Petra Schwalie

PhD Student 2008-2012

University of Cambridge and EMBL-EBI

Publications

• MC Ward, MD Wilson, NL Barbosa-Morais, D Schmidt, R Stark, Q Pan, PC Schwalie, S Menon, M Lukk, S Watt, D Thybert, C Kutter, K Kirschner, P Flicek, BJ Blencowe, DT Odom. Latent regulatory potential of human-specific repetitive elements. Mol Cell 2013;49(2):262–272. doi:10.1016/j.molcel.2012.11.013
• PC Schwalie, MC Ward, CE Cain, AJ Faure, Y Gilad, DT Odom, P Flicek. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol 2013;14(12):R148. doi:10.1186/gb-2013-14-12-r148
• T Schauer, PC Schwalie, A Handley, CE Margulies, P Flicek, AG Ladurner. CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System. Cell Rep 2013;5(1):271–282. doi:10.1016/j.celrep.2013.09.001
• A Scally, JY Dutheil, LW Hillier, GE Jordan, I Goodhead, J Herrero, A Hobolth, T Lappalainen, T Mailund, T Marques-Bonet, S McCarthy, SH Montgomery, PC Schwalie, YA Tang, MC Ward, Y Xue, B Yngvadottir, C Alkan, LN Andersen, Q Ayub, EV Ball, K Beal, BJ Bradley, Y Chen, CM Clee, S Fitzgerald, TA Graves, Y Gu, P Heath, A Heger, E Karakoc, A Kolb-Kokocinski, GK Laird, G Lunter, S Meader, M Mort, JC Mullikin, K Munch, TD O’Connor, AD Phillips, J Prado-Martinez, AS Rogers, S Sajjadian, D Schmidt, K Shaw, JT Simpson, PD Stenson, DJ Turner, L Vigilant, AJ Vilella, W Whitener, B Zhu, DN Cooper, de P Jong, ET Dermitzakis, EE Eichler, P Flicek, N Goldman, NI Mundy, Z Ning, DT Odom, CP Ponting, MA Quail, OA Ryder, SM Searle, WC Warren, RK Wilson, MH Schierup, J Rogers, C Tyler-Smith, R Durbin. Insights into hominid evolution from the gorilla genome sequence. Nature 2012;483(7388):169–175. doi:10.1038/nature10842
• AJ Faure, D Schmidt, S Watt, PC Schwalie, MD Wilson, H Xu, RG Ramsay, DT Odom, P Flicek. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Res 2012;22(11):2163–2175. doi:10.1101/gr.136507.111
• D Schmidt, PC Schwalie, MD Wilson, B Ballester, A Gonçalves, C Kutter, GD Brown, A Marshall, P Flicek, DT Odom. Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages. Cell 2012;148(1-2):335–348. doi:10.1016/j.cell.2011.11.058
• D Schmidt, MD Wilson, B Ballester, PC Schwalie, GD Brown, A Marshall, C Kutter, S Watt, CP Martinez-Jimenez, S Mackay, I Talianidis, P Flicek, DT Odom. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding. Science 2010;328(5981):1036–1040. doi:10.1126/science.1186176