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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
...reviewers and Ahmet Denli for improving our manuscript.Author contributions: J.E.M. and Y.L. conceived the study and designed the experiments and analysis. I.D., J.M., and J.E.M. collected the data. Y.L. and I.D. performed DNA extractions. Y.L., W.v.d.B., and I.D. performed the data analysis. J.E.M. and Y ...
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Research: Rtt109 slows replication speed by histone N-terminal acetylation
- Nelly Frenkel,
- Felix Jonas,
- Miri Carmi,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. March 2021 31: 426-435; Published in Advance February 9, 2021, doi:10.1101/gr.266510.120
..., Studitsky VM, Reinberg D. 2003. FACT facilitates transcription-dependent nucleosome alteration. Science 301: 10901093. doi:10.1126/science.1085703 Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM. 2008. Molecular functions of the histone acetyltransferase chaperone ...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...304.e18. doi:10.1016/j.cell.2017.12.014 Deshpande AS, Ulahannan N, Pendleton M, Dai X, Ly L, Behr JM, Schwenk S, Liao W, Augello MA, Tyer C, et al. 2022. Identifying synergistic high-order 3D chromatin conformations from -scale nanopore concatemer sequencing. Nat Biotechnol 40: 14881499. doi:10.1038/s ...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
..., Koutseva N, Zaghlul S, Graves T, Rock S, et al. 2014. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508: 494499. doi:10.1038/nature13206 Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large s with single-molecule sequencing ...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...-S, Friedman JM, Birol I. 2021. Straglr: discovering and genotyping tandem repeat expansions using whole long-read sequences. Genome Biol 22: 224. doi:10.1186/s13059-021-02447-3 Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, et al. 2022 ...
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Research: Assessment of palindromes as platforms for DNA amplification in breast cancer
- Jamie Guenthoer,
- Scott J. Diede,
- Hisashi Tanaka,
- Xiaoyu Chai,
- Li Hsu,
- Stephen J. Tapscott,
- and Peggy L. Porter
Genome Res. February 2012 22: 232-245; Published in Advance July 13, 2011, doi:10.1101/gr.117226.110
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Research: Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging
- Aaron R. Jeffries,
- Reza Maroofian,
- Claire G. Salter,
- Barry A. Chioza,
- Harold E. Cross,
- Michael A. Patton,
- Emma Dempster,
- I. Karen Temple,
- Deborah J.G. Mackay,
- Faisal I. Rezwan,
- Lise Aksglaede,
- Diana Baralle,
- Tabib Dabir,
- Matthew F. Hunter,
- Arveen Kamath,
- Ajith Kumar,
- Ruth Newbury-Ecob,
- Angelo Selicorni,
- Amanda Springer,
- Lionel Van Maldergem,
- Vinod Varghese,
- Naomi Yachelevich,
- Katrina Tatton-Brown,
- Jonathan Mill,
- Andrew H. Crosby,
- and Emma L. Baple
Genome Res. July 2019 29: 1057-1066; Published in Advance June 3, 2019, doi:10.1101/gr.243584.118
...Research Council (MRC) grant G1001931 (to E.L.B.), MRC grant G1002279 (to A.H.C.), and MRC grants MR/M008924/1 and MR/K013807/1 (to J.M.).Author contributions: E.L.B., A.H.C., and J.M. conceived the study. R.M. and B.A.C. performed the genetic analysis. A.R.J. and R.M. performed LUMA global methylation ...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
....genome.org .] Article is online at http://www.genome.org/cgi/doi/10.1101/gr.086652.108 . Copyright 2009 by Cold Spring Harbor Laboratory Press Joshua Akey Akey JoshuaM Akey Akey, Joshua M Joshua Akey, J.M JM Akey Joshua M, Akey Akey, JM Akey, J J Akey J.M. Akey Joshua M Akey Joshua M. Joshua M Akey ...
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Research: Evolution of splicing regulatory networks in Drosophila
- C. Joel McManus,
- Joseph D. Coolon,
- Jodi Eipper-Mains,
- Patricia J. Wittkopp,
- and Brenton R. Graveley
Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
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ARTICLE: Direct cDNA selection with DNA microdissected from mouse chromosome 16: isolation of novel clones and construction of a partial transcription map of the C3-C4 region.
- J Wei,
- M E Hodes,
- Y Wang,
- Y Feng,
- B Ghetti,
- and S R Dlouhy
Genome Res. August 1996 6: 678-687; doi:10.1101/gr.6.8.678
....C. and Lander. E.S. 1994 . A genetic map of the mouse with 4,006 simple sequence length polymorphisms. Nature Genet. 7 : 220 245 . Dufresne-Zacharia, M.-C., , Dahmane, N. , Theophile, D. , Orti, R. , Chettouh, Z. , Sinet, P.-M. , Delabar. J.-M. Dufresne-Zacharia, M.-C., Dahmane, N. Theophile, D. Orti, R ...

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