Searching journal content for articles similar to Muthappan et al. 21 (4): 626.

Displaying results 1-10 of 3157
For checked items
  1. Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
    • Siavash Raeisi Dehkordi,
    • Zhaoyang Jia,
    • Joey Estabrook,
    • Jen Hauenstein,
    • Neil Miller,
    • Naz Güleray-Lafci,
    • Jürgen Neesen,
    • Alex Hastie,
    • Alka Chaubey,
    • Andy Wing Chun Pang,
    • Paul Dremsek,
    • and Vineet Bafna
    Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
    ...of lower complexity (Fig. 2C). The distribution of the SV sizes suggests good representation of each SV type (Supplemental Fig. S2).View larger version: In this window In a new window Figure 2. Validation statistics on simulated and clinical karyotypes. Each plot displays a 3D histogram of Jaccard score...
    OPEN ACCESS ARTICLE
  2. Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
    • Sophia N. Lee,
    • Erin C. Banda,
    • Lu Qiao,
    • Sarah L. Thompson,
    • Karan Singh,
    • Ryan A. Hagenson,
    • Teresa Davoli,
    • Stefan F. Pinter,
    • and Jason M. Sheltzer
    Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
    ...of the alterations in this proband are typical for this condition (Okur et al. 2021).View larger version: In this window In a new window Figure 1. Karyotype of the invdupdel(8p) proband iPSC line. (A) Schematic listing commonly observed symptoms in individuals affected by invdupdel(8p). (B) Diagram delineating...
  3. Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
    • Vishvak Raghavan,
    • Yumin Zheng,
    • Yue Li,
    • and Jun Ding
    Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
    ...to generate animated visualizations of single-cell interactions and provides flexibility in modifying agent behavior rules, facilitating thorough exploration of both close and distant cellular communications. Furthermore, CellAgentChat leverages ABM features to enable intuitive in silico perturbations via...
    OPEN ACCESS ARTICLE
  4. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    ..., scRNA-seq captures gene expression profiles, whereas scDNAm data reflects DNAmethylation levels. These biologically rooted representational differences can lead to misaligned embeddings for the same cell type across modalities. To enforce modality-consistent and translatable latent representations...
    OPEN ACCESS ARTICLE
  5. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...of the upregulated genes affected by HBV integration, suggesting that HBV-Enh I plays an important role in gene transcriptional activation.View larger version: In this window In a new window Figure 7. Cis-activation role of HBV-Enh I. (A) Schematic representation of the HBV integration locus and the constitution...
  6. Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
    • Basanta Bista,
    • Laura González-Rodelas,
    • Lucía Álvarez-González,
    • Zhi-qiang Wu,
    • Eugenia E. Montiel,
    • Ling Sze Lee,
    • Daleen B. Badenhorst,
    • Srihari Radhakrishnan,
    • Robert Literman,
    • Beatriz Navarro-Dominguez,
    • John B. Iverson,
    • Simon Orozco-Arias,
    • Josefa González,
    • Aurora Ruiz-Herrera,
    • and Nicole Valenzuela
    Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
    ...in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear s. Namely, whole- comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of reshuffling in Apalone (Trionychidae) whose karyotype...
    OPEN ACCESS ARTICLE
  7. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...in dimensionality reduction and data simulation. These individual genotype sequences can then be decomposed into latent representations and reconstruction errors (residuals), which provide a sparse representation useful for lossless compression. We show that different populations have differentiated compression...
    OPEN ACCESS ARTICLE
  8. Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
    • Damira Veseljak,
    • Evelin Despot-Slade,
    • Marin Volarić,
    • Lucija Horvat,
    • Tanja Vojvoda Zeljko,
    • Nevenka Meštrović,
    • and Brankica Mravinac
    Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
    ...the chromosomal distribution of the low-copy-number satellites obtained in silico, we experimentally analyzed six of them with a proportion between 0.01% and 0.05%. We found that satDNAs with a proportion higher than 0.02% had a broader chromosomal distribution (Supplemental Fig. S3A–C), whereas sat...
  9. Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
    • Igor Rodrigues Costa,
    • Francisco Prosdocimi,
    • and W. Bryan Jennings
    Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
    ...In silico phylogenomics using complete genomes: a case study on the evolution of hominoids Igor Rodrigues Costa 1 , 3 , Francisco Prosdocimi 1 , 3 and W. Bryan Jennings 2 1Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica...
  10. Resource: The SynMall resource for characterizing the functional impact of synonymous variation
    • Chen Ye,
    • Xiaoyan Li,
    • Na Cheng,
    • Yansen Su,
    • and Junfeng Xia
    Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
    ..., and protein levels. These include both handcrafted features and embeddings from large language models to support advanced representation learning. To prioritize pathogenic sSNVs, we have developed SynScore, a machine learning framework that integrates ACMG guidelines and diverse biological characteristics...
For checked items

Search Results

Next 10 » 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. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research