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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...concept. Palaeontologia Electronica 21: 1–25. doi:10.26879/750 ↵Berv JS, Field DJ. 2018. Genomic signature of an avian Lilliput Effect across the K-Pg extinction. Syst Biol 67: 1–13. doi:10.1093/sysbio/syx064 ↵Berv JS, Singhal S, Field DJ, Walker-Hale N, McHugh SW, Shipley JR, Miller ET, Kimball RT, Braun...
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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
...chromosomes over large genomic regions.The evolution of sex chromosomes represents one of the major innovations of inheritance and plays a core role in sexual evolution in the animal kingdom (Charlesworth 1991; Wright et al. 2016). In species with genetic sex determination mechanisms, sex chromosomes carry...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...to disease risk. Collecting sequencing data from families allows us to identify genomic events such as meiotic crossovers and shared genetic material between family members that is impossible to detect in unrelated individuals.Crossover detection using family data is one of the major approaches used to study...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity...
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Research: Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability
- Richard J. Wang,
- Gregg W.C. Thomas,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Harshavardhan Doddapaneni,
- Donna M. Muzny,
- John P. Capitanio,
- Predrag Radivojac,
- Jeffrey Rogers,
- and Matthew W. Hahn
Genome Res. June 2020 30: 826-834; Published in Advance May 27, 2020, doi:10.1101/gr.255174.119
.... Veenman & Zonen, B.V., Wageningen, The Netherlands. ↵Rogers J, Garcia R, Shelledy W, Kaplan J, Arya A, Johnson Z, Bergstrom M, Novakowski L, Nair P, Vinson A, et al. 2006. An initial genetic linkage map of the rhesus macaque (Macaca mulatta) using human microsatellite loci. Genomics 87: 30–38. doi:10...
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Research: Direct estimate of the rate of germline mutation in a bird
- Linnéa Smeds,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. September 2016 26: 1211-1218; Published in Advance July 13, 2016, doi:10.1101/gr.204669.116
...H Ellegren Anna Smeds Qvarnström, Anna Linnéa Hans, Ellegren Hans Ellegren Hans 1549-5469 10.1101/gr.204669.116 genome;gr.204669.116 1088-9051 Direct estimate of the rate of germline mutation in a bird Smeds et al. Avian mutation rate Direct estimate of the rate of germline mutation in a bird Linnéa...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum Alistair Miles 1 , 2 , Zamin Iqbal 3 , Paul Vauterin 1 , Richard Pearson 1 , 2 , Susana Campino 2 , Michel Theron 2 , Kelda...
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Research: Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
- Martin Völker,
- Niclas Backström,
- Benjamin M. Skinner,
- Elizabeth J. Langley,
- Sydney K. Bunzey,
- Hans Ellegren,
- and Darren K. Griffin
Genome Res. April 2010 20: 503-511; Published in Advance March 31, 2010, doi:10.1101/gr.103663.109
...support for the notion of recombination-based processes playing a major role in avian genome evolution. Footnotes ↵ 5 Corresponding author. E-mail D.K.Griffin@kent.ac.uk ; fax 44 (0) 1227-763912. [Supplemental material is available online at http://www.genome.org . The array CGH...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
..., Angela Tam 14 , Richard Moore 14 , Martin Hirst 14 , 15 , Marco A. Marra 14 , Baoxue Zhang 2 , 18 , Joseph F. Costello 5 , 18 and Ting Wang 1 , 18 1 Department of Genetics, Center for Genome Sciences and Systems...
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Research: Sequence shortening in the rodent ancestor
- Steve Laurie,
- Macarena Toll-Riera,
- Núria Radó-Trilla,
- and M. Mar Albà
Genome Res. March 2012 22: 478-485; Published in Advance November 29, 2011, doi:10.1101/gr.121897.111
...Avancxats (M.M.A.). References Alba MM, Guigo R. 2004. Comparative analysis of amino acid repeats in rodents and humans. Genome Res 14: 549–554. Axelsson E, Ellegren H. 2009. Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection...

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