Publications

Publications from 2019

1. “Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir”, Conor Slattery,Paul D. Cotter and Paul W. O’Toole
2. “Prediction of 24-hour milk yield and composition in dairy cows from a single part-day yield and sample”, McParland, S., Coughlan, B., Enright, B., O’Keeffe, M., O’Connor, R., Feeney, L., Berry, D.P.
3. “Improvement of Feed Efficiency in Pigs through Microbial Modulation via Fecal Microbiota Transplantation in Sows and Dietary Supplementation of Inulin in Offspring”, Ursula M. McCormack, Tânia Curião, Barbara U. Metzler-Zebeli, Toby Wilkinson, Henry Reyer, Fiona Crispie, Paul D. Cotter, Christopher J. Creevey, Gillian E. Gardiner, Peadar G. Lawlor
4. “A large interactive visual database of copy number variants discovered in taurine cattle”, Kommadath, A., Grant, J.R., Krivushin, K., Butty, A.M., Baes, C.F., Carthy, T.R., Berry, D.P. and Stothard, P.
5. Feed efficiency and carcass metrics in growing cattle, David N Kelly, Craig Murphy, Roy D Sleator, Michelle M Judge, Stephen B Conroy, Donagh P Berry
6. “Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields”, Donagh P Berry, Thierry Pabiou, Rory Fanning, Ross D Evans, Michelle M Judge
7. “Potential exists to change, through breeding, the yield of individual primal carcass cuts in cattle without increasing overall carcass weight”, Michelle M Judge, Thierry Pabiou, Jessica Murphy, Stephen B Conroy, P J Hegarty, Donagh P Berry
8. “Predicted carcass meat yield and primal cut yields in cattle divergent in genetic merit for a terminal index”, Stephen M Connolly, Andrew R Cromie, Roy D Sleator, Donagh P Berry
9. “Associations between colostrum management, passive immunity, calf-related hygiene practices, and rates of mortality in preweaning dairy calves”, J.Barry, E.A.M.Bokkers, D.P.Berry, I.J.M.de Boer, J.McClure, E.Kennedy
10. “Choice of artificial insemination beef bulls used to mate with female dairy cattle”, D.P.Berry, S.C.Ring, A.J.Twomey, R.D.Evans
11. “Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population”, D. C. Purfield, R. D. Evans and D. P. Berry
12. “Leveraging Social Network Analysis for Characterizing Cohesion of Human-Managed Animals”, Dixon Vimalajeewa  ; Sasitharan Balasubramaniam ; Bernadette O’Brien ; Chamil Kulatunga ; Donagh P. Berry
13. “Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice”, Raul Cabrera-Rubio, Angela M. Patterson, Paul D. Cotter & Naiara Beraza
14. Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis, David Lynch, Paula M. O’Connor, Paul D. Cotter, Colin Hill, Des Field,Maire Begley
15. “Genetics of bull semen characteristics in a multi-breed cattle population.”, Berry DP, Eivers B, Dunne G, McParland S
16. “How herd best linear unbiased estimates impact the progress achievable from gains in additive and non-additive genetic merit”, F.L.Dunne, S.McParland, M.M.Kelleher, S.W.Walsh, D.P.Berry
17. “Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle”, Twomey, A.J., Berry, D.P., Evans, R.D., Diherty, M.L., Grham, D.,A., and Purfield D. C.
18. “Nanoimprint Lithography–Based Fabrication of Plasmonic Array of Elliptical Nanoholes for Dual-Wavelength, Dual-Polarisation Refractive Index Sensing”, Robinson, Caoimheand Justice, Johnand Pet, Jarnoand Karppinen, Mikkoand Corbett, Brianand O’Riordan, Alanand Lovera, Pierre
19. “Moving Forward with Molecular Communication: from Theory to Human Health Applications”, Ian F Akyildiz, Massimiliano Pierobon, Sasitharan Balasubramaniam
20. “Co-simulation of electricity distribution networks and peer to peer energy trading platforms”, B.P. Hayes, S. Thakur, J.G. Breslin
21. “Weather forecasts to enhance an Irish grass growth model”, J.McDonnell, C.Brophy, E.Ruelle, L.Shalloo, K.Lambkin D.Hennessy
22. “Effect of parity weighting on milk production forcast models”, Zhang F., Upton J., Shalloo L. and Murphy M.D.
23. “Bioengineering nisin to overcome the nisin resistance protein”, Des Field, Tony Blake, Harsh Mathur, Paula M. O’ Connor, Paul D. Cotter, R. Paul Ross, Colin Hill
24. “Cattle stratified on genetic merit segregate on carcass characteristics, but there is scope for improvement”, Donagh P Berry, Thierry Pabiou, Denis Brennan, Patrick J Hegarthy, Michelle M Judge
25. “Dietary α-lactalbumin alters energy balance, gut microbiota composition and intestinal nutrient transporter expression in high-fat diet-fed mice”, Serena Boscaini, Raul Cabrera-Rubio, John R. Speakman, Paul D. Cotter, John F. Cryan and Kanishka N. Nilaweera
26. “Dressing percentage and the differential between live weight and carcass weight in cattle are influenced by both genetic and non-genetic factors”, Jessica M Coyne, Ross D Evans, Donagh P Berry
27. “Factors associated with the weight of individual primal cuts and their inter-relationship in cattle”, Michelle M Judge, Thierry Pabiou, Stephen Conroy, Rory Fanning, Martin Kinsella, Diarmaid Aspel, Andrew R Cromie, Donagh P Berry
28. “Genetic parameters for animal mortality in pasture-based, seasonal-calving dairy and beef herds”, S.C. Ring, R.D.Evans, M.L.Doherty, D.P.Berry
29. “Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs”, Héctor Argüello, Jordi Estellé, Finola C. Leonard, Fiona Crispie, Paul D. Cotter, Orla O’Sullivan, Helen Lynch, Kavita Walia, Geraldine Duffy, Peadar G. Lawlor, Gillian E. Gardiner
30. “Lactobacillus gasseri APC 678 Reduces Shedding of the Pathogen Clostridium difficile in a Murine Model”, Lisa Quigley, Mairéad Coakley, Debebe Alemayehu, Mary C. Rea, Patrick G. Casey, Órla O’Sullivan, Eileen Murphy, Barry Kiely, Paul D. Cotter, Colin Hill and R. Paul Ross
31. “The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline”, Mahdi Ghanbari, Viviana Klose, Fiona Crispie & Paul D. Cotter
32. “The effect of ovine milk fermentation on the antithrombotic properties of polar lipids”, Ronan Lordan, Aaron M.Walsh, Fiona Crispie, LauraFinnegan, Paul D.Cotter, Ioannis Zabetakis
33. “Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits”, Daniel Martins, Michael T Barros, Sasitharan Balasubramaniam
34. “An Information Theoretic Framework to Analyze Molecular Communication Systems Based on Statistical Mechanics”, Ian F. Akyildiz, Massimiliano Pierobon, Sasitharan Balasubramaniam
35. “Genetic (co)variances between milk mineral concentration and chemical composition in lactating Holstein-Friesian dairy cows”, G. Visentin, G. Niero, D. P. Berry, A. Costa, M. Cassandro, M. De Marchi and M. Penasa
36. “Scenarios to limit environmental nitrogen losses from dairy expansion.”, Hoekstra NJ, Schulte RPO, Forrestal PJ, Hennessy D, Krol DJ, Lanigan GJ, Müller C, Shalloo L, Wall DP, Richards KG
37. “Setting targets for the Irish Dairy Industry”, L. Shalloo and L. Hanrahan
38. “Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials”, Marija Miljkovic, Sofija Jovanovic, Paula M. O’Connor, Nemanja Mirkovic, Branko Jovcic, Brankica Filipic, Miroslav Dinic, David John Studholme, Djordje Fira, Paul D. Cotter, Milan Kojic
39. “Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters”, Colin Fogarty, Catherine M. Burgess, Paul D. Cotter, Raul Cabrera‐Rubio, Paul Whyte, Conor Smyth, Declan J. Bolton
40. “Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components”, Cathy Lordan, Dinesh Thapa, R. Paul Ross & Paul D. Cotter
41. “An examination of the effects of labor efficiency on the profitability of grass-based, seasonal-calving dairy farms.”, Deming J, Kinsella J, O’Brien B, Shalloo L
42. “Effect of introducing weather parameters on the accuracy of milk production forecast models.”, F. Zhang, J. Upton, L. Shalloo, P. Shine, M. D. Murphy.
