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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
...quantified the total microbial abundance across all samples and found that GF bees harbored negligible microbiota (traditionally defined as 105 CFUs), whereas CV bees exhibited high and variable microbial loads, ranging from 109 to 1010 CFUs (Fig. 3C). 16s rRNA sequencing data from bee gut further revealed...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology Abigail L. Lind1,2, Nathan A. McDonald2,3, Elias R. Gerrick4, Ami S. Bhatt5,6 and Katherine S. Pollard1,7,8 1Gladstone Institute for Data Science...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.Whole- sequences serve as a fundamental blueprint for life, providing the foundation for a broad range of life science research. The s of prokaryotes, that is, archaea and bacteria, are typically smaller (<10...
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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
..., to provide comprehensive open-access metagenomics data from multiple research centers. Therefore, an in-depth analysis of the impact of the gut microbiome on health and disease will be used to facilitate future studies to reveal the critical role of the gut microbiome in maintaining human health...
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Research: Rapid evolution and strain turnover in the infant gut microbiome
- Daisy W. Chen and
- Nandita R. Garud
Genome Res. June 2022 32: 1124-1136; Published in Advance May 11, 2022, doi:10.1101/gr.276306.121
..., University of California, Los Angeles, California 90095-1606, USA; 4Department of Human Genetics, University of California, Los Angeles, California 90095-1606, USA Corresponding author: ngarud@ucla.eduAbstractAlthough the ecological dynamics of the infant gut microbiome have been intensely studied...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed s from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs...
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Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
- Zhoutao Chen,
- Long Pham,
- Tsai-Chin Wu,
- Guoya Mo,
- Yu Xia,
- Peter L. Chang,
- Devin Porter,
- Tan Phan,
- Huu Che,
- Hao Tran,
- Vikas Bansal,
- Justin Shaffer,
- Pedro Belda-Ferre,
- Greg Humphrey,
- Rob Knight,
- Pavel Pevzner,
- Son Pham,
- Yong Wang,
- and Ming Lei
Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
...fragment into small subfragments, which later become the inserts of a sequencing library. These methods can be classified into two categories: synthetic long reads (SLRs) and linked-reads. SLR methods, for example, LFR (Peters et al. 2012), LRseq (Voskoboynik et al. 2013), and TSLR (Bankevich and Pevzner...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...and Wakefield 2009; Hansen et al. 2010; Li et al. 2010; Trapnell et al. 2010; Garber et al. 2011; Roberts et al. 2011; Kivioja et al. 2012; Risso et al. 2014; Bray et al. 2016; Love et al. 2016; Patro et al. 2017; Davies et al. 2021). Examples include: GC bias, which links read abundance to GC...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
..., the clearest one against GA-rich repeats in the human . However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw...

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