Publications

Gottschalk, P., K. Klumpp, R. Cardinael, E. Ceschia, S. Diop, L. Genesio, M.I. Khalil, B. Krujit, E. Lugato, J.-L. Roujean, P. Sieber and B. Osborne. 2025. Reflecting on surface albedo and climate. Climate Research (In Press).

Sheikh, S. and M.I. Khalil. 2025. Automating Spatial Data Integration for HOLOS-IE: Irish Case Study with Soil and Land Cover. Land (Environmental and Earth Sciences). https://doi.org/10.20944/preprints202507.0992.v1

Siddique, M., R. Collier, A. Barry and M. I. Khalil. 2025. Stakeholder Perspectives on Current Agri-Environmental Measures and HOLOS-IE Digital Platform Development. MDPI Agronomy. DOI:10.20944/preprints202502.1916.v1

Khalil MI and Walkiewicz A. 2024. The contribution of managed forestry and the driving variables in climate change mitigation and adaptation. Frontiers in Forestry and Global Change 7:1521968. doi: 10.3389/ffgc.2024.1521968. Click here

Walkiewicz, A., Bulaka, P., Khalil, M. I., and Osborne, B. 2024. Assessment of soil CO₂, CH₄, and N₂O fluxes and their drivers, and their contribution to the climate change mitigation potential of forest soils in the Lublin region of Poland. Eur. J. For. Res. doi: 10.1007/s10342-024-01739-0. Click here

Khalil M.I., B.A. Osborne and A. Wingler. 2024. Towards net zero emissions without compromising agricultural sustainability: what is achievable? Nutrient Cycling in Agroecosystems. Click here

Khalil M.I. and B. Osborne. 2022. Developing climate‑resilient agri‑environmental production systems. Nutrient Cycling in Agroecosystems. Click here