43. “Structure, stability and water adsorption on ultra-thin TiO2 supported on TiN”, José Julio Gutiérrez Moreno, Marco Fronzi, Pierre Lovera , Alan O’Riordan , Michael J. Ford , Wenjin Li and Michael Nolan
44. VAssociating cow characteristics with mobility scores in pasture-based dairy cows.”, O’Connor AH, Bokkers EAM, de Boer IJM, Hogeveen H, Sayers R, Byrne N, Ruelle E, Shalloo L
45. “Evaluation and application potential of an accelerometer-based collar device for measuring grazing behavior of dairy cows.V, Werner J, Umstatter C, Leso L, Kennedy E, Geoghegan A, Shalloo L, Schick M, O’Brien B
46. “A breeding index to rank beef bulls for use on dairy females to maximize profit”, D.P.Berry, P.R.Amer, R.D.Evans, T.Byrne, A.R.Cromie, F.Hely
47. “Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake”, Ursula M. McCormack, Tânia Curião, Barbara U. Metzler-Zebeli, Elizabeth Magowan, Donagh P. Berry, Henry Reyer, Maria L. Prieto, Stefan G. Buzoianu, Michael Harrison, Natalie Rebeiz, Fiona Crispie, Paul D. Cotter, Orla O’Sullivan, Gillian E. Gardiner, Peadar G. Lawlor
48. “Leveraging Fog Analytics for Real-Time Animal Localization in IoT-Enabled Dairy Farms.”, K. Bhargava, S. Ivanov, D. McSweeney,W. Donnelly.
49. “Genomic Regions Associated With Gestation Length Detected Using Whole-Genome Sequence Data Differ Between Dairy and Beef Cattle.”, Purfield DC, Evans RD, Carthy TR, Berry DP
50. “Candidate genes associated with the heritable humoral response to Mycobacterium avium subspecies paratuberculosisin dairy cows have factors in common with gastrointestinal diseases in humans”, McGovern, S. P., Purfield, D. C., Ring, S. C., Carthy, T. R., Graham, D. A., & Berry, D. P
51. “A description and evaluation of the physical and financial characteristics of dairy farms operating on soil types classified as poorly drained and associated with high rainfall”, Liam Hanrahan, Pat Tuohy, Noirin McHugh, James O’Loughlin, Brian Moran, Pat Dillon, James Breen, Michael Wallace, Laurence Shalloo
52. “Linkage between Predictive Transmitting Ability of a Genetic Index (EBI), Potential Milk Production and a Dynamic Model (PBHDM)”, Ruelle e., Delaby L. and Shalloo L
53. “Effect of parity weighting on milk production forecast models”, F. Zhang, J. Upton, L. Shalloo, M.D. Murphy
54. “Leveraging Social Network Analysis “for Evaluating Animal Cohesion.”, Dixon Vimalajeewa, Chamil Kulatunga, Sasitharan Balasubramaniam, Brendatte O’Brien, Donagh P Berry
55. “Dietary alpha-lactalbumin alters energy balance, gut microbiota composition and intestinal nutrient transporter expression in high-fat diet fed mice”, Serena Boscaini, Raul Cabrera-Rubio, John R. Speakman, Paul D. Cotter, John F. Cryan and Kanishka N. Nilaweera
56. “Development of a welfare assessment protocol for dairy calves from birththrough to weaning”, J Barry, E Kennedy, R Sayers, IJM de Boer and EAM Bokkers
57. “A mating advice system in dairy cattle incorporating genomic information”, Carthy TR, McCarthy J, Berry DP
58. “Effect of teatcup removal settings on milking efficiency and milk quality in a pasture-based automatic milking system”, Silva Boloña, P., D. J. Reinemann, and J. Upton
59. “Pasture allowance, duration, and stage of lactation—Effects on early and total lactation animal performance”, Emer Kennedy
60. “Predicting the dry matter intake of grazing dairy cows using infrared reflectance spectroscopy analysis”, Emer Kennedy
61. “First evidence of production of the lantibiotic nisin P”, Paul Cotter

Publications from 2020

1. “Observed progeny performance validates the benefit of mating genetically elite beef sires to dairy females”, D.P.Berry & S.C.Ring.
2. “Dairy-derived peptides for satiety”, Alina Kondrashina, André Brodkorb, Linda Giblin. 
3. “Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds”, Jennifer L. Doyle, Donagh P. Berry, Roel F. Veerkamp, Tara R. Carthy, Ross D. Evans, Siobhán W. Walsh & Deirdre C. Purfield.
4. “Electrochemical-Based Serological Detection of Bovine Immunoglobulin G in Calves”, Caoimhe Robinson, Niamh Creedon, Riona Sayers, Emer Kennedy, Alan O Riordan.
5. “Grazing Cow Behavior and Lameness”, Niall W. O’Leary, Daire. T. Byrne, Pauline Garcia, Jessica Werner, Morgan Cabedoche, and Laurence Shalloo.
6. “Electrochemical Detection of Free-Chlorine in Water Samples Facili-tated by in-situpH Controlusing Interdigitated Microelectrodes”, Ian Seymour, Benjamin O’Sullivan, Pierre Lovera, James F. Rohan, and Alan O’Riordan.
7. “The use of subjectively assessed muscular and skeletal traits on live cattle to aid in differentiation between animal genetically divergent in carcass kill out metrics”, D.P.Berry J.M.Coyne J.Doyle R.D.Evans.
8. “Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle”, Pierce Rafter, Isobel Claire Gormley, Andrew C. Parnell, John Francis Kearney & Donagh P. Berry.
9. “A Wristwatch-BasedWireless Sensor Platform for IoT Health Monitoring Applications”, Sanjeev Kumar, John L. Buckley, John Barton, Melusine Pigeon, Robert Newberry, Matthew Rodencal, Adhurim Hajzeraj, Tim Hannon, Ken Rogers, Declan Casey, Donal O’Sullivan and Brendan O’Flynn.
10. “Highly Sensitive SERS Detection of Neonicotinoid Pesticides. Complete Raman Spectral Assignment of Clothianidin and Imidacloprid”, Niamh Creedon, Pierre Lovera, Jose Julio Gutierrez Moreno, Michael Nolan, Alan O’Riordan.
11. “Grazing Cow Behavior’s Association with Mild and Moderate Lameness”, Niall W. O’Leary, Daire. T. Byrne, Pauline Garcia, Jessica Werner, Morgan Cabedoche and Laurence Shalloo.
12. “Energy-Aware Tracking of Mobile Targets by Bacterial Nanonetworks”, Nabiul Islam; Saswati Pal; Sasitharan Balasubramaniam; Sudip Misra.
13. “Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle”, Deirdre C Purfield, Ross D Evans, Donagh P Berry.
14. “The probiotic L. casei LC-XCAL™ improves metabolic health in a diet-induced obesity mouse model without altering the microbiome”, Calum J. Walsh , Selena Healy , Paul W. O’Toole , Eileen F. Murphy & Paul D.Cotter.
15. “Good Counterfactuals and Where to Find Them: A Case-Based Technique for Generating Counterfactuals for Explainable AI (XAI)”, Mark T. Keane & Barry Smyth.
