Publications

Bhattacharjee, A.; Banani Roy, C.; Kevin Schneider, C. A.; Roy, B.; Schneider, K. A. Supporting Program Comprehension by Generating Abstract Code Summary Tree. 2022, 22, 81–85. https://doi.org/10.1145/3510455.3512793.

David, E.; Serouart, M.; Smith, D.; Madec, S.; Velumani, K.; Liu, S.; Wang, X.; Pinto, F.; Shafiee, S.; Tahir, I. S. A.; Tsujimoto, H.; Nasuda, S.; Zheng, B.; Kirchgessner, N.; Aasen, H.; Hund, A.; Sadhegi-Tehran, P.; Nagasawa, K.; Ishikawa, G.; Dandrifosse, S.; Carlier, A.; Dumont, B.; Mercatoris, B.; Evers, B.; Kuroki, K.; Wang, H.; Ishii, M.; Badhon, M. A.; Pozniak, C.; LeBauer, D. S.; Lillemo, M.; Poland, J.; Chapman, S.; de Solan, B.; Baret, F.; Stavness, I.; Guo, W. Global Wheat Head Detection 2021: An Improved Dataset for Benchmarking Wheat Head Detection Methods. Plant Phenomics 2021, 2021, 2023. https://doi.org/10.34133/2021/9846158.

Ebersbach, J.; Khan, N. A.; McQuillan, I.; Higgins, E. E.; Horner, K.; Bandi, V.; Gutwin, C.; Vail, S. L.; Robinson, S. J.; Parkin, I. A. P. Exploiting High-Throughput Indoor Phenotyping to Characterize the Founders of a Structured B. Napus Breeding Population. Front Plant Sci 2022, 12, 3192. https://doi.org/10.3389/FPLS.2021.780250.

Huang, D.; Stavness, I. Large Growth Deformations of Thin Tissue Using Solid-Shells. IEEE Trans Vis Comput Graph 2023, 29 (03), 1893–1909. https://doi.org/10.1109/TVCG.2022.3217008.

Mardanisamani, S.; Eramian, M. Segmentation of Vegetation and Microplots in Aerial Agriculture Images: A Survey. The Plant Phenome Journal 2022, 5 (1), e20042. https://doi.org/10.1002/PPJ2.20042.

Mostafa, S.; Mondal, D.; Beck, M. A.; Bidinosti, C. P.; Henry, C. J.; Stavness, I. Leveraging Guided Backpropagation to Select Convolutional Neural Networks for Plant Classification. Front Artif Intell 2022, 5, 98. https://doi.org/10.3389/FRAI.2022.871162.

O. Vasquez, H. Hesseln and S. J. Smyth. 2022. Canadian Consumer Preferences Regarding Gene-Edited Food Products. Frontiers in Genome Editing, 4, 854334.

Pixley, K. v.; Falck-Zepeda, J. B.; Paarlberg, R. L.; Phillips, P. W. B.; Slamet-Loedin, I. H.; Dhugga, K. S.; Campos, H.; Gutterson, N. Genome-Edited Crops for Improved Food Security of Smallholder Farmers. Nature Genetics 2022 54:4 2022, 54 (4), 364–367. https://doi.org/10.1038/s41588-022-01046-7.

Seidenthal, K.; Panjvani, K.; Chandnani, R.; Kochian, L.; Eramian, M. Iterative Image Segmentation of Plant Roots for High-Throughput Phenotyping. Scientific Reports 2022 12:1 2022, 12 (1), 1–21. https://doi.org/10.1038/s41598-022-19754-9.

Ubbens, J.; Feldmann, M. J.; Stavness, I.; Sharpe, A. G. Quantitative Evaluation of Nonlinear Methods for Population Structure Visualization and Inference. G3 Genes|Genomes|Genetics 2022, 12 (9). https://doi.org/10.1093/G3JOURNAL/JKAC191.

Ugochukwu, A. I.; Phillips, P. W. B. Data Sharing in Plant Phenotyping Research: Perceptions, Practices, Enablers, Barriers and Implications for Science Policy on Data Management. The Plant Phenome Journal 2022, 5 (1), e20056. https://doi.org/10.1002/PPJ2.20056.

Wang, S.; 0000-0002-0526-0843. Set-Stat-Map: Visualizing Spatial Data with Mixed Numeric and Categorical Attributes. 2023.

