Publications

Paper Application
Emily Breeze, Elizabeth Harrison, Stuart McHattie, Linda Hughes, Richard Hickman, Claire Hill, Steven Kiddle, Youn-sung Kim, Christopher A. Penfold, Dafyd Jenkins, Cunjin Zhang, Karl Morris, Carol Jenner, Stephen Jackson, Brian Thomas, Alexandra Tabrett, Roxane Legaie, Jonathan D. Moore, David L. Wild, Sascha Ott, David Rand, Jim Beynon, Katherine Denby, Andrew Mead, and Vicky Buchanan-Wollaston. High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation. The Plant Cell, 2011. doi:10.1105/tpc.111.083345 Gradient Tool
Jason Piper, Markus C. Elze, Pierre Cauchy, Peter N. Cockerill, Constanze Bonifer, and Sascha Ott. Wellington: A Novel Method for the Accurate Identification of Digital Genomic Footprints from DNase-Seq Data. Nucleic Acids Research, 2013. doi:10.1093/nar/gkt850 Wellington-footprint
Jason Piper, Salam A Assi, Pierre Cauchy, Christophe Ladroue, Peter N Cockerill, Constanze Bonifer, and Sascha Ott. Wellington-Bootstrap: Differential DNase-Seq Footprinting Identifies Cell-Type Determining Transcription Factors. BMC Genomics, 2015. doi:10.1186/s12864-015-2081-4 Wellington-bootstrap
Ian J. Mackay, Pauline Bansept-Basler, Toby Barber, Alison R. Bentley, James Cockram, Nick Gosman, Andy J. Greenland, Richard Horsnell, Rhian Howells, Donal M. O’Sullivan, Gemma A. Rose, and Phil J. Howell. Multiparental Populations: An Eight-Parent Multiparent Advanced Generation Inter-Cross Population for Winter-Sown Wheat: Creation, Properties, and Validation, G3, 2014. doi:10.1534/g3.114.012963
Ramirez-Gonzalez, R.H., Uauy, C. and Caccamo, M. PolyMarker: A fast polyploid primer design pipeline., Bioinformatics, 2015. In press. doi:10.1093/bioinformatics/btv069
Emily Breeze, Elizabeth Harrison, Stuart McHattie, Linda Hughes, Richard Hickman, Claire Hill, Steven Kiddle, Youn-sung Kim, Christopher A. Penfold, Dafyd Jenkins, Cunjin Zhang, Karl Morris, Carol Jenner, Stephen Jackson, Brian Thomas, Alexandra Tabrett, Roxane Legaie, Jonathan D. Moore, David L. Wild, Sascha Ott, David Rand, Jim Beynon, Katherine Denby, Andrew Mead, and Vicky Buchanan-Wollaston, High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation, Plant Cell, 2011, doi: 10.1105/tpc.111.083345 HMT
Nathaniel J. Davies, Peter Krusche, Eran Tauber and Sascha Ott, Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals, BMC Evolutionary Biology, doi: 10.1186/s12862-015-0499-6 APPLES – Conservation Tool
Laura Baxter, Aleksey Jironkin, Richard Hickman, Jay Moore, Christopher Barrington, Peter Krusche, Nigel P. Dyer, Vicky Buchanan-Wollaston, Alexander Tiskin, Jim Beynon, Katherine Denby, and Sascha Ott, Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants, Plant Cell, 2012, doi:10.1105/tpc.112.103010 APPLES – Conservation Tool
Krzysztof Polanski, Johanna Rhodes, Claire Hill, Peijun Zhang, Dafyd J. Jenkins, Steven J. Kiddle, Aleksey Jironkin, Jim Beynon, Vicky Buchanan-Wollaston, Sascha Ott and Katherine J. Denby, Wigwams: identifying gene modules co-regulated across multiple biological conditions, Bioinformatics, 2014, doi:10.1093/bioinformatics/btt728 Wigwams
Emma J Cooke, Richard S Savage, Paul DW Kirk, Robert Darkins and David L Wild, Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements, BMC Bioinformatics, 2011, doi: 10.1186/1471-2105-12-399 BHC
Christopher A. Penfold, David L. Wild, How to infer gene networks from expression profiles, revisited, Interface Focus, 2011, doi: 10.1098/rsfs.2011.0053 CSI
Christopher A. Penfold, Vicky Buchanan-Wollaston, Katherine J. Denby, and David L. Wild, Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks, Bioinformatics, 2012, doi:10.1093/bioinformatics/bts222 hCSI
Christopher A. Penfold, Jonathan B. A. Millar and David L. Wild, Inferring orthologous gene regulatory networks using interspecies data fusion, Bioinformatics, 2015, 10.1093/bioinformatics/btv267 OCSI
Steven J. Kiddle, Oliver P. F. Windram, Stuart McHattie, Andrew Mead, Jim Beynon, Vicky Buchanan-Wollaston, Katherine J. Denby, and Sach Mukherjee, Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana, Bioinformatics, 2010, doi:10.1093/bioinformatics/btp673 TCAP
Oliver Stegle, Katherine J. Denby, Emma J. Cooke, David L. Wild, Zoubin Ghahramani, and Karsten M. Borgwardt, A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series, Journal of Computational Biology, 2010. doi:10.1089/cmb.2009.0175. GP2S