16. “Animal-level factors associated with the achievement of desirable specifications in Irish beef carcasses graded using the EUROP classification system”, David Kenny, Craig P Murphy, Roy D Sleator, Michelle M Judge, Ross D Evans, Donagh P Berry.
17. “Cow and herd-level risk factors associated with mobility scores in pasture-based dairy cows”, A.H.O’Connor, E.A.M.Bokkers, I.J.M.de Boer, H.Hogeveen, R.Sayers, N.Byrne, E.Ruelle, B.Engel, L.Shalloo
18. “Validation of an Automated Body Condition Scoring System Using 3D Imaging”, Niall O’ Leary, Lorenzo Leso, Frank Buckley, Jonathon Kenneally, Diarmuid McSweeney and Laurence Shalloo.
19. “Feed and production efficiency of young crossbred beef cattle stratified on a terminal total merit index”, David N. Kelly, Stephen B. Conroy, Craig P. Murphy, Roy D. Sleator, and Donagh P. Berry.
20. “Large variability in feeding behavior among crossbred growing cattle”, David. N. Kelly, Roy. D. Sleator, Craig. P. Murphy, Stephen. B. Conroy, Michelle. M Judge, and Donagh. P. Berry.
21. “Short communication: Animal-level factors associated with whether a dairy female is mated to a dairy or beef bull”, D.P.Berry & S.C.Ring.
22. “Short communication: The beef merit of the sire mated to a dairy female affects her subsequent performance”, D.P.Berry & S.C.Ring.
23. “Kefir microbial composition is a deciding factor in the physiological impact of kefir in a mouse model of obesity”, Benjamin C. T. Bourrie, Tingting Ju, Janelle M. Fouhse, Andrew J. Forgie, Consolato Sergi, Paul D. Cotter and Benjamin P. Willing.
24. “The E ect of Compositional Changes Due to Seasonal Variation on Milk Density and the Determination of Season-Based Density Conversion Factors for Use in the Dairy Industry”, Puneet Parmar, Nicolas Lopez-Villalobos, John T. Tobin, Eoin Murphy, Arleen McDonagh, Shane V. Crowley, Alan L. Kelly and Laurence Shalloo.
25. “Distributed Denial of Service Cyberbioattack Affecting Bacteria-based Biosensing Systems”, Sergio Lopez Bernal, Daniel Perez Martins, Alberto Huertas Celdran.
26. “Simultaneous Detection of Copper, Lead and Mercury in River Water with In-Situ pH Control Using Electrochemical Stripping Techniques”, Bernardo Patella, Benjamin O’Sullivan, Robert Daly, Pierre Lovera, Rosslinda Inguanta, Alan O’Riordan.
27. “Elimination of Oxygen Interference in the Electrochemical Detection of Monochloramine, Using In-Situ pH Control at Interdigitated Electrodes”, Ian Seymour, Benjamin O’Sullivan, Pierre Lovera, Alan O’Riordan, James Rohan.
28. “Identifying artificially drained pasture soils using machine learning and Earth observation imagery”, Rob O’Hara, Stuart Green, Tim McCarthy, Conor Cahalane, Owen Fenton, Pat Tuohy.
29. “Delivery of β-carotene to the in vitro intestinal barrier using nanoemulsions with lecithin or sodium caseinate as emulsifiers”, Ariadna Gasa-Falcon, Elena Arranz, Isabel Odriozola-Serrano, Olga Martín-Belloso & Linda Giblin.
30. “Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality”, Aaron M. Walsh, Guerrino Macori, Kieran N. Kilcawley & Paul D. Cotter.
31. “A Model-Agnostic Approach to Quantifying the Informativeness of Explanation Methods for Time Series Classification”, Thu Trang Nguyen, Thach Le Nguyen, and Georgiana Ifrim.
32. “Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament”, Roy Costilla, Kathryn E. Kemper, Enda M. Byrne, Laercio R. Porto-Neto, Roberto Carvalheiro, Deirdre C. Purfield, Jennifer L. Doyle, Donagh P. Berry, Stephen S. Moore, Naomi R. Wray & Ben J. Hayes. 
33. “Evolving Intelligent Reflector Surface towards 6G for Public Health: Application in Airborne Virus Detection”, Harun Siljak, Nouman Ashraf, Michael Taynnan Barros, Daniel Perez Martins, Bernard Butler, Arman Farhang, Nicola Marchetti, Sasitharan Balasubramaniam.
34. “On Generating Plausible Counterfactual and Semi-Factual Explanations for Deep Learning”, Eoin M. Kenny and Mark T. Keane.
35. “Play MNIST For Me! User Studies on the Effects of Post-Hoc, Example-Based Explanations & Error Rates on Debugging a Deep Learning, Black-Box Classifier”, Courtney Ford, Eoin M. Kenny & Mark T. Keane.
36. “Hydrogel-based Bio-nanomachine Transmitters for Bacterial Molecular Communications”, Daniel P. Martins, Huong Q.-O’Reilly, Lee Coffey, Paul D. Cotter & Sasitharan Balasubramaniam.
37. “Instance-Based Counterfactual Explanations for Time Series Classification”, Eoin Delaney, Derek Greene and Mark T. Keane.
38. “Good Counterfactuals and Where to Find Them: A Case-Based Technique for Generating Counterfactuals for Explainable AI (XAI)”, Mark T. Keane and Barry Smyth.
39. “Development and evaluation of a processing sector model for butter manufacture using a mass balance technique at two dairy processing sites”, Puneet Parmar, Nicolas Lopez‐Villalobos, John T Tobin, Eoin Murphy, Shane V Crowley, Alan L Kelly, Laurence Shalloo.
40. “Carcass and efficiency metrics of beef cattle differ by whether the calf was born in a dairy or a beef herd”, A J Twomey, S C Ring, N McHugh, D P Berry.
41. “Stereochemistry of Astaxanthin Biosynthesis in the Marine Harpacticoid Copepod Tigriopus Californicus”, Alfonso Prado-Cabrero, Ganjar Saefurahman and John M. Nolan.
42. “Block Chain and Internet of Nano-Things for Optimizing Chemical Sensing in Smart Farming”, Dixon Vimalajeewa, Subhasis Thakur, John Breslin, Donagh P. Berry, Sasitharan Balasubramaniam.
43. “An Examination of the State-of-the-Art for Multivariate Time Series Classification”, Bhaskar Dhariyal, Thach Le Nguyen, Severin Gsponer and Georgiana Ifrim.
44. “An index framework founded on the future profit potential of female beef cattle to aid the identification of candidates for culling”, F. L. Dunne, D. P. Berry M. M. Kelleher, R. D. Evans, S. W. Walsh and P. R. Amer.
45. “Suboptimal mobility in spring calving, pasture-based dairy systems: causes and economic consequences.”, Aisling H. O’Connor.
46. “Extracting Pasture Phenotype and Biomass Percentages using Weakly Supervised Multi-target Deep Learning on a Small Dataset”, Badri Narayanan, Mohamed Saadeldin, Paul Albert, Kevin McGuinness, and Brian Mac Namee.
47. “Effect of temperature on raw whole milk density and its potential impact on milk payment in the dairy industry”, Puneet Parmar Nicolas Lopez‐Villalobos John T. Tobin Eoin Murphy Frank Buckley Shane V. Crowley Alan L. Kelly Laurence Shalloo.
48. “The effects of sustained fitness improvement on the gut microbiome: A longitudinal, repeated measures case-study approach.”, Wiley Barton, Owen Cronin, Isabel Garcia-Perez, Ronan Whiston, Elaine Holmes, Trevor Woods, Catherine B. Molloy, Michael G. Molloy Fergus Shanahan, Paul D. Cotter, Orla O’Sullivan.
49. “A Model of Decentralized Social Internet of Things using Blockchain Offline Channels”, Subhasis Thakur; John G. Breslin.
