BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

174 related articles for article (PubMed ID: 34965583)

  • 1. ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.
    Suryatenggara J; Yong KJ; Tenen DE; Tenen DG; Bassal MA
    Brief Bioinform; 2022 Jan; 23(1):. PubMed ID: 34965583
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.
    Szalkowski AM; Schmid CD
    Brief Bioinform; 2011 Nov; 12(6):626-33. PubMed ID: 21059603
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Novel ChIP-seq simulating program with superior versatility: isChIP.
    Subkhankulova T; Naumenko F; Tolmachov OE; Orlov YL
    Brief Bioinform; 2021 Jul; 22(4):. PubMed ID: 33320934
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Evaluation of algorithm performance in ChIP-seq peak detection.
    Wilbanks EG; Facciotti MT
    PLoS One; 2010 Jul; 5(7):e11471. PubMed ID: 20628599
    [TBL] [Abstract][Full Text] [Related]  

  • 6. RECAP reveals the true statistical significance of ChIP-seq peak calls.
    Chitpin JG; Awdeh A; Perkins TJ
    Bioinformatics; 2019 Oct; 35(19):3592-3598. PubMed ID: 30824903
    [TBL] [Abstract][Full Text] [Related]  

  • 7. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
    Yan H; Evans J; Kalmbach M; Moore R; Middha S; Luban S; Wang L; Bhagwate A; Li Y; Sun Z; Chen X; Kocher JP
    BMC Bioinformatics; 2014 Aug; 15(1):280. PubMed ID: 25128017
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.
    Eder T; Grebien F
    Genome Biol; 2022 May; 23(1):119. PubMed ID: 35606795
    [TBL] [Abstract][Full Text] [Related]  

  • 9. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.
    Chung D; Park D; Myers K; Grass J; Kiley P; Landick R; Keleş S
    PLoS Comput Biol; 2013; 9(10):e1003246. PubMed ID: 24146601
    [TBL] [Abstract][Full Text] [Related]  

  • 10. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.
    Ho JW; Bishop E; Karchenko PV; Nègre N; White KP; Park PJ
    BMC Genomics; 2011 Feb; 12():134. PubMed ID: 21356108
    [TBL] [Abstract][Full Text] [Related]  

  • 11. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
    Qin Q; Mei S; Wu Q; Sun H; Li L; Taing L; Chen S; Li F; Liu T; Zang C; Xu H; Chen Y; Meyer CA; Zhang Y; Brown M; Long HW; Liu XS
    BMC Bioinformatics; 2016 Oct; 17(1):404. PubMed ID: 27716038
    [TBL] [Abstract][Full Text] [Related]  

  • 12. An integrated software system for analyzing ChIP-chip and ChIP-seq data.
    Ji H; Jiang H; Ma W; Johnson DS; Myers RM; Wong WH
    Nat Biotechnol; 2008 Nov; 26(11):1293-300. PubMed ID: 18978777
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Epigenetic analysis: ChIP-chip and ChIP-seq.
    Pellegrini M; Ferrari R
    Methods Mol Biol; 2012; 802():377-87. PubMed ID: 22130894
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.
    Stanton KP; Jin J; Lederman RR; Weissman SM; Kluger Y
    Nucleic Acids Res; 2017 Dec; 45(21):e173. PubMed ID: 28981893
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Unified Analysis of Multiple ChIP-Seq Datasets.
    Ma G; Babarinde IA; Zhuang Q; Hutchins AP
    Methods Mol Biol; 2021; 2198():451-465. PubMed ID: 32822050
    [TBL] [Abstract][Full Text] [Related]  

  • 16. PeakRanger: a cloud-enabled peak caller for ChIP-seq data.
    Feng X; Grossman R; Stein L
    BMC Bioinformatics; 2011 May; 12():139. PubMed ID: 21554709
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes.
    Sharma V; Majumdar S
    BMC Bioinformatics; 2020 Feb; 21(1):65. PubMed ID: 32085702
    [TBL] [Abstract][Full Text] [Related]  

  • 18. A comparison of peak callers used for DNase-Seq data.
    Koohy H; Down TA; Spivakov M; Hubbard T
    PLoS One; 2014; 9(5):e96303. PubMed ID: 24810143
    [TBL] [Abstract][Full Text] [Related]  

  • 19. An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
    Mercier E; Droit A; Li L; Robertson G; Zhang X; Gottardo R
    PLoS One; 2011 Feb; 6(2):e16432. PubMed ID: 21358819
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Design and analysis of ChIP-seq experiments for DNA-binding proteins.
    Kharchenko PV; Tolstorukov MY; Park PJ
    Nat Biotechnol; 2008 Dec; 26(12):1351-9. PubMed ID: 19029915
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.