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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...discovery: uTR, TRF, and vamos. Our findings indicate that MotifScope identified a greater number of motifs and reflected the actual repeat sequence more accurately than other tools. Additionally, we show potential applications of MotifScope in population genetics to explore population stratification due...
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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
...transcriptomic data. Our23 results demonstrate that spRefine yields more robust cell- and spot-level represen-24 tations after denoising and imputation, substantially improving data integration.25 In addition, spRefine serves as a strong framework for model pre-training and26 the discovery of novel biological...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...‘predictor genes’ (those used to embed PCs) contribute to predict each response in the PC space. Repeating this for multiple response genes yields cell-specific coexpression networks (CSNs). C. Network Ensemble Construction: Collecting all CSNs form a network ensemble, which is a cell × response × predictor...
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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
...with LLOKI-CAE, we use a conditional autoencoder to integrate data across ST technologies, using LLOKI-FP embeddings as input features for each cell. Our integration strategy combines three loss functions: (1) reconstruction loss to preserve accurate data representations; (2) triplet loss to enhance...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...step in this process is the prediction of a consensus sequence derived from long reads, providing a highly accurate reconstruction of the original template (e.g., circular RNA). This step requires in silico intervention and typically employs widely used tandem repeat detection tools for consensus...
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Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
- An Wang,
- Stephanie Hicks,
- Donald Geman,
- and Laurent Younes
Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
...(see Supplemental Fig. S6 for matching quality comparisons on all 10x Genomics reference clusters). This result highlights geneCover's ability to enhance the resolution of spatial transcriptomics discovery, particularly in identifying highly refined spatial organizations, using a compact and minimally...
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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
....g., combining information from whole-transcriptome platforms with lower spatial resolution with platforms that measure expression of a limited number of genes at high spatial resolution). Such integration could assist in two tasks: (1) predicting the expression of genes that are missing in the high resolution...
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Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
- Hang Zhang,
- Yi Zhang,
- Kai Ming Ting,
- Jie Zhang,
- and Qiuran Zhao
Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
...to this work. Corresponding authors: tingkm@nju.edu.cn, zhangj_ai@nju.edu.cnAbstractSpatial transcriptomics are a collection of technologies that have enabled characterization of gene expression profiles and spatial information in tissue samples. Existing methods for clustering spatial transcriptomics data...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...those motifs that were detected by both HOMER and MEME-Suite were considered as true signals and used for the downstream analysis. We performed motif discovery in the 200-bp region around the center of the enhancers. For HOMER, the masked version of the s was used. We used 20,934 control sequences...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...RNA production from distal promoters. The discovery of the SV40 viral enhancer was a landmark event more than 40 years ago. The 72 bp DNA sequence encoding the SV40 enhancer increased the expression of a reporter gene by more than two orders of magnitude in a manner that was largely independent of its position...

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