Searching journal content for articles similar to Allen et al. 14 (1): 142.

Displaying results 1-10 of 2041

For checked items

view abstracts
download to citation manager

Select this article
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
...using this method requires a substantial amount of computing resources, posing a significant challenge for researchers with limited computing capabilities. To address these challenges, several models of modest size have been proposed to improve the performance of gene expression prediction by utilizing...
OPEN ACCESS ARTICLE
Select this article
Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...and enable independent feature importance 331 assessment(Wang et al. 2020; Zhu et al. 2025a), and 3) incorporation of in silico mutational 332 landscapes (Chen et al. 2022) and gene-editing datasets. Multimodal integration will advance 333 phenotype prediction from single-source models to large...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
Select this article
Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
OPEN ACCESS ARTICLE
Select this article
Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...module further improves model interpretability. Extensive tests on eight diseases and two quantitative traits demonstrate the superiority of PRS-Net over multiple baseline PRS methods in disease prediction and gene discovery.A standard clumping and thresholding (C + T) PRS integrates not only -wide...
OPEN ACCESS ARTICLE
Select this article
Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...) Collection and preprocessing of snRNA-seq and snATAC-seq data sets in physical space. (B) Multiple analysis to identify an AD-associated gene list including differential gene expression analysis; identification of cCRE; cell type–specific, AD-associated risk variants; and peak-to-gene linkages. (C) Two...
OPEN ACCESS ARTICLE
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
...to increase the stability of results in case of strong technical variation and batch effects. UCell is solely based on Mann–Whitney U statistics (Andreatta and Carmona 2021) and is expected to be robust against technical variation as it only uses per-cell gene rank information. JASMINE computes scores...
OPEN ACCESS ARTICLE
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulatory events occur at TF binding sites some distance from the TSS, and predicting these is crucial in computational genetics. TF binding operates within a topologically associating domain typically upstream of the TSS but sometimes within the gene. However, predicting the boundaries of this domain...
OPEN ACCESS ARTICLE
Select this article
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
...and size of the edges correspond to the probability assigned by PRISM-GRN in the predicted GRN. (C) GO enrichment analysis results for the 25 genes in CD4 naive cells. The FDR indicates the significance of enrichment, with P-values corrected for multiple testing using the Benjamini–Hochberg procedure...
Select this article
Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
.... Order determined by a coin flip. Corresponding author: braphael@princeton.eduAbstractSpatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active...
OPEN ACCESS ARTICLE
Select this article
Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...-positive/false-negative rates of the manually predicted IG genes in these assemblies.Figure 1A illustrates the IterativeIGDetective pipeline with emphasis on detecting V genes. It starts by identifying a contig (or multiple contigs) containing the IGH locus in the target species and finding candidate RSSs in this locus based...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Allen et al. 14 (1): 142.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: