Lee Coffey

Lee Coffey
Waterford Institute of Technology | WIT · Department of Science

About

147
Publications
4,331
Reads
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313
Citations
Additional affiliations
January 2005 - December 2012
Waterford Institute of Technology

Publications

Publications (147)
Article
Full-text available
This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used in the sequencing pipeline in order to allow the perpetrators to gain control over the resources used...
Preprint
Full-text available
This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used in the sequencing pipeline in order to allow the perpetrators to gain control over the resources used...
Article
Full-text available
Biocomputing systems based on engineered bacteria can lead to novel tools for environmental monitoring and detection of metabolic diseases. In this paper, we propose a Bacterial Molecular Computing on a Chip (BMCoC) using microfluidic and electrochemical sensing technologies. The computing can be flexibly integrated into the chip, but we focus on e...
Conference Paper
Full-text available
Synthetic biology has utilised engineering concepts for the rational design of biocompatible systems. Here we utilise two bacterial populations to create a modulated molecular channel coding scheme for molecular communications systems. We believe this approach can drive the development of more reliable biocompatible molecular communications systems...
Article
Full-text available
The current treatment for the acquired retinal vasculopathies involves lifelong repeated intravitreal injections of either anti-vascular endothelial growth factor (VEGF) therapy or modulation of inflammation with steroids. Consequently, any treatment modification that decreases this treatment burden for patients and doctors alike would be a welcome...
Preprint
Full-text available
Biocomputing systems based on engineered bacteria can lead to novel tools for environmental monitoring and detection of metabolic diseases. In this paper, we propose a Bacterial Molecular Computing on a Chip (BMCoC) using microfluidic and electrochemical sensing technologies. The computing can be flexibly integrated into the chip, but we focus on e...
Preprint
Full-text available
Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the emission of a superfolded green fluorescence protein from a bacterial population that will flow through hydrogel, w...
Article
Full-text available
A comprehensive series of optimization studies including pH, solvent and temperature were completed on the nitrile hydrolyzing Rhodococcus erythropolis bacterium SET1 with the substrate 3‐hydroxybutyronitrile. These identified temperature of 25 °C and pH of 7 as the best conditions to retain enantioselectivity and activity. The effect of the additi...
Conference Paper
The article focuses on the information security risks that arise from the use of dubious software as part of a DNA-sequencing pipeline. We show how the perpetrator can use a biologically engineered sample that contains the remote machine's IP address and port number to trigger Trojan spyware previously dormant, and create a connection to the remote...
Article
In this work, a series of novel organocatalysts derived from unique unnatural β‐amino acid scaffold were synthesized and further developed to enhance the desired catalytic properties. Their evaluation was carried out in the asymmetric crossed‐aldol condensation of isatin and enolizable ketone donors. Following a systematic study of the reaction par...
Article
Full-text available
We present the work towards strengthening the security of DNA-sequencing functionality of future bioinformatics systems against bio-computing attacks. Recent research has shown how using common tools, a perpetrator can synthesize biological material, which upon DNA-analysis opens a cyber-backdoor for the perpetrator to hijack control of a computati...
Article
Full-text available
Nitrilase enzymes (EC 3.5.5.1) are responsible for the direct hydration of nitriles to their corresponding carboxylic acids and ammonia. The utilization of nitrilase enzymes in biocatalysis toward bio‐pharmaceuticals and industrial applications facilitates the move towards green chemistry. The body of research presented describes a novel clade‐spec...
Article
Full-text available
Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data are needed, and one promising media is the DNA. This storage solution provides numerous advantages, which includ...
Article
A metagenomic approach was used to search for novel nitrile hydrolyzing enzymes from environmental samples. Nitrile compounds are versatile and can be converted into amides, amines, imines, oximes, carboxylic acids, esters and alcohols, encompassing a large group of economically important synthetic intermediates. The pharmaceutical industry particu...
Article
Aldoxime dehydratase catalyses the conversion of aldoximes to their corresponding nitriles. Utilization of the aldoxime-nitrile metabolising enzyme pathway can facilitate the move towards a greener chemistry. In this work, a real-time PCR assay was developed for the detection of aldoxime dehydratase genes in aldoxime/nitrile metabolising microorgan...
Poster
Full-text available
High ammonia concentrations in groundwater can have serious ecological consequences, such as fish kills and algal blooms. Ammonia contamination can be remediated by the biological conversion of ammonium into nitrate (nitrification) and its subsequent reduction into nitrite (denitrification). At a former landfill site with ammonia-contaminated groun...
Poster
Full-text available
High ammonia concentrations in groundwater can have serious ecological consequences, such as fish kills and algal blooms. Ammonia contamination can be remediated by the biological conversion of ammonium into nitrate (nitrification) and its subsequent reduction into nitrite (denitrification). Ammonia-contaminated groundwater from a former landfill s...
Article
Assessment of Rhodococcus erythropolis SET1, a novel nitrile hydrolysing bacterial isolate, has been undertaken with 34 nitriles, 33 chiral and 1 prochiral. These substrates consist primarily of β-hydroxy nitriles with varying alkyl and aryl groups at the β position and containing in several compounds different substituents α to the nitrile. In the...
Poster
R. erythropolis SET-1 was identified as a promising nitrile metabolising isolate due to it's ability to degrade 3-Hydroxybutyronitrile to 3-Hydroxybutyric acid with a high level of enantioselectivity. In order to exploit the nitrile metabolising activity displayed, the gene of interested should be identified. Previous attempts to identify the gene...
Article
Nitrile hydrolysing enzymes have found wide use in the pharmaceutical industry for the production of fine chemicals. This work presents a strategy that facilitates the rapid identification of bacterial isolates demonstrating nitrile hydrolysing activity. The strategy incorporates toxicity, starvation and induction studies along with subsequent colo...
Article
Full-text available
Developing strategies to maintain biodiversity requires baseline information on the current status of each individual species. The development of genetic techniques and their application to noninvasively collected samples have the potential to yield information on the structure of elusive animal populations and so are important tools in conserva-ti...
Article
Full-text available
We have developed TaqMan based assays for species-specific identification of two species of squirrel found in the British Isles, the native red squirrel (Sciurus vulgaris) and the introduced north American grey squirrel (Sciurus carolinensis). These assays correctly identified tissue and hair samples of both species and there was no cross-species a...
Article
The aim was to investigate pathogen survival during composting of pig manure solids with and without bulking agents in two trials of 56 days duration, each with four treatments. Salmonella was detected in the sawdust and straw bulking agents but was undetectable in the compost, except in one treatment at day 0. Enteric indicator organisms were redu...
Article
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation...
Article
Full-text available
To enhance the information pertaining to the epidemiology of a collection of 378 Listeria spp. isolates obtained from several food-processing plants in Ireland over a 3-year period (2004-2007). The collection was characterized by pulsed-field gel electrophoresis (PFGE). The most prevalent pulse-type was PFGE profile I (n=14·5%) that consisted mainl...

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