Journal Article

Achtman, Mark (2016) How old are bacterial pathogens? Proceeding of the Royal Society B, 286 (1836). ISSN 0962-8452.

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 ISSN 1553-7390.

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 ISSN 1553-7374.

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 ISSN 1553-7390.

Achtman, Mark and Zhou, Zhemin (2020) Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. Philosophical Transactions of the Royal Society B: Biological Sciences, 375 (1812). 20190573. doi:10.1098/rstb.2019.0573 ISSN 0962-8436.

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 ISSN 2045-2322.

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 ISSN 1750-2640.

Alberti, Fabrizio, Kaleem, Saraa and Weaver, Jack (2020) Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research. Biology Open, 9 (12). bio056010. doi:10.1242/bio.056010 ISSN 2046-6390.

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 ISSN 1471-2164.

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 ISSN 1553-7390.

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 ISSN 0022-0957.

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. ISSN 1176-9343.

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 ISSN 1471-2229.

Amourda, Christopher and Saunders, Timothy E. (2020) The mirtron miR-1010 functions in concert with its host gene SKIP to balance elevation of nAcRβ2. Scientific Reports, 10 (1). 1688. doi:10.1038/s41598-020-58655-7 ISSN 2045-2322.

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 ISSN 0261-4189.

(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 ISSN 1471-2164.

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 ISSN 1664-302X.

(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 ISSN 1932-6203.

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 ISSN 1932-6203.

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 ISSN 1932-6203.

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 ISSN 1471-2164.

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 ISSN 0305-1048.

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 ISSN 2398-6182.

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 ISSN 1940-9990.

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 ISSN 2041-1723.

(2014) Uterine selection of human embryos at implantation. Scientific Reports, 4 . 3894. doi:10.1038/srep03894 ISSN 2045-2322.

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 ISSN 1367-4803.

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 ISSN 2045-7758.

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 ISSN 1752-4571.

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 ISSN 0378-1135.

Camsund, Daniel, Jaramillo, Alfonso and Lindblad, Peter (2021) Engineering of a promoter repressed by a light-regulated transcription factor in escherichia coli. BioDesign Research, 2021 (9857418). doi:10.34133/2021/9857418 ISSN 2693-1257.

Capalbo, Luisa, Bassi, Zuni I., Geymonat, Marco, Todesca, Sofia, Copoiu, Liviu, Enright, Anton J., Callaini, Giuliano, Riparbelli, Maria Giovanna, Yu, Lu, Choudhary, Jyoti S., Ferrero, Enrico, Wheatley, Sally, Douglas, Max E., Mishima, Masanori and D'Avino, Pier Paolo (2019) The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. Nature Communications, 10 (1). 4513. doi:10.1038/s41467-019-12507-9 ISSN 2041-1723.

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 ISSN 0028-0836.

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 ISSN 1752-0509.

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 ISSN 0264-410X.

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 ISSN 0214-6282.

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 ISSN 1751-7907.

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 ISSN 1614-2942.

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 ISSN 1553-7390.

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 ISSN 1471-2180.

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 ISSN 1664-302X.

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 ISSN 0737-4038.

Chew, Ting Gang, Lim, Tzer Chyn, Osaki, Yumi, Huang, Junqi, Kamnev, Anton, Osumi, Masako and Balasubramanian, Mohan K. (2020) Inhibition of cell membrane ingression at the division site by cell wall in fission yeast. Molecular Biology of the Cell, 31 (21). pp. 2306-2314. doi:10.1091/mbc.E20-04-0245 ISSN 1059-1524.

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 ISSN 1471-2164.

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 ISSN 1471-2148.

Clifton, Rachel, Giebel, Katharina, Liu, Nicola, Purdy, Kevin J. and Green, Laura E. (2019) Sites of persistence of Fusobacterium necrophorum and Dichelobacter nodosus: a paradigm shift in understanding the epidemiology of footrot in sheep. Scientific Reports, 9 (1). 14429. doi:10.1038/s41598-019-50822-9 ISSN 2045-2322.

