BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

136 related articles for article (PubMed ID: 37012226)

  • 1. 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]  

  • 2. Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis.
    Yu J; Leng J; Hou Z; Sun D; Wu LY
    Brief Bioinform; 2024 Jan; 25(2):. PubMed ID: 38493346
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. 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]  

  • 5. Deciphering cell types by integrating scATAC-seq data with genome sequences.
    Zeng Y; Luo M; Shangguan N; Shi P; Feng J; Xu J; Chen K; Lu Y; Yu W; Yang Y
    Nat Comput Sci; 2024 Apr; 4(4):285-298. PubMed ID: 38600256
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 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. 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]  

  • 9. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq.
    Zhang G; Fu Y; Yang L; Ye F; Zhang P; Zhang S; Ma L; Li J; Wu H; Han X; Wang J; Guo G
    Dev Cell; 2024 Mar; 59(6):793-811.e8. PubMed ID: 38330939
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace.
    Tayyebi Z; Pine AR; Leslie CS
    Nat Methods; 2024 Jun; 21(6):1014-1022. PubMed ID: 38724693
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types.
    Kim SS; Truong B; Jagadeesh K; Dey KK; Shen AZ; Raychaudhuri S; Kellis M; Price AL
    Nat Commun; 2024 Jan; 15(1):563. PubMed ID: 38233398
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
    Mimitou EP; Lareau CA; Chen KY; Zorzetto-Fernandes AL; Hao Y; Takeshima Y; Luo W; Huang TS; Yeung BZ; Papalexi E; Thakore PI; Kibayashi T; Wing JB; Hata M; Satija R; Nazor KL; Sakaguchi S; Ludwig LS; Sankaran VG; Regev A; Smibert P
    Nat Biotechnol; 2021 Oct; 39(10):1246-1258. PubMed ID: 34083792
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Fundamental and practical approaches for single-cell ATAC-seq analysis.
    Shi P; Nie Y; Yang J; Zhang W; Tang Z; Xu J
    aBIOTECH; 2022 Sep; 3(3):212-223. PubMed ID: 36313930
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Profiling single-cell chromatin accessibility in plants.
    Marand AP; Zhang X; Nelson J; Braga Dos Reis PA; Schmitz RJ
    STAR Protoc; 2021 Sep; 2(3):100737. PubMed ID: 34430912
    [TBL] [Abstract][Full Text] [Related]  

  • 15. HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.
    Zhang W; Cui Y; Liu B; Loza M; Park SJ; Nakai K
    Brief Bioinform; 2024 Mar; 25(3):. PubMed ID: 38581422
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen.
    Li Z; Kuppe C; Ziegler S; Cheng M; Kabgani N; Menzel S; Zenke M; Kramann R; Costa IG
    Nat Commun; 2021 Nov; 12(1):6386. PubMed ID: 34737275
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq.
    Cui Z; Cui Y; Gao Y; Jiang T; Zang T; Wang Y
    Front Genet; 2021; 12():658352. PubMed ID: 33889181
    [TBL] [Abstract][Full Text] [Related]  

  • 18. scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data.
    Hu K; Liu H; Lawson ND; Zhu LJ
    Front Cell Dev Biol; 2022; 10():981859. PubMed ID: 36238687
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. 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]  

    [Next]    [New Search]
    of 7.