Searching journal content for articles similar to Alkema et al. 14 (7): 1362.

Displaying results 1-10 of 6128
For checked items
  1. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...and gastrointestinal tracts and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest...
  2. 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
    ...states, implicitly assuming static regulatory programs and potentially missing 16 subtle, dynamic variation in regulation across individual cells. To address these limitations, 17 we introduce NeighbourNet (NNet), a method that constructs cell-specific coexpression 18 networks. NNet first applies...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  3. 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
    ...-GRN's adaptability across diverse real-world biological contexts. Finally, practical applications and biological analyses reveal that PRISM-GRN facilitates the identification of cell type–specific or context-specific regulatory relationships and core regulators under different biological research scenarios...
  4. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...be conserved across multiple lineages. For bacteria that engage in frequent interspecific gene transfer, even the gold-standard criterion demanding the same debilitating mutation(s) in two outgroup lineages may, in fact, be too permissive and should instead require their presence in more than two outgroup...
  5. Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
    • Kangli Wang,
    • Weikun Xia,
    • Yingli Gu,
    • Songpeng Zu,
    • Qian Yang,
    • Maria Luisa Amaral,
    • Yaozhi Wang,
    • Allen Wang,
    • Xiang-Dong Fu,
    • William C. Mobley,
    • and Bing Ren
    Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
    ..., which may differ 392 substantially across species due to evolutionary divergence in regulatory architecture. The 393 limited coverage and underrepresentation of certain cell types in both datasets may further 394 constrain the ability to detect conserved regulatory relationships. More comprehensive...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  6. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...al. 2016, 2018; Avsec et al. 2021b). We reasoned that this multitask strategy could favor detection of pervasive regulatory sites present across multiple cell types to the detriment of more cell-selective features (Schreiber et al. 2020; Kathail et al. 2024). We compared peaks called from Enformer...
  7. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...aspect of host defence 409 mechanisms conserved across vertebrates. In this study, we combined RNA-seq, ATAC-seq 410 and ChIP-seq to investigate the regulatory landscape underlying the antiviral response in 411 Atlantic salmon following poly I:C stimulation, a mimic of double-stranded RNA viruses. Our...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  8. Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
    • Fan Feng,
    • Sean Moran,
    • Anders S. Hansen,
    • Xiaotian Zhang,
    • and Jie Liu
    Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
    ...signal based on its neighbors.Quagga efficiently detects stripes across diverse cell types, sequencing depths, resolutions, and 3C methodsWe applied Quagga to call stripes from Hi-C contact maps of different cell lines. Quagga found 4133 stripes for GM12878 at 10 kb resolution, 10,398 for H1, 2908 for K...
    OPEN ACCESS ARTICLE
  9. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ...DNA sequences, epigenomic signals, and chromatin contact data in stages. Although these models achieve remarkable predictive performance, their effectiveness is constrained by the scarce availability of extra data across different cell types or by the requirement of elaborately preparing data...
    OPEN ACCESS ARTICLE
  10. Method: Unified integration of spatial transcriptomics across platforms with LLOKI
    • Ellie Haber,
    • Ajinkya Deshpande,
    • Jian Ma,
    • and Spencer Krieger
    Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
    ..., LLOKI-FP alone, although yielding a moderate biological conservation score (0.44), performed poorly in batch correction (0.31), highlighting the importance of LLOKI-CAE in aligning LLOKI-FP embeddings across batches.To further evaluate the importance of the OT alignment step in LLOKI-FP, we compared...
    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. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research