50. “The effects of cow genetic group on the density of raw whole milk”, P. Parmar, N. Lopez-Villalobos, J.T. Tobin, E. Murphy, F. Buckley, A. McDonagh, J.A. O’Mahony, S.V. Crowley, A.L. Kelly, L. Shalloo.
51. “An Edge Colouring-based Collaborative Routing Protocol for Blockchain Offline Channels”, Subhasis Thakur; John G. Breslin.

Publications from 2021

1. “Towards Designing an Explainable-AI based Solution for Livestock Mart Industry”, Parit Mehta, Rudresh Dwivedi, Ciaran Feeney, Pankesh Patel, Muhammad Intizar Ali & John Breslin.
2. “IMPAQT Miniaturized Underwater Acoustic Telemetry Platform: Transmitter Node System Design”, Hamed Jafarzadeh, Marco Belcastro & Brendan O’Flynn.
3. “Interpretable Classification of Human Exercise Videos through Pose Estimation and Multivariate Time Series Analysis”, Ashish Singh, Binh Thanh Le, Thach Le Nguyen, Darragh Whelan, Martin O’Reilly, Brian Caulfield & Georgiana Ifrim.
4. “A Service-based Joint Model Used for Distributed Learning: Application for Smart Agriculture”, Dixon Vimalajeewa, Chamil Kulatunga, Donagh Berry & Sasitharan Balasubramaniam.
5. “A review of precision technologies in pasture-based dairying systems”, L. Shalloo, T. Byrne, L. Leso, E. Ruelle, K. Starsmore, A. Geoghegan, J. Werner & N. O’Leary.
6. “A Theoretical and Experimental Study of Electrochemical pH Control at Gold Interdigitated Microband Arrays”, Bernardo Patella, Robert Daly, Ian Seymour, Pierre Lovera, James Rohan, Rosslinda Inguanta, Alan O’Riordan & Benjamin O’Sullivan.
7. “Short communication: Differences in genetic merit for visually-assessed body condition score materialises as phenotypic differences in tactile-based body condition score in commercial dairy cows”, D.P.Berry & M.M.Kelleher.
8. “Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle”, Jennifer L Doyle, Deirdre C Purfield, Tom Moore, Tara R Carthy, Siobhan W Walsh, Roel F Veerkamp, Ross D Evans & Donagh P Berry.
9. “If Only We Had Better Counterfactual Explanations: Five Key Deficits to Rectify in the Evaluation of Counterfactual XAI Techniques”, Mark T. Keane, Eoin M. Kenny, Eoin Delaney & Barry Smyth.
10. “Theoretical Models for Underwater RFID and the Impact of Water Salinity on the Design of Wireless Systems”, Peres, Caroline; Pigeon, Melusine; Rather, Nadeem; Gawade, Dinesh; Buckley, John; Jafarzadeh, Hamed; O’Flynn, Brendan.
11. “Towards Designing Computer Vision-based Explainable-AI Solution: A Use Case of Livestock Mart Industry”, Devam Dave, Het Naik, Smiti Singhal, Rudresh Dwivedi and Pankesh Patel.
12. “Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence-dependent fashion”, Héctor Argüello, Irene Magdalena Rodríguez-Gómez, Jose María Sánchez-Carvajal, Francisco José Pallares, Iván Díaz, Raúl Cabrera-Rubio, Fiona Crispie, Paul D. Cotter, Enric Mateu, Gerard Martín-Valls, Librado Carrasco, Jaime Gómez-Laguna.
13. “Characterising soil moisture regimes on poorly drained soils in Ireland using optical satellite derived vegetation indices and the OPTRAM model”, Rumia Basu, Colin Brown, Patrick Tuohy & Eve Daly.
14. “Prediction of genetic merit for live weight and body condition score in dairy cows using routinely available linear type and carcass data”, D.P.Berry, R.D.Evans & M.M.Kelleher.
15. Advances of plant-based structured food delivery systems on the in vitro digestibility of bioactive compounds”,
    Talita A. Comunian,Stephan Drusch & André Brodkorb.
16. “On-body Edge Computing through E-Textile Programmable Logic Array”, Frances Cleary, David Henshall & Sasitharan Balasubramaniam.
17. “Post-Hoc Explanation Options for XAI in Deep Learning: The Insight Centre for Data Analytics Perspective”, Eoin M. Kenny, Eoin D. Delaney, Derek Greene & Mark T. Keane.
18. “Co-clustering of time-dependent data via Shape Invariant Model”, Alessandro Casa, Charles Bouveyron, Elena Erosheva & Giovanna Menardi.
19. “Handling Climate Change Using Counterfactuals: Using Counterfactuals in Data Augmentation to Predict Crop Growth in an Uncertain Climate Future”, Mohammed Temraz, Eoin M. Kenny, Elodie Ruelle, Laurence Shalloo, Barry Smyth & Mark T. Keane.
20. “Platinum Interdigitated Electrode Arrays for Reagent-free Detection of Copper”, Robert Daly, Tarun Narayan, Alan O’Riordan & Pierre Lovera.
21. “Microfluidic-based Bacterial Molecular Computing on a Chip”, Daniel P. Martins, Michael Taynnan Barros, Benjamin O’Sullivan, Ian Seymour, Alan O’Riordan, Lee Coffey,
    Joseph Sweeney, & Sasitharan Balasubramaniam.
22. “Assessment of the biological activity of fish muscle protein hydrolysates using in vitro model systems”, Shauna Heffernan, Linda Giblin & Nora O’Brien.
23. “Digestive System Dynamics in Molecular Communication Perspectives”, Dixon Vimalajeewa & Sasitharan Balasubramaniam.
24. “Cross-sectional analyses of a national database to determine if superior genetic merit translates to superior dairy cow performance”, S.C.Ring, R.D.Evans, A.R.Cromie & D.P.Berry.
25. “NFC Sensing of Tear Fluid for Animal health Monitoring”, Melusine Pigeon; Nadeem Rather; Brendan O’Flynn & John Buckley.
26. “Twin Systems for DeepCBR: A Menagerie of Deep Learning and Case-Based Reasoning Pairings for Explanation and Data Augmentation”, Mark T. Keane, Eoin M. Kenny, Eoin Delaney, Mohammed Temraz, Derek Greene & Barry Smyth.
27. “Greenhouse gas emissions and nitrogen efficiency of dairy cows of divergent economic breeding index under seasonal pasture-based management”, B.Lahart, L.Shalloo, J.Herron, D.O’Brien, R.Fitzgerald, T.M.Boland & F.Buckley.
28. “Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes”, Oleksandr Nychyk, WileyBarton, Agata M.Rudolf, Serena Boscaini, Aaron Walsh, Thomaz F.S.Bastiaanssen, Linda Giblin, Paul Cormican, Liang Chen, Yolanda Piotrowicz, Davina Derous, Áine Fanning, Xiaofei Yin, Jim Grant, Silvia Melgar, Lorraine Brennan, Sharon E.Mitchell, John F.Cryan & Kanishka N.Nilaweera.
29. “A Bandwidth Enhanced Sub-GHz Wristwatch Antenna using an Optimized Feed Structure”, Sanjeev Kumar; Robert Newberry; Tim Hannon; John Barton; Matthew Rodencal; Melusine Pigeon; William G. Scanlon & Brendan O’Flynn.
30. “Rescaling genetic expression of carcass traits in cattle by environment using herd best linear unbiased estimates (BLUEs)”, David Kenny, Roy D.Sleator,Craig P.Murphy, Ross D.Evans & Donagh P.Berry.
31. “Herd solutions from genetic evaluations can be used as a tool to rescale the expected expression of genetic potential in cattle”, David Kenny, Roy D. Sleator, Craig P. Murphy, Ross D. Evans,
    & Donagh P. Berry.
32. “Carotenoids in Milk and the Potential for Dairy Based Functional Foods”, Ruth Conboy Stephenson, R. Paul Ross & Catherine Stanton.
33. “Mid-infrared spectroscopy and milk quality traits: a data analysis competition at the International Workshop on Spectroscopy and Chemometrics 2021”, Maria Frizzarin, Antonio Bevilacqua, Bhaskar Dhariyal, Katarina Domijan, Federico Ferraccioli, Elena Hayes, Georgiana Ifrim, Agnieszka Konkolewska, Thach Le Nguyen, Uche Mbaka, Giovanna Ranzato, Ashish Singh, Marco Stefanucci, & Alessandro Casa.
34. “Incorporation of the grazing utilization subindex and new updates to the Pasture Profit Index”, T.Tubritt, L.Shalloo, T.J.Gilliland, N.McHugh & M.O’Donovan.
35. “A Graph-based Molecular Communications Model Analysis of the Human Gut Bacteriome”, Samitha Somathilaka, Daniel P. Martins, Wiley Barton, Orla O’Sullivan, Paul D. Cotter & Sasitharan Balasubramaniam.
36. “Uncertainty Estimation and Out-of-Distribution Detection for Counterfactual Explanations: Pitfalls and Solutions”, Eoin Delaney, Derek Greene & Mark Keane.
37. “Channel Capacity of Starch and Glucose Molecular Communications in the Small Intestine Digestive Tract”, Dixon Vimalajeewa & Sasitharan Balasubramaniam.

Publications from 2022

1. “Mapping grassland management and habitats with satellite and ground level imagery through machine learning”, O’Hara R.1,2, Saad M.2,3, Zimmermann J.1 , Green S.1 , Finn J.4 , Mac Namee B.3 , McGuinness K.5 and O’Connor N.5
2. “The role of remote sensing in practical grassland farming”, Green S.1 , O’Hara R.1,2 and Zimmermann J.
3. “Next generation IMPAQT miniaturized underwater transmitter system design”, Jafarzadeh, Hamed; Belcastro, Marco; O’Flynn, Brendan
4. “The Repeatability of Grazing Efficiency as a Perennial Ryegrass Variety Trait”, Tomás Tubritt, Luc Delaby and Michael O’Donovan
5. “A novel RCS based CRFID tag design”, Rather, Nadeem; Buckley, John; O’Flynn, Brendan; Pigeon, Melusine
6. “Nearest Neighbour-Based Data Augmentation for Time Series Forecasting”, Duncan Wallace, Eoin Delaney, Mark T. Keane, and Derek Greene
7. “In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort”, Laura Wosinska, Calum J. Walsh, Paula M. O’Connor, Elaine M. Lawton, Paul D. Cotter, Caitriona M. Guinane and Orla O’Sullivan
8. “Towards On-Device AI and Blockchain for 6G enabled Agricultural Supply-chain Management”, Muhammad Zawish, Nouman Ashraf, Rafay Iqbal Ansari, Steven Davy, Hassaan Khaliq Qureshi, Nauman Aslam, Syed Ali Hassan
9. “Using deep learning to classify grassland management intensity in ground-level photographs for more automated production of satellite land use maps”, Mohamed Saadeldin, Rob O’Hara, Jesko Zimmermann, BrianMac Namee, Stuart Green.
10. “Predicting livestock behaviour using accelerometers: A systematic review of processing techniques for ruminant behaviour prediction from raw accelerometer data”, L.Riaboff, L.Shallooc, A.F.Smeaton, S.Couvreur, A.Madouasse, M.T.Keane.
11. “A multimodality test outperforms three machine learning classifiers for identifying and mapping paddocks using time series satellite imagery”, Rob O’Hara, Jesko Zimmermann & Stuart Green.
12. “Feature selection for genomic prediction of perennial ryegrass forage quality”, Agnieszka Konkolewska, Patrick Conaghan, Dan Milbourne, Michael Dineen, Susanne Barth, Rachel Keirse and Stephen Byrne
13. “Intensive production of the harpacticoid copepod Tigriopus californicus in a zero-effluent ‘green water’ bioreactor”, Alfonso Prado-Cabrero, Rafael Herena-Garcia & John M. Nolan.
14. “Optimization of Waiting Time for Electric Vehicles Using a Fuzzy Inference System”, Shahid Hussain; Yun-Su Kim; Subhasis Thakur; John G. Breslin.
15. “Presence and Germination of the Probiotic Bacillus subtilis DE111 ® in the Human Small Intestinal Tract: A Randomized, Crossover, Double-Blind, and Placebo-Controlled Study”, Joan Colom, Daniela Freitas, Annie Simon, Andre Brodkorb, Martin Buckley, John Deaton, Alison M Winger.
16. “A direct comparison of 2D versus 3D diffusion analysis at nanowire electrodes: A finite element analysis and experimental study”, Benjamin O’ Sullivan, Shane O’ Sullivan, Tarun Narayan, Han Shao, Bernardo Patella, Ian Seymour, Rosalinda Inguanta, Alan O’ Riordan.
17. “Are subjectively scored linear type traits suitable predictors of the genetic merit for feed intake in grazing Holstein-Friesian dairy cows?”, M.Williams, C.P.Murphy, R.D.Sleator, S.C.Ring, D.P.Berry.
18. “Exploiting genetic variability in the trajectory of lactation yield and somatic cell score with each progressing parity” M.Williams, R.D.Sleator, C.P.Murphy, J.McCarthy, D.P.Berry
19. “Blue Whiting (Micromesistius poutassou) Protein Hydrolysates Increase GLP-1 Secretion and Proglucagon Production in STC-1 Cells Whilst Maintaining Caco-2/HT29-MTX Co-Culture Integrity” Shauna Heffernan ,Leo Nunn, Pádraigín A. Harnedy-Rothwell, Snehal Gite , Jason Whooley ,Linda Giblin,Richard J. FitzGerald and Nora M. O’Brien
20. “Electrochemical Synthesis of Zinc Oxide Nanostructures on Flexible Substrate and Application as an Electrochemical Immunoglobulin-G Immunosensor” Bernardo Patella, Nadia Moukri , Gaia Regalbuto, Chiara Cipollina, Elisabetta Pace, Serena Di Vincenzo, Giuseppe Aiello, Alan O’Riordan and Rosalinda Inguanta
21. “FuzzyAct: A Fuzzy-based Framework for Temporal Activity Recognition in IoT Applications using RNN and 3D-DWT”
    Fayaz Ali Dharejo; Muhammad Zawish; Yuanchun Zhou; Steven Davy; Kapal Dev; Sunder Ali Khowaja; Yanjie Fu; Nawab Muhammad Faseeh Qureshi
22. “Laser-Induced Graphene Supercapacitors by Direct Laser Writing of Cork Natural Substrates” Alessandra Imbrogno, Jahidul Islam, Chiara Santillo, Rachele Castaldo, Labrini Sygellou, Cathal Larrigy, Richard Murray, Eoghan Vaughan, Md. Khairul Hoque, Aidan J. Quinn, and Daniela Iacopino*
23. “A novel minimal set decode-amplify-forward (MS-DAF) relaying scheme for MIMO-NOMA” Muhammad Zeeshan, Mahnoor Ajmal, Muhammad Umar Farooq & Tabinda Ashraf 
24. “Highly sensitive pesticide detection using electrochemically prepared Silver-Gum Arabic nanocluster SERS substrates” Yuqing Yang, Alan O’Riordan,Pierre Lovera
25. “Features of Explainability: How users understand counterfactual and causal explanations for categorical and continuous features in XAI” Greta Warren, Mark Keane, Ruth M.J. Byrne
26. “Multi-Component Optimization and Efficient Deployment of Neural-Networks on Resource-Constrained IoT Hardware” Bharath Sudharasan, Dineshkumar Sundaram, Pankesh Patel, John G. Breslin, Muhammad Intizar Ali, Schahram Dustdar, Albert Zomaya, and Rajiv Ranjan
27. “Preliminary Classification of Selected Farmland Habitats in Ireland Using Deep Neural Networks” Abraham, Lizy, Steven Davy, Muhammad Zawish, Rahul Mhapsekar, John A. Finn, and Patrick Moran.
