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. 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. ISSN 1553-7374

Achtman, Mark and Zhou, Zhemin. (2014) Distinct genealogies for plasmids and chromosome. PLoS Genetics, Volume 10 (Number 12). Article number e1004874. ISSN 1553-7390

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. ISSN 1750-2640

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. ISSN 1471-2164

Allaby, Robin G.. (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany, Vol.61 (No.4). pp. 935-944. 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). ISSN 1471-2229

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. 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. 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). 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. 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. 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 . ISSN 0305-1048

Bowyer, Jack, 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 . ISSN 1940-9990 (In Press)

Brodel, Andreas K., Jaramillo, Alfonso and Isalan, Mark. (2016) Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nature Communications, 7 . 13858 . ISSN 2041-1723

. (2014) Uterine selection of human embryos at implantation. Scientific Reports, Volume 4 . Article number 3894. 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 . 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. 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. 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. ISSN 0378-1135

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. ISSN 0737-4038

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. ISSN 1471-2164

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

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. 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. 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. ISSN 1553-7390

Davies, Lawrence O., Schäfer, Hendrik, Marshall, Samantha, Bramke, Irene, Oliver, Robin G. and Bending, Gary D.. (2013) Light structures phototroph, bacterial and fungal communities at the soil surface. PLoS One, Volume 8 (Number 7). Article number e69048. 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). 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. 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. ISSN 1553-7390

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

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. ISSN 1932-6203

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. ISSN 1756-3305

. (2013) Esperanto for histones : CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Research, Volume 21 (Number 2). pp. 101-106. 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). 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. 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. 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. ISSN 1932-6203

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. ISSN 1083-6489

Featherstone, Katie, Hey, K., 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. 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. ISSN 1553-7358

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. ISSN 0305-1048

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. ISSN 1053-8119

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. ISSN 0027-8424

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. ISSN 1471-213x

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. ISSN 1553-7390

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. ISSN 1471-2407

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. ISSN 1355-8382

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. ISSN 0040-5809

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. ISSN 1932-6203

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). ISSN 1545-7885

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. ISSN 1751-7362

Haworth, Claire M. A. and Davis, Oliver S. P. . (2014) From observational to dynamic genetics. Frontiers in Genetics, Volume 5 . Article number 6. ISSN 1664-8021

Hebenstreit, Daniel. (2012) Methods, challenges and potentials of single cell RNA-seq. Biology, Volume 1 (Number 3). pp. 658-667. ISSN 2079-7737

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. ISSN 1465-4644

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., 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. ISSN 0960-7412

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. ISSN 1932-6203

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

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. ISSN 1389-2029

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. ISSN 1755-8166

Iqbal, Mudassar, Mast, Yvonne, Amin, Rafat, Hodgson, D. A. (David A.), Wohlleben, W. and Burroughs, Nigel John. (2012) Extracting regulator activity profiles by integration of de novo motifs and expression data : characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Nucleic Acids Research, Vol.40 (No.12). pp. 5227-5239. ISSN 0305-1048

Jaakola, Laura, Poole, Mervin, Jones, Matthew O., Kämäräinen-Karppinen, Terttu, Koskimäki, Janne J., Hohtola, Anja, Häggman, Hely, Fraser, Paul D., Manning, Kenneth, King , Graham J., Thomson, H. (Helen) and Seymour, G. B. (Graham B.). (2010) A SQUAMOSA MADS-box gene involved in the regulation of anthocyanin accumulation in bilberry fruits. Plant Physiology, Vol.153 (No.4). ISSN 0032-0889

Jadhav, Vaibhav, Hackl, Matthias, Druz, Aliaksandr, Shridhar, Smriti, Chung, Cheng-Yu, Heffner, Kelley M., Kreil, David, Betenbaugh, Mike, Shiloach, Joseph, Barron, Niall, Grillari, Johannes and Borth, Nicole. (2013) CHO microRNA engineering is growing up : recent successes and future challenges. Biotechnology Advances, Volume 31 (Number 8). pp. 1501-1513. ISSN 0734-9750

Jenkins, Dafyd J., Finkenstädt, Bärbel and Rand, D. A. (David A.). (2013) A temporal switch model for estimating transcriptional activity in gene expression. Bioinformatics, Volume 29 (Number 9). pp. 1158-1165. ISSN 1367-4803

Jenkins, Dafyd J. and Stekel, Dov. (2010) De novo evolution of complex, global and hierarchical gene regulatory mechanisms. Journal of Molecular Evolution, Vol.71 (No.2). pp. 128-140. ISSN 0022-2844

Jenkins, Paul, Song, Yun S. and Brem, Rachel B.. (2012) Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. PLoS One, Volume 7 (Number 11). Article number e46947. ISSN 1932-6203

Jensen, Brita Dahl, Vicente, Joana G., Manandhar, Hira Kaji and Roberts, Steven J.. (2010) Occurrence and diversity of Xanthomonas campestris pv. campestris in vegetable brassica fields in Nepal. Plant Disease, Vol.94 (No.3). pp. 298-305. ISSN 0191-2917

. (2013) An integrated model of the transcriptome of HER2-positive breast cancer. PLoS One, Volume 8 (Number 11). Article number e79298. ISSN 1932-6203

Kang, Jing, Ph.D., Xu, Bing, Yao, Ye, Lin, Wei, Hennessy, Conor, Fraser, Peter and Feng, Jianfeng. (2011) A dynamical model reveals gene co-localizations in nucleus. PLoS Computational Biology, Vol.7 (No.7). e1002094. ISSN 1553-734X

Kantsler, Vasily, Dunkel, Jörn, Blayney, Martyn and Goldstein, Raymond E.. (2014) Rheotaxis facilitates upstream navigation of mammalian sperm cells. eLife, Volume 3 . Article number e02403. ISSN 2050-084X

Karikari, Thomas K., Quansah, Emmanuel and Mohamed, Wael M. Y.. (2015) Widening participation would be key in enhancing bioinformatics and genomics research in Africa. Applied & translational genomics, 6 . pp. 35-41. ISSN 2212-0661

Keeling, Matthew James and White, Peter. (2011) Targeting vaccination against novel infections : risk, age and spatial structure for pandemic influenza in Great Britain. Journal of the Royal Society - Interface, Vol.8 (No.58). pp. 661-670. ISSN 1742-5662

Kelly, M. Ann , Rees, Simon D., Hydrie, M. Zafar I., Shera, A. Samad, Bellary, Srikanth, O'Hare, J. Paul, Kumar, Sudhesh, Taheri, S., Basit, Abdul and Barnett, Anthony H.. (2012) Circadian gene variants and susceptibility to type 2 diabetes : a pilot study. PLoS ONE, Vol.7 (No.4). e32670. ISSN 1932-6203

Kerr, Gary W., Sarkar, Sourav, Tibbles, Katherine L., Petronczki, Mark, Millar, Jonathan B. A. and Arumugam, Prakash . (2011) Meiotic nuclear divisions in budding yeast require PP2ACdc55-mediated antagonism of Net1 phosphorylation by Cdk. The Journal of Cell Biology, Vol.193 (No.7). pp. 1157-1166. ISSN 0021-9525

Kiddle, Steven J., Windram, Oliver P., McHattie, Stuart, Mead, A., Beynon, Jim, Buchanan-Wollaston, Vicky, Denby, Katherine J. and Mukherjee, Sach. (2009) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics, Vol.26 (No.3). pp. 355-362. ISSN 1367-4811

Kochunov, Peter, Glahn, David C., Nichols, Thomas E., Winkler, Anderson M., Hong, Elliot L., Holcomb, Henry H., Stein, Jason L., Thompson, Paul M., Curran, Joanne E., Carless, Melanie A., Olvera, Rene L., Johnson, Matthew P., Cole, Shelley A., Kochunov, Valeria, Kent, Jack and Blangero, John. (2011) Genetic analysis of cortical thickness and fractional anisotropy of water diffusion in the brain. Frontiers in Neuroscience, Vol.5 . p. 120. ISSN 1662-4548

Komorowski, Michal, Finkenstädt, Bärbel, Harper, Claire V. and Rand, D. A. (David A.). (2009) Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics, Vol.10 (No.343). ISSN 1471-2105

. (2011) Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript. Human Genetics, Vol.129 (No.6). pp. 687-694. ISSN 1432-1203

. (2013) Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. Human Molecular Genetics, Volume 22 (Number 12). pp. 2520-2528. ISSN 0964-6906

Krishna, Ritesh V., Li, Chang-Tsun and Buchanan-Wollaston, Vicky. (2010) A temporal precedence based clustering method for gene expression microarray data. BMC Bioinformatics, Vol.11 . Article 68. ISSN 1471-2105

Kushwaha, Manish, Rostain, William, Prakash, Satya, Duncan, John and Jaramillo, Alfonso. (2016) Using RNA as molecular code for programming cellular function. ACS Synthetic Biology, 5 (8). pp. 795-809. ISSN 2161-5063

Lenartowski, Robert, Suwińska, Anna, Prusińska, Justyna, Gumowski, Krzysztof and Lenartowska, Marta. (2014) Molecular cloning and transcriptional activity of a new Petunia calreticulin gene involved in pistil transmitting tract maturation, progamic phase, and double fertilization. Planta, Volume 239 (Number 2). pp. 437-454. ISSN 0032-0935

. (2010) The genome of a pathogenic rhodococcus : cooptive virulence underpinned by key gene acquisitions. PLoS Genetics, Volume 6 (Number 9). Article number e1001145. ISSN 1553-7390

Lloret-Llinares, Marta, Pérez-Lluch, Sílvia, Rossell, David, Morán, Tomás, Ponsa-Cobas, Joan, Auer, Herbert, Corominas, Montserrat and Azorín, Fernando. (2012) dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes. Nucleic Acids Research, Volume 40 (Number 19). pp. 9493-9505. ISSN 0305-1048

Love, Christopher G., Graham, Neil S. , Ó Lochlainn, Seosamh, Bowen, Helen C., May, Sean T., White, Philip J., Broadley, Martin R., Hammond, John P. and King , Graham J.. (2010) A Brassica exon array for whole-transcript gene expression profiling. PL o S One, Vol.5 (No.9). ISSN 1932-6203

Lowry, Kym, Woodman, Andrew, Cook, Jonathan P. and Evans, D. J. (David J.). (2014) Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length 'imprecise' intermediates. PLoS Pathogens, Volume 10 (Number 6). Article number e1004191. ISSN 1553-7374

Marenduzzo, Davide, Micheletti, C. (Cristian) and Cook, P. R.. (2006) Entropy-driven genome organization. Biophysical Journal, Vol.90 (No.10). pp. 3712-3721. ISSN 0006-3495

Martens, Harald, Veflingstad, Siren R., Plahte, Erik, Martens, M. (Magni), Bertrand, Dominique and Omholt, Stig W.. (2009) The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors. BMC Systems Biology, Volume 3 . Article number 87. ISSN 1752-0509

McFadden, Nora, Arias, Armando, Dry, Inga, Bailey, Dalan, Witteveldt, Jeroen, Evans, D. J. (David J.), Goodfellow, Ian and Simmonds, Peter. (2013) Influence of genome-scale RNA structure disruption on the replication of murine norovirus--similar replication kinetics in cell culture but attenuation of viral fitness in vivo. Nucleic Acids Research, Volume 41 (Number 12). pp. 6316-6331. ISSN 0305-1048

Melillo, Paolo, Pecchia, Leandro, Testa, Francesco, Rossi, Settimio, Bennett, Jean, M.D. and Simonelli, Francesca. (2012) Pupillometric analysis for assessment of gene therapy in Leber Congenital Amaurosis patients. BioMedical Engineering OnLine, Volume 11 (Number 1). Article number 40. ISSN 1475-925X

Michniewski, Slawomir, Redgwell, Tamsin, Scanlan, David J. and Millard, Andrew D.. (2017) Draft genome sequence of Bacteriophage vB_Eco_swan01. Genome Announcements, 5 (28). pp. 1-17. e00501. ISSN 2169-8287

Moatsou, Dafni, Li, Jian, Ranji, Arnaz, Pitto-Barry, Anaïs, Ntai, Ioanna, Jewett, Michael C. and O’Reilly, Rachel K.. (2015) Self-assembly of temperature-responsive protein–polymer bioconjugates. Bioconjugate Chemistry, 26 (9). pp. 1890-1899. ISSN 1043-1802

Morris, S. J. (Susan J.), Farley, Daniel C. and Leppard, K. N. (Keith N.). (2010) Generation of cell lines to complement Adenovirus vectors using recombination-mediated cassette exchange. BioMed Central Ltd., Vol.10 (No.92). Article No.92. ISSN 1472-6750

Breast Cancer Association Consortium (Including: Muir, Kenneth (Kenneth R.), Lophatananon, Artitaya and Stewart-Brown, Sarah L.). (2013) FGF receptor genes and breast cancer susceptibility : results from the Breast Cancer Association Consortium. British Journal of Cancer, Volume 110 (Number 4). pp. 1088-1100. ISSN 0007-0920

Breast Cancer Association Consortium (Including: Muir, Kenneth (Kenneth R.), Lophatananon, Artitaya and Stewart-Brown, Sarah L.). (2015) Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2. Human Molecular Genetics, Volume 24 (Number 10). pp. 2966-2984. Article number 2966. ISSN 0964-6906

Naylor, Richard William and Jones, E. A.. (2009) Notch activates Wnt-4 signalling to control medio-lateral patterning of the pronephros. Development , Vol.136 (No.21). pp. 3585-3595. ISSN 0950-1991

Nell, Sandra, Eibach, Daniel, Montano, Valeria, Maady, Ayas, Nkwescheu, Armand, Siri, Jose, Elamin, Wael F., Falush, Daniel, Linz, Bodo, Achtman, Mark, Moodley, Yoshan and Suerbaum, Sebastian. (2013) Recent acquisition of Helicobacter pylori by Baka Pygmies. PLoS Genetics, 9 (9). e1003775. ISSN 1553-7390

Nicodemi, Mario and Prisco, Antonella. (2007) Self-assembly and DNA binding of the blocking factor in X chromosome inactivation. PLoS Computational Biology, Vol.3 (No.11). pp. 2135-2142. ISSN 1553-734X

Nicodemi, Mario and Prisco, Antonella. (2009) Thermodynamic pathways to genome spatial organization in the cell nucleus. Biophysical Journal, Vol.96 (No.6). pp. 2168-2177. ISSN 0006-3495

Noda-Garcia, Lianet, Camacho-Zarco, Aldo R., Medina-Ruíz, Sophía, Gaytán, Paul, Carrillo-Tripp, Mauricio, Fülöp, Vilmos and Barona-Gómez, Francisco. (2013) Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer. Molecular Biology and Evolution, Volume 30 (Number 9). pp. 2024-2034. ISSN 0737-4038

Oakley, Brian B., Dowd, Scot E. and Purdy, Kevin J.. (2011) ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples. FEMS Microbiology Ecology, Vol.77 (No.1). pp. 17-27. ISSN 1574-6941

Orozco, Gisela, Goh, Chee L., Al Olama, Ali Amin, Benlloch, Sara, Govindasami, Koveela, Guy, Michelle, Muir, Kenneth, Giles, Graham, Severi, Gianluca, Neal, David E., Hamdy, Freddie C., Donovan, Jenny, Kote-Jarai, Zsofia, Easton, Douglas F., Eyre, Steve and Eeles, Rosalind A.. (2011) Common genetic variants associated with disease from genome-wide association studies are mutually exclusive in prostate cancer and rheumatoid arthritis. BJU International, Volume 111 (Number 7). pp. 1148-1155. ISSN 1464-1603

Papanayotou, Costis, Benhaddou, Ataaillah, Camus, Anne, Perea-Gomez, Aitana, Jouneau, Alice, Mezger, Valérie, Langa, Francina, Ott, Sascha, Sabéran-Djoneidi, Délara and Collignon, Jérôme. (2014) A novel Nodal enhancer dependent on pluripotency factors and Smad2/3 signaling conditions a regulatory switch during epiblast maturation. PLoS Biology, Volume 12 (Number 6). Article number e1001890. ISSN 1545-7885

. (2013) Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus. BMC Genomics, Volume 14 (Number 1). Article number 663. ISSN 1471-2164

Penfold, Christopher A., Brown, Paul E., Lawrence, Neil (Neil D.) and Goldman, Alastair S. H.. (2012) Modeling meiotic chromosomes indicates a size dependent contribution of telomere clustering and chromosome rigidity to homologue juxtaposition. PLoS Computational Biology, Vol.8 (No.5). e1002496. ISSN 1553-7358

Penfold, Christopher A., Shifaz, Ahmed, Brown, Paul E., Nicholson, Ann and Wild, David L.. (2015) CSI : A nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data. Statistical Applications in Genetics and Molecular Biology, Volume 14 (Number 3). pp. 307-310. ISSN 1544-6115

Penman, Bridget S., Gupta, Sunetra and Buckee, Caroline O.. (2012) The emergence and maintenance of sickle cell hotspots in the Mediterranean. Infection, Genetics and Evolution , 12 (7). pp. 1543-1550. ISSN 1567-1348

Penman, Bridget S., Gupta, Sunetra and Weatherall, David J.. (2015) Epistasis and the sensitivity of phenotypic screens for beta thalassaemia. British Journal of Haematology, 169 (1). pp. 117-128. ISSN 0007-1048

Perez Sepulveda, Blanca M., Redgwell, Tamsin, Rihtman, Branko, Pitt, Frances Diana, Scanlan, David J. , Millard, Andrew D. and Hantke, Klaus. (2016) Marine phage genomics : the tip of the iceberg. FEMS Microbiology Letters, 363 (15). ISSN 0378-1097

Piersma, Sjouke, Denham, Emma, Drulhe, Samuel, Tonk, Rudi H. J., Schwikowski, Benno and Dijl, Jan Maarten van. (2013) TLM-Quant : an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells. PLoS One, Volume 8 (Number 7). Article number e68696. ISSN 1932-6203

Piper, Jason, Elze, Markus C., Cauchy, Pierre, Cockerill, Peter N., Bonifer, Constanze and Ott, Sascha. (2013) Wellington : a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Research, Volume 41 (Number 21). Article number e201. ISSN 0305-1048

. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genetics, Vol.6 (No.2). e1000843. ISSN 1553-7390

Polanski, Krzysztof , Rhodes, Johanna, Hills, Claire E., Zhang, Peijun, Jenkins, Dafyd J., Kiddle, Steven J., Jironkin, Aleksey, Beynon, Jim, Buchanan-Wollaston, Vicky, Ott, Sascha and Denby, Katherine J.. (2014) Wigwams : identifying gene modules co-regulated across multiple biological conditions. Bioinformatics, Volume 30 (Number 7). pp. 962-970. ISSN 1367-4803

Pontiroli, Alessandra, Khera, Tanya T., Oakley, Brian B., Mason, Sam, Dowd, Scot E., Travis, Emma Rachel, Erenso, Girum, Aseffa, Abraham, Courtenay, Orin and Wellington, E. M. H.. (2013) Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity. PLoS One, Volume 8 (Number 7). Article number e68648. ISSN 1932-6203

Pontiroli, Alessandra, Travis, Emma Rachel, Sweeney, F. P., Porter, David, Gaze, William H., Mason, Sam, Hibberd, V., Holden, Jennifer, Courtenay, Orin and Wellington, E. M. H.. (2011) Pathogen quantitation in complex matrices : a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition. PLoS One, Vol.6 (No.3). Article number e17916. ISSN 1932-6203

Páez, Carlos J., Schulz, Peter A., Wilson, Neil R. and Roemer, Rudolf A.. (2012) Robust signatures in the current–voltage characteristics of DNA molecules oriented between two graphene nanoribbon electrodes. New Journal of Physics, Vol.14 (No.9). 093049. ISSN 1367-2630

Quince, Christopher , Lanzen, Anders, Davenport, Russell J. and Turnbaugh, Peter J.. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, Volume 12 (Number 1). Article number 38. ISSN 1471-2105

Rahmanpour, Rahman and Bugg, Tim. (2013) Assembly in vitro of rhodococcus jostii RHA1 encapsulin and peroxidase DypB to form a nano-compartment. FEBS Journal, Volume 280 (Issue 9). pp. 2097-2104. ISSN 1742-464x

Rasmussen, Carl Edward, De la Cruz, Bernard J., Ghahramani, Zoubin and Wild, David L.. (2009) Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures. IEEE - ACM Transactions on Computational Biology and Bioinformatics, Vol.6 (No.4). pp. 615-628. ISSN 1545-5963

Ray, Swagat and Anderson, Emma C.. (2016) Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction. Scientific Reports, 6 . 22461. ISSN 2045-2322

Rees, Simon D., Hydrie, M. Zafar I., O'Hare, J. Paul, Kumar, Sudhesh, Shera, A. Samad, Basit, Abdul, Barnett, A. H. and Kelly, M. Ann. (2011) Effects of 16 genetic variants on fasting glucose and type 2 diabetes in South Asians : ADCY5 and GLIS3 variants may predispose to type 2 diabetes. PLoS ONE, Vol.6 (No.9). ISSN 1932-6203

Reid, J. E. (John E.), Evans, Kenneth J., Dyer, Nigel, Wernisch, Lorenz and Ott, Sascha. (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics, Vol.11 (Article 30). ISSN 1471-2164

Reid, J. E. (John E.), Ott, Sascha and Wernisch, Lorenz. (2009) Transcriptional programs : modelling higher order structure in transcriptional control. BMC Bioinformatics, Vol.10 . Article no. 218. ISSN 1471-2105

Remenyi, Judit, van den Bosch, Mirjam W. M., Palygin, Oleg, Mistry, Rajen B., McKenzie, Colin, Macdonald, Andrew, Hutvagner, Gyorgy, Arthur, J. Simon C., Frenguelli, Bruno G. and Pankratov, Yuriy. (2013) miR-132/212 knockout mice reveal roles for these miRNAs in regulating cortical synaptic transmission and plasticity. PLoS One, Volume 8 (Number 4). Article number e62509. ISSN 1932-6203

. (2013) Tetrahydropyrazolo[1,5-a]Pyrimidine-3-Carboxamide and N-Benzyl-6′,7′-Dihydrospiro[Piperidine-4,4′-Thieno[3,2-c]Pyran] analogues with bactericidal efficacy against Mycobacterium tuberculosis targeting MmpL3. PLoS One, Volume 8 (Number 4). Article number e60933. ISSN 1932-6203

Rodrigo, Guillermo, Majer, Eszter, Prakash, Satya, Daros, Jose Antonio, Jaramillo, Alfonso and Poyatos, Juan F.. (2015) Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells. Biophysical Journal, 109 (5). pp. 1070-1076. ISSN 0006-3495

Rodrigo, Guillermo, Prakash, Satya, Cordero, Teresa, Kushwaha, Manish and Jaramillo, Alfonso. (2016) Functionalization of an antisense small RNA. Journal of Molecular Biology, 428 Part B (5). pp. 889-892. ISSN 0022-2836

Rodrigo, Guillermo, Prakash, Satya, Shen, Shensi, Majer, Eszter, Daròs, José-Antonio and Jaramillo, Alfonso. (2017) Model-based design of RNA hybridization networks implemented in living cells. Nucleic Acids Research . gkx698. ISSN 0305-1048 (In Press)

Rognes, Torbjørn, Flouri, Tomáš, Nichols, Ben, Quince, Christopher and Mahé, Frédéric. (2016) VSEARCH : a versatile open source tool for metagenomics. PeerJ, 4 . e2584. ISSN 2167-8359

Russell, Claire L., Smith, Edward M., Calvo-Bado, Leo A., Green, Laura E., Wellington, E. M. H., Medley, Graham, Moore, Lynda J. and Grogono-Thomas, Rosemary. (2014) Multiple locus VNTR analysis highlights that geographical clustering and distribution of Dichelobacter nodosus, the causal agent of footrot in sheep, correlates with inter-country movements. Infection, Genetics and Evolution , Volume 22 (Number 1). pp. 273-279. ISSN 1567-1348

Sawlekar, Rucha, Montefusco, Francesco, Kulkarni, Vishwesh V. and Bates, Declan. (2016) Implementing nonlinear feedback controllers using DNA strand displacement reactions. IEEE Transactions on NanoBioscience . ISSN 1536-1241 (In Press)

Schweiger, W. (Wolfgang), Steiner, B. (Barbara), Ametz, Christian, Siegwart, Gerald, Wiesenberger, Gerlinde, Berthiller, Franz, Lemmens, Marc, Jia, Haiyan, Adam, G. (Gerhard), Muehlbauer, Gary J., Kreil, David and Buerstmayr, Hermann. (2013) Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa-5A, identifies novel candidate genes. Molecular Plant Pathology, Volume 14 (Number 8). pp. 772-785. ISSN 1464-6722

