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Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
The exciting possibilities in the field of new quantum technologies extend far beyond the well-reported application of quantum computing. Precision timing, gravity sensors and imagers, cryptography, navigation, metrology, energy harvesting…
The increasing demands for computing performance have been a reality regardless of the requirements for smaller and more energy efficient devices. Throughout the years, the strategy adopted by industry was to increase the robustness of a…
The planned high-luminosity upgrade of the Large Hadron Collider (LHC) at CERN will bring much higher data rates that are far above the capabilities of currently installed software-based data processing systems. Therefore, new methods must…
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and…
Neuromorphic computing and, in particular, spiking neural networks (SNNs) have become an attractive alternative to deep neural networks for a broad range of signal processing applications, processing static and/or temporal inputs from…
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
Synthetic Biology is the new engineering-based approach to biology that includes applications of designing complex biological devices. At present, it is not yet clear what will emerge as the defining principles of Synthetic Biology. One…
Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
In early-stage architectural design, optimization algorithms are essential for efficiently exploring large and complex design spaces under tight computational constraints. While prior research has benchmarked various optimization methods,…
Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Energy efficiency is a corner stone of sustainability in data center and high-performance networking. However, at present there is a notable structural mismatch between network silicon development targets and network equipment utilization…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a…
Drug discovery is lengthy and expensive, with traditional computer-aided design facing limits. This paper examines integrating quantum computing across the drug development cycle to accelerate and enhance workflows and rigorous…