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Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
A cellular automaton is a deterministic and exactly computable dynamical system which mimics certain fundamental aspects of physical dynamics such as spatial locality and finite entropy. CA systems can be constructed which have additional…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and,…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
We present a scalable, robust approach to creating quantum programs of arbitrary size and complexity. The approach is based on the true abstraction of the problem. The quantum program is expressed in terms of a high-level model together…
Biomolecular computers, along with quantum computers, may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing of data, expanded capacity of storing…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
Modern computer vision systems increasingly encounter performance limitations in data-scarce domains, where collecting large-scale, high-quality labeled data is costly or impractical. While controllable diffusion models enable scalable…
In this paper, we introduce SynthAI, a new method for the automated creation of High-Level Synthesis (HLS) designs. SynthAI integrates ReAct agents, Chain-of-Thought (CoT) prompting, web search technologies, and the Retrieval-Augmented…
The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central…
We introduce Synapse motivated by the needs to estimate and emulate workload execution characteristics on high-performance and distributed heterogeneous resources. Synapse has a platform independent application profiler, and the ability to…
Symmetry principles play an important role in geometry, and physics, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest. Biological systems are often…
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation,…
The human immune system protects the human body against various pathogens like e.g. biological viruses and bacteria. Artificial immune systems reuse the architecture, organization, and workflows of the human immune system for various…
Causal inference is essential for developing and evaluating medical interventions, yet real-world medical datasets are often difficult to access due to regulatory barriers. This makes synthetic data a potentially valuable asset that enables…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Quantum computing systems depend on the principles of quantum mechanics to perform multiple challenging tasks more efficiently than their classical counterparts. In classical software engineering, the software life cycle is used to document…