Journal Article

Achtman, Mark (2016) How old are bacterial pathogens? Proceeding of the Royal Society B, 286 (1836).

Achtman, Mark (2011) A broad brush, global overview of bacterial sexuality. PLoS Genetics, Volume 7 (Number 8). Article number e1002255. doi:10.1371/journal.pgen.1002255

Achtman, Mark, Wain, John, Weill, François-Xavier, Nair, Satheesh, Zhou, Zhemin, Sangal, Vartul, Krauland, Mary G., Hale, James L., Harbottle, Heather, Uesbeck, Alexandra, Dougan, Gordon, Harrison, Lee H. and Brisse, Sylvain (2012) Multilocus sequence typing as a replacement for serotyping in salmonella enterica. PLoS Pathogens, Volume 8 (Number 6). Article number e1002776. doi:10.1371/journal.ppat.1002776

Achtman, Mark and Zhou, Zhemin (2014) Distinct genealogies for plasmids and chromosome. PLoS Genetics, Volume 10 (Number 12). Article number e1004874. doi:10.1371/journal.pgen.1004874

Adams, Sally, Pathak, Prachi, Shao, Hongguang, Lok, James B. and Pires-da Silva, André Francisco (2019) Liposome-based transfection enhances RNAi and CRISPR-1 mediated mutagenesis in non-model nematode systems. Scientific Reports, 9 . 483. doi:10.1038/s41598-018-37036-1

Agoti, Charles N., Gitahi, Caroline W., Medley, Graham, Cane, Patricia and Nokes, D. James (2013) Identification of group B respiratory syncytial viruses that lack the 60-nucleotide duplication after six consecutive epidemics of total BA dominance at coastal Kenya. Influenza and Other Respiratory Viruses, Volume 7 (Number 6). pp. 1008-1012. doi:10.1111/irv.12131

Alikhan, Nabil-Fareed, Petty, Nicola K., Ben Zakour, Nouri L. and Beatson, Scott A. (2011) BLAST Ring Image Generator (BRIG) : simple prokaryote genome comparisons. BMC Genomics, Volume 12 (Number 1). Article number 402. doi:10.1186/1471-2164-12-402

Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J. and Achtman, Mark (2018) A genomic overview of the population structure of Salmonella. PLoS Genetics, 14 (4). e1007261. doi:10.1371/journal.pgen.1007261

Allaby, Robin G. (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany, Vol.61 (No.4). pp. 935-944. doi:10.1093/jxb/erp382

Allaby, Robin G. and Woodwark, Mathew (2007) Phylogenomic analysis reveals extensive phylogenetic mosaicism in the Human GPCR Superfamily. Evolutionary Bioinformatics, Vol.3 . pp. 357-370.

Allender, Charlotte J. and King , Graham J. (2010) Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers. BMC Plant Biology, Vol.10 (Article 54). doi:10.1186/1471-2229-10-54

Apta-Smith, Michael James, Hernandez Fernaud, Juan Ramon and Bowman, Andrew J. (2018) Evidence for the nuclear import of histones H3.1 & H4 as monomers. EMBO Journal, 37 (19). e98714. doi:10.15252/embj.201798714

(2018) The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water. BMC Genomics, 19 (1). 832. doi:10.1186/s12864-018-5163-2

Barnett, James P., Millard, Andrew D., Ksibe, Amira Z., Scanlan, David J., Schmid, Ralf and Blindauer, Claudia A. (2012) Mining genomes of marine cyanobacteria for elements of zinc homeostasis. Frontiers in Microbiology, Volume 3 . Article number 142. doi:10.3389/fmicb.2012.00142

(2011) Association between Prostinogen (KLK15) genetic variants and prostate cancer risk and aggressiveness in Australia and a meta-analysis of GWAS data. PLoS ONE, Vol.6 (No.11). e26527. doi:10.1371/journal.pone.0026527

Australian Ovarian Cancer Study Group, Peter MacCallum Hospital (Melbourne, Vic.). Cancer Institute, Ovarian Cancer Association (Including:

). (2011) Functional polymorphisms in the TERT promoter are associated with risk of serous epithelial ovarian and breast cancers. PLoS ONE, Vol.6 (No.9). doi:10.1371/journal.pone.0024987

Bingle, Lewis E. H., Constantinidou, Chrystala, Shaw, Robert K., Islam, Md. Shahidul, Patel, Mala, Snyder, Lori A. S., Lee, David J., Penn, C. W., Busby, Stephen J. W. and Pallen, Mark J. (2014) Microarray analysis of the ler regulon in enteropathogenic and enterohaemorrhagic escherichia coli strains. PLoS One, Volume 9 (Number 1). e80160. doi:10.1371/journal.pone.0080160

Blanc-Mathieu, Romain, Verhelst, Bram, Derelle, Evelyne, Rombauts, Stephane, Bouget, François-Yves , Carré, Isabelle A., Château, Annie, Eyre-Walker, Adam, Grimsley, Nigel, Moreau, Hervé, Piégu, Benoit, Rivals, Eric , Schackwitz, Wendy, Peer, Yves van de and Piganeau, Gwenaël (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics, Volume 15 . pp. 1-11. Article number 1103. doi:10.1186/1471-2164-15-1103

Blin, Kai, Wolf, Thomas, Chevrette, Marc G., Lu, Xiaowen, Schwalen, Christopher J., Kautsar, Satria A., Suarez Duran, Hernando G., Emmanuel de los Santos, L. C., Kim, Hyun Uk, Nave, Mariana, Dickschat, Jeroen S., Mitchell, Douglas A., Shelest, Ekaterina, Breitling, Rainer, Takano, Eriko, Lee, Sang Yup, Weber, Tilmann and Medema, Marnix H. (2017) antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Research . doi:10.1093/nar/gkx319

Bowyer, Jack E., Hsiao, Victoria, Wong, Wilson W. and Bates, Declan (2017) Mechanistic modelling of a recombinase-based two-input temporal logic gate. Engineering Biology, 1 (1). pp. 40-50. doi:10.1049/enb.2017.0006

Bowyer, Jack E., Zhao, Jia, Subsoontorn, Pakpoom, Wong, Wilson, Rosser, Susan and Bates, Declan (2016) Mechanistic modeling of a rewritable recombinase addressable data module. IEEE Transactions on Biomedical Circuits and Systems, 10 (6). pp. 1161-1170. doi:10.1109/TBCAS.2016.2526668

Brodel, Andreas K., Jaramillo, Alfonso and Isalan, Mark (2016) Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nature Communications, 7 . 13858 . doi:10.1038/ncomms13858

(2014) Uterine selection of human embryos at implantation. Scientific Reports, Volume 4 . Article number 3894. doi:10.1038/srep03894

Brown, Paul E., Baxter, Laura, Hickman, Richard J., Beynon, Jim, Moore, Jonathan D. and Ott, Sascha (2013) MEME-LaB : motif analysis in clusters. Bioinformatics . doi:10.1093/bioinformatics/btt248

Bräutigam, Katharina, Vining, Kelly J., Lafon-Placette, Clément, Fossdal, Carl G., Mirouze, Marie, Jose, Gutiérrez-Marcos, Fluch, Silvia, Fraga, Mario Fernández, Guevara, M. Ángeles, Abarca, Dolores, Johnsen, Øystein, Maury, Stéphane, Strauss, Steven H., Campbell, Malcolm M., Rohde, Antje, Díaz-Sala, Carmen and Cervera, María-Teresa (2013) Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecology and Evolution, Volume 3 (Number 2). pp. 399-415. doi:10.1002/ece3.461

Busi, R. (Roberto), Neve, Paul and Powles, Stephen B. (2013) Evolved polygenic herbicide resistance in Lolium rigidum by low-dose herbicide selection within standing genetic variation. Evolutionary Applications, Volume 6 (Number 2). pp. 231-242. doi:10.1111/j.1752-4571.2012.00282.x

Calvo-Bado, Leo A., Green, Laura E., Medley, Graham, Ul-Hassan, Atiya, Buller, Nicky B., Kaler, Jasmeet, Russell, Claire L., Kennan, Ruth M., Rood, Julian I., Wellington, E. M. H. and Grogono-Thomas, Rosemary (2010) Detection and diversity of a putative novel heterogeneous polymorphic proline-glycine repeat (Pgr) protein in the footrot pathogen Dichelobacter nodosus. Veterinary Microbiology, Vol.147 (No.3-4). pp. 358-366. doi:10.1016/j.vetmic.2010.06.024

Social Science Genetic Association Consortium (SSGAC) (Including: Cappuccio, Francesco). (2016) Genome-wide association study identifies 74 loci associated with educational attainment. Nature, 533 . pp. 539-542. doi:10.1038/nature17671

Carrera, Javier and Jaramillo, Alfonso (2013) Automated design of bacterial genome sequences. BMC Systems Biology, Volume 7 (Number 1). Article number 108. doi:10.1186/1752-0509-7-108

Carson, Connor, Antoniou, Maria, Begoña Ruiz-Argüello, Maria, Alcami, Antonio, Christodoulou, Vasiliki , Messaritakis, Ippokratis, Blackwell, Jenefer M. and Courtenay, Orin (2008) A prime/boost DNA/Modified vaccinia virus Ankara vaccine expressing recombinant Leishmania DNA encoding TRYP is safe and immunogenic in outbred dogs, the reservoir of zoonotic visceral leishmaniasis. Vaccine, Vol.27 (No.7). pp. 1080-1086. doi:10.1016/j.vaccine.2008.11.094

Carter, Anthony D., Bonyadi, Roxanna and Gifford, Miriam L. (2013) The use of fluorescence-activated cell sorting in studying plant development and environmental responses. The International Journal of Developmental Biology, Volume 57 . pp. 545-552. doi:10.1387/ijdb.130195mg

