Searching journal content for articles similar to Zhang et al. 35 (10): 2339.

Displaying results 1-10 of 4937
For checked items
  1. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...labels are directly encoded, it makes the unrealistic assumption that all cells with the same condition share the same effect.Here, we introduce Adaptive Layering of Phenotypic and Integrative Noise Extraction (ALPINE), a novel, flexible approach designed to address the complexities of multicondition...
  2. Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
    • Yingxin Lin,
    • Tung-Yu Wu,
    • Xi Chen,
    • Sheng Wan,
    • Brian Chao,
    • Jingxue Xin,
    • Jean Y.H. Yang,
    • Wing H. Wong,
    • and Y.X. Rachel Wang
    Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
    ...ATAC-seq data, the data integration problem, essential for accurate cell type identification, has been mostly treated as a standalone challenge. Here we present scTIE, a unified method that integrates temporal multimodal data and infers regulatory relationships predictive of cellular state changes. scTIE uses...
    OPEN ACCESS ARTICLE
  3. Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
    • Marcel Tarbier,
    • Sebastian D. Mackowiak,
    • Vaishnovi Sekar,
    • Franziska Bonath,
    • Etka Yapar,
    • Bastian Fromm,
    • Omid R. Faridani,
    • Inna Biryukova,
    • and Marc R. Friedländer
    Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
    ...relatively low sensitivity.View larger version: In this window In a new window Figure 1. miRNA profiling in single mouse embryonic stem cells (mESCs) by Small-seq. (A) Number of distinct miRNAs detected in each single cell. (B) Top 25 miRNAs in mESCs. The number of detected molecules was estimated using...
    OPEN ACCESS ARTICLE
  4. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...of development, aging, and cancer. Cell lineage trees represent the evolutionary history of cells sampled from an organism. Recent developments in single-cell sequencing have greatly facilitated the inference of cell lineage trees. However, single-cell data are sparse and noisy, and the size of single-cell data...
    OPEN ACCESS ARTICLE
  5. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...sizes for reliable GCN inference. recount3, a data set with 316,443 processed human RNA-seq samples, provides an opportunity to improve network reconstruction. However, GCN inference from public data is challenged by confounders and inconsistent labeling. To address this, we develop a pipeline...
    OPEN ACCESS ARTICLE
  6. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...with at least one CNA, ichorCNA allows direct estimation of the TF, with inferred TFs above 0.03 considered to be reliable (Adalsteinsson et al. 2017). In 13/14 patient samples, we reliably detected TFs from the cfDNA-derived CNA profile. While HCs had a median TF of 0.016 (range 0.003–0.032), TFs of cancer...
    OPEN ACCESS ARTICLE
  7. Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
    • Song Zhang,
    • Chao Wang,
    • Shenghua Qin,
    • Choulin Chen,
    • Yongzhou Bao,
    • Yuanyuan Zhang,
    • Lingna Xu,
    • Qingyou Liu,
    • Yunxiang Zhao,
    • Kui Li,
    • Zhonglin Tang,
    • and Yuwen Liu
    Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
    ...targets and tagmentation (CUT&Tag) to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages, and investigated how SEs influence skeletal muscle development. We identify three SE families with distinct temporal dynamics...
  8. Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
    • Charlie Y. Shi,
    • Lara E. Elcavage,
    • Raghu R. Chivukula,
    • Joanna Stefano,
    • Benjamin Kleaveland,
    • and David P. Bartel
    Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
    ...-sensitive miRNAs identified in mouse cells to 58, representing 48 miRNA families. A summary of the ZSWIM8-sensitivity profiles for the 53 miRNAs found to be at least marginally sensitive in embryonic tissues revealed distinct, context-specific patterns of sensitivity (Fig. 4B). For example, some mi...
    OPEN ACCESS ARTICLE
  9. Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
    • Jordan H. Little,
    • Guillermo Hoffmann Meyer,
    • Aakash Grover,
    • Alex Michael Francette,
    • Raghavendran Partha,
    • Karen M. Arndt,
    • Martin Smith,
    • Nathan Clark,
    • and Maria Chikina
    Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
    ...) in parallel. Thus, by identifying genes with correlated changes in branch-specific RERs, functional relationships between genes can be inferred.Evolutionary rate covariation (ERC) is a measure that quantifies the correlation of the RERs of a pair of genes across all branches in a phylogeny, both internal...
  10. Method: Bayesian inference of sample-specific coexpression networks
    • Enakshi Saha,
    • Viola Fanfani,
    • Panagiotis Mandros,
    • Marouen Ben Guebila,
    • Jonas Fischer,
    • Katherine H. Shutta,
    • Dawn L. DeMeo,
    • Camila M. Lopes-Ramos,
    • and John Quackenbush
    Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
    ...equally to this work. Corresponding author: johnq@hsph.harvard.eduAbstractGene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring coexpression...
    OPEN ACCESS ARTICLE
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. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research