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 *

122 related articles for article (PubMed ID: 37425672)

  • 1. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
    Bryce-Smith S; Burri D; Gazzara MR; Herrmann CJ; Danecka W; Fitzsimmons CM; Wan YK; Zhuang F; Fansler MM; Fernández JM; Ferret M; Gonzalez-Uriarte A; Haynes S; Herdman C; Kanitz A; Katsantoni M; Marini F; McDonnel E; Nicolet B; Poon CL; Rot G; Schärfen L; Wu PJ; Yoon Y; Barash Y; Zavolan M
    bioRxiv; 2023 Jun; ():. PubMed ID: 37425672
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
    Bryce-Smith S; Burri D; Gazzara MR; Herrmann CJ; Danecka W; Fitzsimmons CM; Wan YK; Zhuang F; Fansler MM; Fernández JM; Ferret M; Gonzalez-Uriarte A; Haynes S; Herdman C; Kanitz A; Katsantoni M; Marini F; McDonnel E; Nicolet B; Poon CL; Rot G; Schärfen L; Wu PJ; Yoon Y; Barash Y; Zavolan M
    RNA; 2023 Dec; 29(12):1839-1855. PubMed ID: 37816550
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation.
    Shah A; Mittleman BE; Gilad Y; Li YI
    Genome Biol; 2021 Oct; 22(1):291. PubMed ID: 34649612
    [TBL] [Abstract][Full Text] [Related]  

  • 4. A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data.
    Chen M; Ji G; Fu H; Lin Q; Ye C; Ye W; Su Y; Wu X
    Brief Bioinform; 2020 Jul; 21(4):1261-1276. PubMed ID: 31267126
    [TBL] [Abstract][Full Text] [Related]  

  • 5. APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.
    Fahmi NA; Ahmed KT; Chang JW; Nassereddeen H; Fan D; Yong J; Zhang W
    BMC Bioinformatics; 2022 Sep; 23(Suppl 3):396. PubMed ID: 36171568
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.
    Long Y; Zhang B; Tian S; Chan JJ; Zhou J; Li Z; Li Y; An Z; Liao X; Wang Y; Sun S; Xu Y; Tay Y; Chen W; Gao X
    Genome Res; 2023 Apr; 33(4):644-657. PubMed ID: 37117035
    [TBL] [Abstract][Full Text] [Related]  

  • 7. APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.
    Ye C; Long Y; Ji G; Li QQ; Wu X
    Bioinformatics; 2018 Jun; 34(11):1841-1849. PubMed ID: 29360928
    [TBL] [Abstract][Full Text] [Related]  

  • 8. PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.
    Jonnakuti VS; Wagner EJ; Maletić-Savatić M; Liu Z; Yalamanchili HK
    Cell Rep Methods; 2024 Feb; 4(2):100707. PubMed ID: 38325383
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.
    Ye W; Lian Q; Ye C; Wu X
    Genomics Proteomics Bioinformatics; 2023 Feb; 21(1):67-83. PubMed ID: 36167284
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data.
    Wang X; Lian Q; Dong H; Xu S; Su Y; Wu X
    Genomics Proteomics Bioinformatics; 2024 Jul; 22(2):. PubMed ID: 39049508
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation.
    Zhang Y; Carrion SA; Zhang Y; Zhang X; Zinski AL; Michal JJ; Jiang Z
    Int J Biol Sci; 2018; 14(12):1709-1714. PubMed ID: 30416385
    [TBL] [Abstract][Full Text] [Related]  

  • 12. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.
    D'Antonio M; D'Onorio De Meo P; Pallocca M; Picardi E; D'Erchia AM; Calogero RA; Castrignanò T; Pesole G
    BMC Genomics; 2015; 16(Suppl 6):S3. PubMed ID: 26046471
    [TBL] [Abstract][Full Text] [Related]  

  • 13. XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.
    Liu Y; Wu P; Zhou J; Johnson-Pais TL; Lai Z; Chowdhury WH; Rodriguez R; Chen Y
    BMC Bioinformatics; 2017 Oct; 18(Suppl 11):384. PubMed ID: 28984183
    [TBL] [Abstract][Full Text] [Related]  

  • 14. TAPAS: tool for alternative polyadenylation site analysis.
    Arefeen A; Liu J; Xiao X; Jiang T
    Bioinformatics; 2018 Aug; 34(15):2521-2529. PubMed ID: 30052912
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.
    Quinn TP; Crowley TM; Richardson MF
    BMC Bioinformatics; 2018 Jul; 19(1):274. PubMed ID: 30021534
    [TBL] [Abstract][Full Text] [Related]  

  • 16. scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data.
    Wu X; Liu T; Ye C; Ye W; Ji G
    Brief Bioinform; 2021 Jul; 22(4):. PubMed ID: 33142319
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.
    Yalamanchili HK; Elrod ND; Jensen MK; Ji P; Lin A; Wagner EJ; Liu Z
    Methods Enzymol; 2021; 655():185-204. PubMed ID: 34183121
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
    Holland CH; Tanevski J; Perales-Patón J; Gleixner J; Kumar MP; Mereu E; Joughin BA; Stegle O; Lauffenburger DA; Heyn H; Szalai B; Saez-Rodriguez J
    Genome Biol; 2020 Feb; 21(1):36. PubMed ID: 32051003
    [TBL] [Abstract][Full Text] [Related]  

  • 19. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.
    Ye C; Zhou Q; Wu X; Yu C; Ji G; Saban DR; Li QQ
    Bioinformatics; 2020 Feb; 36(4):1262-1264. PubMed ID: 31557285
    [TBL] [Abstract][Full Text] [Related]  

  • 20. PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data.
    Jonnakuti VS; Wagner EJ; Maletić-Savatić M; Liu Z; Yalamanchili HK
    bioRxiv; 2023 Jan; ():. PubMed ID: 36747700
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.