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 *

173 related articles for article (PubMed ID: 37497729)

  • 1. AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data.
    Tian L; Xie Y; Xie Z; Tian J; Tian W
    Brief Bioinform; 2023 Sep; 24(5):. PubMed ID: 37497729
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. simATAC: a single-cell ATAC-seq simulation framework.
    Navidi Z; Zhang L; Wang B
    Genome Biol; 2021 Mar; 22(1):74. PubMed ID: 33663563
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data.
    Lee MYY; Kaestner KH; Li M
    Genome Biol; 2023 Oct; 24(1):244. PubMed ID: 37875977
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Systematic benchmarking of single-cell ATAC-sequencing protocols.
    De Rop FV; Hulselmans G; Flerin C; Soler-Vila P; Rafels A; Christiaens V; González-Blas CB; Marchese D; Caratù G; Poovathingal S; Rozenblatt-Rosen O; Slyper M; Luo W; Muus C; Duarte F; Shrestha R; Bagdatli ST; Corces MR; Mamanova L; Knights A; Meyer KB; Mulqueen R; Taherinasab A; Maschmeyer P; Pezoldt J; Lambert CLG; Iglesias M; Najle SR; Dossani ZY; Martelotto LG; Burkett Z; Lebofsky R; Martin-Subero JI; Pillai S; Sebé-Pedrós A; Deplancke B; Teichmann SA; Ludwig LS; Braun TP; Adey AC; Greenleaf WJ; Buenrostro JD; Regev A; Aerts S; Heyn H
    Nat Biotechnol; 2024 Jun; 42(6):916-926. PubMed ID: 37537502
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Benchmarking automated cell type annotation tools for single-cell ATAC-seq data.
    Wang Y; Sun X; Zhao H
    Front Genet; 2022; 13():1063233. PubMed ID: 36583014
    [TBL] [Abstract][Full Text] [Related]  

  • 7. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.
    Yan G; Song D; Li JJ
    Nat Commun; 2023 Nov; 14(1):7482. PubMed ID: 37980428
    [TBL] [Abstract][Full Text] [Related]  

  • 8. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.
    Lin Y; Wu TY; Wan S; Yang JYH; Wong WH; Wang YXR
    Nat Biotechnol; 2022 May; 40(5):703-710. PubMed ID: 35058621
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Cellcano: supervised cell type identification for single cell ATAC-seq data.
    Ma W; Lu J; Wu H
    Nat Commun; 2023 Apr; 14(1):1864. PubMed ID: 37012226
    [TBL] [Abstract][Full Text] [Related]  

  • 10. CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal.
    Lyu Z; Dahal S; Zeng S; Wang J; Xu D; Joshi T
    Genes (Basel); 2024 Jul; 15(7):. PubMed ID: 39062661
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets.
    Erbe R; Kessler MD; Favorov AV; Easwaran H; Gaykalova DA; Fertig EJ
    Nucleic Acids Res; 2020 Jul; 48(12):e68. PubMed ID: 32392348
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility using scRNA-Seq and scATAC-Seq.
    Weir K; Leavey P; Santiago C; Blackshaw S
    J Vis Exp; 2021 Mar; (169):. PubMed ID: 33779599
    [TBL] [Abstract][Full Text] [Related]  

  • 13. scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization.
    Yan X; Zheng R; Chen J; Li M
    Bioinformatics; 2023 Aug; 39(8):. PubMed ID: 37584660
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A Unified Deep Learning Framework for Single-Cell ATAC-Seq Analysis Based on ProdDep Transformer Encoder.
    Wang Z; Zhang Y; Yu Y; Zhang J; Liu Y; Zou Q
    Int J Mol Sci; 2023 Mar; 24(5):. PubMed ID: 36902216
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?
    Liu Y; Zhang J; Wang S; Zeng X; Zhang W
    Brief Bioinform; 2022 Jan; 23(1):. PubMed ID: 34718405
    [TBL] [Abstract][Full Text] [Related]  

  • 16. scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data.
    Jiang Y; Hu Z; Lynch AW; Jiang J; Zhu A; Zeng Z; Zhang Y; Wu G; Xie Y; Li R; Zhou N; Meyer C; Cejas P; Brown M; Long HW; Qiu X
    bioRxiv; 2024 Mar; ():. PubMed ID: 37333088
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Evaluation of classification in single cell atac-seq data with machine learning methods.
    Guo H; Yang Z; Jiang T; Liu S; Wang Y; Cui Z
    BMC Bioinformatics; 2022 Sep; 23(Suppl 5):249. PubMed ID: 36131234
    [TBL] [Abstract][Full Text] [Related]  

  • 18. CAraCAl: CAMML with the integration of chromatin accessibility.
    Schiebout C; Frost HR
    BMC Bioinformatics; 2024 Jun; 25(1):212. PubMed ID: 38872103
    [TBL] [Abstract][Full Text] [Related]  

  • 19. SCALE method for single-cell ATAC-seq analysis via latent feature extraction.
    Xiong L; Xu K; Tian K; Shao Y; Tang L; Gao G; Zhang M; Jiang T; Zhang QC
    Nat Commun; 2019 Oct; 10(1):4576. PubMed ID: 31594952
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Protocol for executing and benchmarking eight computational doublet-detection methods in single-cell RNA sequencing data analysis.
    Xi NM; Li JJ
    STAR Protoc; 2021 Sep; 2(3):100699. PubMed ID: 34382023
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.