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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...the potential design for iterative improvement of such models by integrating synthetic regulatory data set. Our work suggests a key role for synthetic regulatory genomics in training future genomic deep learning models.ResultsEnformer performance predicting synthetic payloadsTo probe the varied performance...
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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
...by CTCF and, thus, that maintained CTCF binding does not alter mitotic chromosome folding. Lastly, we compare mitotic Hi-C data generated in this study in mouse with public data in human and chicken. We do not find any cell type–specific differences; however, we find a difference between species...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer Gabriela D.A. Guardia1,5, Carlos H. dos Anjos1,5, Aline Rangel-Pozzo2, Filipe F. dos Santos1,3, Alexander Birbrair4, Paula F. Asprino1, Anamaria A. Camargo1 and Pedro A.F. Galante1 1...
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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
...for human Chromosome 8 by Logsdon et al. (2021) are specialized tools for reconstructing segmental duplications or centromeres, they were designed for error-prone long reads. To the best of our knowledge, there is no specialized assembler for reconstructing repeats that uses PacBio HiFi reads exclusively...
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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. April 2026 36: 661-670; 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 Saether1,2,6, Angelo Salazar Mantero1,3,6, Marlene Ek1,3, Maria Pettersson1,3, Elisabeth Syk Lundberg1,3, Christopher M. Grochowski4, Claudia M...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...constructed the miRNA-mediated regulatory network of mouse early embryos specific to diapause. We find that individual miRNAs contribute to the combinatorial regulation by the network, and the perturbation of the network compromises embryo survival in diapause. We further identified the nutrient...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...the investigation of potential sexualization of sex chromosomes and its correlation with sexual dimorphism in moustache toads.We generated a high-quality chromosome-scale assembly as a reference , in conjunction with phased haplotype s and transcriptomic data from both sexes. We identified the sex chromosomes...
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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
...).Chromosome fusions involving X/Z often synchronously generate sex-limited chromosomes, neo-Y/W, that degenerate through the suppression of recombination. Hemizygosity of genes linked to the neo-X/Z Chromosome then selects for dosage compensation (Natri et al. 2013; Sigeman et al. 2021). This process occurs...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
..., generating additional noise in the graph. This prevents automated resolution which requires support from at least twice as many ONT UL reads as the next best. A path consistent with the largest number of ONT UL sequences was selected.In the maize assembly, three chromosomes (Chr 1, 8, and 9) had four...
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Method: Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
- Brendan L. O'Connell,
- Ruth V. Nichols,
- Dmitry Pokholok,
- Jerushah Thomas,
- Sonia N. Acharya,
- Andrew Nishida,
- Casey A. Thornton,
- Marissa Co,
- Andrew J. Fields,
- Frank J. Steemers,
- and Andrew C. Adey
Genome Res. February 2023 33: 208-217; Published in Advance February 15, 2023, doi:10.1101/gr.276655.122
...University, Knight Cardiovascular Institute, Portland, Oregon 97239, USA Corresponding author: adey@ohsu.eduAbstractHere we present advancements in single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve...
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