Aug 2026· Institutional Research Information System (Università degli Studi di Trento)
Abstract
In Bacteria and Archaea, mobile genetic elements (MGEs) are extremely diverse in terms of size, structure and mobilization mechanism, ranging from minimal non-autonomous sequences (<100 bp) to complex elements (>100,000 bp) capable of mobilizing many passenger genes. MGEs drive genome evolution and horizontal gene transfer (HGT), shaping the dissemination of functional traits across species, including antimicrobial resistance genes (ARGs) and virulence factors. Despite their importance, the distribution and transmission of MGEs in complex microbial communities remains understudied, largely due to the lack of methods for their systematic identification in metagenomic data and the limited scope of existing databases. In this thesis, I developed a comparative genomics framework to systematically identify insertions flanked by conserved regions in 1,345,857 prokaryotic genomes. This approach reconstructed 9,008,672 insertion clusters (ICs), capturing 61.4% of MGEs in public databases while revealing a vast diversity of previously uncharacterized elements. Integrating homology annotations, structural motif detection and machine learning predictions, I assigned 29.2% of ICs to known MGE classes, expanding their diversity by 32-fold. Functional analyses showed that ICs are enriched in canonical MGE-associated traits, such as ARGs, virulence factors, secondary metabolic pathways and prokaryotic defense systems. Mapping ICs across isolate genomes revealed extensive HGT across the prokaryotic tree of life, providing direct evidence of mobilization, and showed that 89.5% of horizontally transferred ICs were previously unknown. Together, these results represent the most comprehensive characterization of the prokaryotic mobilome to date and reveal a large diversity of uncharacterized elements, providing a resource for the exploration of MGEs at the metagenomic scale. In the second part of this thesis, I leverage large metagenomic data to explore the diversity of programmable nucleases for the development of new genome editing tools. CRISPR-Cas systems, which provide adaptive immunity against MGEs, have been widely repurposed for genome editing. However, clinical applications of currently available Cas nucleases remain limited by several factors, including activity, specificity, targeting requirements and efficient in vivo delivery. In particular, the widely used SpCas9 is not compatible with single adeno-associated viral (AAV) vector delivery, due 8 to its size, and is restricted to targets flanked by an NGG protospacer adjacent motif (PAM). To address these limitations, I developed a computational pipeline to identify and characterize TnpB proteins, compact programmable nucleases encoded by widespread MGE families (IS200/605 and IS607). By analyzing 330,895 TnpB orthologs from 14,127 species, I selected 25 candidates for experimental characterization. This led to the identification of ISPmu1, a TnpB from Pasteurella multocida that is active in human cells and represents a promising candidate for the development of compact genome editors. In parallel, I developed PAMpredict, a computational tool to accurately predict the PAM sequence of Cas9 nucleases. Applying this tool at scale revealed that natural PAM diversity across prokaryotes is sufficient to target almost all disease-causing mutations in the human genome with allele specificity. Overall, this thesis demonstrates that large metagenomic data enables the systematic exploration and characterization of MGEs and programmable nucleases across prokaryotes.
Some claim that especially in the field of agile software development the research lags years behind of the practice. In this paper, we characterize the status and main challenges for research on agile software development, and propose a preliminary roadmap, focusing on providing more empirical research, primarily on experienced agile teams and organizations, connecting better to existing streams of research in more established fields, giving more attention to management-oriented approaches, and finally give more emphasis to the core ideas in agile software development in order to increase our understanding. We hope that this preliminary roadmap serves as a starting point for creating a common research agenda and enables the generation of fruitful discussions and research results from the field.
Torgeir Dingsøyr, T. Dybå, P. Abrahamsson· Agile Conference· 91 citations· ⚡7
The happy-productive worker thesis states that happy workers are more productive. Recent research in software engineering supports the thesis, and the ideal of flourishing happiness among software developers is often expressed among industry practitioners. However, the literature suggests that a cost-effective way to foster happiness and productivity among workers could be to limit unhappiness. Psychological disorders such as job burnout and anxiety could also be reduced by limiting the negative experiences of software developers. Simultaneously, a baseline assessment of (un)happiness and knowledge about how developers experience it are missing. In this paper, we broaden the understanding of unhappiness among software developers in terms of (1) the software developer population distribution of (un)happiness, and (2) the causes of unhappiness while developing software. We conducted a large-scale quantitative and qualitative survey, incorporating a psychometrically validated instrument for measuring (un)happiness, with 2 220 developers, yielding a rich and balanced sample of 1318 complete responses. Our results indicate that software developers are a slightly happy population, but the need for limiting the unhappiness of developers remains. We also identified 219 factors representing causes of unhappiness while developing software. Our results, which are available as open data, can act as guidelines for practitioners in management positions and developers in general for fostering happiness on the job. We suggest considering happiness in future studies of both human and technical aspects in software engineering.
D. Graziotin, Fabian Fagerholm, Xiaofeng Wang et al.· International Conference on...· 84 citations· ⚡6
To compete in this age of disruption, large companies cannot rely on cost efficiency, lead time reduction and quality improvement. They are now looking for ways to innovate like startups. Meanwhile, the awareness and use of the Lean startup approach have grown rapidly amongst the software startup community in recent years. This study investigates how Lean internal startup facilitates software product innovation in large companies and identifies its enablers and inhibitors. A multiple case study approach is followed in the investigation. Two software product innovation projects from two large companies are examined, using a conceptual framework that is based on the method-in-action framework and extended with the previously developed Lean-Internal Corporate Venture model. Seven face-to-face in-depth interviews of the employees with different roles are conducted. Within-case analysis and cross-case comparison are applied to draw the findings from the cases. A generic process flow summarises the common key processes of Lean internal startups. The findings suggest that an internal startup that is initiated management or employees faces different challenges. A list of enablers of applying Lean startup in large companies are identified, including top management support and cross-functional team. Both cases face different inhibitors due to the different process of inception, objective of the team and type of the product. Our contributions are threefold. First, this study is one of the first attempt to investigate the use of Lean startup approach in large companies empirically. Second, the study shows the potential of the method-in-action framework to investigate the Lean startup approach in non-startup context. The third is a general process of Lean internal startup and the evidence of the enablers and inhibitors of implementing it, which are both theory-informed and empirically grounded.
Henry Edison, Nina M. Smørsgård, Xiaofeng Wang et al.· Journal of Systems and Softw...· 78 citations· ⚡6
In this paper, we present a novel approach to improving software quality and efficiency through a Large Language Model (LLM)-based model designed to review code and identify potential issues. Our proposed LLM-based AI agent model is trained on large code repositories. This training includes code reviews, bug reports, and documentation of best practices. It aims to detect code smells, identify potential bugs, provide suggestions for improvement, and optimize the code. Unlike traditional static code analysis tools, our LLM-based AI agent has the ability to predict future potential risks in the code. This supports a dual goal of improving code quality and enhancing developer education by encouraging a deeper understanding of best practices and efficient coding techniques. Furthermore, we explore the model's effectiveness in suggesting improvements that significantly reduce post-release bugs and enhance code review processes, as evidenced by an analysis of developer sentiment toward LLM feedback. For future work, we aim to assess the accuracy and efficiency of LLM-generated documentation updates in comparison to manual methods. This will involve an empirical study focusing on manually conducted code reviews to identify code smells and bugs, alongside an evaluation of best practice documentation, augmented by insights from developer discussions and code reviews. Our goal is to not only refine the accuracy of our LLM-based tool but also to underscore its potential in streamlining the software development lifecycle through proactive code improvement and education.
Z. Rasheed, Malik Abdul Sami, Muhammad Waseem et al.· arXiv.org· 62 citations· ⚡3
Agile methods continue to gain popularity. In particular, the Scrum method appears to be on the verge of becoming a de-facto standard in the industry, leading the so called Agile movement. While there are success stories and recommendations, there is little scientifically valid evidence of the challenges in the adoption of Agile methods in general, and Scrum in particular. Little, if anything, is empirically known about the application and adoption of Scrum in a multi-team and multi-project situation. The authors carried out an ethnographically informed longitudinal case study in industrial settings and closely followed how the Scrum method was adopted in a 20-person department, working in a simultaneous multi-project R&D environment. Altogether 10 challenges pertinent to the case of multi-team multi-project Scrum adoption were identified in the study. The authors contend that these results carry great relevance for other industrial teams. Future research avenues arising from the study are indicated.
A. Marchenko, P. Abrahamsson· Agile Conference· 59 citations· ⚡11
Systematic literature review (SLR) is foundational to evidence-based research, enabling scholars to identify, classify, and synthesize existing studies to address specific research questions. Conducting an SLR is, however, largely a manual process. In recent years, researchers have made significant progress in automating portions of the SLR pipeline to reduce the effort and time required for high-quality reviews; nevertheless, there remains a lack of AI-agent-based systems that automate the entire SLR workflow. To this end, we introduce a novel multi-AI-agent system designed to fully automate SLRs. Leveraging large language models (LLMs), our system streamlines the review process to enhance efficiency and accuracy. Through a user-friendly interface, researchers specify a topic; the system then generates a search string to retrieve relevant academic papers. Next, an inclusion/exclusion filtering step is applied to titles relevant to the research area. The system subsequently summarizes paper abstracts and retains only those directly related to the field of study. In the final phase, it conducts a thorough analysis of the selected papers with respect to predefined research questions. This paper presents the system, describes its operational framework, and demonstrates how it substantially reduces the time and effort traditionally required for SLRs while maintaining comprehensiveness and precision. The code for this project is available at: https://github.com/GPT-Laboratory/SLR-automation .
Malik Abdul Sami, Z. Rasheed, Kai-Kristian Kemell et al.· arXiv.org· 43 citations· ⚡2
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