Wang, S.; Mondal, D.; Sadri, S.; Roy, C. K.; Famiglietti, J. S.; Schneider, K. A. SET-STAT-MAP: Extending Parallel Sets for Visualizing Mixed Data. IEEE Pacific Visualization Symposium 2022, 2022-April, 151–160. https://doi.org/10.1109/PACIFICVIS53943.2022.00024.

Bose P, Mehrabi S, Mondal D. Faster multi-sided one-bend boundary labelling. InInternational Workshop on Algorithms and Computation 2021 Feb 28 (pp. 116-128).

Espenant J, Mondal D. StreamTable: An Area Proportional Visualization for Tables with Flowing Streams. arXiv preprint arXiv:2103.15037. 2021 Mar 28.

Gleim, SW, Gray, RS & Smyth, SJ. 2021. Forensics at the Port: Can Diagnostic Testing Benefit Trade? Sustainability, 13, 1, 106. https://dx.doi.org/10.3390/su13010106.

Khodabandehloo, H.; Roy, B.; Mondal, M.; Roy, C.; Schneider, K. 2021 IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER) 2021.

Lam, K.; Gutwin, C.; Klarkowski, M.; Cockburn, A. The Effects of System Interpretation Errors on Learning New Input Mechanisms. Proceedings of the Conference on Human Factors in Computing Systems. Yokohama, Japan. ACM Press. January 15, 2021.

Mondal, M.; Roy, C.; Roy, B.; Schneider, K.  “FLeCCS: A Technique for Suggesting Fragment-Level Similar Co-change Candidates.” 2021 IEEE/ACM 29th International Conference on Program Comprehension (ICPC), 2021 pp. 160-171. doi: 10.1109/ICPC52881.2021.00024

Mondal, S., Saifullah, K., Bhattacharjee, A., Masudur Rahman, M. and Roy, C. K. 2021. Early Detection and Guidelines to Improve Unanswered Questions on Stack Overflow. In 14th Innovations in Software Engineering Conference (formerly known as India Software Engineering Conference) (ISEC 2021). Association for Computing Machinery, New York, NY, USA, Article 9, 1–11. DOI:https://doi.org/10.1145/3452383.3452392

Mondal, Saikat & Uddin, Gias & Roy, Chanchal. (2021). Rollback Edit Inconsistencies in Developer Forum. 10.1109/MSR52588.2021.00050. ArchiNet: A Concept-token based Approach for Determining Architectural Change Categories

Saifullah, C, Asaduzzaman, M. & Roy, C. (2021). COSTER: A Tool for Finding Fully Qualified Names of API Elements in Online Code Snippets. Automatic Identification of Rollback Edit with Reasons in Stack Overflow Q&A Site

Singh KD, Duddu HS, Vail S, Parkin I, Shirtliffe SJ. UAV-Based Hyperspectral Imaging Technique to Estimate Canola (Brassica napus L.) Seedpods Maturity. Canadian Journal of Remote Sensing. 2021 Jan 2;47(1):33-47.

Keshav D. Singh, Hema S. N. Duddu, Sally Vail, Isobel Parkin & Steve J. Shirtliffe (2021) UAV-Based Hyperspectral Imaging Technique to Estimate Canola (Brassica napus L.) Seedpods Maturity, Canadian Journal of Remote Sensing.

Lam, K.; Gutwin, C.; Klarkowski, M.; Cockburn, A. The Effects of System Interpretation Errors on Learning New Input Mechanisms. Proceedings of the Conference on Human Factors in Computing Systems. Yokohama, Japan. ACM Press. January 15, 2021.

W. Gleim, R. S. Gray and S. J. Smyth. 2021. Forensics at the Port: Can Diagnostic Testing Benefit Trade? Sustainability, 13, 1, 106.

Ahasanuzzaman, M.; Asaduzzaman, M.; Roy, C. K.; Schneider, K. A. CAPS: A Supervised Technique for Classifying Stack Overflow Posts Concerning API Issues. Empir. Softw. Eng. 2020. https://doi.org/10.1007/s10664-019-09743-4

Aich, S.; Yamazaki, M.; Taniguchi, Y.; Stavness, I. Multi-Scale Weight Sharing Network for Image Recognition. Pattern Recognit. Lett. 2020. https://doi.org/10.1016/j.patrec.2020.01.011

Alba, O. S.; Syrovy, L. D.; Duddu, H. S. N.; Shirtliffe, S. J. Increased Seeding Rate and Multiple Methods of Mechanical Weed Control Reduce Weed Biomass in a Poorly Competitive Organic Crop. F. Crop. Res. 2020. https://doi.org/10.1016/j.fcr.2019.107648

Awada, L., P. Phillips, & S. Smyth. 2020. The Adoption of Automated Phenotyping by Plant Breeders” in “Intelligent Image Analysis for Plant Phenotyping”, Ashok Samal (Editor), Sruti Das Choudhury (Editor), ISBN 9781138038554, CRC Press, Taylor & Francis Group

Awada, L.; Phillips, P.W.B. The distribution of returns from land efficiency improvement in multistage production systems. Canadian Journal of Agricultural Economics. November 4, 2020. https://doi.org/10.1111/cjag.12260

Ayalew, T.; Ubbens, J.; Stavness, I. Unsupervised Domain Adaptation for Plant Organ Counting. Computer Vision Problems in Plant Phenotyping Workshop. August 28, 2020.

Bandi, V.; Gutwin, C. Interactive Exploration of Genomic Conservation. Graphics Interface 2020 Conference. Toronto, Canada. CHCCS Press. May 15, 2020.

Bandi, V.; Roy, C. K.; Gutwin, C. Clone Swarm: A Cloud Based CodeClone Analysis Tool. In IWSC 2020 – Proceedings of the 2020 IEEE 14th International Workshop on Software Clones; 2020. https://doi.org/10.1109/IWSC50091.2020.9047642

Bazghaleh, N.; Mamet, S.D.; Bell, J.K.; Morales Moreira, Z.; Taye, Z.M.; Williams-Johnson, S.; Arcand, M.M.; Lamb, E.G.; Shirtliffe, S.; Vail, S.; Siciliano, S.D.; Helgason, B. An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus. Data in Brief. 2020, 31, 106143. https://doi.org/10.1016/j.dib.2020.106143

Bazghaleh, N.; Mamet, S.D.; Bell, J.K.; Morales Moreira, Z.; Taye, Z.M.; Williams-Johnson, S.; Arcand, M.M.; Lamb, E.G.; Shirtliffe, S.; Vail, S.; Siciliano, S.D.; Helgason, B. An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus. Data in Brief. 2020, 30, 105467.

Bekele EK, Nosworthy MG, Henry CJ, Shand PJ, Tyler RT. Oxidative stability of direct‐expanded chickpea–sorghum snacks. Food Science & Nutrition. 2020 Aug;8(8):4340-51.

Bell, J. K.; Siciliano, S. D.; Lamb, E. G. A Survey of Invasive Plants on Grassland Soil Microbial Communities and Ecosystem Services. Sci. Data 2020. https://doi.org/10.1038/s41597-020-0422-x

Bernard, J.; McQuillan, I. Inferring Temporal Parametric L-systems Using Cartesian Genetic Programming. 32nd International Conference on Tools with Artificial Intelligence (ICTAI). Baltimore, Md., USA. 2020, 580-588.

Bhattacharjee, A.; Nath, S. S.; Zhou, S.; Chakroborti, D.; Roy, B.; Roy, C. K.; Schneider, K. An Exploratory Study to Find Motives Behind CrossPlatform Forks from Software Heritage Dataset. In Proceedings of the 17th International Conference on Mining Software Repositories; MSR ’20; Association for Computing Machinery: New York, NY, USA, 2020; pp 11–15. https://doi.org/10.1145/3379597.3387512

Chakroborti, D.; Roy, B.; Nath, S.S. Designing for Recommending Intermediate States in A Scientific Workflow Management System. ACM Digital Library. 5, 198:1-198:29. https://doi.org/10.1145/3457145

Costa, D.; Aziz, U.; Elliott, J.; Baulch, H.; Roy, B.; Schneider, K.; Pomeroy, J. The Nutrient App: Developing a smartphone application for on-site instantaneous community-based NO3 and PO4 monitoring. Environmental Modelling & Software. 2020, 133, 104829. https://doi.org/10.1016/j.envsoft.2020.104829

David E, Madec S, Sadeghi-Tehran P, Aasen H, Zheng B, Liu S, Kirchgessner N, Ishikawa G, Nagasawa K, Badhon MA, Pozniak C. Global Wheat Head Detection (GWHD) dataset: a large and diverse dataset of high-resolution RGB-labelled images to develop and benchmark wheat head detection methods. Plant Phenomics. 2020 Aug 20.

Gleim, SW, Gray, RS & Smyth, SJ. 2021. Forensics at the Port: Can Diagnostic Testing Benefit Trade? Sustainability, 13, 1, 106. https://dx.doi.org/10.3390/su13010106.

Gutwin, C.; van der Kamp, M.; Storring, J.; Cockburn, A.; Phillips, C. Testing the Limits of the Spatial Approach: Comparing Retrieval and Revisitation Performance of Spatial and Paged Data Organizations for Large Item Sets. Proceedings of Graphics Interface 2020. Toronto, Canada. CHCCS Press. May 15, 2020.

Habibullah, M.; Mohebian, M.R.; Soolanayakanahally, R.; Bahar, A.N.; Vail, S.; Wahid, K.A.; Dinh, A. 2020. Low-Cost Multispectral Sensor Array for Determining Leaf Nitrogen Status. Nitrogen. 1, 1, 67-80. MDPI. doi: 10.3390/nitrogen1010007

Halcro, K.; McNabb, K.; Lockinger, A.; Socquet-Juglard, D.; Bett, K.; Noble, S. The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples. Plant Methods. 2020, 16, 49. https://doi.org/10.1186/s13007-020-00591-8

Hasan MR, Mondal D, Gutwin C. Tracing shapes with eyes: design and evaluation of an eye tracking based approach. InProceedings of the 11th Augmented Human International Conference 2020 May 27 (pp. 1-4)

Hossain, M.M.; Roy, B.; Roy, C.K.; Schneider, K.A. VizSciFlow: A Visually Guided Scripting Framework for Supporting Complex Scientific Data Analysis. Journal of Proceedings of the ACM on Human-Computer Interaction. 2020, 4, 34 pages.

Khaled Saifullah, C. M.; Asaduzzaman, M.; Roy, C. K. Exploring Type Inference Techniques of Dynamically Typed Languages. In SANER 2020 – Proceedings of the 2020 IEEE 27th International Conference on Software Analysis, Evolution, and Reengineering; 2020. https://doi.org/10.1109/SANER48275.2020.9054814

Khan, N. A.; Lyon, O. A. S.; Eramian, M.; McQuillan, I. A Novel Technique Combining Image Processing, Plant Development Properties, and the Hungarian Algorithm, to Improve Leaf Detection in Maize. 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), Seattle, WA, USA. 2020, 330-339. doi: 10.1109/CVPRW50498.2020.00045.

Khan, N.; Stavness, I. Pruning Convolutional Filters Using Batch Bridgeout. IEEE Access. 8, 212003-212012. IEEE. 10.1109/ACCESS.2020.3040256

Lassoued, R.; Macall, D.; Smyth, S.J.; Phillips, P.W.B.; Hesseln, H. How should we regulate products of new breeding techniques? Opinion of surveyed experts in plant biotechnology. Biotechnology Reports. 2020, 26, e00460.

Li, G.; Wu, Y.; Roy, C. K.; Sun, J.; Peng, X.; Zhan, N.; Hu, B.; Ma, J. SAGA: Efficient and Large-Scale Detection of Near-Miss Clones with GPU Acceleration. In SANER 2020 – Proceedings of the 2020 IEEE 27th International Conference on Software Analysis, Evolution, and Reengineering; 2020. https://doi.org/10.1109/SANER48275.2020.9054832

Liu, N.; Zhao, L.; Tang, L.; Stobbs, J.; Parkin, I.; Kunst, L.; Karunakaran, C. Mid-Infrared Spectroscopy Is a Fast Screening Method for Selecting Arabidopsis Genotypes with Altered Leaf Cuticular Wax. Plant Cell Environ. 2020. https://doi.org/10.1111/pce.13691

Macall, D. M.; Smyth, S. J. Ex-Ante Impact Assessment of GM Maize Adoption in El Salvador. GM Crop. Food 2020. https://doi.org/10.1080/21645698.2019.1706424

Mairena, A.; Gutwin, C.; Dechant, M.; Cockburn, A. A Baseline Study of Emphasis Effects in Information Visualization. Proceedings of Graphics Interface 2020. Toronto, Canada, CHCCS Press. May 15, 2020.

Mondal, M., Roy, C. & Schneider, Kevin. (2020). A Fine-Grained Analysis on the Inconsistent Changes in Code Clones. 2020 IEEE International Conference on Software Maintenance and Evolution (ICSME). 220-231. 10.1109/ICSME46990.2020.00030.

Mondal, M.; Roy, B.; Roy, C. K.; Schneider, K. A. Associating Code Clones with Association Rules for Change Impact Analysis. In SANER 2020 – Proceedings of the 2020 IEEE 27th International Conference on Software Analysis, Evolution, and Reengineering; 2020. https://doi.org/10.1109/SANER48275.2020.9054846

Mondal, M.; Roy, B.; Roy, C. K.; Schneider, K. A. HistoRank: History-Based Ranking of Co-Change Candidates. In SANER 2020 – Proceedings of the 2020 IEEE 27th International Conference on Software Analysis, Evolution, and Reengineering; 2020. https://doi.org/10.1109/SANER48275.2020.9054869

Mondal, M.; Roy, B.; Roy, C.K.; Schneider, K.A. ID-correspondence: A Measure for Detecting Evolutionary Coupling. Empirical Software Engineering Journal. 26, 1-34. https://link.springer.com/article/10.1007/s10664-020-09921-9

Mondal, M.; Roy, C. K.; Roy, B.; Schneider, K. A. Investigating the Relationship between Evolutionary Coupling and Software BugProneness. In CASCON 2019 Proceedings – Conference of the Centre for Advanced Studies on Collaborative Research – Proceedings of the 29th Annual International Conference on Computer Science and Software Engineering; 2020.

Mondal, M.; Roy, C. K.; Roy, B.; Schneider, K. A. Ranking Co-Change Candidates of Micro-Clones. In CASCON 2019 Proceedings – Conference of the Centre for Advanced Studies on Collaborative Research – Proceedings of the 29th Annual International Conference on Computer Science and Software Engineering; 2020.

Mondal, M.; Roy, C. K.; Schneider, K. A. A Survey on Clone Refactoring and Tracking. J. Syst. Softw. 2020. https://doi.org/10.1016/j.jss.2019.110429

Mondal, M.;Roy, B.; Roy, C.K.; Schneider, K.A. Investigating Near-Miss Micro-Clones in Evolving Software. Proceedings of the 28th ACM/IEEE International Conference on Program Comprehension (ICPC 2020). Seoul, South Korea. 2020, 11 pages.

Mostaeen, G.; Roy, B.; Roy, C.K.; Schneider, K.; Svajlenko, J. A machine learning based framework for code clone validation. Journal of Systems and Software. 2020, 169, 110686. https://doi.org/10.1016/j.jss.2020.110686

Nadim, M.; Mondal, M.; Roy, C. K. Evaluating Performance of Clone Detection Tools in Detecting Cloned Cochange Candidates. In 2020 IEEE 14th International Workshop on Software Clones (IWSC); 2020; pp 15–21. https://doi.org/10.1109/IWSC50091.2020.9047639

Nafi, K. W.; Roy, B.; Roy, C. K.; Schneider, K. A. A Universal Cross Language Software Similarity Detector for Open Source Software Categorization. J. Syst. Softw. 2020. https://doi.org/10.1016/j.jss.2019.110491

Nielsen, K. Using UAV-Based Imagery to Determine Volume, Groundcover, and Growth Rate Characteristics of Lentil (Lens culinaris Medik.). M.Sc. Thesis, University of Saskatchewan. 2020.

Nilsen, K. T.; Walkowiak, S.; Xiang, D.; Gao, P.; Quilichini, T. D.; Willick, I. R.; Byrns, B.; N’Diaye, A.; Ens, J.; Wiebe, K.; Ruan, Y.; Cuthbert, R. D.; Craze, M.; Wallington, E. J.; Simmonds, J.; Uauy, C.; Datla, R.; Pozniak, C. J. Copy Number Variation of TdDof Controls Solid-Stemmed Architecture in Wheat. Proc. Natl. Acad. Sci. U. S. A. 2020, 117 (46), 28708–28718. https://doi.org/10.1073/pnas.2009418117

Nilsen, K. T.; Walkowiak, S.; Xiang, D.; Gao, P.; Quilichini, T. D.; Willick, I. R.; Byrns, B.; N’Diaye, A.; Ens, J.; Wiebe, K.; Ruan, Y.; Cuthbert, R. D.; Craze, M.; Wallington, E. J.; Simmonds, J.; Uauy, C.; Datla, R.; Pozniak, C. J. Copy Number Variation of TdDof Controls Solid-Stemmed Architecture in Wheat. Proceedings of the National Academy of Sciences 2020, 202009418.

Pass, B.; Kim, Y.-H.; Schneider, D. Optimal Transport and Barycenters for Dendritic Measures. Pure Appl. Anal. 2020.

Qi P, Samadi N, Chapman D. X-ray Spectral Imaging Program: XSIP. Journal of Synchrotron Radiation. 2020 Nov 1; 27(6).

Siegmund, J.; Roy, C.K. Preface to the special issue on program comprehension. Empir Software Eng. 2020, 25, 3, 2137–2139. https://doi.org/10.1007/s10664-020-09806-x

Siri, J.N.; Parkin, I.; Sharpe, A. Using Simulated Annealing to Declutter Genome Visualizations. Proceeding of the Thirty-Third International FLAIRS Conference. 2020, 201-204.

Smyth, S. J. The Human Health Benefits from GM Crops. Plant Biotechnol. J. 2020. https://doi.org/10.1111/pbi.13261

Smyth, S. J.; Macall, D. M.; Phillips, P. W. B.; de Beer, J. Implications of Biological Information Digitization: Access and Benefit Sharing of Plant Genetic Resources. J. World Intellect. Prop. 2020. https://doi.org/10.1111/jwip.12151

Smyth, S.J.; Sutherland, C. Assessing Innovative Sustainability. Report submitted to the Agri-Food Innovation Council. May 2020.

Smyth, SJ, & Charles, TC. 2020. Impacts on International Research Collaborations from DSI/ABS Uncertainty. Trends in Biotechnology, https://doi.org/10.1016/j.tibtech.2020.10.011

Smyth, SJ, Gleim, SW & Lubieniechi, S. 2020. Regulatory Barriers to Innovative Plant Breeding in Canada. Frontiers in Genome Editing, 2,

Smyth, SJ. 2020. Regulatory Barriers to Improving Global Food Security. Global Food Security, 26, Article 100440. https://doi.org/10.1016/j.gfs.2020.100440.

Sutherland, C; Sim, C.;Gleim, S.; Smyth, S.J. Canadian Consumer Insights on Agriculture: Addressing the Knowledge-Gap. J Agr Food Inform. 2020, 21, 50-72.

Sutherland, C.; Sim, C.; Gleim, S.; Smyth, S. J. Consumer Insights on Canada’s Food Safety and Food Risk Assessment System. J. Agric. Food Res. 2020. https://doi.org/10.1016/j.jafr.2020.100038

Tasim, J.; Mondal, D. Data Reduction and Deep-Learning Based Recovery for Geospatial Visualization and Satellite Imagery. IEEE International Conference on Big Data (IEEE BigData-MLBD 2020). 2020. 10.1109/BigData50022.2020.9378008

Tidemann, B. D.; Harker, K. N.; Johnson, E. N.; Willenborg, C. J.; Shirtliffe, S. J. Time of Wild Oat (Avena Fatua) Panicle Clipping Influences Seed Viability. Weed Sci. 2020. https://doi.org/10.1017/wsc.2020.19

Torres-Tello, J.; Venkatachalam, S.; Moreno, L.; Ko, S.-B. Ensemble Learning for Improving Generalization in Aeroponics Yield Prediction. 2020 IEEE International Symposium on Circuits and Systems (ISCAS). Sevilla, Spain. 2020. 10.1109/ISCAS45731.2020.9181283

Ubbens, J.; Cieslak, M.; Prusinkiewicz, P.; Parkin, I.; Ebersbach, J.; Stavness, I. Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies. Plant Phenomics 2020. https://doi.org/10.34133/2020/5801869

Ubbens, J.R.; Ayalew, T.W.; Shirtliffe, S.; Josuttes, A.; Pozniak, C.; Stavness, I. Auto Count: Unsupervised Segmentation and Counting of Organs in Field Images. European Conference on Computer Vision 2020. August 23, 2020. Virtual Conference.

Walkowiak, S.; Gao, L.; Monat, C.; Haberer, G.; Kassa, M.T.; Brinton, J.; Ramirez-Gonzalez, R.H.; Kolodziej, M.C.; Delorean, E.; Thambugala, D.; Klymiuk, V.; Byrns, B.; Gundlach, H.; Bandi, V.; Siri, J.N.; Nilsen, K.; Aquino, C.; Himmelbach, A.; Copetti, D.; Ban, T.; Venturini, L.; Bevan, M.; Clavijo, B.; Koo, D.-H.; Ens, J.; Wiebe, K.; N’Diaye, A.; Fritz, A.K.; Gutwin, C.; Fiebig, A.; Fosker, C.; Fu, B.X.; Accinelli, G.G.; Gardner, K.A.; Fradgley, N.; Gutierrez-Gonzalez, J.; Halstead-Nussloch, G.; Hatakeyama, M.; Koh, C.S.; Deek, J.; Costamagna, A.C.; Fobert, P.; Heavens, D.; Kanamori, H.; Kawaura, K.; Kobayashi, F.; Krasileva, K.; Kuo, T.; McKenzie, N.; Murata, K.; Nabeka, Y.; Paape, T.; Padmarasu, S.; Percival-Alwyn, L.; Kagale, S.; Scholz, U.; Sese, J.; Juliana, P.; Singh, R.; Shimizu-Inatsugi, R.; Swarbreck, D.; Cockram, J.; Budak, H.; Tameshige, T.; Tanaka, T.; Tsuji, H.; Wright, J; Wu, J.; Steuernagel, B.; Small, I.; Cloutier, S.; Keeble-Gagnère, G.; Muehlbauer, G.; Tibbets, J.; Nasuda, S.; Melonek, J.; Hucl, P.J.; Sharpe, A.G.; Clark, M; Legg, E.; Bharti, A.; Langridge, P.; Hall, A.; Uauy, C.; Mascher, M.; Krattinger, S.G.; Handa, H.; Shimizu, K.K.; Distelfeld, A.; Chalmers, K.; Keller, B.; Mayer, K.F.X.; Poland, J.; Stein, N.; McCartney, C.A.; Spannagl, M.; Wicker, T.; Pozniak, C.J. Multiple wheat genomes reveal global variation in modern breeding. Nature. 588, 277-283. Springer Nature. https://doi.org/10.1038/s41586-020-2961-x

Wu, M.; Wang, P.; Yin, K.; Cheng, H.; Xu, Y.; Roy, C. K. LVMapper: A LargeVariance Clone Detector Using Sequencing Alignment Approach. IEEE Access 2020. https://doi.org/10.1109/ACCESS.2020.2971545

Chaudhary, R.; Koh, C.S.; Kagale, S.; Tang, L.; Wu, S.W.; Lv, Z.; Mason, A.S.; Sharpe, A.G.; Diederichsen, A.; Parkin, I.A.P. Assessing Diversity in the Camelina Genus Provides Insights into the Genome Structure of Camelina sativa. G3: Genes, Genomes, Genetics. 2020, 10 (4), 1297-1308.

Lassoued, R, Smyth, J.S, Phillips, P.W.B. Regulation of gene editing for crop improvement: A global expert opinion. Ag-West bio-Bulletin Oct 2020.

2020. Smyth and T. C. Charles. 2020. Impacts on International Research Collaborations from DSI/ABS Uncertainty. Trends in Biotechnology.
2021. Smyth. 2020. Regulatory Barriers to Improving Global Food Security. Global Food Security, 26, Article 100440.

Siegmund, J.; Roy, C.K. Preface to the special issue on program comprehension. Empir Software Eng. 2020, 25, 3, 2137–2139.

Mayra S, Espana C, and Deters R. (2019) Access Control Management for Plant Phenotyping Using Integrated Blockchain. Proceedings of the 2019 ACM International Symposium on Blockchain and Secure Critical Infrastructure. BSCI '19, pp 39-46.

Singh K. D., Shirtliffe S. J., and Duddu H. S. N. (2019) The Role of Bi-Directional Reflectance Correction in UAV-based Hyperspectral Imaging to Improve Data Robustness. 10th Workshop on Hyperspectral Imaging and Signal Processing: Evolution in Remote Sensing (WHISPERS). pp 1-5.

Ademola A. Adenle, E. Jane Morris, Denis J. Murphy, Peter W.B. Phillips, Eduardo Trigo, Peter Kearns, Yun-He Li, Hector Quemada, José Falck-Zepeda, John Komen. In Press. Rationalising the Governance of GM Technologies in Developing Countries. Nature Biotechnology.

Bernard, J. & McQuillan, I. (2018). A Fast and Reliable Hybrid Approach for Inferring L-systems. The 2018 Conference on Artificial Life: A Hybrid of the European Conference on Artificial Life (ECAL) and the International Conference on the Synthesis and Simulation of Living Systems (ALIFE) 2018 : 444-451 

Bernard J. & McQuillan I. (2018) New Techniques for Inferring L-systems Using Genetic Algorithm. In: Korošec P., Melab N., Talbi EG. (eds) Bioinspired Optimization Methods and Their Applications. BIOMA 2018. Lecture Notes in Computer Science, vol 10835. 

Bernard and I. McQuillan, "Inferring Stochastic L-Systems Using a Hybrid Greedy Algorithm," 2018 IEEE 30th International Conference on Tools with Artificial Intelligence (ICTAI), Volos, 2018, pp. 600-607.

de Beer, J., & Jain, V.(2018). Inclusive Innovation in Biohacker Spaces: The Role of Systems and Networks. Technology Innovation Management Review, 8(2): 27-37.

Gleim, S., & Smyth, S. J. (2018). Scientific underpinnings of biotechnology regulatory frameworks. New Biotechnology, 42, 26-32. doi:10.1016/j.nbt.2018.01.004

Hema S.N. Duddu, Vladimir Pajic, Scott D. Noble, Karen K. Tanino & Steven J. Shirtliffe (2018): Image-Based Rapid Estimation of Frost Damage in Canola (Brassica napus L.), Canadian Journal of Remote Sensing, DOI: 10.1080/07038992.2018.1462660 

Judith F. Islam, Manishankar Mondal, Chanchal K. Roy, Kevin A. Schneider, (2018) Comparing Software Bugs in Clone and Nonclone Codes: An Empirical Study, International Journal of Software Engineering and Knowledge Engineering Vol. 27, Nos. 9&10 1–20

 Maru A, Berne D, De Beer J, Ballantyne P, Pesce V, Kalyesubula S, Fourie N, Addison C, Collet A, Chaves J. (2018). Digital and Data-Driven Agriculture: Harnessing the Power of Data for Smallholders. F1000Research.

McQuillan, I., Bernard, J. & Prusinkiewicz, P. (2018). Algorithms for Inferring Context-Sensitive L-Systems. In: Stepney S., Verlan S. (eds) Unconventional Computation and Natural Computation. UCNC2018. Lecture Notes in Computer Science, vol 10867. 

Shifting the limits in wheat research and breeding using a fully annotated reference genome; P2IRC authors include: Andrew Sharpe, Curtis Pozniak (full list of authors included in article)

Scott Biden, Stuart J. Smyth & David Hudson (2018): The economic and environmental cost of delayed GM crop adoption: The case of australia's GM canola moratorium, GM Crops & Food, DOI: 10.1080/21645698.2018.1429876

Avni R, Nave M, Barad O, Baruch K,Twardziok S, Gundlach H, Hale I, Masche M. et al (2017)  Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 6346, 93-97.

Banani Roy, Amit Kumar Mondal, Chanchal K. Roy, Kevin A. Schneider, Kawser Wazed, (2017)Towards a Reference Architecture for Cloud-Based Plant Genotyping and Phenotyping Analysis Frameworks", The 2017 International Conference on Software Architecture (ICSA 2017), pp. 41-50, Gothenburg, Sweden, April 2017. 

de Beer, Jeremy.(2017) Ownership of Open Data: Governance Options for Agriculture and Nutrition. F1000Research.

Feret, J.-B., A. Gitelson, S.D. Noble, and S. Jacquemoud. (2017). PROSPECT-D: towards modeling leaf optical properties through a complete lifecycle. Remote Sensing of Environment. 193: 204-215.

Runions, A, Tsiantis, M, Prusinkiewicz, P (2017) A common developmental program can produce diverse leaf shapes.   New Phytologist   216   Issue: 2   401-418

Samaniego, M, and Deters R  (2017)  Virtual Resources & Blockchain for Configuration Management in IoT.  Journal of Ubiquitous Systems & Pervasive Networks 9(2): 1-13.

Smyth, S. J. (2017). Genetically modified crops, regulatory delays, and international trade. Food and Energy Security, 6(2), 78-86. doi:10.1002/fes3.100

Stuart J. Smyth, William A. Kerr & Richard S. Gray (2017) Regulatory barriers to international scientific innovation: approving new biotechnology in North America, Canadian Foreign Policy Journal, 23:2, 134-145, DOI: 10.1080/11926422.2016.1190771

Ubbens, J. R., Cieslak, M., Prusinkiewicz, P. & Stavness, I. (2017). Using Plant Models in Deep Learning for High-Throughput Phenotyping. BMC Plant Methods

Ubbens, J. R. & Stavness, I. (2017). Deep Plant Phenomics: A Deep Learning Platform for Complex Plant Phenotyping Tasks.  Frontiers in Plant Science, 8: 1190 1-11

Cieslak M, Cheddadi I, Boudon F, Baldazzi V, Genard M, Godin C, Berti N. (2016) Integrating Physiology and Architecture in Models of Fruit Expansion.  Frontiers in Plant Science 9, 1739

Lomotey, Richard K., and Ralph Deters, 2016, MUBaaS: mobile ubiquitous brokerage as a service, J. World Wide Web 19(1):5-19