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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read sequencing Kristine Bilgrav Saether,1,2,6 Angelo Salazar Mantero,1,3,6 Marlene Ek,1,3 Maria Pettersson,1,3 Elisabeth Syk Lundberg,1,3 Christopher M. Grochowski,4 Claudia M...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...Automated interpretable artificial intelligence genomic prediction with AlGP 1 Running title: Interpretable AI for Genomic Prediction 2 Lei Wei1, Ziqin Jiang2, Baoliang Fan3, Yidan Yan1, Zhenqiang Xu2, Xiaoxiang Hu1,4*, Yuzhe 3 Wang1,4* 4 1. State Key Laboratory of Animal Biotech Breeding, College...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...assembly G and HiFi reads H will be denoted by RA.G.H. For example, the RAmbler assembly using the HG38 assembly and the HG00733 HiFi reads will be called RA.HG38.HG00733.We focused on five complex repetitive regions within the human : the centromeres of Chromosome 8 and X, and three noncentromeric regions...
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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
...size and chromosome dimensions, with the exception of recent reports in budding yeast and the Xenopus embryo (Kakui et al. 2022; Zhou et al. 2023). It would be interesting to support our findings with experimental data capturing ratios of condensin I and II across different species. Although we assume...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...observed in mice (Vara et al. 2021), muntjac deer (Yin et al. 2021), and yeast (Di Stefano et al. 2020). This specific chromosome structuring could be significant, as multiple-level chromatin organization has been shown to influence gene expression, recombination, and mutation in various species (Li et al...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...to UV mutagenesis. However, the impact of genomic context and chromatin architecture on CPD deamination rates in cells remains poorly understood. Here, we develop a method known as dCPD-seq to map deaminated CPDs (dCPDs) across the of repair-deficient yeast cells at single-nucleotide resolution. Our d...
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Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
...in most eukaryotes. DNA replication origins, origin binding proteins, and replication timing of centromere DNA are important determinants of centromere function. The epigenetically regulated regional centromeres in the budding yeast Candida albicans have unique DNA sequences that replicate earliest...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...of genetically modified human hematopoietic progenitor cells. PLoS One 8: e59594. doi:10.1371/journal.pone.0059594 ↵Crabtree AM, Kizer EA, Hunter SS, Van Leuven JT, New DD, Fagnan MW, Rowley PA. 2019. A rapid method for sequencing double-stranded RNAs purified from yeasts and the identification of a potent K1...
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Research: Identification and characterization of centromeric sequences in Xenopus laevis
- Owen K. Smith,
- Charles Limouse,
- Kelsey A. Fryer,
- Nicole A. Teran,
- Kousik Sundararajan,
- Rebecca Heald,
- and Aaron F. Straight
Genome Res. June 2021 31: 958-967; Published in Advance April 19, 2021, doi:10.1101/gr.267781.120
...centromere formation in vertebrates.Perturbing centromere function in cells often leads to cell death; thus, cell-free systems using budding yeast and Xenopus laevis egg extracts have been invaluable for studying centromere and kinetochore assembly (Ng and Carbon 1987; Hyman et al. 1992; Sorger et al. 1994...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...to merge individual tissue markers into 10,183 marker clusters. For every marker cluster, the fraction of tissue-specific DNA fragments at all markers within the cluster was calculated, which was used as the input vector for two DNNs with three dense hidden layers each. To avoid model overfitting, a batch...
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