Searching journal content for articles similar to Dai et al. 32 (9): 1787.

Displaying results 1-10 of 5593

For checked items

view abstracts
download to citation manager

Select this article
Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...intratumoral heterogeneity (Shi et al. 2022), have been used to generate high-quality sequencing data and minimize confoundment by nontumor components. These organoid models also enable high-throughput drug screening, providing valuable insights into therapeutic responses for PAAD, a disease notorious for its...
OPEN ACCESS ARTICLE
Select this article
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
...regulation, and cell differentiation. Nevertheless, StripeDiff does not provide a user-friendly package to directly call all stripes with common contact map files.Here we introduce Quagga, a statistically rigorous, algorithmically efficient, and interpretable tool to identify stripes. Quagga's biggest...
OPEN ACCESS ARTICLE
Select this article
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...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...Scope and vamos original successfully characterized the two alleles as (TCTA)11 and (TCTA)12TTTA(TCTA)2 while uTR, TRF, and vamos efficient failed to identify the TTTA motif in the second allele.Joint motif discovery and annotation across multiple sMotifScope offers the capability to analyze multiple samples...
OPEN ACCESS ARTICLE
Select this article
Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
..., there are several automatic tools available that allow de novo discovery and annotation of TE insertions, e.g., RepeatModeler2 (RM2) (Flynn et al. 2020), REPET (Flutre et al. 2011), and EDTA (Ou et al. 2019) (for a more comprehensive list visit: https://tehub.org/) (Elliott et al. 2021). However, libraries produced...
OPEN ACCESS ARTICLE
Select this article
Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
- Han Shu,
- Jing Chen,
- Chang Xu,
- Jialu Hu,
- Yongtian Wang,
- Jiajie Peng,
- Qinghua Jiang,
- Xuequn Shang,
- and Tao Wang
Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
...observed in the 10x Visium data set. This trend continued in the Stereo-seq data set, confirming successful integration across donors. Additionally, we evaluated computational efficiency. stMSA processed up to 20 slices with <12 GB of GPU memory, whereas Stitch3D, SPACEL, and SEDR struggled to handle...
Select this article
Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...phenotype (Nevins and Potti 2007). One key application of signature scoring is cell annotation, as it offers a highly efficient and reliable method for classifying cells into types and states (Neftel et al. 2019). Notably, the quality of gene signatures plays a critical role in this process, as the accuracy...
OPEN ACCESS ARTICLE
Select this article
Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
..., facilitating the development of future targeted therapeutics.In this study, we aim to address the knowledge gap by performing single-cell RNA sequencing to profile m6A RNA methylation patterns in individual cells of the hippocampus. A myriad of different m6A sequencing detection methods exist, such as m6A RNA...
OPEN ACCESS ARTICLE
Select this article
Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage s publicly available. Importantly, as the number of sequenced s increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior...
OPEN ACCESS ARTICLE
Select this article
Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
- Hang Zhang,
- Yi Zhang,
- Kai Ming Ting,
- Jie Zhang,
- and Qiuran Zhao
Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
...cluster and to discover clusters of dissimilar characteristics. The identified transcriptomically similar clusters assist in further characterizing tissue organization and uncovering potential biomarkers or therapeutic targets.Existing methods for spatial domain detection have primarily focused on data...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Dai et al. 32 (9): 1787.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: