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Research: Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu,
- Katie Evans,
- Patrick van Eijk,
- Mark Bennett,
- Richard M. Webster,
- Matthew Leadbitter,
- Yumin Teng,
- Raymond Waters,
- Stephen P. Jackson,
- and Simon H. Reed
Genome Res. October 2016 26: 1376-1387; Published in Advance July 28, 2016, doi:10.1101/gr.209106.116
...-wide UV-induced DNA repair is organized around gene structure. (A) A linear plot of a section of Chromosome 14 showing 3D-DIP-Chip results from wild-type cells. The black line shows the mean (n = 3) CPD level observed immediately after UV irradiation (100 J/m2, shading highlights the SEM). Gray dots ...
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Research: High-throughput functional comparison of promoter and enhancer activities
- Thomas A. Nguyen,
- Richard D. Jones,
- Andrew R. Snavely,
- Andreas R. Pfenning,
- Rory Kirchner,
- Martin Hemberg,
- and Jesse M. Gray
Genome Res. August 2016 26: 1023-1033; Published in Advance June 16, 2016, doi:10.1101/gr.204834.116
...D Jones Jesse M Richard Jesse M, Gray Martin Hemberg Pfenning, Andreas R Andreas R, Pfenning Richard D, Jones Jones, RD Hemberg Martin Jesse Gray Martin Thomas Jones, R.D Rory ThomasA Nguyen Nguyen, Thomas A JesseM Gray Snavely, A.R J.M. Gray Nguyen, T Andrew R Snavely Nguyen, TA Andreas Pfenning Andreas ...
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LETTER: Genomic signatures of positive selection in humans and the limits of outlier approaches
- Joanna L. Kelley,
- Jennifer Madeoy,
- John C. Calhoun,
- Willie Swanson,
- and Joshua M. Akey
Genome Res. August 2006 16: 980-989; Published in Advance July 6, 2006, doi:10.1101/gr.5157306
...Press JoshuaM Akey Willie Swanson Swanson JC Calhoun JohnC Calhoun John JM Akey Joanna Kelley Calhoun Kelley, J Calhoun, J J.M. Akey Joanna L Kelley Swanson, Willie Jennifer, Madeoy Joshua M Akey Madeoy Jennifer J.L. Kelley Akey, Joshua M Joanna L, Kelley Joshua Kelley, Joanna L Swanson Willie ...
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Letter: Extreme variability among mammalian V1R gene families
- Janet M. Young,
- Hillary F. Massa,
- Li Hsu,
- and Barbara J. Trask
Genome Res. January 2010 20: 10-18; Published in Advance December 1, 2009, doi:10.1101/gr.098913.109
...Spring Harbor Laboratory Press BJ Trask Young, J.M Young, J Barbara J, Trask Young, JM H Massa Barbara Trask Hsu, Li Li Janet M, Young H.F. Massa Massa, H.F Janet M Young Trask, B.J Young Hillary F, Massa L Hsu Trask, BJ Janet M Hillary Massa Janet Young Janet JanetM Young Young, Janet M Hillary ...
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ARTICLE: Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria.
- T Koeuth,
- J Versalovic,
- and J R Lupski
Genome Res. November 1995 5: 408-418; doi:10.1101/gr.5.4.408
...in prokaryotic s. J. Bacteriol. 174: 4525 4529. 2. . Higgins, C.F., , Ames, G.F.L. , Barnes, W.M. , Clement, J.M. , Hofnung. M. Higgins, C.F., Ames, G.F.L. Barnes, W.M. Clement, J.M. and Hofnung. M. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298: 760 762. 3. . Gilson, E ...
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Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
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Research: Genetic and phenotypic intra-species variation in Candida albicans
- Matthew P. Hirakawa,
- Diego A. Martinez,
- Sharadha Sakthikumar,
- Matthew Z. Anderson,
- Aaron Berlin,
- Sharvari Gujja,
- Qiandong Zeng,
- Ethan Zisson,
- Joshua M. Wang,
- Joshua M. Greenberg,
- Judith Berman,
- Richard J. Bennett,
- and Christina A. Cuomo
Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
..., Diego A Wang, J.M Matthew Z, Anderson Gujja, Sharvari JM Greenberg Anderson, Matthew Z D Martinez Ethan, Zisson Cuomo, Christina A Martinez Sharadha, Sakthikumar Joshua M Bennett Richard J. Sakthikumar, S MP Hirakawa Bennett, R.J Zeng, Qiandong Martinez, DA Hirakawa, M Joshua Greenberg C.A. Cuomo ...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...of moss plants with knockout of PSEP1 (Supplemental Fig. S13AC; Supplemental Table S6). The phenotypes of psep3 KO and PSEP3 OE lines grown on BCD medium: (I,L) wild type; (J,M) knockout of PSEP3; (K,N) overexpression of PSEP3. (O) Diameter of moss plants with knockout of PSEP3 (Supplemental Fig. S13G ...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...initially analyzed CPD deamination in yeast genomic DNA that was UV-irradiated in vitro. To quantify the kinetics of CPD deamination in naked DNA in vitro, isolated yeast genomic DNA was UV-irradiated (600 J/m2 of UVC based on our previous calibration) and subsequently incubated for various times at 37C ...
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Research: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112

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