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 ISSN 1743-422X.

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 ISSN 1932-6203.

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 ISSN 1553-7390.

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 ISSN 2041-1723.

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 ISSN 1932-6203.

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 ISSN 1474-7596.

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 ISSN 1932-6203.

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. ISSN 0869-6918.

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 ISSN 1553-7390.

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, 46 (22). e134. doi:10.1093/nar/gky783 ISSN 0305-1048.

Didelot, Xavier, Siveroni, Igor and Volz, Erik M. (2021) Additive uncorrelated relaxed clock models for the dating of genomic epidemiology phylogenies. Molecular Biology and Evolution, 38 (1). pp. 307-317. msaa193. doi:10.1093/molbev/msaa193 ISSN 1537-1719.

Dijkman, Patricia M., Muñoz-García, Juan C., Steven R., Lavington, Suemy Kumagai, Patricia , dos Reis, Rosana I., Yin, Daniel , Stansfeld, Phillip J., Costa-Filho, Antonio José and Watt , Anthony (2020) Conformational dynamics of a G protein-coupled receptor helix 8 in lipid membranes. Science Advances, 6 (33). eaav8207. doi:10.1126/sciadv.aav8207 ISSN 2375-2548.

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. ISSN 1756-8935.

Dong, Yuxiang, Liu, Jiliang, Lu, Xuanzhao, Duan, Jialin, Zhou, Liqi, Dai, Lizhi, Ji, Min, Ma, Ningning, Wang, Yong, Wang, Peng, Zhu, Jun-Jie, Min, Qianhao, Gang, Oleg and Tian, Ye (2022) Two-stage assembly of nanoparticle superlattices with multiscale organization. Nano Letters, 22 (9). pp. 3809-3817. doi:10.1021/acs.nanolett.2c00942 ISSN 1530-6984.

(2020) Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria. Frontiers in Microbiology, 11 . 567431. doi:10.3389/fmicb.2020.567431 ISSN 1664-302X.

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 ISSN 1932-6203.

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 ISSN 2167-8359.

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 ISSN 1756-3305.

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 ISSN 2405-4712.

(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 ISSN 0967-3849.

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 ISSN 1471-2199.

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 ISSN 0981-9428.

(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 ISSN 1944-3277.

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 ISSN 1932-6203.

Fan, Xijian, Zhou, Rui, Tjahjadi, Tardi, Das Choudhury, Sruti and Ye, Qiaolin (2022) A segmentation-guided deep learning framework for leaf counting. Frontiers in Plant Science, 13 . 844522. doi:10.3389/fpls.2022.844522 ISSN 1664-462X.

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. ISSN 1364-906X.

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 ISSN 0246-0203.

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 ISSN 1083-6489.

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. doi:10.7554/eLife.08494 ISSN 2050-084X.

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 ISSN 1553-7358.

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 ISSN 2397-7000.

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 ISSN 0305-1048.

Foo, Mathias, Kim, Jongrae and Bates, Declan (2019) Modelling and control of gene regulatory networks for perturbation mitigation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16 (2). pp. 583-595. doi:10.1109/TCBB.2017.2771775 ISSN 1545-5963.

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 ISSN 0958-1669.

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Cavallaro, Massimo, Wang, Yuexuan, Hebenstreit, Daniel and Dutta, Ritabrata (2021) Bayesian inference of PolII dynamics over the exclusion process. (Submitted)

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

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

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Charlton, Georgina (2020) Proteomic analysis of drought & oxidative stress in Arabidopsis thaliana & Zea mays. 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.

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Chew, Yean Ming (2022) Allosteric effects of taxol and kinesin on single isoform microtubule lattices. PhD thesis, University of Warwick.