28. “5G/SDR-Assisted Cognitive Communication in UAV Swarms: Architecture and Applications” Muhammad Zeeshan, Muhammad Umar Farooq, Kashif Shahzad, Adnan Akhunzada
29. “Fast Channel Selection for Scalable Multivariate Time Series Classification” Bhaskar Dhariyal, Thach Le Nguyen, Georgiana Ifrim
30. “A Short Tutorial for Time Series Classification and Explanation with MrSQM” Thach Le Nguyen and Georgiana Ifrim
31. “Addressing out-of-distribution label noise in webly-labelled data” Paul Albert, Diego Ortego, Eric Arazo, Noel O’Connor and Kevin McGuinness
32. “Forecasting for Sustainable Dairy Produce: Enhanced Long-Term, Milk-Supply Forecasting Using k-NN for Data Augmentation, with Prefactual Explanations for XAI” Eoin Delaney, Derek Greene, Laurence Shalloo, Mike Lynch and Mark T. Keane
33. “The role of compute nodes in privacy-aware decentralized AI” Joana Tirana, Christodoulos Pappas, Dimitris Chatzopoulos, Spyros Lalis, Manolis Vavalis 
34. Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites: Claudia Marcela Arenas-Gómez, Enriqueta Garcia-Gutierrez, Juan S. Escobar & Paul D. Cotter
35. Linear type trait genetic trends in Irish Holstein-Friesian dairy animals: Donagh Berry, Siobhan Ring & Margaret Kelleher
36. Energy-aware AI-driven Framework for Edge Computing-based IoT Applications: Muhammad  Zawish, , Nouman Ashraf, Rafay  Ansari and Steven Davy
37. Milk Oligosaccharides: Hannah Masterson, Tadasu Urashima, Rebecca A. Owens & Rita M. Hickey
38. Simultaneous detection of copper and mercury in water samples using in-situ pH control with electrochemical stripping techniques: Bernardo Patella, Tarun Narayan, Benjamin O’Sullivan, Robert Daly, Claudio Zanca, Pierre Lovera, Rosalinda Inguanta, Alan O’Riordan
39. Modeling the economic impacts of mobility scores in dairy cows under Irish spring pasture-based management: Aisling O’Connor, Laurence Shalloo, Eddie Bokkers, Imke de Boer, Henk Hogeveen, Riona Sayers, Nicky Byrne, Elodie Ruelle
40. T. Wedage, B. Butler, S. Balasubramaniam, M. C. Vuran and Y. Koucheryavy, “Path Loss Analysis of Terahertz Communication in Mars’ Atmospheric Conditions,” 2022 IEEE International Conference on Communications Workshops (ICC Workshops), Seoul, Korea, Republic of, 2022, pp. 1225-1230, doi: 10.1109/ICCWorkshops53468.2022.9814599

Publications from 2023

1. “Classification of cowdiet based on milk Mid Infrared Spectra: A data analysis competition at the ‘‘International Workshop on Spectroscopy and Chemometrics 2022’’”, Maria Frizzarin, Giulio Visentin, Alessandro Ferragina, Elena Hayes, Antonio Bevilacqua, Bhaskar Dhariyal, Katarina Domijan, Hussain Khan, Georgiana Ifrim, Thach Le Nguyen, Joe Meagher, Laura Menchetti, Ashish Singh, Suzy Whoriskey, Robert Williamson, Martina Zappaterra, Alessandro Casa
2. “Mid infrared spectroscopy and milk quality traits: A data analysis competition at the “International Workshop on Spectroscopy and Chemometrics 2021”, Maria Frizzarin, Antonio Bevilacqua, Bhaskar Dhariyal, Katarina Domijan, Federico Ferraccioli, Elena Hayes, Georgiana Ifrim, Agnieszka Konkolewska, Thach Le Nguyen, Uche Mbaka, Giovanna Ranzato, Ashish Singh, Marco Stefanucci, Alessandro Casa
3. “Edge-AI Implementation for Milk Adulteration Detection”, Mhapsekar, R.R., Abraham, L., O’Shea, N., Davy, S.
4. “Towards Resource-aware DNN Partitioning for Edge Devices with Heterogeneous Resources”, Zawish, M., Abraham, L., Dev, Davy, K.
5. “Climate Change Sensing through Terahertz Communications: A Disruptive Application of 6G Networks”, Wedage, L.T., Butler, B., Balasubramaniam, S., Koucheryavy, Y., Jornet, J.M.
6. “Realizing Molecular Machine Learning through Communications for Biological AI: Future Directions and Challenges”, Balasubramaniam, S., Somathilaka, S., Sun, S., Ratwatte, A., Pierobon, M.
7. “Comparative Analysis of Terahertz Propagation Under Dust Storm Conditions on Mars and Earth”, Wedage, L.T., Butler, B., Balasubramaniam, S., Koucheryavy, Y., Vuran, M.C.
8. “Evaluating Enteric Methane Emissions within a Herd of Genetically Divergent Grazing Dairy Cows”, Lahart, B., Buckley, F., Herron, J., Fitzgerald, R., Fitzpatrick, E., Galvin, N., Shalloo, L.
9. “Predicting Methane Emissions of Individual Grazing Dairy Cows from Spectral Analyses of their Milk Samples”, McParland, S., Frizzarin, M., Lahart, B., Kennedy, M., Shalloo, L., Egan, M., Starsmore, K., Berry, D.P.
10. “Use of Reconstituted Kefir Consortia to Determine the Impact of Microbial Composition on Kefir Metabolite Profiles”, Bourrie, B.C.T., Diether, N., Dias, R.P., Nam, S.L., Paulina de la Mata, A., Forgie, A.J., Gaur, G., Harynuk, J.J., Gänzle, M., Cotter, P.D., Willing, B.P.
11. “Genomic Prediction of Seasonal Forage Yield in Perennial Ryegrass”, Konkolewska, A., Phang, S., Conaghan, P., Milbourne, D., Lawlor, A., & Byrne, S.
12. “Revealing Gene Regulation-based Neural Network Computing in Bacteria”, Somathilaka, S.S., Balasubramaniam, S., Martins, D.P., Li, X.
13. “Mapping the Available Evidence on the Impact of Ingested Live Microbes on Health: A Scoping Review Protocol”, Mukherjee, A., Iyer, A., Gomez-Sala, B., O’Connor, E., Kenny, J.G., Cotter, P.D.
14. “Counterfactual Explanations for Misclassified Images: How Human and Machine Explanations Differ”, Delaney, E., Pakrashi, A., Greene, D., Keane, M.T.
15. “Characterising Sustainability Certification Standards in Dairy Production”, McGarr-O’Brien, K., Herron, J., Shalloo, L., De Boer, I.J.M., De Olde, E.M.
16. “Methods to Mitigate Escherichia Coli Blooms in Ex Vivo Colon Model Experiments Using the Micro-Matrix Bioreactor Fermentation System”, Mathur, H., Mechoud, M., Matthews, C., Lordan, C., Fitzgerald, J.A., Beresford, T., Cotter, P.D.
17. “Detecting the Halyomorpha Halys Using a Low-Power Edge-Based Monitoring System”, Kargar, A., Zorbas, D., Gaffney, M., O’Flynn, B.
18. “Evaluating the Effects of Grass Management Technologies on the Physical, Environmental, and Financial Performance of Irish Pasture-based Dairy Farms”, Palma-Molina, P., Hennessy, T., Dillon, E., Onakuse, S., Moran, B., Shalloo, L.
19. “Characterising Sustainability Certification Standards in Dairy Production”, McGarr-O’Brien, K., Herron, J., Shalloo, L., De Boer, I.J.M., De Olde, E.M.
