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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...a genomic basis to study host-microbe interactions, and we demonstrate its utility in identifying candidate pathways in the bacteria affecting chemotaxis behavior and survival in the nematodes. Second, we generate nematode transcriptomes of P. pacificus nematodes on 38 bacterial diets and characterize 60...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
..., Bethlehem, Pennsylvania 18015, USA Corresponding author: matthew.pollard95@gmail.comAbstractMammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative...
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Resource: Global compositional and functional states of the human gut microbiome in health and disease
- Sunjae Lee,
- Theo Portlock,
- Emmanuelle Le Chatelier,
- Fernando Garcia-Guevara,
- Frederick Clasen,
- Florian Plaza Oñate,
- Nicolas Pons,
- Neelu Begum,
- Azadeh Harzandi,
- Ceri Proffitt,
- Dorines Rosario,
- Stefania Vaga,
- Junseok Park,
- Kalle von Feilitzen,
- Fredric Johansson,
- Cheng Zhang,
- Lindsey A. Edwards,
- Vincent Lombard,
- Franck Gauthier,
- Claire J. Steves,
- David Gomez-Cabrero,
- Bernard Henrissat,
- Doheon Lee,
- Lars Engstrand,
- Debbie L. Shawcross,
- Gordon Proctor,
- Mathieu Almeida,
- Jens Nielsen,
- Adil Mardinoglu,
- David L. Moyes,
- Stanislav Dusko Ehrlich,
- Mathias Uhlen,
- and Saeed Shoaie
Genome Res. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
...indicates ES = 0.3; the red dotted line indicates ES = 0.5; and each dot in the plot represents one MSP within one disease cohort. Acronyms are as follows: (ACVD) acute coronary cardiovascular disease, (Ob) obesity, (CRC) colorectal cancer, (NSCLC) non-small-cell lung cancer, (RCC) renal cell carcinoma...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...short- and long-term pathologies associated with these exposures, which include altered growth (intrauterine growth restriction, small for gestational age), abnormal organ development, and development of disease (such as obesity, diabetes, hypertension, cancer) and disorders (attention...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
...plasticity by a viral RNA. Nature 511: 366–369. doi:10.1038/nature13378 ↵Cuevas-Sierra A, Ramos-Lopez O, Riezu-Boj JI, Milagro FI, Martinez JA. 2019. Diet, gut microbiota, and obesity: links with host genetics and epigenetics and potential applications. Adv Nutr 10: S17–S30. doi:10.1093/advances/nmy078 ↵de...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
...of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current annotations and thus permit their inclusion in hypotheses and models, which...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
..., Michal JJ, Kovac M, Jiang Z. 2013. Obesity gene atlas in mammals. J Genomics 1: 45–55. Larson G, Dobney K, Albarella U, Fang M, Matisoo-Smith E, Robins J, Lowden S, Finlayson H, Brand T, Willerslev E, et al. 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication...
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Method: Enhanced virome sequencing using targeted sequence capture
- Todd N. Wylie,
- Kristine M. Wylie,
- Brandi N. Herter,
- and Gregory A. Storch
Genome Res. December 2015 25: 1910-1920; Published in Advance September 22, 2015, doi:10.1101/gr.191049.115
..., St. Louis, Missouri 63110, USA; 2McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA Corresponding author: wylie_t@kids.wustl.edu ↵ 3 These authors contributed equally to this work. Abstract...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...is the most commonly used inbred strain in biomedical research, develops diet-induced obesity, has a high preference for ethanol, and demonstrates late-onset hearing loss (McClearn and Rodgers 1961; Surwit et al. 1988; Zheng et al. 1999). These susceptibilities are in contrast to other inbred strains...
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Research: Sympatric chimpanzees and gorillas harbor convergent gut microbial communities
- Andrew H. Moeller,
- Martine Peeters,
- Jean-Basco Ndjango,
- Yingying Li,
- Beatrice H. Hahn,
- and Howard Ochman
Genome Res. October 2013 23: 1715-1720; Published in Advance June 26, 2013, doi:10.1101/gr.154773.113
...heterogeneity in a patchy ecosystem. Proc Natl Acad Sci 104: 2761–2766. Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL. 2012. Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Integrative Physiol. 4: 738–747. Serion M, Luche E, Gres...

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