Castro, Thiago L. P., Seyffert, Nubia, Ramos, Rommel T. J., Barbosa, Silvanira, Carvalho, Rodrigo D. O., Pinto, Anne Cybelle, Carneiro, Adriana Ribeiro, Silva, Wanderson Marques, Pacheco, Luis G. C., Downson, Christopher G., Schneider, Maria P. C., Miyoshi, Anderson, Azevedo, V. (Vasco) and Silva, Artur (2013) Ion torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method. Microbial Biotechnology, Volume 6 (Number 2). pp. 168-177. doi:10.1111/1751-7915.12020

Cevik, Volkan, Ryder, Carol D., Popovich, Alexandra, Manning, Kenneth, King , Graham J. and Seymour, G. B. (Graham B.) (2010) A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.). Tree Genetics & Genomes, Vol.6 (No.2). pp. 271-279. doi:10.1007/s11295-009-0247-4

Chan, Andrew H., Jenkins, Paul and Song, Yun S. (2012) Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, Vol.8 (No.12). e1003090. doi:10.1371/journal.pgen.1003090

Chan, Jacqueline, Halachev, Mihail R., Loman, Nicholas J., Constantinidou, Chrystala and Pallen, Mark J. (2012) Defining bacterial species in the genomic era : insights from the genus Acinetobacter. BMC Microbiology, 12 (1). 302. doi:10.1186/1471-2180-12-302

Chan, Jacqueline, Millard, Andrew D., Mann, Nicholas H. and Schäfer, Hendrik (2014) Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Frontiers in Microbiology, Volume 5 . Article number 506. doi:10.3389/fmicb.2014.00506

Chan, Yi-Wah, Mohr, Remus, Millard, Andrew D., Holmes, Antony B., Larkum, Anthony W. D., Whitworth, Anna L., Mann, Nicholas H., Scanlan, David J., Hess, Wolfgang R. and Clokie, Martha R. J. (2011) Discovery of cyanophage genomes which contain mitochondrial DNA polymerase. Molecular Biology and Evolution, Vol.28 (No.8). pp. 2269-2274. doi:10.1093/molbev/msr041

The Genographic Consortium (Including: Clarke, Andrew C., Prost, Stefan, Stanton, Jo-Ann L., White, W Timothy J., Kaplan, Matthew E. and Matisoo-Smith, Lisa). (2014) From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics, Volume 15 (Number 1). Article number 68. doi:10.1186/1471-2164-15-68

Click, Arielle, Savaliya, Chandni H, Kienle, Simone, Herrmann, Matthias and Pires-da Silva, André Francisco (2009) Natural variation of outcrossing in the hermaphroditic nematode Pristionchus pacificus. BMC Evolutionary Biology, Volume 9 (Number 1). Article no.75. doi:10.1186/1471-2148-9-75

Clokie, Martha R. J., Millard, Andrew D. and Mann, Nicholas H. (2010) T4 genes in the marine ecosystem: studies of the T4-like cyanophages and their role in marine ecology. Virology Journal, Volume 7 . Article number 291. doi:10.1186/1743-422X-7-291

Constantinidou, Chrystala, Sergeant, Martin J., Cogan, Tristan, Penn, Charles W. and Pallen, Mark J. (2012) High-throughput sequencing of 16S rRNA gene amplicons : effects of extraction procedure, primer length and annealing temperature. PLoS One, Volume 7 (Number 5). Article number e38094. doi:10.1371/journal.pone.0038094

Dame, Remus T. (Remus Thei), Kalmykowa, Olga J. and Grainger, David C. (2011) Chromosomal macrodomains and associated proteins : implications for DNA organization and replication in gram negative bacteria. PLoS Genetics, Vol.7 (No.6). e1002123. doi:10.1371/journal.pgen.1002123

Darlington, Alexander P. S., Kim, Juhyun, Jiménez, José I. and Bates, Declan (2018) Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nature Communications, 9 (1). 695. doi:10.1038/s41467-018-02898-6

Davies, Lawrence O., Schäfer, Hendrik, Marshall, Samantha, Bramke, Irene, Oliver, Robin G. and Bending, G. D. (2013) Light structures phototroph, bacterial and fungal communities at the soil surface. PLoS One, Volume 8 (Number 7). Article number e69048. doi:10.1371/journal.pone.0069048

Davis, Seth J. and Millar, A. J. (Andrew J.) (2001) Watching the hands of the Arabidopsis biological clock. Genome Biology, Vol.2 (No.3). doi:10.1186/gb-2001-2-3-reviews1008

Dealtry, Simone, Ding, Guo-Chun, Weichelt, Viola, Dunon, Vincent, Schlüter, Andreas, Martini, María Carla, Papa, María Florencia Del, Lagares, Antonio, Amos, Gregory C. A., Wellington, E. M. H., Gaze, William H., Sipkema, Detmer, Sjöling, Sara, Springael, Dirk, Heuer, Holger, Elsas, J. D. van, Thomas, Christopher M. and Smalla, Kornelia (2014) Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats. PLoS One, Volume 9 (Number 2). Article number e89922. doi:10.1371/journal.pone.0089922

Devran, Z., Süğüt, M. A. , Gözel, U. , Tör, Mahmut and Elekçioglu, I. H. (2008) Analysis of genetic variation between populations of Meloidogyne spp. from Turkey. Russian Journal of Nematology, Vol.16 (No.2). pp. 143-149.

