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Research: Systems genetics of the Drosophila metabolome
- Shanshan Zhou,
- Fabio Morgante,
- Matthew S. Geisz,
- Junwu Ma,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 392-405; Published in Advance November 6, 2019, doi:10.1101/gr.243030.118
...al. 2008). However, to date, a comprehensive integration of -wide variants with variation in gene expression, the metabolome, and organismal phenotype along with metabolome-based phenotypic prediction has not been reported for any genetically well-defined model organism population, and few studies...
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Research: Cellular age explains variation in age-related cell-to-cell transcriptome variability
- Ming Yang,
- Benjamin R. Harrison,
- and Daniel E.L. Promislow
Genome Res. November 2023 33: 1906-1916; Published in Advance November 16, 2023, doi:10.1101/gr.278144.123
...in the transcriptome differ among organs (Schaum et al. 2020). Similar among-organ differences are seen in the aging of the proteome (Ori et al. 2015). However, these observations are based on analysis of bulk tissue, which masks variation among cells within tissues (e.g., Ibañez-Solé et al. 2022). Analysis of aging...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and meta atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures...
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Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
- William R. Thomas,
- Cecilia Baldoni,
- Yuanyuan Zeng,
- David Carlson,
- Julie Holm-Jacobsen,
- Marion Muturi,
- Dominik von Elverfeldt,
- Tue B. Bennike,
- Dina K.N. Dechmann,
- John Nieland,
- Angelique P. Corthals,
- and Liliana M. Dávalos
Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
...the trajectory of size plasticity. We focused on blood, which circulates metabolites, and the liver, a key site of metabolic regulation including lipid and glucose processing. By integrating phenotypic, metabolomic, transcriptomic, and proteomic data, our study aims to identify the molecular pathways...
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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
...in understudied lineages like ruminants. 113 In this study, we aimed to comprehensively characterize the coevolutionary dynamics of 114 KZFPs and TEs across 32 ruminant s. We sought to use a k-mer-based approach to 115 overcome limitations of conserved sequence methods and identify taxon-specific expansions 116...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...assemble a high-quality, telomere-to-telomere haplotype of A. avenae. Transcriptomic analyses reveal distinct sets of genes involved in responses to desiccation and freezing stress. Notably, under desiccation stress, several desiccation-tolerance genes exhibit allelic imbalance expression. Among these, we...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...and flexibility in real-world applications. Furthermore, expanding the model to incorporate other omic data, such as single-cell proteomics or metabolomics, could provide a more comprehensive understanding of cellular functions and regulatory networks, thus further improving the robustness and versatility of sc...
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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
...or transcriptomics to metabolomics, to comprehensively evaluate and improve CAMUS. In the future, a dedicated database of data sets and methods should be established, integrating CAMUS to assist users in selecting reference data and annotation methods.MethodsData preprocessingWe processed the count matrices for sc...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...previous studies characterizing transcriptomic (Hu et al. 2007; Kemmeren et al. 2014), metabolomic (Shakoury-Elizeh et al. 2010; Mülleder et al. 2016; Zelezniak et al. 2018), and proteomic (Messner et al. 2023) responses to genetic perturbations, the exact chromatin-mediated mechanisms enacting...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...behavior, the potential involvement of RNA editing in gut–brain interactions remains unexplored. Here, we perform comparative transcriptomic analyses between heads of germ-free (GF) versus conventional (CV) honeybees. A total of 1528A-to-I editing sites are identified in honeybee heads, among which...

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