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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- 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 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...Talent Development Program of 586 China Agricultural University) for the financial support. We thank the Lab members that 587 gave constructive suggestions to this project. 588 589 Authors’ contributions 590 Y.Duan, W.C., X.Z., and S.L. conceptualized and supervised this work. Y.Duan, M.H., L.Y., 591 L...
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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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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...in biology, including reports on best practice guidelines for various genomic analysis pipelines, such as RNA-seq (Conesa et al. 2016), ChIP-seq (Landt et al. 2012), and ATAC-seq (Yan et al. 2020), as well as the Reproducibility Project: Cancer Biology (Center of Open Sciences and Science Exchange...
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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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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
...continents provides a valuable knowledge resource for researchers investigating the impact of the microbiome on individual health parameters. This open-access atlas will be updated routinely with the new publicly available gut metagenomics data, including the recently announced One Million Microbiome Project...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
...data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal...
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Insight/Outlook: The ethics of conducting molecular autopsies in cases of sudden death in the young
- Amy L. McGuire,
- Quianta Moore,
- Mary Majumder,
- Magdalena Walkiewicz,
- Christine M. Eng,
- John W. Belmont,
- Salma Nassef,
- Sandra Darilek,
- Katie Rutherford,
- Stacey Pereira,
- Steven E. Scherer,
- V. Reid Sutton,
- Dwayne Wolf,
- Richard A. Gibbs,
- Roger Kahn,
- Luis A. Sanchez,
- and the Molecular Autopsy Consortium of Houston (MATCH)
Genome Res. September 2016 26: 1165-1169; Published in Advance July 13, 2016, doi:10.1101/gr.192401.115
...for their contributions. Funding for this project was provided by the National Institute of Justice, 2010-DN-BX-K230 (R.K.) and the Baylor College of Medicine President's Circle (A.L.M., Q.M.).Footnotes ↵7 Additional members of the MATCH Consortium: Eric Boerwinkle, L. Maximilian Buja, Tom Caskey, Sherhonda Harper...
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Resource: The NIH Human Microbiome Project
- The NIH HMP Working Group,
- Jane Peterson,
- Susan Garges,
- Maria Giovanni,
- Pamela McInnes,
- Lu Wang,
- Jeffery A. Schloss,
- Vivien Bonazzi,
- Jean E. McEwen,
- Kris A. Wetterstrand,
- Carolyn Deal,
- Carl C. Baker,
- Valentina Di Francesco,
- T. Kevin Howcroft,
- Robert W. Karp,
- R. Dwayne Lunsford,
- Christopher R. Wellington,
- Tsegahiwot Belachew,
- Michael Wright,
- Christina Giblin,
- Hagit David,
- Melody Mills,
- Rachelle Salomon,
- Christopher Mullins,
- Beena Akolkar,
- Lisa Begg,
- Cindy Davis,
- Lindsey Grandison,
- Michael Humble,
- Jag Khalsa,
- A. Roger Little,
- Hannah Peavy,
- Carol Pontzer,
- Matthew Portnoy,
- Michael H. Sayre,
- Pamela Starke-Reed,
- Samir Zakhari,
- Jennifer Read,
- Bracie Watson,
- and Mark Guyer
Genome Res. December 2009 19: 2317-2323; Published in Advance October 9, 2009, doi:10.1101/gr.096651.109
....S. investigators conducting research projects that have similar goals. Specifically, researchers who are using 16S rRNA gene or whole- shotgunmetagenomic analyses to study changes in the human microbiome in health and disease or who are generating a significant number of reference microbial sequences are welcome...
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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
...(216 tRNA isodecoders) and mitochondrial tRNAs (22 tRNA isoacceptors) of the +DM and −DM libraries using the R (version 4.0.1) (R Core Team 2020) packages FactoMineR (version 2.4) (Lê et al. 2008) and factoextra (version 1.0.7) (https://CRAN.R-project.org/package=factoextra), respectively. The PCAs...
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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
...249 healthy adults from the Human Microbiome Project (HMP) (The Human Microbiome Project Consortium 2012; Lloyd-Price et al. 2017) and 185 healthy adults from Qin et al. (2012; Table 1) to compare the evolutionary dynamics in adults versus infants. These data sets were chosen because...

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