Searching journal content for articles similar to Gao et al. 30 (8): 1170.

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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...from 96.5% to 96.9% for C. briggsae isolates and from 98.3% to 99.2% for C. nigoni ones, suggesting that the quality is on par with that of the reference s (Supplemental Table S1). To ensure consistency and minimize potential biases in gene family comparisons, we applied a uniform gene prediction...
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Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
...by using population variant data in pan graph references (Garrison et al. 2018; Sirén et al. 2021).Parent-child trios provide evidence of sequence transmission between generations. This helps to identify which variants in the child occurred as de novo mutations, because these variants will generally...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...genotypes and phenotypes derived from collections of families. GPF allows interactive exploration of genetic variants, enrichment analysis for de novo mutations, phenotype/genotype association tools, and secure data sharing. GPF is used to disseminate two family collection data sets, SSC and SPARK...
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Research: Extensive variation in germline de novo mutations in Poecilia reticulata
- Yuying Lin,
- Iulia Darolti,
- Wouter van der Bijl,
- Jake Morris,
- and Judith E. Mank
Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
..., is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation (DNM) to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize germline DNMs in three large guppy families. Our results suggest...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...of the mammalian . We use whole- sequencing to identify de novo mutations in cohorts of age-matched ART-derived and naturally conceived mice. Our reliance on mice of a single inbred strain background allows us to rigorously control for potential genetic influences and environmental exposures on mutation rates...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...the likelihood of finding all de novo MEIs. MELT uses a transposon reference file to identify and characterize nonreference MEIs for each transposon family (Gardner et al. 2017). In contrast, RUFUS and the recently published TranSurVeyor identify breakpoints regardless of the transposon family, each producing...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...asked whether integration of predicted splicing-altering mutations with other genetic evidence can help to formally prioritize NDD-risk genes using a rigorous statistical framework (Methods). Specifically, we used two models to identify candidate risk genes based on the burden of de novo variants, model...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...in the database (Daubin and Ochman 2004a; Yomtovian et al. 2010; Vakirlis and Kupczok 2024; Pereira et al. 2025).De novo gene birth is the most tractable and traceable of these three routes because it is possible, in principle, to identify the ancestral noncoding sequence from which the new gene formed. Based...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...that early feature extraction, rather than downstream architecture, is the primary determinant of prediction accuracy. A comprehensive evaluation of these models on ATAC-seq signal prediction at 4-bp resolution in a cell type–specific manner identifies the ConvNeXt-based dilated CNN as the most robust...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...for Evolutionary Biology, 24306 Plön, Germany Corresponding author: elcortegano@protonmail.comAbstractAll forms of genetic variation originate from new mutations, making it crucial to understand their rates and mechanisms. Here, we use long-read sequencing from Pacific Biosciences (PacBio) to investigate de novo...
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