Schwentner, Raphaela, Papamarkou, Theodore, Kauer, Maximilian O., Stathopoulos, Vassilios, Yang, Fan, Bilke, Sven, Meltzer, Paul S., Girolami, Mark and Kovar, Heinrich. (2015) EWS-FLI1 employs an E2F switch to drive target gene expression. Nucleic Acids Research . ISSN 0305-1048 (In Press)

Scialdone, Antonio and Nicodemi, Mario. (2008) Mechanics and dynamics of X-chromosome pairing at X inactivation. PL o S Computational Biology, Vol.4 (No.12). ISSN 1553-734X

Selama, Okba, Amos, Gregory C. A., Djenane, Zahia, Borsetto, Chiara, Laidi, Rabah Forar, Porter, David, Nateche, Farida, Wellington, E. M. H. and Hacène, Hocine. (2014) Screening for genes coding for putative antitumor compounds, antimicrobial and enzymatic activities from haloalkalitolerant and haloalkaliphilic bacteria strains of Algerian Sahara soils. BioMed Research International, 2014 . Article number 317524. ISSN 2314-6133

Sgamma, Tiziana, Jackson, Alison C., Muleo, Rosario, Thomas, Brian and Massiah, Andrea J.. (2014) TEMPRANILLO is a regulator of juvenility in plants. Scientific Reports, Volume 4 . Article number 3704. ISSN 2045-2322

Shah, Kunal M., Webber, Jason, Dr., Carzaniga, Raffaella, Taylor, Deborah M., Fusi, Luca, Clayton, Aled, Brosens, Jan J., Hartshorne, Geraldine M. and Christian, Mark. (2013) Induction of microRNA resistance and secretion in differentiating human endometrial stromal cells. Journal of Molecular Cell Biology, Volume 5 (Number 1). pp. 67-70. ISSN 1674-2788

Shi, Xiao Li, Marie, D., Jardillier, Ludwig, Scanlan, David J. and Vaulot, Daniel. (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS One, Vol.4 (No.10). Article No. e7657. ISSN 1932-6203

Shih, Chi-Tin, Wells, Stephen A., Hsu, Ching-Ling, Cheng, Yun-Yin and Roemer, Rudolf A.. (2012) The interplay of mutations and electronic properties in disease-related genes. Scientific Reports, Vol.2 (No.272). ISSN 2045-2322

Shrestha, Ram, Lubinsky, Baruch, Bansode, Vijay B., Moinz, Mónica B. J., McCormack, Grace P. and Travers, Simon A.. (2014) QTrim : a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform. BMC Bioinformatics, Volume 15 (Number 1). Article number 33. ISSN 1471-2105

Sidda, John D., Song, Lijang, Poon, Vincent, Al-Bassam, Mahmoud, Lazos, Orestis, Buttner, Mark J., Challis, Gregory L. and Corre, Christophe. (2014) Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chemical Science, Volume 5 . pp. 86-89. ISSN 2041-6520

Sirinukunwattana, Korsuk, Savage, Richard S., Bari, Muhammad F., Snead, David R. J. and Rajpoot, Nasir M. (Nasir Mahmood). (2013) Bayesian hierarchical clustering for studying cancer gene expression data with unknown statistics. PLoS One, 8 (10). e75748. ISSN 1932-6203

Smith, Edward M., Littrell, Jack and Olivier, M. (Michael). (2007) Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays. Genomics Proteomics & Bioinformatics, Vol.5 (No.3-4). pp. 256-259. ISSN 1672-0229

Smith, Edward M., Zhang, Y., Baye, T. M., Gawrieh, S., Cole, R., Blangero, J., Carless, Melanie A., Curran, Joanne E., Dyer, T. D., Abraham, L. J., Moses, E. K. (Eric Keith), Kissebah, Ahmed, Martin, L. J. (Lisa J.) and Olivier, M. (Michael). (2010) INSIG1 influences obesity-related hypertriglyceridemia in humans. Journal of Lipid Research, Vol.51 . pp. 701-708. ISSN 0022-2275

Smith, Oliver , Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun and Allaby, Robin G.. (2014) Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Scientific Reports, Volume 4 . Article number 5559. ISSN 2045-2322

Smith, Oliver , Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun and Allaby, Robin G.. (2014) A complete ancient RNA genome : identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Scientific Reports, Volume 4 . Article number 4003. ISSN 2045-2322

Snyder, Lori A. S., Loman, Nicholas J., Linton, James D., Langdon, Rebecca R., Weinstock, George M., Wren, Brendan and Pallen, Mark J.. (2010) Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. BMC Genomics, Volume 11 (Number 1). Article number 67. ISSN 1471-2164

Soyer, Orkun S. and Pfeiffer, Thomas. (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology, Volume 6 (Number 8). Article no. e1000907. ISSN 1553-7358

Srinivasan, Rajagopalan and Balasubramanian, M. J.. (2014) Bacteria spring a surprise. eLife, Volume 3 . Article number e03435. ISSN 2050-084X

Steinacher, Arno, Bates, Declan, Akman, Ozgur E. and Soyer, Orkun S.. (2016) Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels. PLoS One, 11 (4). e0153295. ISSN 1932-6203

Steinberg, Deborah Lynn. (2009) The search for the Jew's gene : science, spectacle, and the ethnic other. MediaTropes, Vol.2 (No.1). pp. 1-23. ISSN 1913-6005

Stock, Emily, Marriott, Anthony C. and Easton, A. J. (Andrew J.). (2014) The host-range tdCE phenotype of Chandipura virus is determined by mutations in the polymerase gene. Journal of General Virology, Volume 95 (Number 1). pp. 38-43. ISSN 0022-1317

Svensson, Per-Arne, Wahlstrand, Björn, Olsson, Maja, Froguel, Philippe, Falchi, Mario, Bergman, Richard N., McTernan, P. G. (Philip G.), Hedner, Thomas, Carlsson, Lena M. S. and Jacobson, Peter. (2014) CDKN2B expression and subcutaneous adipose tissue expandability : possible influence of the 9p21 atherosclerosis locus. Biochemical and Biophysical Research Communications, Volume 446 (Number 4). pp. 1126-1131. ISSN 0006-291X

Tandonnet, Sophie and Pires-da Silva, Andre. (2016) Phenotypic plasticity and developmental innovations in nematodes. Current Opinion in Genetics and Development, 39 . pp. 8-13. ISSN 0959-437X

Tesfaye, Mesfin, Silverstein, Kevin AT., Nallu, Sumitha, Wang, Lin, Botanga, Christopher J., Gomez, S. Karen, Costa, Liliana M., Harrison, Maria J., Samac, Deborah A., Glazebrook, Jane, Katagiri, Fumiaki, Gutierrez-Marcos, José F. and VandenBosch, Kathryn A.. (2013) Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes. PLoS One, Volume 8 (Number 3). Article no. e58992. ISSN 1932-6203

Theisen, Ulrike, Straube, Anne and Steinberg, Gero. (2008) Dynamic rearrangement of nucleoporins during fungal "open" mitosis. Molecular Biology of the Cell, Volume 19 (Number 3). pp. 1230-1240. ISSN 1059-1524

Traka, Maria H., Saha, Shikha, Huseby, Stine, Kopriva, Stanislav, Walley, Peter Glen, Barker, Guy C., Moore, Jonathan D., Mero, Gene, van den Bosch, Frans, Constant, Howard, Kelly, Leo, Schepers, Hans, Boddupalli, Sekhar and Mithen, Richard F.. (2013) Genetic regulation of glucoraphanin accumulation in Beneforté® broccoli. New Phytologist, Volume 198 (Number 4). pp. 1085-1095. ISSN 0028-646X

Turner, Matthew S. . (2000) Two time constants for the binding of proteins to DNA from micromechanical data. Biophysical Journal, Vol.78 (No.2). pp. 600-607. ISSN 0006-3495

Valdes, Ana M., Doherty, Sally A., Muir, Kenneth, Wheeler, Margaret, Maciewicz, Rose A., Zhang, Weiya and Doherty, Michael. (2013) The genetic contribution to severe post-traumatic osteoarthritis. Annals of the Rheumatic Diseases, Volume 72 (Number 10). pp. 1687-1690. ISSN 0003-4967

Valdes, Ana M., Doherty, Sally A., Muir, Kenneth, Zhang, Weiya, Maciewicz, Rose A., Wheeler, Margaret, Arden, N., Cooper, Cyrus and Doherty, Michael. (2012) Genetic contribution to radiographic severity in osteoarthritis of the knee. Annals of the Rheumatic Diseases, Vol.71 (No.9). pp. 1537-1540. ISSN 0003-4967

. (2011) Large scale replication study of the association between HLA class II/BTNL2 variants and osteoarthritis of the knee in European-descent populations. PLoS ONE, Vol.6 (No.8). ISSN 1932-6203

. (2011) The Ile585Val TRPV1 variant is involved in risk of painful knee osteoarthritis. Annals of the Rheumatic Diseases, Vol.70 (No.9). pp. 1556-1561. ISSN 0003-4967

Vlisidou, Isabella, Dowling, Andrea J., Evans, Iwan R., Waterfield, Nicholas R., ffrench-Constant, Richard H. and Wood, W. (Will). (2009) Drosophila embryos as model systems for monitoring bacterial infection in real time. PLoS Pathogens, Volume 5 (Number 7). Article number e1000518. ISSN 1553-7374

Vrljicak, P., Tao, S., Varshney, G. K., Quach, H. N. B., Joshi, A., LaFave, M. C., Burgess, S. M. and Sampath, Karuna. (2016) Genome-wide analysis of transposon and retroviral insertions reveals preferential integrations in regions of DNA flexibility. G3 : Genes Genomes Genetics, 6 (4). pp. 805-817. ISSN 2160-1836

Wang, Weishan, Yang, Tongjian, Li, Yihong, Li, Shanshan, Yin, Shouliang, Styles, Kathryn, Corre, Christophe and Yang, Keqian. (2016) Development of a synthetic oxytetracycline-inducible expression system for streptomycetes using de novo characterized genetic parts. ACS Synthetic Biology, 5 (7). pp. 765-773. ISSN 2161-5063

