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[50] Richard M Leggett and Dan MacLean (2014) Reference-free SNP detection: Dealing with the Data Deluge BMC Genomics In Press.
[49] Dan MacLean (2014) Out of the woods. Ash dieback and the future of emergent pathogenomics Molecular Plant Pathology vol. 1 pp. 1--4 doi:10.1111/mpp.12086 LINK
[48] Shunichi Kosugi, Satoshi Natsume, Kentaro Yoshida, Dan MacLean, Liliana Cano, Sophien Kamoun and Ryohei Terauchi (2013) Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data PloS ONE vol. 10 pp. e75402 doi:10.1371/journal.pone.0075402 LINK
[47] Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga {\'S}liwka, Leighton Pritchard, Graham J Etherington, Dan MacLean, Peter J Cock, Richard M Leggett, Glenn J Bryan and others (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations The Plant Journal vol. 3 pp. 530--544 doi:10.1111/tpj.12307 LINK
[46] Dan MacLean, Kentaro Yoshida, Anne Edwards, Lisa Crossman, Bernardo Clavijo, Matt Clark, David Swarbreck, Matthew Bashton, Patrick Chapman, Mark Gijzen and others (2013) Crowdsourcing genomic analyses of ash and ash dieback-power to the people GigaScience vol. 1 pp. 2 doi:10.1186/2047-217X-2-2 LINK
[45] Liliana M Cano, Sylvain Raffaele, Riston H Haugen, Diane GO Saunders, Lauriebeth Leonelli, Dan MacLean, Saskia A Hogenhout and Sophien Kamoun (2013) Major Transcriptome Reprogramming Underlies Floral Mimicry Induced by the Rust Fungus Puccinia monoica in Boechera stricta PloS ONE vol. 9 pp. e75293 doi:10.1371/journal.pone.0075293 LINK
[44] Dario Cantu, Vanesa Segovia, Dan MacLean, Rosemary Bayles, Xianming Chen, Sophien Kamoun, Jorge Dubcovsky, Diane GO Saunders and Cristobal Uauy (2013) Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors BMC Genomics vol. 1 pp. 270 doi:10.1186/1471-2164-14-270 LINK
[43] Rhys A Farrer, Daniel A Henk, Dan MacLean, David J Studholme and Matthew C Fisher (2013) Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects Scientific Reports pp. doi:doi:10.1038/srep01512 LINK
[42] Graham J Etherington and Dan MacLean (2013) SVGenes: a library for rendering genomic features in scalable vector graphic format Bioinformatics vol. 15 pp. 1890--1892 doi:10.1093/bioinformatics/btt294 LINK
[41] Richard M Leggett, Ricardo H Ramirez-Gonzalez, Walter Verweij, Cintia G Kawashima, Zamin Iqbal, Jonathan DG Jones, Mario Caccamo and Dan MacLean (2013) Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs PloS ONE vol. 3 pp. e60058 doi:10.1371/journal.pone.0060058 LINK
[40] Dan MacLean (2013) Changing the rules of the game eLife pp. doi:10.7554/eLife.01294 LINK
[39] Ricardo Ramirez-Gonzalez, Raoul JP Bonnal, Mario Caccamo, Dan MacLean and others (2012) Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. Source Code for Biology and Medicine vol. 6 pp. doi:10.1186/1751-0473-7-6 LINK
[38] Raoul JP Bonnal, Jan Aerts, George Githinji, Naohisa Goto, Dan MacLean, Chase A Miller, Hiroyuki Mishima, Massimiliano Pagani, Ricardo Ramirez-Gonzalez, Geert Smant and others (2012) Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics Bioinformatics vol. 7 pp. 1035--1037 doi:10.1093/bioinformatics/bts080 LINK
[37] Dan MacLean and Sophien Kamoun (2012) Big data in small places Nature Biotechnology vol. 1 pp. 33--34 doi:10.1038/nbt.2079 LINK
[36] GJ Etherington and D MacLean (2012) BIOINFORMATIK-Analyse von Next Generation-Sequenzierungsdaten BIOforum-Forschung und Entwicklung vol. 1 pp. 34
[35] David EL Cooke, Liliana M Cano, Sylvain Raffaele, Ruairidh A Bain, Louise R Cooke, Graham J Etherington, Kenneth L Deahl, Rhys A Farrer, Eleanor M Gilroy, Erica M Goss and others (2012) Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen PLoS Pathogens vol. 10 pp. e1002940 doi:10.1371/journal.ppat.1002940 LINK
[34] Martina Beck, Ji Zhou, Christine Faulkner, Dan MacLean and Silke Robatzek (2012) Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting The Plant Cell Online vol. 10 pp. 4205--4219 doi:10.1105/tpc.112.100263 LINK
[33] John Walshaw, Graham J Etherington and Dan MacLean (2011) Next-Generation Sequencing Approaches to Metagenomics Metagenomics: Current Innovations and Future Trends pp. 63
[32] Dent Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo, Daniel R Zerbino, Mark Diekhans and others (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods Genome Research vol. 12 pp. 2224--2241 doi:10.1101/gr.126599.111 LINK
[31] Eric Kemen, Anastasia Gardiner, Torsten Schultz-Larsen, Ariane C Kemen, Alexi L Balmuth, Alexandre Robert-Seilaniantz, Kate Bailey, Eric Holub, David J Studholme, Dan MacLean and others (2011) Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana PLoS Biology vol. 7 pp. e1001094 doi:10.1371/journal.pbio.1001094 LINK
[30] JP Carr, Mathew Lewsey, J Westwood, Heiko Ziebell, Dan MacLean, A Kleczkowski, M Stevens and John A Walsh (2011) The effects of cucumber mosaic virus 2b protein on methyl jasmonate induced transcriptional responses and plant-aphid interactions in Arabidopsis Proceedings of the 27th Annual Meeting of American Society for Virology pp.
