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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...RNAs. Next, based on the BSJs, the annotated host transcripts of the circRNAs were identified, and the HTS reads containing both BSJs and intronic sequences between circularized exons were used to identify candidate EIciRNAs. Selection of HTS reads containing both intronic sequences and BSJs ruled out...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...of G4s identified with each of the two methods is provided as well as the top 50 longest G4s for each of the two methods. Through the page, users can then select and see the full list of G4 sequences with additional annotation. Annotation features for each G4 sequence include the presence of genes (CDS...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., providing actionable insights into ensemble architecture design in DL frameworks.Comparison with existing predictorsTo verify the performance of EnDeep4mC, we systematically compared it against five DL models (4mCCNN, Deep4mC, Hyb4mC, DeepSF-4mC, and EpiTEAmDNA) and one traditional ML model (4mc...
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Method: spRefine denoises and imputes spatial transcriptomics 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 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...et al (2024). We used the 10X Visium dataset from SpatialLIBD207 Maynard et al (2021) for evaluation. This dataset contains multiple slides and also208 offers expert annotation of spot types to validate the preservation of biological sig-209 nals. Our selected baselines provide recommended hyper...
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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
...CREs in open chromatin regions together with ChIP-seqs of transcription factors and histone modifications to predict the expression level of target genes. EPInformer (Lin et al. 2024) introduced an efficient deep-learning framework based on the transformer architecture to predict gene expression by integrating...
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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
...indirect or secondary effects. Compared with RNAi or CRISPR knockout, degrons can thus reveal more immediate transcriptional dependencies on the TF of interest.In practice, combining depletion strategies with the precise transcriptional readouts discussed in this section provides a robust framework...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...analysis, providing comprehensive exploration of gene expression across diverse biological contexts. However, RNA-seq data are susceptible to various biases that can significantly compromise the accuracy and reliability of transcript quantification. This study investigates the influence of high...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...though the Human Genome Organization Gene Nomenclature Committee (HGNC) has annotated 19,261 protein coding genes in the human (Seal et al. 2023), only 4923 genes have been associated with human phenotypes according to the Online Mendelian Inheritance in Man (OMIM) (Hamosh et al. 2021). In addition...
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Research: Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
- Guifeng Wei,
- Mafalda Almeida,
- Greta Pintacuda,
- Heather Coker,
- Joseph S. Bowness,
- Jernej Ule,
- and Neil Brockdorff
Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
...and intron-of-origin.Most exonic methylations are enriched around stop-codon regions, as previously noted (Dominissini et al. 2012; Meyer et al. 2012), but intronic methylation sites are fairly evenly distributed relative to host transcripts (Supplemental Fig. S3E). Therefore, we queried in particular...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...and complex diseases. Its ability to align multislice data, compensate for the lack of SC resolution, and integrate information across different levels provides a robust framework for advancing biological and disease research. In clinical pathology, STMSC has the potential to assist in tumor classification...

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