Searching journal content for articles similar to King et al. 13 (5): 896.

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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
...score stability and cross-signature comparability, achieving cell-state annotation accuracy comparable to supervised methods. We demonstrate the practical utility of ANS by developing and validating a gene signature to differentiate cancer-associated fibroblasts from malignant cells undergoing...
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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
...interpretability, we performed cCRE prioritization, pattern analysis, and motif discovery.Experimental results confirm the superiority of ScPGE over existing models, showing that ScPGE can predict RNA-seq or CAGE-seq gene expression accurately by modeling the relationships between cCREs and target genes...
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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
..., such as known patterns of driver mutual exclusivity (Bokhari et al. 2020). Biological pathways can provide insights into the timing of driver events in a tumor cohort by mapping predicted pathogenic mutations to genes in KEGG pathways (Kanehisa et al. 2019) and estimating the order in which hallmark pathways...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...shows high accuracy in selecting the best methods on the 80 scST data sets (82.5%) and five scATAC-seq data sets (100.0%), illustrating its universal applicability. In addition, we utilize the CAMUS score with other metrics to predict the annotation accuracy, providing direct guidance on whether...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...) Pipeline for prediction of gene expression and active promoter regions based on the annotations (Methods). (C) Annotations predict gene expression and active promoter with high AUC. Vertical axis indicates the area under the receiver-operator curve (AUC) for predicting RNA-seq expression from labels...
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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...at the gene's promoter (Zhang and Hardison 2017; Libbrecht et al. 2019; Daneshpajouh et al. 2022), but such prediction tasks are useful for the purpose of comparing different annotations but do not serve as a realistic evaluation of the annotations themselves. This study introduces SAGAconf as a comprehensive...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...sRNA-seq and RNA-seq is not due to codetection of housekeeping genesThe association between small RNA and total RNA expression could be partly owing to the codetection of highly expressed housekeeping genes. To rule this out, we functionally annotated the top 10% of the highest expressed genes form...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...-length transcriptome sequencing data from seven paired tumor and nontumor tissues. We characterized HBV integration patterns at both the genomic and transcriptomic levels, as well as their regulatory effects on human SVs and gene expression in the human . Notably, the tissues were obtained from patients under 30 years...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...species, and the intrinsic uncertainty in the discovery of functional coding and noncoding elements in newly assembled s (Yandell and Ence 2012).Currently, annotation approaches can be broadly divided into three main types: evidence-based methods, ab initio, and evidence-driven gene predictions (Yandell...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...of California Santa Cruz, Santa Cruz, California 95064, USA Corresponding author: vollmers@ucsc.eduAbstractGenerating an accurate and complete annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive...
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