Conference Proceedings

• Khalil M.I., Badhan,S., Mahjabin,S., ., Tasos,C., Aaron,M., Rakin, SA, Herron, J., Roland, K., Bruce,O. and Rem,C. 2025. HOLOS-IE Digital Platform for Carbon Footprint Assessment: A Dairy Farm Case Study. Presented at the 9^th GGAA Conference held in Nairobi, Kenya from 5-9 October 2025.
• Khalil M.I., Badhan,S., Mahjabin,S., Roland,K., Bruce,O., Rem,C., Tasos,C., Aaron,M., Shakeef, R., Jonathan, H. 2025.”HOLOS-IE: A System Model for Assessing Carbon Emissions and Balance in Agricultural Systems. EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025. https://doi.org/10.5194/egusphere-egu25-12648.                                                                                                                                                                                     
• Meng, X., Khalil, M.I., and Osborne, B. 2025. Enhancing crop yield, carbon sequestration, and greenhouse gas mitigation through organic matter inputs: long-term grassland farming observations and DNDC model predictions, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-20890, https://doi.org/10.5194/egusphere-egu25-20890, 2025.
• Chen, Y. B., M. Necpalova, and M. I. Khalil. 2025. Reframing Grassland-Livestock Systems for Sustainable Land Transitions: A Digital Modelling Approach Aligned with Climate and Nature-Based Goals. In Proceedings of the 2nd International Electronic Conference on Land, 4–5 September 2025, MDPI: Basel, Switzerland. https://sciforum.net/paper/view/23465
• Chen, Y B., M. Necpalova, D. P. Bu, and M. I. Khalil. 2025. Developing Grassland System Modules for HOLOS-IE Focusing on Carbon Footprint Accounting Driven by Soils, Climate and Management Approaches. ENVIRON 2025 University College Dublin (UCD). https://www.researchgate.net/publication/390105329.
• Siddique, M., R. Collier, B. Sen, S. Pogue, A. McPherson, R. Kröbel, B. Osborne, P. O’Brien, and M.I. Khalil. 2024. Integrating Agroforestry Systems into HOLOS-IE Software: Impact on Farm-Level Carbon Emissions in Ireland. Presented at Ireland’s Future Food Systems Research Symposium on 4 December 2024 at University College Dublin, Dublin, Ireland. Click here
• Meng, X., M.I. Khalil, and B. Osborne. 2024. Assessing the soil carbon storage and GHG emissions of grasslands using the DNDC model. Environ 2024, Waterford, Ireland. https://pure.ulster.ac.uk/ws/portalfiles/portal/157076024/Environ_2024_detailed _programme.pdf
• Chen, Y.B., M. Necpalova, D. P. Bu, and M. I. Khalil. 2024. Towards a HOLOS-IE Module for Grassland Systems and Carbon Footprint Accounting Driven by Soils, Climate and Management Approaches. Presented at Ireland’s Future Food Systems Research Symposium on 4 December 2024 at University College Dublin, Dublin, Ireland. Click here
• Siddique M., R. Collier, B. Sen, A. McPherson, S. Pogue, R. Kröbel, B. Osborne, P. O’Brien and M.I. Khalil. 2024. In: ISCRAES Book of Abstracts Series III (M.I. Khalil, Ed.). Published in 2024 by the ISCRAES 2024 Organising Committee in collaboration with Prudence College Dublin. p39. Click here
• Chatzichristou A. A., J.D. Herron, M. Wallace M., M. Necpalova, M.I. Khalil and B. Osborne. 2024. Development of an Integrated Farming Systems Bio-economic Model for HOLOS-IE. In: ISCRAES Book of Abstracts Series III (M.I. Khalil, Ed.). Published in 2024 by the ISCRAES 2024 Organising Committee in collaboration with Prudence College Dublin. p32. Click here
• Khalil, M.I., B. Sen, M. Siddique, B. Osborne, P. O’Brien and R. Collier. 2024. HOLOS-IE: Bridging Gaps for Sustainable Agriculture and Carbon Netrality. In: Book of Abstracts. In: ISCRAES Book of Abstracts Series III (M.I. Khalil, Ed.). Published in 2024 by the ISCRAES 2024 Organising Committee in collaboration with Prudence College Dublin. p43 Click here
• Khalil M. I. 2024. Assessing Agri-Environmental Footprints and Pathways to Net-Zero: Insights from ProcessBased and Whole-Farm Models. Paper presented at the EJP Annual Science days and General Meeting 2024 held from 10-14 June 2024 in Vilnious, Lithuania. Click here
• Khalil M.I., B. Sen, M. Siddique, A. McPherson, R. Kröbel, B. Osborne, P. O’Brien, and R. Collier. 2024. Unveiling HOLOS-IE: A Cutting-Edge Tool for Predicting Carbon-to-Environmental Footprints and Enabling Sustainable Agricultural System Management. Paper presented at the 9th International Symposium on Soil Organic Matter held from 26-31 May 2024 at UM6P, Benguerrir, Morocco.
• Siddique M., R. Collier, B. Sen, S. Pogue, A. McPherson, R. Kröbel, B. Osborne, C. Farrelly and M.I. Khalil. 2024. Creating an Agroforestry Module on the HOLOS-IE Digital Platform for Assessing Carbon-Neutral Agricultural Farming. Presented at the Environ 2024 held at SETU, Waterford, Ireland.  
• Khalil M.I., R. Collier, C. Farrelly, B. Sen and M. Siddique. 2023. Towards a System-Based Digital Platform For Agriculture Land Use Planning, Management Decision and Inventory Reporting. Presented at the SI-IRC Research Summit held from 20-21 November 2023 in Cork, Ireland. 2023. Click here
• Siddique M., R. Collier, B. Sen, A.T. Chowdhury and M.I. Khalil. 2023. Developing an agroforestry module for HOLOS-IE digital platform to assess total carbon footprint. Presented at the International Agroforestry Conference held from 16-17 November 2023 in Cork, Ireland. Click here
• Khalil M.I., M. Siddique and A. T. Chowdhury. 2023. Towards a System-Based Digital Platform For Agriculture Land Use Planning, Management Decision and Inventory Reporting. Presented at the Climate-KIC conference held on 28 October 2023 at UCD, Dublin, Ireland. Click here
• Khalil M.I. and B. Osborne. 2023. Using Whole Farm Modelling to Inform Land Use Planning for Greenhouse Gas Emissions Mitigation and Offsetting. Presented at AGMIP9: Modelling the Future of Food 26-30 June 2023, Columbia University, New York, USA. Click here
• Khalil M.I. 2023. Towards a Systems-based Digital Platform for Agricultural Land Use Planning, Management Decisions, and Inventory Reporting. Presented at the BONARES 2023 Conference “Soil as a sustainable resource” held from 15-17 May 2023, Berlin, Germany. Click here

Newsletters/Bulletins/B/Vlogs

• Cox. T. 2024.  ReLive – working together for circular agriculture. Click here
• Chatzichristou T. 2024. Analysis: mixed farming systems are a potential solution to bridging the gap between agriculture’s economic and environmental challenges. In: Can farms combining livestock and crops improve sustainability? RTÉ Radio 1. Click here