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Clarke, Scott T. (2022) A study of oscillatory cortical behaviours and traveling waves during cytokinesis in the zebrafish embryo. PhD thesis, University of Warwick.

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Cooper, Daniel D. (2019) What underlies the benefits of environmental enrichment on the brain? : investigation of a neurotrophin-stimulaed kinase reveals its role in regulating sociability and experience-dependent changes in hippocampal gene expression. PhD thesis, University of Warwick.

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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, Philip R. (2020) Understanding mammalian gene expression noise as a function of cell growth. 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.

Dawson, Alexander Takahide Takao (2021) A multi-omics study of tapping and ethylene induction in Hevea brasiliensis. 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.

Fernandes Duarte, Filipe Alexandre (2021) Investigating chromatin domain structures in living cells using histone pulse-labelling approaches. PhD thesis, University of Warwick.

Ford, Emma (2021) The nature of chromosome segregation errors in the early mitotic divisions of human embryos. PhD thesis, University of Warwick.

Fullwood, Alexander James (2019) Biochemical investigations of TetR-family regulators that control antibiotic biosynthesis in Streptomyces bacteria. PhD thesis, University of Warwick.

Garbutt, Lauren A (2022) Characterisation of a novel transgenic mouse for tissue- and cell-specific recording of circadian rhythms. PhD thesis, University of Warwick.

Germanova, Tsvetelina E. (2021) Functional organisation of the human kinetochore and roles of the Ska complex. PhD thesis, University of Warwick.

Healey, Joseph R. J. (2018) Photorhabdus virulence cassettes: understanding the structure, and genomic role, of a novel bacterial protein delivery mechanism. PhD thesis, University of Warwick.

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

Ignatieva, Anastasia (2021) Population genetics models for viral data with recombination. PhD thesis, University of Warwick.

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

Jackisch, Laura (2019) Molecular mechanisms of adipose tissue mitochondrial (mal)adaptation in obesit. 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.

Jones, Matthew (2022) Transcriptional noise and Pol2 recycling. 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.

Lam, Jenna Hoi-Yan (2019) Condition-dependent transcriptional landscape of Campylobacter jejuni. PhD thesis, University of Warwick.

Li, Stephen (2022) Transcriptomic analysis predicts the identities and biological roles of Campylobacter jejuni small RNAs. PhD thesis, University of Warwick.

Lipecki, Julia (2020) Computational approaches for determination of transcriptomic and epigenomic states. PhD thesis, University of Warwick.

Liu, Hsiao (2019) Grape evolution in the human environment. PhD thesis, University of Warwick.

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

Liyanagedera, Sahan B. W. (2022) Optimisation of cell-free transcription/translation systems for phage therapy. PhD thesis, University of Warwick.

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

Lones, Emma (2020) Analysis of the mechanism of recruitment of the helicase Sen1 at the replisome and its role in the maintenance of genomic stability. PhD thesis, University of Warwick.

Lovell, Alan D. (2000) Population structure of three commercially important species in the Gulf of Guinea. 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.

Maguire, Rosanne (2022) Strategic and responsive breeding of common bean varieties (Phaseolus vulgaris L.) for the UK market. PhD thesis, University of Warwick.

Manoharan, Shathviga (2022) Investigation into the temperature-dependent regulation of virulence factors in Bacillus cereus G9241, the causative agent of an anthrax-like disease. PhD thesis, University of Warwick.

Maple, Robert (2019) Meiosis associated Argonautes in male reproductive development. PhD thesis, University of Warwick.

Martucci, Sophie Marie (2020) The role and mechanisms of action of PMLII on regulating gene expression. 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.

Michniewski, Slawomir (2020) Phages infecting marine Vibrios: prevalence, diversity and role in the dissemination of antibiotic resistance genes. PhD thesis, University of Warwick.

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

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Rangama, Marie Séverine (2020) Characterisation of a subset of Escherichia coli river isolates and their role in the environmental resistome. PhD thesis, University of Warwick.

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