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Method: Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
- Seyed Ali Madani Tonekaboni,
- Parisa Mazrooei,
- Victor Kofia,
- Benjamin Haibe-Kains,
- and Mathieu Lupien
Genome Res. October 2019 29: 1733-1743; Published in Advance September 18, 2019, doi:10.1101/gr.248658.119
...suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell 159: 11261139. doi:10.1016/j.cell.2014.10.024 Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, et al. 2018. The chromatin accessibility landscape of primary human cancers ...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
.... doi:10.3791/52246 Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, et al. 2010. A map of open chromatin in human pancreatic islets. Nat Genet 42: 255259. doi:10.1038/ng.530 Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp ...
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In memoriam: Sydney Brenner—a personal perspective
- Byrappa Venkatesh
Genome Res. June 2019 29: vii-ix; doi:10.1101/gr.251918.119
...conserved regulatory elements with the model of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci 92: 16841688. doi:10.1073/pnas.92.5.1684 Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. 2002. Whole- shotgun assembly and analysis ...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...376. Axelsson E, Ratnakumar A, Arendt M-L, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K. 2013. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495: 360364. Brsch-Haubold AG, Montero I, Konrad K, Haubold B. 2014. Genome ...
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Research: An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
- Djivan Prentout,
- Olga Razumova,
- Bénédicte Rhoné,
- Hélène Badouin,
- Hélène Henri,
- Cong Feng,
- Jos Käfer,
- Gennady Karlov,
- and Gabriel A.B. Marais
Genome Res. February 2020 30: 164-172; Published in Advance February 7, 2020, doi:10.1101/gr.251207.119
...://creativecommons.org/licenses/by-nc/4.0/.References Ahmed S, Cock JM, Pessia E, Luthringer R, Cormier A, Robuchon M, Sterck L, Peters AF, Dittami SM, Corre E, et al. 2014. A haploid system of sex determination in the brown alga Ectocarpus sp. Curr Biol 24: 19451957. doi:10.1016/j.cub.2014.07.042 Alexander SP. 2016. Therapeutic ...
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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
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Research: LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- Jan Attig,
- George R. Young,
- Louise Hosie,
- David Perkins,
- Vesela Encheva-Yokoya,
- Jonathan P. Stoye,
- Ambrosius P. Snijders,
- Nicola Ternette,
- and George Kassiotis
Genome Res. October 2019 29: 1578-1590; Published in Advance September 19, 2019, doi:10.1101/gr.248922.119
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Method: Identifying loci under positive selection in complex population histories
- Alba Refoyo-Martínez,
- Rute R. da Fonseca,
- Katrín Halldórsdóttir,
- Einar Árnason,
- Thomas Mailund,
- and Fernando Racimo
Genome Res. September 2019 29: 1506-1520; Published in Advance July 30, 2019, doi:10.1101/gr.246777.118
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Method: Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
- Timothy M. Freeman,
- Genomics England Research Consortium,
- Dennis Wang,
- and Jason Harris
Genome Res. March 2020 30: 415-426; Published in Advance March 10, 2020, doi:10.1101/gr.255349.119
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Research: Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation
- Tingting Guo,
- Qi Mu,
- Jinyu Wang,
- Adam E. Vanous,
- Akio Onogi,
- Hiroyoshi Iwata,
- Xianran Li,
- and Jianming Yu
Genome Res. May 2020 30: 673-683; Published in Advance April 16, 2020, doi:10.1101/gr.255703.119
...to Heilongjiang Province, northern limit of China. J Integr Plant Biol 57: 698707. doi:10.1111/jipb.12326 Li X, Guo TT, Mu Q, Li XR, Yu JM. 2018. Genomic and environmental determinants and their interplay underlying phenotypic plasticity. Proc Natl Acad Sci 115: 66796684. doi:10.1073/pnas.1718326115 Ma JF ...

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