Wang, Yin, Wang, Xi, Wohland, Thorsten and Sampath, Karuna. (2016) Extracellular interactions and ligand degradation shape the nodal morphogen gradient. eLife, 5 . e13879. ISSN 2050-084X

Wentzel, Alexander, Bruheim, Per, Øverby, Anders, Jakobsen, Øyvind M, Sletta, Håvard, Omara, Walid A. M., Hodgson, D. A. (David A.) and Ellingsen, Trond E.. (2012) Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2). BMC Systems Biology, Volume 6 . Article number 59. ISSN 1752-0509

Williams, Tiffany M., Loman, Nicholas J., Ebruke, Chinelo, Musher, Daniel M., Adegbola, Richard A., Pallen, Mark J., Weinstock, George M. and Antonio, Martin. (2012) Genome analysis of a highly virulent serotype 1 strain of streptococcus pneumoniae from West Africa. PLoS One, Volume 7 (Number 10). Article number e26742. ISSN 1932-6203

Willox, Anna K., Sahraoui, Yasmina M. E. and Royle, Stephen J.. (2014) Non-specificity of Pitstop 2 in clathrin-mediated endocytosis. Biology Open, Volume 3 (Number 5). pp. 326-331. ISSN 2046-6390

Woodcock, Dan J., Vance, Keith W., Komorowski, Michal, Koentges, Georgy, Finkenstädt, Bärbel and Rand, D. A. (David A.). (2013) A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number. Bioinformatics, Volume 29 (Number 12). pp. 1519-1525. ISSN 1367-4803

Woolley, Michael J., Watkins, Harriet A., Taddese, Bruck, Karakullukcu, Z. Gamze, Barwell, James, Smith, Kevin J., Hay, Debbie L., Poyner, David, Reynolds, Christopher A. and Conner, Alex C.. (2013) The role of ECL2 in CGRP receptor activation : a combined modelling and experimental approach. Journal of The Royal Society Interface, Volume 10 (Number 88). p. 20130589. ISSN 1742-5689

Wright, Jordan L., Atwan, Zeenah, Morris, S. J. (Susan J.) and Leppard, K. N. (Keith N.). (2015) The human adenovirus type 5 L4 promoter is negatively regulated by TFII-I and by L4-33K. Journal of Virology, Volume 89 (Number 14). pp. 1-36. ISSN 0022-538X

Yuan, Yinyin, Li, Chang-Tsun and Windram, Oliver P.. (2011) Directed partial correlation : inferring large-scale gene regulatory network through induced topology disruptions. PL o S One, Vol.6 (No.4). ISSN 1932-6203

Zhang, Junlong, Zhang, F. (Fang), Didelot, Xavier, Bruce, Kimberley D., Cagampang, Felino R., Vatish, Manu, Hanson, Mark A., Lehnert, Hendrik, Ceriello, Antonio and Byrne, Christopher D.. (2009) Maternal high fat diet during pregnancy and lactation alters hepatic expression of insulin like growth factor-2 and key microRNAs in the adult offspring. BMC Genomics, Vol.10 (No.478). ISSN 1471-2164

Zhou, Zhemin, McCann, Angela, Litrup, Eva, Murphy, Ronan, Cormican, Martin, Fanning, Seamus, Brown, Derek, Guttman, David S., Brisse, Sylvain and Achtman, Mark. (2013) Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica serovar agona. PLoS Genetics, 9 (4). e1003471. ISSN 1553-7390

Zou, Cunlu, Ladroue, Christophe, Guo, Shuixia and Feng, Jianfeng. (2010) Identifying interactions in the time and frequency domains in local and global networks : a Granger causality approach. BMC Bioinformatics, Vol.11 . Article 337. ISSN 1471-2105

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

Conference Item

Bryson, K., Luck, Michael (Michael M.), Joy, Mike, Jones, D. T., Nicolas, P., Bessieres, P. and Gibrat, J.-F. (2002) From GeneWeaver to Agmial. In: Network Tools and Applications in Biology Workshop on Agents in Bioinformatics (NETTAB 2002), Bologna, Italy, 12-14 Jul 2002

Law, Timothy R., Hancox, Ian, Cheng, Tammy M. K., Chaleil, Raphael A. G., Wright, Steven A., Bates, Paul A. and Jarvis, Stephen A. (2016) Optimisation of a molecular dynamics simulation of chromosome condensation. In: 28th International Symposium on Computer Architecture and High Performance Computing, LA, USA, 26 -28 Oct 2016. Published in: Proceedings of 28th International Symposium on Computer Architecture and High Performance Computing (In Press)

Yuan, Yinyin and Li, Chang-Tsun (2009) Inferring causal relations from multivariate time series : a fast method for large-scale gene expression data. In: BioInformatics and BioEngineering (BIBE), 2009 Ninth IEEE International Conference on, Tʻai-chung shih (Taiwan), 2009 pp. 92-99.

Report

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

Thesis or Dissertation

Abouna, Sylvie (2009) Non-beta-cell progenitors in pregnant mice and the origin and functionality of beta-cells after diabetic recovery in a c-Myc ablation model. PhD thesis, University of Warwick.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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