Searching journal content for articles similar to Chiu et al. 25 (2): 257.

Displaying results 1-10 of 4066
For checked items
  1. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Le Cao
    Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...1Scalable cell-specific coexpression networks for granular regulatory 2 pattern discovery with NeighbourNet 3 Yidi Deng1,2, Jiadong Mao1,† & Jarny Choi3,† & Kim-Anh Lê Cao1,*,† 4 1Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, 5 3010, Australia 6...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  2. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...55421, USA Corresponding author: jshaw@ds.dfci.harvard.eduAbstractReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized...
  3. Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
    • Daijun Zhang,
    • Ren Qi,
    • Xun Lan,
    • and Bin Liu
    Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
    ...as a multislice joint analysis framework featuring a precorrection mechanism that enables the precise identification of complex spatial domains, advancing disease pathology insights. STMSC assumes that precise three-dimensional (3D) reconstruction is essential for an in-depth investigation of tissue components...
  4. Research: microRNA target prediction programs predict many false positives
    • Natalia Pinzón,
    • Blaise Li,
    • Laura Martinez,
    • Anna Sergeeva,
    • Jessy Presumey,
    • Florence Apparailly,
    • and Hervé Seitz
    Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
    ...in microRNA target identification Genome Research 237 www..org observed decrease in target mRNAs upon ceRNA knock-down. Consequently, the consensus now states that mRNAs are unlikely to exert any noticeable titration of miRNAs in the general case (Garcia et al. 2011; Wee et al. 2012; Denzler et al. 2014...
  5. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ..., reconstructing cell type–specific networks and allowing in silico T perturbations to reveal dynamic regulatory mechanisms. The knowledge-primed model SupirFactor (Tjärnberg et al. 2024) embeds the prior GRN directly into deep learning architectures, enabling biologically interpretable GRN predictions while...
  6. Research: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
    • Lili Tang,
    • Fei Huang,
    • Wuxin You,
    • Ansgar Poetsch,
    • Rafael Henrique Nóbrega,
    • Deborah Mary Power,
    • Tengfei Zhu,
    • Kaiqiang Liu,
    • Hong-Yan Wang,
    • Qian Wang,
    • Xiwen Xu,
    • Bo Feng,
    • Manfred Schartl,
    • and Changwei Shao
    Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
    ....uni-wuerzburg.de, shaocw@ysfri.ac.cnAbstractCompeting endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement of noncoding RNAs (ncRNAs) as ceRNA in genotypic sex determination (GSD) and environmental sex determination (ESD) in fish is unknown. The Chinese tongue sole, which has both GSD...
    OPEN ACCESS ARTICLE
  7. 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
    ...provide insights into processes that are simultaneously activated in different biological states (Becker et al. 2023). However, most methods for constructing coexpression networks estimate an aggregate network for the entire population (Langfelder and Horvath 2008; Dawson et al. 2012; Lemoine et al. 2021...
    OPEN ACCESS ARTICLE
  8. Method: Spatial Cellular Networks from omics data with SpaCeNet
    • Stefan Schrod,
    • Niklas Lück,
    • Robert Lohmayer,
    • Stefan Solbrig,
    • Dennis Völkl,
    • Tina Wipfler,
    • Katherine H. Shutta,
    • Marouen Ben Guebila,
    • Andreas Schäfer,
    • Tim Beißbarth,
    • Helena U. Zacharias,
    • Peter J. Oefner,
    • John Quackenbush,
    • and Michael Altenbuchinger
    Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124
    ...of correlation in spatial transcriptomics data by extending the concept of CI to spatially distributed information, facilitating the reconstruction of both the intracellular and the intercellular interaction networks with single-cell spatial resolution. SpaCeNet was developed to address the diversity of cellular...
  9. Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
    • Chuanyuan Wang and
    • Zhi-Ping Liu
    Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
    ...space modeling, DigNet is robust to the presence of noise in scRNA-seq data and the sparsity of GRNs. Benchmark evaluation results against more than a dozen state-of-the-art network inference methods demonstrate that DigNet achieves superior performance across various single-cell GRN reconstruction...
    OPEN ACCESS ARTICLE
  10. Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
    ...identification within a large, complex cell population. In this study, we developed a subclone clustering method based on a fused lasso model, referred to as FLCNA, which can simultaneously detect CNAs in single-cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering...
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