Under the microscope: From pathogens to probiotics and back

References

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• Sleator RD. Phylogenetics. Arch Microbiol 2011; 193:235-9; PMID:21249334; http://dx.doi.org/10.1007/s00203-011-0677-x
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• Sleator RD. A beginner's guide to phylogenetics. Microb Ecol 2013; 66:1-4; PMID:23624570; http://dx.doi.org/10.1007/s00248-013-0236-x
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• Henry M, O'Sullivan O, Sleator RD, Coffey A, Ross RP, McAuliffe O, O'Mahony JM. In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil. Gene 2010; 453:9-23; PMID:20064590; http://dx.doi.org/10.1016/j.gene.2009.12.007
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• Sleator RD. An overview of the current status of eukaryote gene prediction strategies. Gene 2010; 461:1-4; PMID:20430068; http://dx.doi.org/10.1016/j.gene.2010.04.008
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• O'Mahony J, Fenton M, Henry M, Sleator RD, Coffey A. Lysins to kill - a tale of viral weapons of mass destruction. Bioeng Bugs 2011; 2:306-8; PMID:22008941; http://dx.doi.org/10.4161/bbug.2.6.16804
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• Lynch KM, Lucid A, Arendt EK, Sleator RD, Lucey B, Coffey A. Genomics of Weissella cibaria with an examination of its metabolic traits. Microbiology 2015; 161:914-30; PMID:25678547; http://dx.doi.org/10.1099/mic.0.000053
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• Sleator RD. An overview of the processes shaping protein evolution. Sci Prog 2010; 93:1-6; PMID:20222353; http://dx.doi.org/10.3184/003685009X12605492662844
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• Sleator RD, Walsh P. An overview of in silico protein function prediction. Arch Microbiol 2010; 192:151-5; PMID:20127480; http://dx.doi.org/10.1007/s00203-010-0549-9
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• Henry M, Coffey A, J OM, Sleator RD. Comparative modelling of LysB from the mycobacterial bacteriophage Ardmore. Bioeng Bugs 2011; 2:88-95; PMID:21636995; http://dx.doi.org/10.4161/bbug.2.2.14138
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• Fenton M, Cooney JC, Ross RP, Sleator RD, McAuliffe O, O'Mahony J, Coffey A. In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAP(K). Bacteriophage 2011; 1:198-206; PMID:23050213; http://dx.doi.org/10.4161/bact.1.4.18245
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• Sleator RD. Proteins: form and function. Bioeng Bugs 2012; 3:80-5; PMID:22095055; http://dx.doi.org/10.4161/bbug.18303
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• Sleator RD. Prediction of protein functions. Methods Mol Biol 2012; 815:15-24; PMID:22130980; http://dx.doi.org/10.1007/978-1-61779-424-7_2
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• Sleator RD. The story of Mycoplasma mycoides JCVI-syn1.0: the forty million dollar microbe. Bioeng Bugs 2010; 1:229-30; PMID:21327053
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• Sleator RD. Ferretting out the facts behind the H5N1 controversy. Bioeng Bugs 2012; 3:139-43; PMID:22402712; http://dx.doi.org/10.4161/bbug.20136
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• Sleator RD. Digital biology: a new era has begun. Bioengineered 2012; 3:311-2; PMID:23099453; http://dx.doi.org/10.4161/bioe.22367
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• Sleator RD. Synthetic ribosomes: making molecules that make molecules. Bioengineered 2013; 4:63-4; PMID:23324614; http://dx.doi.org/10.4161/bioe.23640
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• Sleator RD, O'Driscoll A. Digitizing humanity. Artificial DNA, PNA & XNA 2013; 4:37-8; PMID:23912716; http://dx.doi.org/10.4161/adna.25489
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• Sleator RD. The synthetic biology future. Bioengineered 2014; 5:69-72; PMID:24561910; http://dx.doi.org/10.4161/bioe.28317
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• Sleator RD. Genetics just got SEXY: Sequences encoding XY. Bioengineered 2014; 5:214-5; PMID:24847983; http://dx.doi.org/10.4161/bioe.29306
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• Sleator RD. The genetic code. Rewritten, revised, repurposed. Artificial DNA, PNA & XNA 2014; 5:e29408; PMID:25483933; http://dx.doi.org/10.4161/adna.29408
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• O'Driscoll A, Daugelaite J, Sleator RD. 'Big data', Hadoop and cloud computing in genomics. J Biomed Inform 2013; 46:774-81; PMID:23872175; http://dx.doi.org/10.1016/j.jbi.2013.07.001
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• Manning T, Sleator RD, Walsh P. Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics. Bioengineered 2014; 5:80-95; PMID:24335433; http://dx.doi.org/10.4161/bioe.26997
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• Manning T, Sleator RD, Walsh P. Naturally selecting solutions: the use of genetic algorithms in bioinformatics. Bioengineered 2013; 4:266-78; PMID:23222169; http://dx.doi.org/10.4161/bioe.23041
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• Walsh P, Carroll J, Sleator RD. Accelerating in silico research with workflows: a lesson in Simplicity. Comput Biol Med 2013; 43:2028-35; PMID:24290918; http://dx.doi.org/10.1016/j.compbiomed.2013.09.011
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• O'Driscoll A, Belogrudov V, Carroll J, Kropp K, Walsh P, Ghazal P, Sleator RD. HBLAST: Parallelised sequence similarity - A Hadoop MapReducable basic local alignment search tool. J Biomed Inform 2015; 54:58-64; PMID:25625550; http://dx.doi.org/10.1016/j.jbi.2015.01.008
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• Walsh P, Bekaert M, Carroll J, Manning T, Kelly B, O'Driscoll A, Lu X, Smith C, Dickinson P, Templeton K, et al. Draft genome sequences of six different staphylococcus epidermidis clones, isolated individually from preterm neonates presenting with sepsis at Edinburgh's royal infirmary. Gen Announc 2015; 3; PMID:25977439; http://dx.doi.org/10.1128/genomeA.00471-15
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Templeton K, Smith C, Dickinson P, O'Driscoll A, et al. Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient. Gen Announc 2014; 2; PMID:25212624
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Templeton K, Smith C, Dickinson P, O'Driscoll A, et al. Draft genome sequence of a staphylococcus aureus isolate taken from the blood of a preterm neonatal blood sepsis patient. Gen Announc 2014; 2; PMID:25212625
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, et al. Draft genome sequence of a streptococcus agalactiae strain isolated from a preterm neonate blood sepsis patient at the royal infirmary, Edinburgh, Scotland. Gen Announc 2014; 2; PMID:25189584
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, et al. Draft genome sequence of a staphylococcus warneri strain isolated from a preterm neonate blood sepsis patient at the royal infirmary, Edinburgh, Scotland. Gen Announc 2014; 2; PMID:25189586
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, et al. Draft genome sequence of an enterococcus faecalis strain isolated from a neonatal blood sepsis patient. Gen Announc 2014; 2; PMID:25212626
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• Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, et al. Draft genome sequence of a serratia marcescens strain isolated from a preterm neonatal blood sepsis patient at the royal infirmary, Edinburgh, Scotland, United Kingdom. Gen Announc 2014; 2; PMID:25212627
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