Didelot, Xavier, Bowden, Rory, Street, Teresa, Golubchik, Tanya, Spencer, Chris, McVean, Gil, Sangal, Vartul, Anjum, Muna F., Achtman, Mark, Falush, Daniel and Donnelly, Peter (2011) Recombination and population structure in salmonella enterica. PLoS Genetics, Volume 7 (Number 7). Article number e1002191. doi:10.1371/journal.pgen.1002191

Didelot, Xavier, Croucher, Nicholas J., Bentley, Stephen D., Harris, Simon R. and Wilson, Daniel J. (2018) Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Research . doi:10.1093/nar/gky783 (In Press)

Docherty, Sophia J., Davis, Oliver S. P., Haworth, Claire M. A., Plomin, Robert and Mill, Jonathan (2009) Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation. Epigenetics & Chromatin, Volume 2 . Article number 3.

Dowling, Andrea J., Wilkinson, Paul A., Holden, Matthew T. G., Quail, Michael A., Bentley, Stephen D., Reger, Julia, Waterfield, Nicholas R., Titball, Richard W. and ffrench-Constant, Richard H. (2010) Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen burkholderia pseudomallei K96243. PLoS One, Volume 5 (Number 12). Article number e15693. doi:10.1371/journal.pone.0015693

Dryer, Nigel P., Shahrazaie, Vahid and Hebenstreit, Daniel (2019) LiBiNorm : an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ, 7 . e6222. doi:10.7717/peerj.6222

Dugassa, Sisay, Lindh, Jenny M, Torr, Steve, Lindsay, Steven W and Fillinger, Ulrike (2014) Evaluation of the influence of electric nets on the behaviour of oviposition site seeking Anopheles gambiae s.s. Parasites & Vectors, Volume 7 (Number 1). Article number 272. doi:10.1186/1756-3305-7-272

Dunham, Lee S. S., Momiji, Hiroshi, Harper, Claire V., Downton, Polly J., Hey, Kirsty L., McNamara, Anne, Featherstone, Karen, Spiller, David G., Rand, David A., Finkenstädt, Bärbel, White, Michael R. H. and Davis, Julian R.E. (2017) Asymmetry between activation and deactivation during a transcriptional pulse. Cell Systems, 5 (6). 646-653.E5. doi:10.1016/j.cels.2017.10.013

(2013) Esperanto for histones : CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Research, Volume 21 (Number 2). pp. 101-106. doi:10.1007/s10577-013-9347-y

Eastwood, Daniel C., Mead, A. (Andrew), Sergeant, Martin J. and Burton, Kerry S. (2008) Statistical modelling of transcript profiles of differentially regulated genes. BMC Molecular Biology, Vol.9 (No.66). doi:10.1186/1471-2199-9-66

Elashry, Abdelnaser, Okumoto, Sakiko, Siddique, Shahid, Koch, Wolfgang, Kreil, David and Bohlmann, Holger (2013) The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis. Plant Physiology and Biochemistry, Volume 70 . pp. 379-386. doi:10.1016/j.plaphy.2013.05.016

(2013) Meeting report : 1st international functional metagenomics workshop May 7–8, 2012, St. Jacobs, Ontario, Canada. Standards in Genomic Sciences, Volume 8 (Number 1). pp. 106-111. doi:10.4056/sigs.3406845

Fabre, Laëtitia, Zhang, Jian, Guigon, Ghislaine, Le Hello, Simon, Guibert, Véronique, Accou-Demartin, Marie, de Romans, Saïana, Lim, Catherine, Roux, Chrystelle, Passet, Virginie, Diancourt, Laure, Guibourdenche, Martine, Issenhuth-Jeanjean, Sylvie, Achtman, Mark, Brisse, Sylvain, Sola, Christophe and Weill, François-Xavier (2012) CRISPR typing and subtyping for improved laboratory surveillance of salmonella infections. PLoS One, Volume 7 (Number 5). Article number e36995. doi:10.1371/journal.pone.0036995

Farrand, Benjamin Matthew (2016) Human embryonic stem cells and patent law in the EU and China : convergence in standards through divergence in institutions. Intellectual Property Quarterly, 3 . pp. 260-277.

