BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

127 related articles for article (PubMed ID: 37546876)

  • 1. Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples.
    Domanskyi S; Srivastava A; Kaster J; Li H; Herlyn M; Rubinstein JC; Chuang JH
    bioRxiv; 2023 Jul; ():. PubMed ID: 37546876
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples.
    Domanskyi S; Srivastava A; Kaster J; Li H; Herlyn M; Rubinstein JC; Chuang JH
    Cell Rep Methods; 2024 May; 4(5):100759. PubMed ID: 38626768
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study.
    Fatemi M; Feng E; Sharma C; Azher Z; Goel T; Ramwala O; Palisoul SM; Barney RE; Perreard L; Kolling FW; Salas LA; Christensen BC; Tsongalis GJ; Vaickus LJ; Levy JJ
    J Pathol Inform; 2023; 14():100308. PubMed ID: 37114077
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Spatial Transcriptomics in Kidney Tissue.
    Raghubar AM; Crawford J; Jones K; Lam PY; Andersen SB; Matigian NA; Ng MSY; Healy H; Kassianos AJ; Mallett AJ
    Methods Mol Biol; 2023; 2664():233-282. PubMed ID: 37423994
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Inferring single-cell spatial gene expression with tissue morphology via explainable deep learning.
    Zhao Y; Alizadeh E; Liu Y; Xu M; Mahoney JM; Li S
    bioRxiv; 2024 Jun; ():. PubMed ID: 38915550
    [TBL] [Abstract][Full Text] [Related]  

  • 6.
    Tippani M; Divecha HR; Catallini JL; Kwon SH; Weber LM; Spangler A; Jaffe AE; Hyde TM; Kleinman JE; Hicks SC; Martinowich K; Collado-Torres L; Page SC; Maynard KR
    Biol Imaging; 2023; 3():e23. PubMed ID: 38510173
    [TBL] [Abstract][Full Text] [Related]  

  • 7. The Overlooked Role of Specimen Preparation in Bolstering Deep Learning-Enhanced Spatial Transcriptomics Workflows.
    Fatemi MY; Lu Y; Diallo AB; Srinivasan G; Azher ZL; Christensen BC; Salas LA; Tsongalis GJ; Palisoul SM; Perreard L; Kolling FW; Vaickus LJ; Levy JJ
    medRxiv; 2023 Oct; ():. PubMed ID: 37873287
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
    Bergenstråhle J; Larsson L; Lundeberg J
    BMC Genomics; 2020 Jul; 21(1):482. PubMed ID: 32664861
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data.
    Lepetit M; Ilie MD; Chanal M; Raverot G; Bertolino P; Arpin C; Picard F; Gandrillon O
    In Silico Biol; 2023; 15(1-2):11-21. PubMed ID: 37927254
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples).
    Antico F; Gai M; Arigoni M
    Methods Mol Biol; 2023; 2584():191-203. PubMed ID: 36495450
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining.
    Srinivasan G; Davis MJ; LeBoeuf MR; Fatemi M; Azher ZL; Lu Y; Diallo AB; Saldias Montivero MK; Kolling FW; Perrard L; Salas LA; Christensen BC; Palys TJ; Karagas MR; Palisoul SM; Tsongalis GJ; Vaickus LJ; Preum SM; Levy JJ
    Pac Symp Biocomput; 2024; 29():477-491. PubMed ID: 38160301
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining.
    Srinivasan G; Davis M; LeBoeuf M; Fatemi M; Azher Z; Lu Y; Diallo A; Montivero MS; Kolling F; Perrard L; Salas L; Christensen B; Palisoul S; Tsongalis G; Vaickus L; Preum S; Levy J
    bioRxiv; 2023 Jul; ():. PubMed ID: 37577612
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Enabling automated and reproducible spatially resolved transcriptomics at scale.
    Stenbeck L; Taborsak-Lines F; Giacomello S
    Heliyon; 2022 Jun; 8(6):e09651. PubMed ID: 35756107
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Use of Deep Learning to Develop and Analyze Computational Hematoxylin and Eosin Staining of Prostate Core Biopsy Images for Tumor Diagnosis.
    Rana A; Lowe A; Lithgow M; Horback K; Janovitz T; Da Silva A; Tsai H; Shanmugam V; Bayat A; Shah P
    JAMA Netw Open; 2020 May; 3(5):e205111. PubMed ID: 32432709
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Spatial transcriptomics reveal basal sex differences in supraoptic nucleus gene expression of adult rats related to cell signaling and ribosomal pathways.
    Nguyen DH; Duque V; Phillips N; Mecawi AS; Cunningham JT
    Biol Sex Differ; 2023 Oct; 14(1):71. PubMed ID: 37858270
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Feasibility of Inferring Spatial Transcriptomics from Single-Cell Histological Patterns for Studying Colon Cancer Tumor Heterogeneity.
    Fatemi MY; Lu Y; Sharma C; Feng E; Azher ZL; Diallo AB; Srinivasan G; Rosner GM; Pointer KB; Christensen BC; Salas LA; Tsongalis GJ; Palisoul SM; Perreard L; Kolling FW; Vaickus LJ; Levy JJ
    medRxiv; 2023 Oct; ():. PubMed ID: 37873186
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics.
    Pavel I; Irina L; Tatiana G; Denis P; Philipp K; Sergei K; Evgeny D
    BMC Genomics; 2023 Mar; 24(1):102. PubMed ID: 36882687
    [TBL] [Abstract][Full Text] [Related]  

  • 19. STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data.
    Xi J; Lee JH; Kang HM; Jun G
    Bioinform Adv; 2022; 2(1):. PubMed ID: 36284674
    [TBL] [Abstract][Full Text] [Related]  

  • 20. MC-ViT: Multi-path cross-scale vision transformer for thymoma histopathology whole slide image typing.
    Zhang H; Chen H; Qin J; Wang B; Ma G; Wang P; Zhong D; Liu J
    Front Oncol; 2022; 12():925903. PubMed ID: 36387248
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.