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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...) from the target organism.DiscussionIn this study, we conducted pairwise tertiary structural comparisons at a proteomic scale and used the structural information to characterize the twilight zone and investigate the evolutionary relationship of genes from distantly related species. The use of protein...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...these findings. We then investigate roles of mitotically bookmarked CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures, such as TADs or loops, at bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data Can Luo1,3, Zimeng Jamie Zhou2,3, Yichen Henry Liu2 and Xin Maizie Zhou1,2 1Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA; 2...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
.... Corresponding authors: smontgom@stanford.edu, mschatz@cs.jhu.edu, wheelerm@stanford.edu, ajbattle@jhu.eduAbstractRare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed...
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Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
...of mutations in human diseases.View larger version: In this window In a new window Figure 1. Proteome-wide structural analysis of mutational hotspots. (A) Data resource of mutational hotspots and workflow of our full-proteome interaction-specific characterization framework. (B) Composition of mutational...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...Systematic identification and characterization of exon–intron circRNAs Yinchun Zhong1,6, Yan Yang2,6, Xiaolin Wang2, Bingbing Ren3, Xueren Wang4,5, Ge Shan2 and Liang Chen1 1Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...↵3 These authors equally contributed to this work. Corresponding author: danxie@scu.edu.cnAbstractSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in -wide selection, is not yet understood. In this study, we built an SV data set based...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine...

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