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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
..., and metabolomics. Each layer offers unique insights into cellular functions and diseases, and various strategies have been developed for data-driven integration (Ritchie et al. 2015; Picard et al. 2021; Hernández-Lemus and Ochoa 2024). Common approaches combine omics layers into a single data set to facilitate...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...heterogeneity and the mechanisms underlying development and disease. However, current GRN inference methods fail to utilize multi-omics data and prior knowledge from a biologically interpretable insight. Therefore, we propose PRISM-GRN, a Bayesian model that seamlessly incorporates known GRNs, along with sc...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...–specific level, revealing a subset of genes that increasingly express with age and are enriched in PD-related pathways, notably in oligodendrocytes at late aging stages. Integration with five public PD single-cell RNA-seq data sets highlights 85 genes consistently differentially expressed with aging and PD. Key...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
.... Gray boxes and lines indicate regions with HCNE matches between species. (H) Heatmap of enrichment of single-gene mouse knockout phenotypes for collections of HCNEs as indicated in D. Significance in −log10(HyperFdrQ) is indicated both relative to the whole and to all HCNEs to account for nonrandom...
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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
.... Corresponding authors: qhjiang@hit.edu.cn, Shang@nwpu.edu.cn, twang@nwpu.edu.cnAbstractSpatial omics (SOs) are powerful methodologies that enable the study of genes, proteins, and other molecular features within the spatial context of tissue architecture. With the growing availability of SO data sets...
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Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
- Hongyang Li and
- Yuanfang Guan
Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
...Hongyang Li and Yuanfang Guan Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: gyuanfan@umich.eduAbstractDecoding the cell type–specific transcription factor (TF) binding landscape at single-nucleotide resolution...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...reveal associations between structural features of protein and evolutionary constraint, providing key functional insights into natural selection.Predicted structural variants provide novel insights into genetic effects on phenotypesTo conduct association analysis based on protein variation, we measured...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...and proteins derived from a single gene and play important functions in the regulation, localization, and function of mRNAs and proteins, ultimately contributing to phenotypic diversity (Mariella et al. 2019; Li et al. 2021). Therefore, it is essential to comprehensively identify global APA events and explore...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...k-mer cross-species profiling reveals taxon-specific TE expansions accompanied 1 by KZFP co-option and functional impacts in ruminants 2 3 Pengju Zhao1,2*, Jiayi He1,2, Chen Peng1,2, Yuelang Zhang1,2, Chong Wang1,2, 4 Dongyou Yu1,2, Lingzhao Fang3*, Zhengguang Wang1,2* 5 6 1Hainan Institute...
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