Chromosome conformation capture methods such as Hi-C and Micro-C have transformed our understanding of genome organisation, revealing architectural features from megabase-scale compartments to kilobase-scale loops. Yet the choice of fragmentation enzyme imposes constraints that shape which features are most readily observed. Restriction enzyme workflows rely on sequence specific cut sites and often use detergent conditions that can perturb chromatin structure, while micrococcal nuclease (MNase) exhibits pronounced sequence specificity and generates termini that require end processing before efficient ligation. These properties add time, introduce variability, and may bias fragment recovery. This thesis develops CAD-C, a chromosome conformation capture method that exploits the apoptotic nuclease CAD (Caspase-Activated DNase) to address these limitations. CAD is a double strand-specific endonuclease that cleaves preferentially in linker DNA between nucleosomes and generates predominantly blunt or near-blunt double-stranded breaks with 5′-phosphate and 3′ hydroxyl termini, the end chemistry preferred by T4 DNA ligase. This native ligation competence can eliminate enzymatic end-repair steps in Direct CAD-C and supports efficient proximity ligation under chromatin-preserving conditions. I first describe the design, expression, and purification of a recombinant CAD construct optimised for chromatin fragmentation. Because CAD requires its inhibitor-chaperone ICAD for proper folding, I developed a dual-cassette bacterial expression system that co-expresses CAD with a TEV cleavable ICAD variant, enabling on-demand activation of the nuclease. I also identify purification conditions that reduce contaminating bacterial nuclease activity and improve preparation quality for controlled chromatin digestion. I next characterise CAD cleavage patterns on crosslinked chromatin and introduce the CHOMP principle (CAD Hindered Overdigestion at Margins of Proteins), which describes how CAD’s steric bulk can bias cleavage toward defined offsets from chromatin-bound proteins, leaving accessible termini available for ligation. This framework provides a conceptual basis for interpreting CAD-C contact maps and the locations where ligation-competent ends form. I then present the CAD-C protocol in three workflow variants: Classic, Express, and Direct. Benchmarking against Micro-C and Hi-C in GM12878, hTERT-RPE1, and K562 cells shows that CAD-C recovers major architectural features, including compartments, domains, and loops, with performance comparable to Micro-C in these datasets. At the same time, CAD-C exhibits a distinctive short-range contact signature and preferentially recovers a subset of active regulatory contacts, including promoter-associated loops. I develop a ligation-gating model to explain how CAD’s native ligation competence can increase near-diagonal contact density while sharpening loop contrast relative to MNase-based methods. Finally, I introduce CADwalks, a per-molecule analytical framework for Direct CAD-C con catemers. Because CAD generates nucleosome-resolution fragments whose boundaries encode protein-DNA footprint information, and because its ligation-ready termini support efficient concate mer formation, CADwalks preserve the relative order, orientation, and co-occurrence of fragments captured on the same concatemer molecule, information that pairwise decomposition discards. At CTCF boundaries, CADwalks reveal a nucleosome-scale directional asymmetry consistent with oriented loop extrusion. This thesis is primarily a tool-development and validation effort. The experimental work em phasizes proof-of-principle demonstrations rather than exhaustive perturbation biology. Together, CAD-C and CADwalks show that changing the chromatin fragmentation enzyme changes not only assay resolution and workflow efficiency, but also the biochemical gate through which contacts are captured. They establish a nucleosome-resolution, per-molecule framework for chromosome con formation capture and provide a foundation for future studies of chromatin architecture, regulatory looping, and gene control.
In the context of cloud computing, risks associated with underlying technologies, risks involving service models and outsourcing, and enterprise readiness have been recognized as potential barriers for the adoption. To accelerate cloud adoption, the concrete barriers negatively influencing the adoption decision need to be identified. Our study aims at understanding the impact of technical and security-related barriers on the organizational decision to adopt the cloud. We analyzed data collected through a web survey of 352 individuals working for enterprises consisting of decision makers as well as employees from other levels within an organization. The comparison of adopter and non-adopter sample reveals three potential adoption inhibitor, security, data privacy, and portability. The result from our logistic regression analysis confirms the criticality of the security concern, which results in an up to 26-fold increase in the non-adoption likelihood. Our study underlines the importance of the technical and security perspectives for research investigating the adoption of technology.
Nattakarn Phaphoom, Xiaofeng Wang, S. Samuel et al.· Journal of Systems and Softw...· 111 citations· ⚡8
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
Affects--emotions and moods--have an impact on cognitive processing activities and the working performance of individuals. It has been established that software development tasks are undertaken through cognitive processing activities. Therefore, we have proposed to employ psychology theory and measurements in software engineering (SE) research. We have called it "psychoempirical software engineering". However, we found out that existing SE research has often fallen into misconceptions about the affect of developers, lacking in background theory and how to successfully employ psychological measurements in studies. The contribution of this paper is threefold. (1) It highlights the challenges to conduct proper affect-related studies with psychology; (2) it provides a comprehensive literature review in affect theory; and (3) it proposes guidelines for conducting psychoempirical software engineering.
D. Graziotin, Xiaofeng Wang, P. Abrahamsson· SSE@SIGSOFT FSE· 56 citations· ⚡4
It is essential for startups to quickly experiment business ideas by building tangible prototypes and collecting user feedback on them. As prototyping is an inevitable part of learning for early stage software startups, how fast startups can learn depends on how fast they can prototype. Despite of the importance, there is a lack of research about prototyping in software startups. In this study, we aimed at understanding what are factors influencing different types of prototyping activities. We conducted a multiple case study on twenty European software startups. The results are two folds; firstly we propose a prototype-centric learning model in early stage software startups. Secondly, we identify factors occur as barriers but also facilitators for prototyping in early stage software startups. The factors are grouped into (1) artifacts, (2) team competence, (3) collaboration, (4) customer and (5) process dimensions. To speed up a startup’s progress at the early stage, it is important to incorporate the learning objective into a well-defined collaborative approach of prototyping.
Anh Nguyen-Duc, Xiaofeng Wang, P. Abrahamsson· International Conference on...· 44 citations· ⚡5
Proteolysis-targeting chimeras (PROTACs) present a potentially effective strategy against various diseases via selective proteolysis. How to increase the efficacy of PROTACs remains challenging. Here, we explore the necessity of the linker, which has been deemed as an integral part of heterobifunctional PROTACs. Adopting single amino acid-based degradation signals, we find that the linker is not a required feature of the PROTACs. Notably, the linker-free PROTAC, Pro-BA, exhibits superior efficacy over its linker-bearing counterparts in degrading EML4-ALK and inhibiting lung cancer cell growth, as Pro-BA induces a stronger interaction between the target and the E3 ubiquitin ligase. Pro-BA is a water-soluble, orally administered degrader that significantly inhibits the tumor growth in a xenograft mouse model. The broad applicability of this linker-free PROTAC strategy is further validated through the development of BCR-ABL degrader. Our study introduces a design paradigm for PROTACs, potentially facilitating the advancement of more efficient therapeutic degraders. Linkers are traditionally seen as important for PROTAC activity. Here, the authors demonstrate that linker-free PROTACs can outperform traditional designs, marking a paradigm shift in PROTAC development for targeted protein degradation.
Designing effective mRNA sequences for therapeutics remains a formidable challenge. Inspired by successes in protein design, language models (LMs) are now being applied to RNA, but progress is often impeded by the lack of comprehensive training data. Existing models are frequently limited to UTR or CDS regions, restricting their application for complete mRNA sequences. We introduce mRNABERT, a robust, all-in-one mRNA designer pre-trained on the largest available mRNA dataset. To enhance performance, we propose a dual tokenization scheme with a cross-modality contrastive learning framework to integrate semantic information from protein sequences. On a comprehensive benchmark, mRNABERT demonstrates state-of-the-art performance, outperforming previous models in the majority of tasks for 5’ UTR and CDS design, RNA-binding protein (RBP) site prediction, and full-length mRNA property prediction. It also surpasses large protein models in several related tasks. In conclusion, mRNABERT’s superior performance across these diverse tasks signifies a substantial leap forward in mRNA research and therapeutic development. Designing complete mRNA sequences for new vaccines and therapies is a complex challenge. Here, the authors develop mRNABERT, a foundational AI model that designs entire mRNA sequences and demonstrates superior performance across comprehensive benchmarks.
Ying Xiong, Aowen Wang, Yu Kang et al.· Nature Communications· 22 citations· ⚡1
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MIT News · Artificial Intelligence· news.mit.eduAug 27, 2026
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