20. “Biocompatible Hydrogel Electrodeposition Enables the Simultaneous Preparation of Multi-Microinterfaces for Ligand Bioconjugation and Multiplexed Electrochemical Detection”, Juska, V.B., Moukri, N., Estrela, P., Maxwell, G.D., Hendriks, S., Santillan-Urquiza, E., O’Brien, B., Patella, B., Inguanta, R., O’Riordan, A.
21. “Utilising Commercial Farm Grass Growth Data to Evaluate Long-term Dry Matter Production of Perennial Ryegrass Varieties”, Hearn, C., Egan, M., Lynch, M.B., Tubritt, T., O’Leary, M., Geoghegan, A., O’Donovan, M.
22. “Sustainable Laser-Induced Graphene Electrochemical Sensors from Natural Cork for Sensitive Tyrosine Detection”, Vaughan, E., Santillo, C., Setti, M., Larrigy, C., Quinn, A.J., Gentile, G., Lavorgna, M., Iacopino, D. 
23. “Cow-level factors associated with nitrogen utilization in grazing dairy cows using a cross-sectional analysis of a large database”, Tavernier, E., Gormley, I.C., Delaby, L., McParland, S., O’Donovan, M., Berry, D.P.
24. “Mean breed performance of the progeny from beef-on-dairy matings”, Berry, D.P., Twomey, A., Ring, S.
25. “Direct Laser Writing of Chitosan–Borax Composites: Toward Sustainable Electrochemical Sensors”, Vaughan, E., Santillo, C., Imbrogno, A., Gentile, G., Quinn, A.J., Kaciulis, S., Lavorgna, M., Iacopino, D.
26. “Can Dietary Proteins Selectively Reduce either the Visceral or Subcutaneous Adipose Tissues?”, Nilaweera, K., Cotter, P.D. 
27. “Deep Learning Assisted Robust Detection Techniques for a Chipless RFID Sensor Tag”, Rather, N., Simorangkir, R.B.V.B., Buckley, J.L., O’Flynn, B., Tedesco, S. 
28. “Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies”, Patangia, D.V., Grimaud, G., Linehan, K., Ross, R.P., Stanton, C.
29. “Usefulness of mid-infrared spectroscopy as a tool to estimate body condition score change from milk samples in intensively-fed dairy cows”, Frizzarin, M., Miglior, F., Berry, D.P., Gormley, I.C., Baes, C.F.
30. “Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome”, Walsh, L.H., Walsh, A.M., Garcia-Perez, I., Crispie, F., Costabile, A., Ellis, R., Finlayson, J., Finnegan, L.A., Claesson, M.J., Holmes, E., Cotter, P.D.
31. “Back to Basics: A Sanity Check on Modern Time Series Classification Algorithms”, Dhariyal, B., Le Nguyen, T., Ifrim, G.
32. “Comparison of Calving and Revenue-Generating Qualities in Beef-Sired Male and Female Progeny from Dairy Cows”, Berry, D.P., Ring, S.
33. “Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science”, Egan, M., Kuscu, M., Barros, M.T., Booth, M., Llopis-Lorente, A., Magarini, M., Martins, D.P., Schäfer, M., Stano, P.
34. “Review: Use of Assisted Reproduction in Seasonal-Calving Dairy Herds”, Butler, S.T., Crowe, A.D., Moore, S.G., Lonergan, P.
35. “Identifying Primary Producers’ Positioning in the Irish Bioeconomy using Social Network Analysis”, Harrahill, K., Macken-Walsh, A., O’Neill, E.
36. “Comparison of the Relative Impacts of Acute Consumption of an Inulin-enriched Diet, Milk Kefir or a Commercial Probiotic Product on the Human Gut Microbiome and Metabolome”, Cotter, P., Walsh, L., Walsh, A., Perez, I.G., Crispie, F., Costabile, A., Ellis, R., Finlayson, J., Finneganan, L., Claesson, M., Holmes, E.
37. “Isolation and Identification of Chlorate-reducing Hafnia sp. from Milk”, McCarthy, W.P., Srinivas, M., Danaher, M., O’Connor, C.O., O’Callaghan, T.F., Van Sinderen, D., Kenny, J., Tobin, J.T.
38. “Brain in the Dark: Design Principles for Neuro-mimetic Learning and Inference”, Bazargani, M.H., Urbas, S., Friston, K.
39. “Categorical and Continuous Features in Counterfactual Explanations of AI Systems”, Warren, G., Byrne, R.M.J., Keane, M.T.
40. “Performance Characterization of a Battery-less NFC Sensor for Museum Artifact Monitoring”, Gawade, D.R., Kumar, S., Simorangkir, R.B.V.B., O’Callaghan, B., Iacopino, D., Rather, N., O’Flynn, B., Buckley, J.L.
41. “Identifying primary producers’ positioning in the Irish bioeconomy using Social Network Analysis”, Harrahill, K., Macken-Walsh, A., O’Neill, E.
42. “Predicting body condition score change in early lactating Irish dairy cows using milk mid infrared spectra”, Frizzarin, M., Gormley, I.C., Berry, D.P., McParland, S.
43. “Effect of delayed timing of artificial insemination with sex-sorted semen on pregnancy per artificial insemination in synchronized dairy heifers managed in a seasonal-calving pasture-based system”, Moore, S.G., Crowe, A.D., Randi, F., Butler, S.T.
44. “Evaluation of Machine Learning Models for a Chipless RFID Sensor Tag”, Rather, N., Simorangkir, R.B.V.B., Buckley, J., O’Flynn, B., Tedesco, S.
45. “An investigation of extracellular vesicles in bovine colostrum, first milk and milk over the lactation curve”, Santoro, J., Mukhopadhya, A., Oliver, C.,  Brodkorb, A., Giblin, L., O’Driscoll, L.
46. “A Rectenna Design With Harmonic Suppression for RF Energy Harvesting Applications”, Moloudian, G., O’Flynn, B., Buckley, J.L. 
47. “Real-time Electrochemical Sensor for Phosphate Sensing in Soil-Water”, Narayan, T., Reidy, M.K., Heelan, S., O’Riordan, A., Shao, H. 
48. “Predicting milk traits from spectral data using Bayesian probabilistic partial least squares regression”, Urbas, S., Lovera, P., Daly, R., O’Riordan, A., Berry, D., Gormley, I.C.
49. “What is to be gained by ensemble models in analysis of spectroscopic data?”, Domijan, K.
50. “Can the Inclusion of Ribwort Plantain or Chicory Increase the Seasonal and Annual Dry Matter Production of Intensive Dairy Grazing Swards?”, Hearn, Ciaran., Egan, Michael., Lynch, Mary Bridget., Flynn, David., O’ Donovan, Michael.
51. “Potential of Raman spectroscopy for in-line measurement of raw milk composition”, Hussain Khan, H.M., McCarthy, Ultan.,  Esmonde-White, Karen., Casey, Imelda., O’Shea, Norah.
52. “Laser Induced Graphene (Lig) Biosensors Derived from Chitosan: Towards Sustainable and Green Electronics”, Hamidi, Hassan., Levieux, Juliette., Larrigy, Cathal., Russo, Alida., Vaughan, Eoghan., Murray, Richard., Quinn, Aidan J., Iacopino, Daniela.
53. “Identifying primary producers’ positioning in the Irish bioeconomy using Social Network Analysis”, Harrahill, Kieran., Macken-Walsh, Aine., O’Neill, Eoin.
54. “Variation in the proportion of the segregating genome shared between full-sibling cattle and sheep”, Kenny, D., Berry, D.P., Pabiou, T. et al.
55. “Mapping the available evidence on the impact of ingested live microbes on health: a scoping review protocol”, Mukherjee, A., Iyer A, Gómez-Sala, B., Kenny, John. G., Cotter, Paul. D.
