Related papers: TinkerCell: Modular CAD Tool for Synthetic Biology
Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performance computational tools. Despite…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Cell tracking remains a pivotal yet challenging task in biomedical research. The full potential of deep learning for this purpose is often untapped due to the limited availability of comprehensive and varied training data sets. In this…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…
The Core Imaging Library (CIL) is an open-source versatile Python framework for solving inverse problems with special emphasis on imaging applications such as computed tomography (CT), using a plug-in architecture for data and operators,…
Crafting computer-aided design (CAD) models has long been a painstaking and time-intensive task, demanding both precision and expertise from designers. With the emergence of 3D generation, this task has undergone a transformative impact,…
This paper introduces the software TiGL: TiGL is an open source high-fidelity geometry modeler that is used in the conceptual and preliminary aircraft and helicopter design phase. It creates full three-dimensional models of aircraft from…
Model-Based Development (MBD) is widely used for embedded controls development, with Matlab Simulink being one of the most used modelling environments in industry. As with all software, Simulink models are subject to evolution over their…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
Live cell culture is crucial in biomedical studies for analyzing cell properties and dynamics in vitro. This study focuses on segmenting unstained live cells imaged with bright-field microscopy. While many segmentation approaches exist for…
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
Round-the-clock monitoring of human behavior and emotions is required in many healthcare applications which is very expensive but can be automated using machine learning (ML) and sensor technologies. Unfortunately, the lack of…
Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets…
Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…
Chimeric Antigen Receptor (CAR) T cell therapy has transformed immunotherapy for resistant cancers, yet it faces major limitations such as lack of persistence, toxicity, exhaustion, and antigen-negative relapse. Enhancing CAR T cells with…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…