Searching journal content for articles similar to Ovchinnikova and Anders 30 (5): 749.

Displaying results 1-10 of 3156

For checked items

view abstracts
download to citation manager

Select this article
Method: Protein domain embeddings for fast and accurate similarity search
- Benjamin Giovanni Iovino,
- Haixu Tang,
- and Yuzhen Ye
Genome Res. September 2024 34: 1434-1444; Published in Advance September 5, 2024, doi:10.1101/gr.279127.124
...embedding matrix: 2d-DCT is first applied to the input embedding matrix to compute frequency coefficients, and then an iDCT is applied to only low-frequency coefficients (discarding the high-frequency ones) to produce a dimension reduced matrix, thus achieving compression of the embedding matrix...
OPEN ACCESS ARTICLE
Select this article
Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...Exploring the epi profiles of repetitive elements with the WashU Repeat Browser Jiawei Shen1, 2, Siyuan Cheng1, Deepak Purushotham1, Xiaoyu Zhuo1, Alan Y. Du1, Wenjin Zhang1, Daofeng Li1, *, Ting Wang1, 2, 3, * Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Resource: PWAS Hub for exploring gene-based associations of common complex diseases
- Guy Kelman,
- Roei Zucker,
- Nadav Brandes,
- and Michal Linial
Genome Res. October 2024 34: 1674-1686; Published in Advance October 15, 2024, doi:10.1101/gr.278916.123
...in the case-control setting to yield statistically significant genes per phenotype. The PWAS Hub offers a user-friendly interface for an in-depth exploration of gene–disease associations from the UK Biobank (UKB). Results from PWAS cover 99 common diseases and conditions, each with over 10,000 diagnosed...
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
...initialization settings based on input types: using all genes (raw init), only highly variable genes (HVG init), dimension-reduced gene expression profiles based on principal component analysis (PCA init), and dual PCA (DPCA init) (Xia et al. 2023). Figure 5F summarizes the matching scores obtained by st...
Select this article
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
...alignment across data sets. Optimal transport-guided feature propagation adjusts data sparsity to match scRNA-seq references through graph-based imputation, enabling single-cell foundation models such as scGPT to generate unified features. Batch alignment then refines scGPT-transformed embeddings...
OPEN ACCESS ARTICLE
Select this article
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
...mouse epididymal fat pad, which prompted further exploration of sex-related differences. Within the sex-specific embeddings, ALPINE correctly captured increased macrophages in male mice, as well as mammary gland epithelial cells unique to female mice (Fig. 5C). In human samples, we see a more even...
Select this article
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
...genes (HVGs) as input through a pair of coupled batchnorm layers to account for large variations in gene expression levels, making it more robust and generalizable. Third, scTIE provides the means to extract interpretable features from the common embedding space by linking the developmental trajectories...
OPEN ACCESS ARTICLE
Select this article
Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
....To further explore the different gene–gene relationships profiled in the HuBMAP (adult human) and human fetal atlases, for each tissue that is common between the two atlases, we identified unique gene modules in the gene-embedding components of each atlas (Supplemental Note 11). Notably, we observed...
OPEN ACCESS ARTICLE
Select this article
Method: A best-match approach for gene set analyses in embedding spaces
- Lechuan Li,
- Ruth Dannenfelser,
- Charlie Cruz,
- and Vicky Yao
Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
...machine-learning tasks, it is intuitive that gene embeddings capture important gene–gene relationship information (Fig. 1A). However, little attention is paid to exploring the resulting embedding spaces, especially for the analyses of gene sets. In standard genomics analyses, gene sets (e.g., a set...
OPEN ACCESS ARTICLE
Select this article
Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
..., and protein levels. These include both handcrafted features and embeddings from large language models to support advanced representation learning. To prioritize pathogenic sSNVs, we have developed SynScore, a machine learning framework that integrates ACMG guidelines and diverse biological characteristics...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ovchinnikova and Anders 30 (5): 749.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: