Paul Walsh

Cork Institute of Technology | CIT · Department of Computer Science

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task...

Background: The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the...

Affective Computing is a rather new and multidisciplinary research field that seeks for sophisticated automation in emotion detection for later analysis. However, the automated emotion detection and analysis require as well comprehensive data management support e.g. to keep control about produced data, to enable its efficient reuse through classifi...

The reduced cost of DNA sequencing allows metagenomics to be applied on a larger scale. With metagenomic analysis, we have better insight into supplement usage, methane production, and feed conversion efficiency in livestock systems. Nevertheless, sequencing machines generate an enormous amount of complex data. Conventional method used in the analy...

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to...

26 selected full papers and 13 short papers (extended abstracts) of the Collaborative European Research Conference (CERC 2019) at Darmstadt University of Applied Sciences – Darmstadt, Germany, March 29-30 2019, https://www.cerc-conf.eu. Proceedings are online under: http://CEUR-WS.org/Vol-2348/

Abstract: The use of serious games to support learning continues to expand across a range of educational and training settings. Hence, a need to better understand how users experience such games has arisen. This study seeks to describe and assess an approach to the evaluation of user-experience applied within the context of a specific serious game...

Advanced genomic technologies such as whole genome sequencing offer scientists unrivaled opportunities to investigate the dynamics of microbial communities in a variety of domains in medicine, life science and agriculture. The robust interpretation of datasets generated by a whole genome sequencing require advanced computational methods that can pe...

Media use cases for emergency services require mission-critical levels of reliability for the delivery of media-rich services, such as video streaming. With the upcoming deployment of the fifth generation (5G) networks, a wide variety of applications and services with heterogeneous performance requirements are expected to be supported, and any migr...

The field of medical information technology is advancing, standards are maturing, and systems such as electronic health records (EHRs) are increasingly being adopted (Yamamoto et al., 2012). However, clinical IT requirements are also continually evolving and expanding rapidly (Anhøj, 2003; Bates et al., 2014). Therefore, more efficient approaches a...

This paper describes a new emotional detection system based on a video feed in real-time. It demonstrates how a bespoke machine learning support vector machine (SVM) can be utilized to provide quick and reliable classification. Features used in the study are 68-point facial landmarks. In a lab setting, the application has been trained to detect six...

People’s worries about robot and AI software and how it can go wrong have led them to think of it and its associated algorithms and programs as being like Mary Shelley’s Frankenstein monster. The term Franken-algorithms has been used. Furthermore, there are concerns about driverless cars, automated General Practitioner Doctors (GPs) and robotic sur...

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires stan...

High-level resistance and treatment failures with ceftriaxone and azithromycin, the first-line agents for gonorrhoea treatment are reported and antimicrobial-resistant Neisseria gonorrhoeae is an urgent public health threat. Our aims were to determine antimicrobial resistance rates, resistance determinants and phylogeny of N. gonorrhoeae in Ireland...

Network slicing has emerged as a major new networking paradigm for meeting the diverse requirements of various vertical businesses in virtualised and softwarised 5G networks. SliceNet is a project of the EU 5G Infrastructure Public Private Partnership (5G PPP) and focuses on network slicing as a cornerstone technology in 5G networks, and addresses...

Semantic applications today provide benefits to numerous organisations in business sectors such as health care, finance, industry, and the public sector. These applications use the semantics of a domain in order to improve usability, correctness, and completeness. Developing semantic applications requires methodological skills, e.g., ontology engin...

Medical consultants face increasing challenges in keeping up-to-date with the rapid development of new treatments and medications. Information providers offer evidence-based medical information services, continuously taking into account new publications and medical developments. This article describes a personalised clinical decision support system...

Background Bioinformatic research is increasingly dependent on large-scale data sets, accessed either from private or public repositories. An example of a public repository is NCBI’s RefSeq. These repositories must decide in what form to make their data available. Unstructured data can be put to almost any use, but are limited in how access to them...

45 Extended abstracts and 19 selected full papers of the Collaborative European Research Conference CERC 2017 Karlsruhe University of Applied Sciences – Karlsruhe, Germany 22 - 23 September 2017 www.cerc–conference.eu

Semantic applications today provide benefits to numerous organisations in business sectors such as health care, finance, industry, and the public sector. These applications use the semantics of a domain in order to improve usability, correctness, and completeness. Developing semantic applications requires methodological skills, e.g., ontology engin...

This paper discusses an opportunity for using affective computing modalities to support the monitoring of emotional wellbeing of older people. The ageing population is escalating and is associated with an increase in the number of persons with dementia. It is also reported that older people can suffer from social isolation and that people with deme...

Neonates and especially premature infants are highly susceptible to infection but still can have a remarkable resilience that is poorly understood. The view that neonates have an incomplete or deficient immune system is changing. Human neonatal studies are challenging, and elucidating host protective responses and underlying cognate pathway biology...

Members of STRING networks.

DEGs between cord and adult DCs.

GPCR SMARTpool RNAi screen.

Precision medicine can be empowered by a personalized approach to patient care based on the patient's unique genomic sequence. To be used in precision medicine, genomic findings must be robust, reproducible, and experimental data capture should adhere to FAIR Data Guiding Principles. Moreover, precision medicine requires standardization that extend...

This paper describes a new prototype for using the Intel RealSenseTM (Intel, 2017) commercial camera system, a support vector machine (SVM) and multiple facial expression databases to predict emotional states with high accuracy. The system, called the Mobile Agitation Tracker, aims to be used for the detection of agitation and discomfort for patien...

Here, we report the draft genome assemblies of 14 azithromycin-resistant Neisseria gonorrhoeae clinical isolates, representing the first such strains identified in Ireland. Among these isolates are the first reported highly resistant strains (MIC >256 mg/liter), which both belonged to the ST1580 sequence type.

The genetics of antibiotic sensitivity in Clostridioides (Clostridium) difficile remain less well defined relative to other clinical pathogens. As part of our microbial genomics program in collaboration with St. James’s Hospital, Dublin, we have sequenced a bank of over 300 C. difficile isolates. We sought to use this genomic data to investigate th...

Sepsis is a life-threatening immune response to bacterial infection that is difficult to accurately diagnose. Little is known about the human neonatal immune system and in clinical practice, there is a low threshold to treat with broad-spectrum antibiotics. This poses complications toward stewardship of antimicrobial resistance and can have iatroge...

This paper examines whether textural generation system imagery evolved with computational aesthetic support can be judged as having aesthetic attributes, both knowing and not knowing its true origins. Such a generation, depicting a digital landscape, is offered to participants to appraise. A fictitious account of the origins of the piece is initial...

The MAT project aims to develop and evaluate an initial set of algorithms that can detect agitation, restlessness and aggression in dementia patients. MAT uses vision based analytics to track a subjects facial expressions in real-time. The first version of MAT has implemented two use cases for the detection of restlessness and aggression. The proje...

In today's world, which has recently seen fractures and isolation forming among states, internationaland interdisciplinary collaboration has become an important source of progress. Collaboration is arich source of innovation and growth and it is the goal of the Collaborative European ResearchConference (CERC 2016) to foster collaboration among frie...

Sequence alignment is a key bioinformatics technique for identifying DNA, RNA and protein sequences that are similar due to functional, structural or evolutionary relationships. This paper focuses on the identification and analysis of messenger RNA (mRNA), type of RNA molecule, that conveys genetic information from DNA to molecular machinery, known...

In recent years, the number of projects producing very large quantities of sequence data for analysis of the community structure and environmental interactions of microbes, has increased dramatically. Yet, the depth of analysis and visualisation performed is very superficial, reflecting an inefficient use of available information and financial reso...

A bioinformatic researcher, when seeking novel ways to process genomic data, will naturally look for a standarad reference genomic database to test their new ideas against. Perhaps the best-known genomic reference is NCBI's Blast[1]. The word 'Blast' can refer both to the database and to the search algorithm used to access it, and in fact this ambi...

Given the rapidly growing number of medical publications and resources, consultants face challenges in keeping up-to-date with current research and patient care best practices. This paper presents the concept and prototypical implementation of a Clinical Decision Support System (CDSS) for personalized medicine. It satisfies information needs of con...

Keywords Bioinformatics pipeline; pathogen biomarker; neonatal sepsis. Abstract Neonatal sepsis is a severe infection with a high mortality rate of newborns worldwide. Currently, standard treatment of bacterial sepsis includes antibiotic prescription. However, the rapid evolution of antibiotic resistance in sepsis pathogens foreshadows the urgent n...

The cost of developing parallelized software is the current significant bottleneck in the bioinformatics pipeline. This paper identifies the use of low-level threading abstractions as one cause for these elevated costs, and proposes alternatives which offer better value. We identify a core set of higher abstractions to accomplish low-cost multi-cor...

Handling the complexity of relevant data requires new techniques about data access, visualization, perception, and interaction for innovative and successful strategies. In order to address human-computer interaction, cognitive eficiency, and interoperability problems, a generic information visualization, user empowerment, as well as service integra...

This paper introduces an approach to develop an up-todate information technology infrastructure that can support Advanced Visual User interfaces for Distributed Big Data Analysis in Virtual Labs to be used in eScience, Industrial Research, and Data Science Education. The paper introduces and motivates the current situation in this application area...

With the advent of next-generation sequencing technology, clinical data sets now contain enormous amounts of valuable genomic information related to a wide range of diseases such as cancer. This data needs to be analysed, managed, stored, visualized and integrated in order to be clinically useful. However, many clinicians and researchers, who need...

Analytics and visualisation of Big Data appearance is still a challenging task. In this paper, the management and visualisation of big data streams will be discussed at hand of data that comes into existence during the care of people with dementia in their own homes. Therein, basic requirements are explored towards the development of a data managem...

This paper reviews recent research relating to the application of bioinformatics approaches to determining HIV-1 protease specificity, outlines outstanding issues, and presents a new approach to addressing these issues. Leading machine learning theory for the problem currently suggests that the direct encoding of the physicochemical properties of t...