanborn AL; Brouhard EA; Hermetz K; Linsenbaum H; Csankovszki G; Lieberman Aiden E; Corces VG
    Genome Res; 2020 Mar; 30(3):447-458. PubMed ID: 32127418
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops.
    Zhou Y; Cheng X; Yang Y; Li T; Li J; Huang TH; Wang J; Lin S; Jin VX
    Genome Med; 2020 Aug; 12(1):69. PubMed ID: 32787954
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Extracting multi-way chromatin contacts from Hi-C data.
    Liu L; Zhang B; Hyeon C
    PLoS Comput Biol; 2021 Dec; 17(12):e1009669. PubMed ID: 34871311
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.
    Fang T; Liu Y; Woicik A; Lu M; Jha A; Wang X; Li G; Hristov B; Liu Z; Xu H; Noble WS; Wang S
    Bioinformatics; 2024 Jun; 40(Supplement_1):i471-i480. PubMed ID: 38940142
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Fine mapping chromatin contacts in capture Hi-C data.
    Eijsbouts CQ; Burren OS; Newcombe PJ; Wallace C
    BMC Genomics; 2019 Jan; 20(1):77. PubMed ID: 30674271
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Rescuing biologically relevant consensus regions across replicated samples.
    Jalili V; Cremona MA; Palluzzi F
    BMC Bioinformatics; 2023 Jun; 24(1):240. PubMed ID: 37286963
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.
    Race AM; Fuchs A; Chung HR
    Sci Rep; 2023 Dec; 13(1):22020. PubMed ID: 38086827
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Comparison of Capture Hi-C Analytical Pipelines.
    Aljogol D; Thompson IR; Osborne CS; Mifsud B
    Front Genet; 2022; 13():786501. PubMed ID: 35198004
    [TBL] [Abstract][Full Text] [Related]  

  • 12. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
    Cairns J; Freire-Pritchett P; Wingett SW; VĂ¡rnai C; Dimond A; Plagnol V; Zerbino D; Schoenfelder S; Javierre BM; Osborne C; Fraser P; Spivakov M
    Genome Biol; 2016 Jun; 17(1):127. PubMed ID: 27306882
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A comprehensive review of bioinformatics tools for chromatin loop calling.
    Liu L; Han K; Sun H; Han L; Gao D; Xi Q; Zhang L; Lin H
    Brief Bioinform; 2023 Mar; 24(2):. PubMed ID: 36882016
    [TBL] [Abstract][Full Text] [Related]  

  • 14. BaRDIC: robust peak calling for RNA-DNA interaction data.
    Mylarshchikov DE; Nikolskaya AI; Bogomaz OD; Zharikova AA; Mironov AA
    NAR Genom Bioinform; 2024 Jun; 6(2):lqae054. PubMed ID: 38774512
    [TBL] [Abstract][Full Text] [Related]  

  • 15. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.
    Li C; Chen X; Chen S; Jiang R; Zhang X
    Bioinformatics; 2023 Aug; 39(8):. PubMed ID: 37494428
    [TBL] [Abstract][Full Text] [Related]  

  • 16. An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line.
    Huang Z; Wang C; Treuter E; Fan R
    STAR Protoc; 2022 Jun; 3(2):101338. PubMed ID: 35496794
    [TBL] [Abstract][Full Text] [Related]  

  • 17. F-Seq2: improving the feature density based peak caller with dynamic statistics.
    Zhao N; Boyle AP
    NAR Genom Bioinform; 2021 Mar; 3(1):lqab012. PubMed ID: 33655209
    [TBL] [Abstract][Full Text] [Related]  

  • 18. SnapHiC2: A computationally efficient loop caller for single cell Hi-C data.
    Li X; Lee L; Abnousi A; Yu M; Liu W; Huang L; Li Y; Hu M
    Comput Struct Biotechnol J; 2022; 20():2778-2783. PubMed ID: 35685374
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.
    Downes DJ; Smith AL; Karpinska MA; Velychko T; Rue-Albrecht K; Sims D; Milne TA; Davies JOJ; Oudelaar AM; Hughes JR
    Nat Protoc; 2023 Oct; 18(10):3155. PubMed ID: 37369851
    [No Abstract]   [Full Text] [Related]  

  • 20. Enhancer hubs and loop collisions identified from single-allele topologies.
    Allahyar A; Vermeulen C; Bouwman BAM; Krijger PHL; Verstegen MJAM; Geeven G; van Kranenburg M; Pieterse M; Straver R; Haarhuis JHI; Jalink K; Teunissen H; Renkens IJ; Kloosterman WP; Rowland BD; de Wit E; de Ridder J; de Laat W
    Nat Genet; 2018 Aug; 50(8):1151-1160. PubMed ID: 29988121
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 6.