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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
...and subjected to principal component analysis (PCA) via the scanpy.tl.pca() function, in which the top 50 principal components were computed. A k-nearest neighbor (KNN) graph was then constructed using 10 neighbors and the first 40 principal components using the scanpy.pp.neighbors() function. Clustering...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...-mer methods generally report a quality value (QV), a log base 10–scaled measure of assembly error, with higher values indicating more accurate assemblies. We find that DeepPolisher improves the k-mer-based assembly QV by 1.8, equivalent to a 34% reduction in errors, which is approximately consistent...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...) PCA plots of both the retina cohort data and the benchmark data. Red denotes the bulk data to be deconvolved; blue denotes the benchmark bulk data; and green denotes the benchmark pseudobulk data. (B,C) Panels demonstrating the robustness of DeMixSC to different reference matrices at both the cell...
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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
...that nanopore-based detection methods depend on machine learning (ML) models to interpret sequencing signals accurately (Liu et al. 2019; Wang et al. 2021; Chen et al. 2025; Galeone et al. 2025). Therefore, developing bioinformatics tools for the large-scale, accurate, and efficient 4mC site identification...
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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
...for identify-252 ing disease-associated clusters. spRefine may work as an effective pre-training253 framework to preserve biological signals with the help of intrinsic gene-gene inter-254 action supported by the embeddings from DNA foundation models. To validate this255 assumption, we collected large-scale...
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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
...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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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
...for practical use.We also aim for improving EquiRep's accuracy. The framework of EquiRep allows it to be improved in several ways. One approach is to enhance matrix refinement, which is crucial for producing accurate equivalence classes. The current method considers three mutually supportive pairs, but it can...
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Method: Matrix sketching framework for linear mixed models in association studies
- Myson Burch,
- Aritra Bose,
- Gregory Dexter,
- Laxmi Parida,
- and Petros Drineas
Genome Res. September 2024 34: 1304-1311; Published in Advance September 4, 2024, doi:10.1101/gr.279230.124
...), as described at http://creativecommons.org/licenses/by/4.0/.References ↵Bose A, Kalantzis V, Kontopoulou EM, Elkady M, Paschou P, Drineas P. 2019. TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes. Bioinformatics 35: 3679–3683. doi:10.1093/bioinformatics/btz157...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...availability of biobank-scale data offers such opportunities, current methods are not efficient at leveraging very large sample sizes. The most accurate methods are still linkage disequilibrium (LD)–based methods that are only tractable for a few hundred samples. In this work, we propose a fast and memory...

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