Searching journal content for articles similar to Szałaj et al. 26 (12): 1697.

Displaying results 1-7 of 7
For checked items
  1. Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
    • Lin Li,
    • Xianbin Su,
    • and Ze-Guang Han
    Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
    ...and assigns gene program activity to individual cells or spatial locations. Through evaluation on both simulated and real biological data sets, DeCEP demonstrates complementary strengths over existing methods by enabling more fine-grained characterization of gene programs within specific contexts...
  2. Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
    • Hossein Salari,
    • Marco Di Stefano,
    • and Daniel Jost
    Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
    ....ResultsQuantitative data-driven modeling of 3D chromosome organizationTo investigate chromatin motion in situations compatible with experiments, we first developed a data-driven polymer model to quantitatively describe the 3D chromatin organization. We modeled chromatin as a coarse-grained heteropolymer (Fig. 2A). Each...
  3. Method: Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
    • Eric E. Schadt,
    • Onureena Banerjee,
    • Gang Fang,
    • Zhixing Feng,
    • Wing H. Wong,
    • Xuegong Zhang,
    • Andrey Kislyuk,
    • Tyson A. Clark,
    • Khai Luong,
    • Alona Keren-Paz,
    • Andrew Chess,
    • Vipin Kumar,
    • Alice Chen-Plotkin,
    • Neal Sondheimer,
    • Jonas Korlach,
    • and Andrew Kasarskis
    Genome Res. January 2013 23: 129-141; Published in Advance October 23, 2012, doi:10.1101/gr.136739.111
    ...1 1 Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA; 2 Pacific Biosciences, Menlo Park, California 94025, USA; 3 Department of Computer Science and Engineering, University of Minnesota...
    OPEN ACCESS ARTICLE
  4. Method: Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning
    • Tian Tian,
    • Cheng Zhong,
    • Xiang Lin,
    • Zhi Wei,
    • and Hakon Hakonarson
    Genome Res. February 2023 33: 232-246; Published in Advance February 27, 2023, doi:10.1101/gr.277068.122
    ...visualization. The deep generative model has recently emerged as a powerful method for representation learning of single-cell genomics data (Ding et al. 2018; Lopez et al. 2018; Ding and Regev 2021; Liu et al. 2021). To integrate data sets from different batches to a joint embedding, we combine the strength...
  5. Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
    • Charlie George Barker,
    • Eirini Petsalaki,
    • Girolamo Giudice,
    • Julia Sero,
    • Emmanuel Nsa Ekpenyong,
    • Chris Bakal,
    • and Evangelia Petsalaki
    Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
    .... For the basal-like cluster, the regulome with the highest normalized enrichment score is SOX2, as well as MSC and HOXA9. Down-regulated regulomes include ZEB2, MYC, ESRRA, and KLF5 (Supplemental Fig. S2D).Assembly of a data-driven cell-shape regulatory networkTo integrate our data-driven GEMs with signaling...
    OPEN ACCESS ARTICLE
  6. ARTICLE: High-Throughput Imaging of Brain Gene Expression
    • Vanessa M. Brown,
    • Alex Ossadtchi,
    • Arshad H. Khan,
    • Simon R. Cherry,
    • Richard M. Leahy,
    • and Desmond J. Smith
    Genome Res. February 1, 2002 12: 244-254; doi:10.1101/gr.204102
    ...: Department of Biomedical Engineering, One Shields Ave, University of California, Davis, CA 95616, USA. ↵ 5 Corresponding author. E-MAIL DSmith@mednet.ucla.edu ; FAX (310) 825-6267. Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.204102...
  7. ARTICLE: Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease
    • Vanessa M. Brown,
    • Alex Ossadtchi,
    • Arshad H. Khan,
    • Simon Yee,
    • Goran Lacan,
    • William P. Melega,
    • Simon R. Cherry,
    • Richard M. Leahy,
    • and Desmond J. Smith
    Genome Res. June 1, 2002 12: 868-884; Published in Advance May 16, 2002, doi:10.1101/gr.229002
    ...H, Khan Ossadtchi Alex Ossadtchi, A RM Leahy Simon V.M. Brown Simon, Yee Leahy 1549-5469 genome;GR-2290R 10.1101/gr.229002 1088-9051 Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse...
For checked items

Search Results

New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research