LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Roller M, Stamper E, Villar D, Izuogu O, Martin F, Redmond AM, Ramachanderan R, Harewood L, Odom DT, Flicek P. Genome Biol. 2021. 22(1):62. Supporting data.
Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome
Í Kongsstovu S, Dahl HA, Gislason H, Homrum E, Jacobsen JA, Flicek P, Mikalsen SO. J Fish Biol. 2020. 97(1):190-201. Supporting data.
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Genome Biol. 2020. 21(1):5. Supporting data.
Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly
Í Kongsstovu S, Mikalsen SO, Homrum EÍ, Jacobsen JA, Flicek P, Dahl HA. Sci Rep. 2019. 9(1):17716. Supporting data.
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Genome Res. 2018. 28(4):448-459. Supporting data.
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Nat Ecol Evol. 2018. 2(1):152-163. Supporting data.
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Nat Commun. 2017. 8(1):1092. Supporting data.
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
Rensch T, Villar D, Horvath J, Odom DT, Flicek P. Genome Biol. 2016. 17(1):139. Supporting data.
Enhancer evolution across twenty mammalian species
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Cell. 2015. 160(3):554-66. Supporting data.
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Genome Res. 2015. 25(2):167-78. Supporting data.
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Genome Biol. 2013. 14(12):R148. Supporting data.
Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cell. 2013. 154(3):530-40. Supporting Data.
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Genome Res. 2012. 22(11):2163-75.
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Cell. 2012, 148(1-2):335-48.
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. Science. 2010. 328(5981):1036-40. Supporting data