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Research: Widespread natural selection on metabolite levels in humans
- Yanina Timasheva,
- Kaido Lepik,
- Orsolya Liska,
- Balázs Papp,
- and Zoltán Kutalik
Genome Res. August 2024 34: 1121-1129; Published in Advance August 16, 2024, doi:10.1101/gr.278756.123
...linked to human diseases, potentially indicating strong stabilizing selection to preserve their levels, the direction and strength of natural selection shaping metabolite levels are generally unknown. Several lines of observations suggest that stabilizing selection on metabolite levels might be prevalent...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...(as illustrated by the four examples in Fig. 4A), we plotted the interextremity CV of the means and the interextremity CV of the CVs on a 2D graph for all strains (Fig. 4B). Here, the CV was chosen to measure variation preferentially over the standard deviation, because it allows direct comparison...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...width. First, it reduces the chromosome into 5′ or 3′ signal vectors. A vertical or horizontal loading matrix is filled, taking a maximum length along the 5′ or 3′ direction on the contact frequency matrix. For example, a horizontal loading matrix has its rows containing the values of the rows...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
..., long-read sequencing-based methods, using single-molecule real-time (SMRT) or nanopore sequencing technology, can directly detect modified bases, eliminating the need for such preprocessing (Moshitch-Moshkovitz et al. 2022; Kong et al. 2023). The SMRT sequencing platform has been adapted for direct RNA...
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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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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
...the pipeline itself. For instance, we are exploring faster local alignment strategies and are considering eliminating redundant steps, such as performing path-finding only once rather than twice as in the current design. We plan to explore these directions to make EquiRep more efficient and scalable...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...direction, both mates’ read directions point toward each other, and the distance between mates does not deviate too much from the mean insert size. In this case, this threshold is approximately six to seven standard deviations from the mean insert size. On average, 99.4% of reads per individual were paired...
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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
...framework for multiple ST analysis tasks, including spatial domain detection and cell cycle identification. Although these methods have successfully analyzed individual slices, they remain limited to two-dimensional (2D) analyses owing to their single-slice focus.As the availability of SO data derived from...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
..., consistent with the conclusions from another independent study (Gohr et al. 2023). These findings suggest that the determinants of splicing order are hardcoded in the .Direct nanopore RNA sequencing (dnRNA-seq) (Garalde et al. 2018) yields long reads that allow for the simultaneous detection of several...
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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
...to detect biologically meaningful signals even without predefined labels. Additionally, as label-free marker gene selection methods like geneCover identify genes from all sources of variability, some genes may capture biological processes that are not directly associated with anatomical structures...

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