56. “Profitable fee controller for payment channel networks”, De Silva, A., Thakur, S., Breslin, J. 
57. “Simultaneous detection of copper and mercury in water samples using in-situ pH control with electrochemical stripping techniques”, Patella, B., Narayan, T., O’Sullivan, B., Daly, R., Zanca, C., Lovera, P., Inguanta, R., O’Riordan, A.
58. “Spectroscopic technologies and data fusion: Applications for the dairy industry”, Hayes, E., Greene, D., O’Donnell, C., O’Shea, N., Fenelon, M.
59. Classification of cow diet based on milk Mid Infrared Spectra: A data analysis competition at the “International Workshop on Spectroscopy and Chemometrics 2022”, Frizzarin, M., Visentin, G., Ferragina, A., Hayes, E., Bevilacqua, A., Dhariyal, B., Domijan, K., Khan, H., Ifrim, G., Le Nguyen, T., Meagher, J., Menchetti, L., Singh, A., Whoriskey, S., Williamson, R., Zappaterra, M., Casa, A.
60. “Amplification-free, highly sensitive electrochemical DNA-based sensor for simultaneous detection of stx1 and stx2 genes of Shiga toxin-producing E. coli (STEC)”, Wasiewska, L.A., Diaz, F.G., Rodrigues Teixeira, S., Burgess, C.M., Duffy, G., O’Riordan, A.
61. “Inferring Gene Regulatory Neural Networks for Bacterial Decision Making in Biofilms”, Somathilaka, S., Martins, D.P., Li, X., Li, Y., Balasubramaniam, S.
62. “Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity?”, Martin, J.G., Cotter, P.D.
63. “Seasonal variation in the Canastra cheese mycobiota”, Martin, J.G.P., Silva, J.M.M., César, I.C.D.R., da Silva, M., Santana, S.A., Veloso, T.G.R., Silva, J.G.E., Ferreira, C.L.L.F., Leech, J., Cotter, P.D.
64. “Bovine Colostrum for Veterinary and Human Health Applications: A Critical Review”, Linehan, K., Ross, P.R., Stanton, C.
65. “Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life”, Roager, H.M., Stanton, C., Hall, L.J.
66. “Explaining Groups of Instances Counterfactually for XAI: A Use Case, Algorithm and User Study for Group-Counterfactuals”, Warren, G., Keane, M.T., Gueret, C., Delaney, E. 
67. “Electrochemical nucleic acid-based sensors for detection of Escherichia coli and Shiga toxin-producing E. coli—Review of the recent developments”, Wasiewska, L.A., Juska, V.B., Seymour, I., Burgess, C.M., Duffy, G., O’Riordan, A. 
68. “Trend analysis and prediction of seasonal changes in milk composition from a pasture-based dairy research herd”, Hayes, E.,  Wallace, D., O’Donnell, C., Greene, D., Hennessy, D., O’Shea, N., Tobin, J.T., Fenelon, M.A.
69. “Microfabrication of a multiplexed device for controlled deposition of miniaturised copper-structures for glucose electro-oxidation in biological and chemical matrices”, Juska, B.V., Maxwell, D.G., O’Riordan, A.
70. “Characterisation of eight cattle with Swyer syndrome by whole-genome sequencing”, Berry, D.P., Herman, E.K., Carthy, T.R., Jennings, R., Bandi-Kenari, N., O’Connor, R.E., Mee, J.F., O’Donovan, J., Mathews, D., Stothard, P. 
71. “Characterising sustainability certification standards in dairy production”, McGarr-O’Brien, K., Herron, J., Shalloo, L., De Boer, I.J.M., De Olde, E.M.
72. “Spectroscopic technologies and data fusion: Applications for the dairy industry”, Hayes, E., Greene, D., O’Donnell, C., O’Shea, N., Fenelon, M.A.
73. “Factors associated with intensity of technology adoption and with the adoption of 4 clusters of precision livestock farming technologies in Irish pasture-based dairy systems”, Palma-Molina, P., Hennessy, T., O’Connor, A.H., Onakuse, S., O’Leary, N., Moran, B., Shalloo, L.
74. “Estimation of body condition score change in dairy cows in a seasonal calving pasture-based system using routinely available milk mid-infrared spectra and machine learning techniques”, Frizzarin, M., Gormley, I.C., Berry, D.P., McParland, S.
75. “Integrated molecular approaches for fermented food microbiome research”, Walsh, A.M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., Cotter, P.D.
76. “Modeling the economic impacts of mobility scores in dairy cows under Irish spring pasture-based management”, O’Connor, A.H., Shalloo, L., Bokkers, E.A.M., de Boer, I.J.M., Hogeveen, H., Sayers, R., Byrne, N., Ruelle, E.
77. “Scalable classifier-agnostic channel selection for multivariate time series classification”, Dhariyal, B., Le Nguyen, T. & Ifrim, G.
78. “Silver nanoparticles – laser induced graphene (Ag NPs – LIG) hybrid electrodes for sensitive electrochemical-surface enhanced Raman spectroscopy (EC-SERS) detection”, Mu, Y., Islam, J., Murray, R., Larrigy, C., Russo, A, Zhang, X., Quinn, A.J., Iacopino, D. 

1. T. Wedage, M. C. Vuran, B. Butler, Y. Koucheryavy and S. Balasubramaniam, “Internet of Paint (IoP): Channel Modeling and Capacity Analysis for Terahertz Electromagnetic Nanonetworks Embedded in Paint,” in IEEE Journal on Selected Areas in Communications, doi: 10.1109/JSAC.2024.3399201
2. Konkolewska A, Frizzarin M. Spectroscopy meets modern statistics: International workshop in April 2024. NIR news. 2024;0(0). doi:10.1177/09603360241252070
3. Delaney, E., Pakrashi, A., Greene, D., & Keane, M. T. (2024). Counterfactual Explanations for Misclassified Images: How Human and Machine Explanations Differ (Abstract Reprint). Proceedings of the AAAI Conference on Artificial Intelligence, 38(20), 22696-22696. https://doi.org/10.1609/aaai.v38i20.30596
4. Tavernier, I.C. Gormley, L. Delaby, M. O’Donovan, D.P. Berry. Genetic covariance components for measures of nitrogen utilization in grazing dairy cows, Journal of Dairy Science, Volume 107, Issue 4, 2024, Pages 2231-2240, https://doi.org/10.3168/jds.2023-24117
5. Eoin M. Kenny, Elodie Ruelle, Mark T. Keane, Laurence Shalloo. A Hybrid Model that Combines Machine Learning and Mechanistic Models for Useful Grass Growth Prediction, Computers and Electronics in Agriculture, Volume 219, 2024, 108805, https://doi.org/10.1016/j.compag.2024.108805.
6. Tirana, J., Tsigkari, D., Iosifidis, G., & Chatzopoulos, D. (2024). Workflow optimization for parallel split learning. arXiv preprint arXiv:2402.10092.
   https://doi.org/10.48550/arXiv.2402.10092
7. Tirana, J., Lalis, S., & Chatzopoulos, D. (2024). MP-SL: Multihop Parallel Split Learning. arXiv preprint arXiv:2402.00208.
   https://doi.org/10.48550/arXiv.2402.00208
8. Anupa De Silva, Subhasis Thakur, and John G Breslin. Card payment protocol for cryptocurrencies with payment channel network. Distributed Ledger Technologies, 2024. https://dl.acm.org/doi/10.1145/3653681
9. Georgiana Ifrim, Romain Tavenard, Anthony Bagnall, Patrick Schaefer, Simon Malinowski, Thomas Guyet, Vincent Lemaire . Advanced Analytics and Learning on Temporal Data, 8th ECML PKDD Workshop, AALTD 2023, Turin, Italy, September 18–22, 2023, Revised Selected Papers, https://link.springer.com/book/10.1007/978-3-031-49896-1