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Method: Defining TP53 pioneering capabilities with competitive nucleosome binding assays
- Xinyang Yu and
- Michael J. Buck
Genome Res. January 2019 29: 107-115; Published in Advance November 8, 2018, doi:10.1101/gr.234104.117
...of a consensus binding site for p53. Nat Genet 1: 4549. doi:10.1038/ng0492-45 Emamzadah S, Tropia L, Halazonetis TD. 2011. Crystal structure of a multidomain human p53 tetramer bound to the natural CDKN1A (p21) p53-response element. Mol Cancer Res 9: 14931499. doi:10.1158/1541-7786.MCR-11-0351 Espinosa JM ...
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Research: Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock
- Ramon Amat,
- René Böttcher,
- François Le Dily,
- Enrique Vidal,
- Javier Quilez,
- Yasmina Cuartero,
- Miguel Beato,
- Eulàlia de Nadal,
- and Francesc Posas
Genome Res. January 2019 29: 18-28; Published in Advance December 6, 2018, doi:10.1101/gr.238527.118
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Research: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast
- Vahid Aslanzadeh,
- Yuanhua Huang,
- Guido Sanguinetti,
- and Jean D. Beggs
Genome Res. February 2018 28: 203-213; Published in Advance December 18, 2017, doi:10.1101/gr.225615.117
...polymerase II. Cell 154: 775788. Brinster RL, Allen JM, Behringer RR, Gelinas RE, Palmiter RD. 1988. Introns increase transcriptional efficiency in transgenic mice. Proc Natl Acad Sci ...
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Research: The peopling of South America and the trans-Andean gene flow of the first settlers
- Alberto Gómez-Carballa,
- Jacobo Pardo-Seco,
- Stefania Brandini,
- Alessandro Achilli,
- Ugo A. Perego,
- Michael D. Coble,
- Toni M. Diegoli,
- Vanesa Álvarez-Iglesias,
- Federico Martinón-Torres,
- Anna Olivieri,
- Antonio Torroni,
- and Antonio Salas
Genome Res. June 2018 28: 767-779; Published in Advance May 7, 2018, doi:10.1101/gr.234674.118
...de Guerra D, Figuera Prez C, Bravi CM, Saunier J, Scheible M, Irwin J, Coble MD, Rodriguez-Larralde A. 2012. Sequence variation of mitochondrial DNA control region in North Central Venezuela. Forensic Sci Int Genet 6: e131e133. de Saint Pierre M, Bravi CM, Motti JM, Fuku N, Tanaka M, Llop E ...
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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...: 904907. Chapman SJ, Hill AV. 2012. Human genetic susceptibility to infectious disease. Nat Rev Genet 13: 175188. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. 2009. BreakDancer: an algorithm for high-resolution mapping of genomic ...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...), and the Chongqing Foundation of Agricultural Development (12404 and 14409). Author contributions:Mingz. L., S.T., J.W., R.L., andX.L. led the experiments and designed the analytical strategy. L.C., D.L., A.J., Yingk. L., S.S., L.Z., Y.J., and L.B. performed animal work and prepared biological samples. L.J., J.M., X ...
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Research: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo
- Andrew E.O. Hughes,
- Connie A. Myers,
- and Joseph C. Corbo
Genome Res. October 2018 28: 1520-1531; Published in Advance August 29, 2018, doi:10.1101/gr.231886.117
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
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Research: Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence
- Christelle Lenain,
- Carolyn A. de Graaf,
- Ludo Pagie,
- Nils L. Visser,
- Marcel de Haas,
- Sandra S. de Vries,
- Daniel Peric-Hupkes,
- Bas van Steensel,
- and Daniel S. Peeper
Genome Res. October 2017 27: 1634-1644; Published in Advance September 15, 2017, doi:10.1101/gr.225763.117
...barrier in lymphoma development. Nature 436: 660665. Bridger JM, Boyle S, Kill IR, BickmoreWA. 2000. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol 10: 149152. Burckstummer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N ...
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Method: Optimizing sparse sequencing of single cells for highly multiplex copy number profiling
- Timour Baslan,
- Jude Kendall,
- Brian Ward,
- Hilary Cox,
- Anthony Leotta,
- Linda Rodgers,
- Michael Riggs,
- Sean D'Italia,
- Guoli Sun,
- Mao Yong,
- Kristy Miskimen,
- Hannah Gilmore,
- Michael Saborowski,
- Nevenka Dimitrova,
- Alexander Krasnitz,
- Lyndsay Harris,
- Michael Wigler,
- and James Hicks
Genome Res. May 2015 25: 714-724; Published in Advance April 9, 2015, doi:10.1101/gr.188060.114
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