Searching journal content for articles similar to Assaf et al. 27 (12): 1988.

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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
...of Drosophila melanogaster (Muller 1928; Bateman 1959; Mukai 1964) and in humans by pedigree analysis (for review, see Nachman 2004). In recent decades, DNA sequencing techniques have greatly enhanced the ability to detect new mutations, allowing the estimation of mutation rates at the molecular level (Halligan...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
....6 cM/Mb (Hemmer et al. 2020), and D. melanogaster of 2.5 cM/Mb (Comeron et al. 2012). However, experimental studies of Drosophila have rarely looked at variation in -wide recombination rates in natural populations of outbred individuals, and wild populations may differ systematically from populations...
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Research: Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans
- Moein Rajaei,
- Ayush Shekhar Saxena,
- Lindsay M. Johnson,
- Michael C. Snyder,
- Timothy A. Crombie,
- Robyn E. Tanny,
- Erik C. Andersen,
- Joanna Joyner-Matos,
- and Charles F. Baer
Genome Res. September 2021 31: 1602-1613; Published in Advance August 17, 2021, doi:10.1101/gr.275372.121
...in Arabidopsis thaliana MA lines cultured under conditions of heat stress (Belfield et al. 2021). Drosophila melanogaster MA lines initiated from s carrying deleterious large-effect mutations experience higher rates of short deletions than wild-type MA lines, thought to be owing to preferential deployment...
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Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
- Ying Zhen,
- Christian D. Huber,
- Robert W. Davies,
- and Kirk E. Lohmueller
Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
...nonsynonymous mutations in humans, mice, and Drosophila melanogaster by examining patterns of polymorphism and divergence. We develop a novel composite likelihood framework to test whether these parameters differ across species. Overall, we reject a model with the same p+ and s+ of beneficial mutations across...
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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
...:10.1038/nrg3483 ↵Tatsumoto S, Go Y, Fukuta K, Noguchi H, Hayakawa T, Tomonaga M, Hirai H, Matsuzawa T, Agata K, Fujiyama A. 2017. Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole sequencing. Sci Rep 7: 13561. doi:10.1038/s41598-017-13919-7 ↵Thomas...
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Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
...then examined whether the preference for damaging G-to-A/C-to-T missense mutations in a population was associated with the primary ADAR sequence motif (Lehmann and Bass 2000; Eggington et al. 2011) at the variants. Indeed, sites of G-to-A/C-to-T missense mutations have a significantly higher percentage...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...in the twentieth century by analysis of mutation accumulation (MA) experiments, in which spontaneous mutations are allowed to accumulate in lines of small effective population size where natural selection is ineffective (Muller 1928; Bateman 1959; Mukai 1964). The advent of whole- sequencing technology led...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...and gene expression variation. Results A sequencing-based map of structural variation in a Drosophila melanogaster population We obtained deep sequencing data for 39 fly lines from the DGRP pilot data set (Table 1; Ayroles et al. 2009; Mackay et al. 2012). 2Corresponding author E-mail jan...
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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
...range in size between 24 and 32 nt in length in most animals. In the model Dipteran, Drosophila melanogaster (Dmel), the small RNAs comprise 258 miRNA genes (Kozomara et al. 2019), approximately 20 large intergenic piRNA cluster loci (Brennecke et al. 2007; Malone et al. 2009; Wen et al. 2014), more...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...accuracy and sensitivity for -wide somatic SNV detection, and (3) minimal positive and negative mutation selection biases.Here, we introduce lineage sequencing (Fig. 1) and its application to clonal cell populations cultured in vitro. In lineage sequencing, one collects specific cells representing...
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