Favaro, Stefano, Feng, Shui and Jenkins, Paul (2019) Bayesian nonparametric analysis of Kingman’s coalescent. Annales de l’Institut Henri Poincaré - Probabilites et Statistiques, 55 (2). pp. 1087-1115. doi:10.1214/18-AIHP910 (In Press)

Fearnhead, Paul, Jenkins, Paul and Song, Yun S. (2015) Tractable diffusion and coalescent processes for weakly correlated loci. Electronic Journal of Probability, Volume 20 . pp. 1-26. Article number 58. doi:10.1214/EJP.v20-3564

Featherstone, Katie, Hey, Kirsty L., Momiji, Hiroshi, McNamara, A. V., Patist, A. L., Woodburn, J., Spiller , D. G., Christian, H. C., McNeilly, A. S., Mullins, J. J. , Finkenstädt, Bärbel, Rand, D. A. (David A.), White, M. R. H. and David, J. R. E. (2016) Spatially coordinated dynamic gene transcription in living pituitary tissue. eLife, 5 . e08494.

Feng, Song, Ollivier, Julien F. and Soyer, Orkun S. (2016) Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Computational Biology, 12 (5). e1004918. doi:10.1371/journal.pcbi.1004918

Ferreira, Eunice A., Pacheco, Catarina C., Pinto, Filipe, Pereira, José, Lamosa, Pedro, Oliveira, Paulo, Kirov, Boris, Jaramillo, Alfonso and Tamagnini, Paula (2018) Expanding the toolbox for Synechocystis sp. PCC 6803 : validation of replicative vectors and characterization of a novel set of promoters. Synthetic Biology, 3 (1). ysy014. doi:10.1093/synbio/ysy014

Font-Burgada, Joan, Reina, Oscar, Rossell, David and Azorin, Fernando (2013) chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. Nucleic Acids Research, Volume 42 (Number 4). pp. 2126-2137. doi:10.1093/nar/gkt1186

Foo, Mathias, Kim, Jongrae and Bates, Declan (2018) Modelling and control of gene regulatory networks for perturbation mitigation. IEEE/ACM Transactions on Computational Biology and Bioinformatics . doi:10.1109/TCBB.2017.2771775 (In Press)

Galizi, Roberto and Jaramillo, Alfonso (2019) Engineering CRISPR guide RNA riboswitches for in vivo applications. Current Opinion in Biotechnology, 55 . pp. 103-113. doi:10.1016/j.copbio.2018.08.007

Ge, Tian, Feng, Jianfeng, Hibar, Derrek P., Thompson, Paul M. and Nichols, Thomas E. (2012) Increasing power for voxel-wise genome-wide association studies : the random field theory, least square kernel machines and fast permutation procedures. NeuroImage, Vol.63 (No.2). pp. 858-873. doi:10.1016/j.neuroimage.2012.07.012

Ge, Tian, Nichols, Thomas E., Lee, Phil H., Holmes, Avram J., Roffman, Joshua L., Buckner, Randy L., Sabuncu , Mert R. and Smoller, Jordan W. (2015) Massively expedited genome-wide heritability analysis (MEGHA). Proceedings of the National Academy of Sciences of the United States of America, Volume 112 (Number 8). pp. 2479-2484. doi:10.1073/pnas.1415603112

Ghafari , Fataneh, Gutierrez , Carlos G. and Hartshorne, Geraldine M. (2007) Apoptosis in mouse fetal and neonatal oocytes during meiotic prophase one. BMC Development Biology, Vol.7 . p. 87. doi:10.1186/1471-213X-7-87

Gifford, Miriam L., Banta, Joshua A., Katari, Manpreet S., Hulsmans, Jo, Chen, Lisa, Ristova, Daniela, Tranchina, Daniel, Purugganan, Michael D., Coruzzi, Gloria, Birnbaum, Kenneth D., Rosas, Ulises and Cibrian-Jaramillo, Angelica (2013) Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genetics, Volume 9 (Number 9). Article number e1003760. doi:10.1371/journal.pgen.1003760

Glaysher, Sharon, Yiannakis, Dennis, Gabriel, Francis G., Johnson, Penny, Polak, Marta E., Knight, Louise A., Goldthorpe, Zoe, Peregrin, Katharine, Gyi, Mya, Modi, Paul, Rahamim, Joe, Smith, Mark E., Amer, Khalil, Addis, B. J., Poole, Matthew, Narayanan, Ajit, Gulliford, Tim J., Andreotti, Peter Eugene and Cree, Ian A. (2009) Resistance gene expression determines the in vitro chemosensitivity of non-small cell lung cancer (NSCLC). BMC Cancer, Vol.9 (No.1). p. 300. doi:10.1186/1471-2407-9-300

Gonçalves Athanasio, Camila , Sommer, Ulf, Viant, Mark R., Chipman, James Kevin and Mirbahai, Leda (2018) Use of 5-azacytidine in a proof-of-concept study to evaluate the impact of pre-natal and post-natal exposures, as well as within generation persistent DNA methylation changes in Daphnia. Ecotoxicology, 27 (5). pp. 556-568. doi:10.1007/s10646-018-1927-3

Gould, Phillip S., Dyer, Nigel P., Croft, Wayne D., Ott, Sascha and Easton, A. J. (Andrew J.) (2014) Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism. RNA, 20 . pp. 373-381. doi:10.1261/rna.041574.113

