Searching journal content for articles similar to Zheng et al. 35 (12): 2734.

Displaying results 1-6 of 6

For checked items

view abstracts
download to citation manager

Select this article
Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
..., such as the joint embedding from deep learning–based methods. This could potentially enhance the performance and robustness of the consensus clustering. Second, the current version of our consensus framework only incorporates seven tools, which is relatively limited considering the vast number of clustering tools...
Select this article
Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...benchmarked (Li et al. 2022). As examples, methods have been proposed to predict unmeasured gene expression by aggregating nearest neighbors of cells for regression (Stuart et al. 2019; Welch et al. 2019; Abdelaal et al. 2020; Shengquan et al. 2021), joint probabilistic modeling (Lopez et al. 2019; Wan et al...
OPEN ACCESS ARTICLE
Select this article
Perspective: Advances in spatial transcriptomic data analysis
- Ruben Dries,
- Jiaji Chen,
- Natalie del Rossi,
- Mohammed Muzamil Khan,
- Adriana Sistig,
- and Guo-Cheng Yuan
Genome Res. October 2021 31: 1706-1718; doi:10.1101/gr.275224.121
...(MNN) approach has been used to align these data types, which results in cell locations mapping (Haghverdi et al. 2018; Hie et al. 2019; Stuart et al. 2019). DEEPsc uses an artificial neural network to predict spatial locations (Maseda et al. 2021). GLUER combines joint NMF, MNN algorithm, and deep...
OPEN ACCESS ARTICLE
Select this article
Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
...cell identity information from transcriptome features solely. In scHGR, transcriptomically distant cells are bridged by homologous genes and their relationships. Attaining homotypic cell communication across species facilitates improving the reliability of cross-species annotation.View larger version...
Select this article
Editorial: RECOMB 2025 Special Issue
- Sriram Sankararaman and
- Bonnie Berger
Genome Res. December 2025 35: v-vi; doi:10.1101/gr.281664.125
.... Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms . Genome Res (this issue) 35 : 2734 – 2743 . doi: 10.1101/gr.280555.125 Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr...
Select this article
Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...effects through explicit modeling of batch information as covariates; and CarDEC (Lakkis et al. 2021) uses a joint autoencoder together with iterative clustering to remove batch effects. Beyond the ability to model all batches simultaneously, an additional advantage of these neural network–based methods...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Zheng et al. 35 (12): 2734.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: