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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...identify syntenic orthologs across the annotated RPRP s using the GET_PANGENES algorithm we developed based on WGA (Contreras-Moreira et al. 2023). Further, we assigned stable identifiers for a pangene set, here defined as a collection of gene models across different varieties in the same genomic location...
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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
...diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS...
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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
.... 2020). We envision that our Integrative Catalog of TADs and TAD boundaries will provide a vital reference map for future studies that want to investigate the disruption of TADs causing phenotypic changes. Genomic variation, including all types of SVs that overlap or intersect with TAD boundaries...
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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...(SNV) data from the Genome Aggregation Database (gnomAD) (Koenig et al. 2024) (Supplemental Table S3). We then used this catalog to investigate the relationship between chromatin state and isoform expression across gene biotypes. We constructed a filtered set of expressed transcripts with well...
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Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
- Wilfried M. Guiblet,
- Michael DeGiorgio,
- Xiaoheng Cheng,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
...Selection and thermostability suggest G-quadruplexes are novel functional elements of the human Wilfried M. Guiblet1,8, Michael DeGiorgio2, Xiaoheng Cheng3, Francesca Chiaromonte4,5,6, Kristin A. Eckert5,7, Yi-Fei Huang3,5 and Kateryna D. Makova3,5 1Bioinformatics and Genomics Graduate Program...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...Building better annotations across the tree of life Adam H. Freedman and Timothy B. Sackton Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138, USA Corresponding author: adamfreedman@fas.harvard.eduAbstractRecent technological advances in long...
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Resource: Lignature provides a curated resource of ligand induced transcriptomic signatures for signaling inference
- Ying Xin,
- Md Amanullah,
- Cheng Qian,
- Chingmo Zhou,
- and Jiang Qian
Genome Res. April 8, 2026 gr.281287.125; Published in Advance April 8, 2026, doi:10.1101/gr.281287.125
...Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 Cold Spring Harbor Laboratory Press 10.1101/gr.281287.125 ;gr.281287.125v1 ;gr.281287.125 gr.281287.125 gr.281287.125 Resource Resource Resources Lignature for signaling inference The Johns Hopkins University School of Medicine...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...a method for detecting telomeric sequences in Saccharomyces cerevisiae s from raw Oxford Nanopore Technologies (ONT) sequencing reads, providing a comprehensive view of TL distributions both -wide and at individual chromosome extremities. We analyze the TL distribution in 100 S. cerevisiae strains...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...understood. Here, we use comparative genomics, expression across multiple ontogenetic stages and tissues, as well as polymorphism data to investigate MHC evolution in newts. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...architectures through 326 replication- or repair-associated templated insertion. 327 328 To elucidate the regulatory consequences of somatic SVs, we performed an 329 enrichment analysis of SV breakpoints across functional genomic regions. Somatic 330 INS, DUP, DEL, and INV exhibited significant enrichment...
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