Griffiths, Robert C., Jenkins, Paul and Lessard, Sabin (2016) A coalescent dual process for a Wright-Fisher diffusion with recombination and its application to haplotype partitioning. Theoretical Population Biology, 112 . pp. 126-138. doi:10.1016/j.tpb.2016.08.007

Halachev, Mihail R., Loman, Nicholas J. and Pallen, Mark J. (2011) Calculating orthologs in bacteria and archaea : a divide and conquer approach. PLoS One, Volume 6 (Number 12). Article number e28388. doi:10.1371/journal.pone.0028388

Harper, Claire V., Finkenstädt, Bärbel, Woodcock, Dan J., Friedrichsen, Sönke, Semprini, Sabrina, Ashall, Louise, Spiller, David G., Mullins, John J., Rand, D. A. (David A.), Davis, Julian R. E. and White, Michael R. H. (2011) Dynamic analysis of stochastic transcription cycles. PLos Biology, Vol.9 (No.4). doi:10.1371/journal.pbio.1000607

Harper, Claire V., Woodcock, Dan J., Lam, Connie, Garcia-Albornoz, Manuel, Adamson, Antony, Ashall, Louise, Rowe, William, Downton, Polly J., Schmidt, Lorraine, West, Simon, Spiller, David G., Rand, David A. and White, Michael R. H. (2018) Temperature regulates NF-κB dynamics and function through timing of A20 transcription. Proceedings of the National Academy of Sciences of the United States of America, 115 (22). E5243-E5249. doi:10.1073/pnas.1803609115

Hartmann, Manuela, Gómez-Pereira, Paola R., Grob, Carolina, Ostrowski, Martin, Scanlan, David J. and Zubkov, Mikhail V. (2014) Efficient CO2 fixation by surface Prochlorococcus in the Atlantic Ocean. The ISME Journal, Volume 8 (Number 11). pp. 2280-2289. doi:10.1038/ismej.2014.56

Haworth, Claire M. A. and Davis, Oliver S. P. (2014) From observational to dynamic genetics. Frontiers in Genetics, Volume 5 . Article number 6. doi:10.3389/fgene.2014.00006

Hebenstreit, Daniel (2012) Methods, challenges and potentials of single cell RNA-seq. Biology, Volume 1 (Number 3). pp. 658-667. doi:10.3390/biology1030658

Hey, Kirsty L., Momiji, Hiroshi, Featherstone, Karen, Davis, Julian R.E., White, Michael R.H., Rand, D. A. (David A.) and Finkenstädt, Bärbel (2015) A stochastic transcriptional switch model for single cell imaging data. Biostatistics, 16 (4). pp. 655-669. doi:10.1093/biostatistics/kxv010

Hickman, Richard J., Hill, C., Penfold, Christopher A., Breeze, Emily, Bowden, Laura, Moore, Jonathan D., Zhang, Peijun, Jackson, Alison C., Cooke, Emma J., Bewicke-Copley, Findlay, Mead, A. (Andrew), Beynon, Jim, Wild, David L., Denby, Katherine J., Ott, Sascha and Buchanan-Wollaston, Vicky (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. The Plant Journal, Volume 75 (Number 1). pp. 26-39. doi:10.1111/tpj.12194

Holmes, Ian, Harris, Keith and Quince, Christopher (2012) Dirichlet multinomial mixtures : generative models for microbial metagenomics. PLoS One, Volume 7 (Number 2). Article number e30126. doi:10.1371/journal.pone.0030126

Hulin, Michelle T., Armitage, Andrew D., Vicente, Joana G., Holub, E. B., Baxter, Laura, Bates, Helen J., Mansfield, John W., Jackson, Robert W. and Harrison, Richard J. (2018) Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium). The New Phytologist, 291 (2). pp. 672-696. doi:10.1111/nph.15182

Hultén, Maj A. (2011) On the origin of crossover interference : a chromosome oscillatory movement (COM) model. Molecular Cytogenetics, Vol.4 (No.10). doi:10.1186/1755-8166-4-10

Hultén, Maj A., Jonasson, Jon, Nordgren, Ann and Iwarsson, Erik (2010) Germinal and somatic trisomy 21 mosaicism : how common is it, what are the implications for individual carriers and how does it come about? Current Genomics, Vol.11 (No.6). pp. 409-419. doi:10.2174/138920210793176056

Hultén, Maj A., Patel, Suketu D., Westgren, Magnus, Papadogiannakis, Nikos, Jonsson, Anna Maria, Jonasson, Jon and Iwarsson, Erik (2010) On the paternal origin of trisomy 21 Down syndrome. Molecular Cytogenetics, Vol.3 (No.1). p. 4. doi:10.1186/1755-8166-3-4