[29] Ricardo Ramirez-Gonzalez, Mario Caccamo and Dan MacLean (2011) Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data Bioinformatics vol. 19 pp. 2754--2755 doi:10.1093/bioinformatics/btr442 LINK
[28] Alexandre Robert-Seilaniantz, Dan MacLean, Yusuke Jikumaru, Lionel Hill, Shinjiro Yamaguchi, Yuji Kamiya and Jonathan DG Jones (2011) The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates The Plant Journal vol. 2 pp. 218--231 doi:10.1111/j.1365-313X.2011.04591.x LINK
[27] Dan MacLean, Vincent Moulton and David J Studholme (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS BMC Bioinformatics vol. 1 pp. 93 doi:10.1186/1471-2105-11-93 LINK
[26] Dan MacLean and David J Studholme (2010) A boolean model of the pseudomonas syringae hrp regulon predicts a tightly regulated system PloS ONE vol. 2 pp. e9101 doi:10.1371/journal.pone.0009101 LINK
[25] Mathew G Lewsey, Alex M Murphy, Dan MacLean, Neil Dalchau, Jack H Westwood, Keith Macaulay, Mark H Bennett, Michael Moulin, David E Hanke, Glen Powell and others (2010) Disruption of two defensive signaling pathways by a viral RNA silencing suppressor Molecular Plant-Microbe Interactions vol. 7 pp. 835--845 doi:10.1094/MPMI-23-7-0835 LINK
[24] David J Studholme, Eric Kemen, Dan MacLean, Sebastian Schornack, Valente Aritua, Richard Thwaites, Murray Grant, Julian Smith and Jonathan DG Jones (2010) Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt FEMS Microbiology Letters vol. 2 pp. 182--192 doi:10.1111/j.1574-6968.2010.02065.x LINK
[23] Dan MacLean, Nataliya Elina, Ericka R Havecker, Susanne B Heimstaedt, David J Studholme and David C Baulcombe (2010) Evidence for large complex networks of plant short silencing RNAs PLoS One vol. 3 pp. e9901 doi:10.1371/journal.pone.0009901 LINK
[22] Sylviane Comparot-Moss, Oliver K{\"o}tting, Michaela Stettler, Christoph Edner, Alexander Graf, Sean E Weise, Sebastian Streb, Wei-Ling Lue, Dan MacLean, Sebastian Mahlow and others (2010) A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves Plant Physiology vol. 2 pp. 685--697 doi:10.1104/pp.109.148981 LINK
[21] Sylvain Raffaele, Rhys A Farrer, Liliana M Cano, David J Studholme, Dan MacLean, Marco Thines, Rays HY Jiang, Michael C Zody, Sridhara G Kunjeti, Nicole M Donofrio and others (2010) Genome evolution following host jumps in the Irish potato famine pathogen lineage Science vol. 6010 pp. 1540--1543 doi:10.1126/science.1193070 LINK
[20] Pawel Durek, Robert Schmidt, Joshua L Heazlewood, Alexandra Jones, Dan MacLean, Axel Nagel, Birgit Kersten and Waltraud X Schulze (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update Nucleic Acids Research vol. suppl 1 pp. D828--D834 doi:10.1093/nar/gkp810 LINK
[19] MG Lewsey, AM Murphy, D MacLean, N Dalchau, J Westwood, K Macaulay, MH Bennett, M Moulin, DE Hanke, G Powell and others (2010) Disruption of the salicylate and jasmonate signaling pathways by the cucumber mosaic virus 2b RNA silencing suppressor vol. 6 pp. S70--S70
[18] Susanne Salomon, Dorit Grunewald, Kurt St{\"u}ber, Sebastian Schaaf, Dan MacLean, Paul Schulze-Lefert and Silke Robatzek (2010) High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis Plant Physiology vol. 3 pp. 1096--1104 doi:10.1104/pp.110.160325 LINK
[17] Dan MacLean and David J Studholme (2009) Bioinformatics aspects of high-throughput sequencing technology pp. 311
[16] Alexandra ME Jones, Dan MacLean, David J Studholme, Antonio Serna-Sanz, Erik Andreasson, John P Rathjen and Scott C Peck (2009) Phosphoproteomic analysis of nuclei-enriched fractions from< i> Arabidopsis thaliana Journal of Proteomics vol. 3 pp. 439--451 doi:10.1016/j.jprot.2009.02.004 LINK
