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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
...coordinates that form an accurate bounding box around detected chromatin stripes. It works on all 3C family sequencing types, including Hi-C, Micro-C, and HiChIP. Quagga uses two major steps to find chromatin stripes. First, Quagga performs a quick screening of potential stripes and determines stripe width...
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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
...in the three coronal mouse brain slices.Figure 3B illustrates the domain detection performance of stMSA relative to the manually annotated structures from the Allen Brain Atlas (Fig. 3A). Moreover, we find that stMSA and STAMP can depict the cross-sections of the hippocampus and its inner subdomains well...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...of transcription factors such as SP1 and CTCF emerged prominently. The majorly identified transcription factors for each cell type were consistent with the findings of ChromBPNet (Pampari et al. 2024) (Supplemental Fig. S5). These findings indicate that the ConvNeXt V2 block effectively captures cell type...
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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
.... Users may find it difficult to decide how much weight to give to each modality, which can impact the clustering results. We suggest starting with the default values in Proust (30 PCs for gene expression and five PCs for images), which have been shown to work well across a range of data sets. However, we...
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Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
.... To systematically evaluate the performances of these four consensus strategies in terms of ST clustering accuracy and stability, we conducted comprehensive simulations and real data applications across different tissue origins and sequencing platforms. The findings of this comprehensive analysis yield a rich source...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...LAD chromatin. One study has indicated that these LADs are more variable and interact with the nuclear periphery for only part of the cell cycle, which is consistent with their facultative heterochromatin character (Tran et al. 2021). This is consistent with our finding that a much larger fraction...
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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
...the latent space is by finding a low-dimensional factorization of scRNA-seq gene expression matrices (Yang and Michailidis 2016; Argelaguet et al. 2018, 2020; Townes et al. 2019; Liu et al. 2020; Qian et al. 2022).Similarly, in the spatial transcriptomics domain, the SRT gene expression is traditionally...
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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
...clock. All these novel biological findings demonstrate the potential of the reference-free450 imputation framework.451 Taken together, our framework should be understood as reference-free with respect452 to external single-cell or spatial atlases, but not devoid of priors. By incorporating453 Enformer...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...to analyze the transcriptome, histone modification patterns, and replication timing of germline stem cell (GSC)–like and somatic cyst stem cell (CySC)–like cells. Single-cell RNA sequencing validates previous findings on GSC–CySC intercellular communication and reveals a high expression of chromatin...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
..., significant interactions are identified and used to calculate the cell type pair score (CTPS) between two clusters. (E) CellAgentChat enables agent-based animation to visualize cell communication, identify significant LR pairs, and simulate receptor blocking to find the most perturbed downstream genes...
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