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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
...referred to as the Southeast Asian deletion (Farashi and Harteveld 2018) (MIM: 604131) (Supplemental Fig. S13).We did not expect to find rare SVs in X-linked OMIM genes in 46,XY samples, since those events would be more likely to be associated with a disease. However, we did find five such events...
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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...Quadrupia provides a comprehensive catalog of G-quadruplexes across s from the tree of life Nikol Chantzi1,11, Akshatha Nayak1,11, Fotis A. Baltoumas2,3,11, Eleni Aplakidou2,3, Shiau Wei Liew4,5, Jesslyn Elvaretta Galuh4,5, Michail Patsakis1, Austin Montgomery1, Camille Moeckel1, Ioannis Mouratidis...
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Research: Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
- Hongru Wang,
- Filipe G. Vieira,
- Jacob E. Crawford,
- Chengcai Chu,
- and Rasmus Nielsen
Genome Res. June 2017 27: 1029-1038; Published in Advance April 6, 2017, doi:10.1101/gr.204800.116
..., possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow. [Supplemental material is available for this article.] Asian cultivated rice is one of the most...
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Resource: Structural variants in 3000 rice genomes
- Roven Rommel Fuentes,
- Dmytro Chebotarov,
- Jorge Duitama,
- Sean Smith,
- Juan Fernando De la Hoz,
- Marghoob Mohiyuddin,
- Rod A. Wing,
- Kenneth L. McNally,
- Tatiana Tatarinova,
- Andrey Grigoriev,
- Ramil Mauleon,
- and Nickolai Alexandrov
Genome Res. May 2019 29: 870-880; Published in Advance April 16, 2019, doi:10.1101/gr.241240.118
...in finding causative variants in -wide association analysis. These new insights into rice biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.Genomics accelerates...
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Research: Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
- Fan Zhang,
- Hongzhang Xue,
- Xiaorui Dong,
- Min Li,
- Xiaoming Zheng,
- Zhikang Li,
- Jianlong Xu,
- Wensheng Wang,
- and Chaochun Wei
Genome Res. May 2022 32: 853-863; Published in Advance April 8, 2022, doi:10.1101/gr.276015.121
...crop species constructed from SGS data and from small/or less representative samples remain to be improved and validated.Here, we report an effort to construct high-quality pan-s for Asian cultivated rice, Oryza sativa L. (OS) using 105 OS accessions representing all of its major populations plus six...
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Research: Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation
- Tingting Guo,
- Qi Mu,
- Jinyu Wang,
- Adam E. Vanous,
- Akio Onogi,
- Hiroyoshi Iwata,
- Xianran Li,
- and Jianming Yu
Genome Res. May 2020 30: 673-683; Published in Advance April 16, 2020, doi:10.1101/gr.255703.119
...of these four genes for the 3010 diverse cultivated rice s from the 3000 Rice Genomes Project (Supplemental Fig. S14; Supplemental Table S9; Wang et al. 2018). From 29 million single-nucleotide polymorphisms (SNPs), there were more than 100 SNPs for each gene (Hd1, Hd2, Hd5, and Hd6). These four genes were...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...and Innovation Centre, Scotland's Rural College, Barony Campus, Dumfries DG1 3NE, UK Corresponding author: michel.georges@uliege.beAbstractWe report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...author: dujuan9981@cau.edu.cnAbstractDiapause represents a crucial adaptive strategy used by insects to cope with changing environmental conditions. In North China, the Asian corn borer (Ostrinia furnacalis) enters a winter larval diapause stage. Although there is growing evidence implicating epigenetic...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...49), and invasive tumorigenic (P90) stages. Additionally, we characterized active enhancers and promoters using H3K27ac ChIP-seq at P90. Our work represents the first time course catalog of in vivo chromatin accessibility and expression during PB progression aiming at identifying new molecular...

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