[15] Brian J Haas, Sophien Kamoun, Michael C Zody, Rays HY Jiang, Robert E Handsaker, Liliana M Cano, Manfred Grabherr, Chinnappa D Kodira, Sylvain Raffaele, Trudy Torto-Alalibo and others (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans Nature vol. 7262 pp. 393--398 doi:doi:10.1038/nature08358 LINK
[14] Dan MacLean, Jonathan DG Jones and David J Studholme (2009) Application of 'next-generation' sequencing technologies to microbial genetics Nature Reviews Microbiology vol. 4 pp. 287--296 doi:doi:10.1038/nrmicro2088 LINK
[13] David J Studholme, Selena G Ibanez, Dan MacLean, Jeffery L Dangl, Jeff H Chang and John P Rathjen (2009) A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528 BMC Genomics vol. 1 pp. 395 doi:10.1186/1471-2164-10-395 LINK
[12] Nalvo F Almeida, Shuangchun Yan, Magdalen Lindeberg, David J Studholme, David J Schneider, Bradford Condon, Haijie Liu, Carlos J Viana, Andrew Warren, Clive Evans and others (2009) A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000 Molecular Plant-Microbe Interactions vol. 1 pp. 52--62 doi:10.1094/MPMI-22-1-0052 LINK
[11] Vladimir T Valkov, Nunzia Scotti, Sabine Kahlau, Dan MacLean, Stefania Grillo, John C Gray, Ralph Bock and Teodoro Cardi (2009) Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control Plant Physiology vol. 4 pp. 2030--2044 doi:10.1104/pp.109.140483 LINK
[10] Dan MacLean, Cheryl A Jerome, Anthony PC Brown and John C Gray (2008) Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis Plant Molecular Biology vol. 5 pp. 475--490 doi:10.1007/s11103-007-9279-z LINK
[9] Simon Moxon, Frank Schwach, Tamas Dalmay, Dan MacLean, David J Studholme and Vincent Moulton (2008) A toolkit for analysing large-scale plant small RNA datasets Bioinformatics vol. 19 pp. 2252--2253 doi:10.1093/bioinformatics/btn428 LINK
[8] Amanda J Cottage, Ellie K Mott, Jun-Hui Wang, James A Sullivan, Dan MacLean, Linh Tran, Mun-Kit Choy, Christine Newell, Tony A Kavanagh, Sue Aspinall and others (2008) GUN1 (GENOMES UNCOUPLED1) encodes a pentatricopeptide repeat (PPR) protein involved in plastid protein synthesis-responsive retrograde signaling to the nucleus pp. 1201--1205
[7] Dan MacLean, Michael A Burrell, David J Studholme and Alexandra ME Jones (2008) PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data BMC Research Notes vol. 1 pp. 30 doi:10.1186/1756-0500-1-30 LINK
[6] Harrold A Burg, Dimitrios I Tsitsigiannis, Owen Rowland, Jane Lo, Ghanasyam Rallapalli, Dan MacLean, Frank LW Takken and Jonathan DG Jones (2008) The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato The Plant Cell Online vol. 3 pp. 697--719 doi:10.1105/tpc.107.056978 LINK
[5] Alan M Magee, Dan MacLean, John C Gray and Tony A Kavanagh (2007) Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development Transgenic Research vol. 4 pp. 415--428 doi:10.1007/s11248-006-9045-z LINK
[4] Elena Anastasiou, Sabine Kenz, Moritz Gerstung, Dan MacLean, Jens Timmer, Christian Fleck and Michael Lenhard (2007) Control of Plant Organ Size by< i> KLUH/< i> CYP78A5-Dependent Intercellular Signaling Developmental Cell vol. 6 pp. 843--856 doi:doi:10.1016/j.devcel.2007.10.001 LINK
[3] J Gray, A Cottage, E Mott and D MacLean (2006) Coordinating chloroplast, mitochondrial and nuclear gene expression vol. 4 pp. S155--S155
[2] Yii Leng Chua, Ellie Mott, Anthony PC Brown, Dan MacLean and John C Gray (2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones The Plant Journal vol. 6 pp. 789--800 doi:10.1111/j.1365-313X.2004.02007.x LINK
[1] John C Gray, James A Sullivan, Jun-Hui Wang, Cheryl A Jerome and Dan MacLean (2003) Coordination of plastid and nuclear gene expression Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences vol. 1429 pp. 135--145 doi:10.1098/rstb.2002.1180 LINK

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