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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
.... 2022). CAMUS continues to select the best annotation method, confirming its robustness and generalizability in the scATAC-seq setting (Supplemental Fig. S7E).CAMUS score helps predict the accuracy of cell type annotationsAlthough CAMUS facilitates the reference and method selection, users may not know...
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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
...MSA against competing methods by integrating two additional mouse brain data sets from FF and FFPE samples. stMSA demonstrated robust accuracy in identifying spatial domains across both preservation protocols (Supplemental Fig. S9) and achieved the highest overall integration scores, highlighting its enhanced...
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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
...for predicting gene expression (ScPGE) from discrete candidate CREs (cCREs). ScPGE assembles DNA sequences, transcription factor (TF) binding scores, and epigenomic tracks from discrete cCREs into three-dimensional tensors, and then models the relationships between cCREs and genes by combining convolutional...
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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: 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
...] in Table 1). In addition to R2 scores, SIID also consistently outperforms other benchmarked methods on four other correlation metrics (Supplemental Methods D.2; Supplemental Table S5; Li et al. 2022). Additionally, SIID shows robust performance in the presence of noise in the spatial mapping matrix...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...focused on proliferation, whereas those associated with decreased gene expression included factors related to maturation and cardiac function, validating the immature state driven by GSK3i (Fig. 1C,D; Supplemental Table S2). Next, we identified TFs that may drive the alterations in cCRE activity and gene...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...proteotranscriptomics assembly (PTA) workflow (Levin and Butter 2022) for high-confidence annotation of protein-coding genes in 12 nematode species. Including a novel machine-learning implementation to score transcript fragmentation, which is a well-known issue of transcriptome assemblies (Treangen and Salzberg 2011...
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Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
- Jens-Uwe Ulrich and
- Bernhard Y. Renard
Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
...the highest F1- and F0.5-scores on the species level for the three mock communities, indicating the robustness of the findings. We attribute this improvement to using syncmers instead of minimizers, applying several iterative filter steps, and applying our EM algorithm for read classification refinement...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...). Identifying genetic variants that drive canine phenotypic variation will further define gene functions.Genetic association studies typically require an initial and robust characterization of a phenotype, a practice that ultimately limits the scope of potential findings to only those that can be recognized...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...and robustness in various analytical contexts.Extensive benchmark testing on simulation data confirms DigNet efficiencyTo evaluate the performance of DigNet in network generation, we develop a simulation scheme for benchmarking gene expression profiles with single-cell GRNs. The rationale for employing simulated...
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