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 *

353 related articles for article (PubMed ID: 28056762)

  • 1. 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]  

  • 2. CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.
    Miura H; Cerbus RT; Noda I; Hiratani I
    Methods Mol Biol; 2025; 2856():79-117. PubMed ID: 39283448
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. 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]  

  • 5. DolphinNext: a distributed data processing platform for high throughput genomics.
    Yukselen O; Turkyilmaz O; Ozturk AR; Garber M; Kucukural A
    BMC Genomics; 2020 Apr; 21(1):310. PubMed ID: 32306927
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Read Mapping for Hi-C Analysis.
    Kelly ST; Tanaka K; Hosaka C; Yuhara S
    Methods Mol Biol; 2025; 2856():25-62. PubMed ID: 39283445
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines.
    Khalil AIS; Muzaki SRBM; Chattopadhyay A; Sanyal A
    BMC Bioinformatics; 2020 Nov; 21(1):506. PubMed ID: 33160308
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.
    Wolff J; Bhardwaj V; Nothjunge S; Richard G; Renschler G; Gilsbach R; Manke T; Backofen R; Ramírez F; Grüning BA
    Nucleic Acids Res; 2018 Jul; 46(W1):W11-W16. PubMed ID: 29901812
    [TBL] [Abstract][Full Text] [Related]  

  • 9. GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.
    Calandrelli R; Wu Q; Guan J; Zhong S
    Genomics Proteomics Bioinformatics; 2018 Oct; 16(5):365-372. PubMed ID: 30553884
    [TBL] [Abstract][Full Text] [Related]  

  • 10. SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.
    Cresswell KG; Stansfield JC; Dozmorov MG
    BMC Bioinformatics; 2020 Jul; 21(1):319. PubMed ID: 32689928
    [TBL] [Abstract][Full Text] [Related]  

  • 11. MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data.
    Khakmardan S; Rezvani M; Pouyan AA; Fateh M; Alinejad-Rokny H
    BMC Genomics; 2020 Mar; 21(1):225. PubMed ID: 32164554
    [TBL] [Abstract][Full Text] [Related]  

  • 12. JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping.
    Ahmed Z; Renart EG; Mishra D; Zeeshan S
    FEBS Open Bio; 2021 Sep; 11(9):2441-2452. PubMed ID: 34370400
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.
    Hansen P; Gargano M; Hecht J; Ibn-Salem J; Karlebach G; Roehr JT; Robinson PN
    Genes (Basel); 2019 Jul; 10(7):. PubMed ID: 31323892
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline.
    Tanizawa H; Chung CY; Fuse SI; Hayashi T; Weisel P; Noma KI
    Methods Mol Biol; 2025; 2856():133-155. PubMed ID: 39283450
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
    Caboche S; Audebert C; Lemoine Y; Hot D
    BMC Genomics; 2014 Apr; 15():264. PubMed ID: 24708189
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution.
    Spill YG; Castillo D; Vidal E; Marti-Renom MA
    Nat Commun; 2019 Apr; 10(1):1938. PubMed ID: 31028255
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
    Kadota M; Nishimura O; Miura H; Tanaka K; Hiratani I; Kuraku S
    Gigascience; 2020 Jan; 9(1):. PubMed ID: 31919520
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.
    MacKay K; Kusalik A
    Brief Funct Genomics; 2020 Jul; 19(4):292-308. PubMed ID: 32353112
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Measuring the reproducibility and quality of Hi-C data.
    Yardımcı GG; Ozadam H; Sauria MEG; Ursu O; Yan KK; Yang T; Chakraborty A; Kaul A; Lajoie BR; Song F; Zhan Y; Ay F; Gerstein M; Kundaje A; Li Q; Taylor J; Yue F; Dekker J; Noble WS
    Genome Biol; 2019 Mar; 20(1):57. PubMed ID: 30890172
    [TBL] [Abstract][Full Text] [Related]  

  • 20. NEAT: a framework for building fully automated NGS pipelines and analyses.
    Schorderet P
    BMC Bioinformatics; 2016 Feb; 17():53. PubMed ID: 26830846
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 18.