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Book Item

Ladroue, Christophe and Kalvala, Sara (2015) Constraint-based genetic compilation. In: Dediu, Adrian-Horia and Hernández-Quiroz, Francisco and Marin-Vide, Carlos and Rosenblueth, David A., (eds.) Algorithms for Computational Biology : Second International Conference, AlCoB 2015, Mexico City, Mexico, August 4-5, 2015, Proceedings. Lecture Notes in Computer Science, 9199 . Springer, pp. 25-38. ISBN 9783319212326

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Journal Item

Retzer, Katarzyna, Singh, Gaurav and Napier, R. (Richard) (2018) It starts with TIRs. Nature Plants, 4 (7). pp. 410-411. doi:10.1038/s41477-018-0196-8

Report

Amos, Martyn, Gibbons, Alan (Alan M.) and Hodgson, D. A. (1996) Error-resistant implementation of DNA computations. University of Warwick. Department of Computer Science. (Department of Computer Science research report). (Unpublished)

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Aldali, Jehad (2018) Investigating the role of MmyB-like pathway-specific transcriptional activators in antibiotic production. PhD thesis, University of Warwick.

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Baker, Paul (Researcher in biological sciences) (1997) The distribution and diversity of actinomycetes in soil fractions. PhD thesis, University of Warwick.

Barona Gómez, Francisco (2003) Functional and structural genomics of amino acid metabolism in Streptomyces coelicolor. PhD thesis, University of Warwick.

Baroncelli, Riccardo (2012) Colletotrichum acutatum sensu lato : from diversity study to genome analysis. PhD thesis, University of Warwick.

Barr, John Nicholas (1993) Expression of the nucleoprotein and phosphoprotein genes of pneumonia virus of mice and specific interactions of the gene products. PhD thesis, University of Warwick.

Barrington, Christopher (2013) Epigenetic responses to environmental stress in plants. PhD thesis, University of Warwick.

Barstow, David A. (1983) Bacillus subtilis and bacillus licheniformis as hosts for genetic manipulation. PhD thesis, University of Warwick.

Bolt, Frances (2009) The population structure of the Corynebacterium diphtheriae group. PhD thesis, University of Warwick.

Broome, Mark John (2008) Interaction of DNA with groove binding ligands. PhD thesis, University of Warwick.

Camacho Aguilar, Elena (2018) New mathematical methods for the study of stem cell differentiation. PhD thesis, University of Warwick.

Carter, Anthony D. (2013) Cell-type specific comparative analysis of lateral root and nodule development at phenotypic and genomic levels. PhD thesis, University of Warwick.

Chen, Jing (2001) Expression of corticotrophin-releasing hormone receptor subtypes in human myometrium and cloning of the promoter region for the CRH receptors type 2. PhD thesis, University of Warwick.

Chen, Xu (Researcher in statistics) (2014) Accelerated estimation and inference for heritability of fMRI data. PhD thesis, University of Warwick.

Clarke, Ian Nicholas (1982) Genomic variation in rotaviruses. PhD thesis, University of Warwick.

Collier, William O. (2017) Gene expression regulation in pneumoviruses. PhD thesis, University of Warwick.

Coveney, Janice (1982) Activation of the ribosomal RNA genes in erythrocyte nuclei of Xenopus laevis. PhD thesis, University of Warwick.

Crickmore, Neil (1987) Analysis of a cell division gene cluster in "Escherichia coli". PhD thesis, University of Warwick.

Dabrowska, Alicja (2017) Opening up the black box of marine phototroph-heterotroph interactions. PhD thesis, University of Warwick.

Darlington, Alexander P. S. (2018) Design of genetic controllers to manage translational resource allocation in synthetic gene networks. PhD thesis, University of Warwick.

Davies, Siân Elizabeth Wynne (2013) Transcription factor interactions at the promoter of the Arabidopsis circadian clock gene LHY. PhD thesis, University of Warwick.

Downton, Polly J. (2012) The cis-regulatory module interactome of vertebrate myoD1. PhD thesis, University of Warwick.

Edworthy, Nicole Lynn (2008) Development and use of avian pneumovirus reverse genetics systems. PhD thesis, University of Warwick.

Holness, Claire Louise Lesley (1989) Isolation and characterisation of mutants of cowpea mosaic virus. PhD thesis, University of Warwick.

Irwin, Stephen D. (1989) Molecular cloning of the major castor bean 25 albumin precursor. PhD thesis, University of Warwick.

Janus, Ulrich (2008) Modelling and analysis of a genetic oscillator in E.coli. PhD thesis, University of Warwick.

Jeziorska, Danuta M. (2011) Identification and functional characterisation of novel conserved Hes1 cis-regulatory modules. PhD thesis, University of Warwick.

Jironkin, Aleksey (2013) Computational and experimental analysis of plant promoters : identifying functional elements. PhD thesis, University of Warwick.

Jones, Joseph Reuben (2016) The application of scattering techniques at complementary length scales to structural studies of clathrin complexes in vitro. PhD thesis, University of Warwick.

Joseph, Maxim B. (2012) Development of methods for combinational approaches to cis-regulatory module interactions. PhD thesis, University of Warwick.

Khalifa, Ashraf (2012) Gene regulation in methanotrophs : evidence from Methylococcus capsulatus (Bath) and Methylosinus trichosporium (OB3b). PhD thesis, University of Warwick.

Koohy, Hashem (2010) Computational prediction of functional similarity of CRMs. PhD thesis, University of Warwick.

Krishna, Ritesh V. (2009) From gene-expressions to pathways. PhD thesis, University of Warwick.

Liverani, Silvia (2009) Bayesian clustering of curves and the search of the partition space. PhD thesis, University of Warwick.

Lloyd, John S. (1997) Heterologous expression and site-directed mutagenesis of soluble methane monoxygenase. PhD thesis, University of Warwick.

Lucciola, Raffaella (2017) Genome-wide mapping of chromatin landscape and regulatory networks in decidualizing human endometrial stromal cells and cultured mesenchymal stem cells. PhD thesis, University of Warwick.

McCormick, Rachel Jacqueline (2001) Investigations into Xpat, a novel gene expressed in the germ plasm and primordial germ cells of Xenopus laevis. PhD thesis, University of Warwick.

McDowell, David Gordon (1990) A study of plasmid biology in Bacillus thuringiensis subspecies kurstaki HD1-Dipel. PhD thesis, University of Warwick.

Meng, Xueqiong (2018) Dissecting the role of PML-II in gene transcription and in IFN alpha-mediated apoptosis. PhD thesis, University of Warwick.

Morris, Nathan (Nathan Z.) (2000) Molecular detection of type II polyketide synthase genes in Cuban soils. PhD thesis, University of Warwick.

Morrissey, Edward R. (2012) Bayesian inference of causal gene networks. PhD thesis, University of Warwick.

Pateman, Cassandra Sophie Catherine (2002) RGS proteins and G protein signalling. PhD thesis, University of Warwick.

Pearson, Neil (Researcher in life sciences) (2013) Ecological genetics of arabidopsis thaliana from reservoir populations in low-disturbance habitats. PhD thesis, University of Warwick.

Plows, David John (1994) Natural and induced variation in the fusion glycoprotein gene of human respiratory syncytial virus subgroup A. PhD thesis, University of Warwick.

Potts, Linda Elizabeth (1980) Structure of the R. vannielii genome. PhD thesis, University of Warwick.

Prakash, Satya (2018) De novo engineering of trans-activating riboswitches in E. coli. PhD thesis, University of Warwick.

Pritchard, Jane (1999) Analysis of drongo, a new Drosophila zinc finger gene expressed during oogenesis and neurogenesis. PhD thesis, University of Warwick.

Puszyk, William Matthew (2008) Epigenetics of cell-free plasma DNA for non-invasive prenatal diagnosis of fetal aneuploidies. PhD thesis, University of Warwick.

Rhodes, Johanna (2012) Identifying gene regulatory networks common to multiple plant stress responses. PhD thesis, University of Warwick.

Robson, Samuel Charles (2008) Life or cell death: identifying c-Myc regulated genes in two distinct tissues. PhD thesis, University of Warwick.

Schafer, David Gerald (2013) Mechanisms underlying epigenetic gene silencing in maize. PhD thesis, University of Warwick.

Seville, Rachel Alice (2001) Annexin IV: a pronephros specific gene with a role in pronephric development. PhD thesis, University of Warwick.

Sharma, Sapna (2013) Reconstructing regulatory networks from high-throughput post-genomic data using MCMC methods. PhD thesis, University of Warwick.

Simmons, Susan (2001) The microbial ecology of acidic environments. PhD thesis, University of Warwick.

Smith, Oliver (2012) Small RNA-mediated regulation, adaptation and stress response in barley archaeogenome. PhD thesis, University of Warwick.

Spensley, Mark (2007) Transcriptional regulation of the arabidopsis circadian clock component LHY. PhD thesis, University of Warwick.

Teo, Alvin (2017) Detergent-free approach to the studies of bacterial cell division membrane proteins using styrene maleic acid copolymer. PhD thesis, University of Warwick.

Tiberi, Simone (2016) Bayesian hierarchical stochastic inference on multiple, single cell, latent states from both longitudinal and stationary data. PhD thesis, University of Warwick.

Usher, Sarah Louise (2009) Nucleosome positioning in Arabidopsis. PhD thesis, University of Warwick.

Walley, Peter Glen (2007) Dissecting the genetic regulation of texture traits in tomato fruit. PhD thesis, University of Warwick.

Webber, P. M. (1993) Analysis of the promoter region of the Xenopus borealis N-Cadherin gene. PhD thesis, University of Warwick.

Whitworth, David E. (1999) Feedback and molecular interactions in the process of light-induced carotenogenesis in Myxococcus xanthus. PhD thesis, University of Warwick.

Zuco, Giuseppina (2017) Ascaroside-induced neuronal reprogramming of the germline in the nematode Auanema freiburgensis. PhD thesis, University of Warwick.