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With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the…
The integration of Large Language Models (LLMs) into scientific workflows presents exciting opportunities to accelerate biomedical discovery. However, the reactive nature of LLMs, which respond only when prompted, limits their effectiveness…
The growing popularity and widespread adoption of large language models (LLMs) necessitates the development of tools that enhance the effectiveness of user interactions with these models. Understanding the structures and functions of these…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
The advent of modern, high-speed electron detectors has made the collection of multidimensional hyperspectral transmission electron microscopy datasets, such as 4D-STEM, a routine. However, many microscopists find such experiments daunting…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
Teleoperation platforms often require the user to be situated at a fixed location to both visualize and control the movement of the robot and thus do not provide the operator with much mobility. One example is in existing robotic surgery…
OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
Photoacoustic (PA) imaging systems based on clinical linear ultrasound arrays have become increasingly popular in translational PA research. Such systems can be more easily integrated in a clinical workflow due to the simultaneous access to…
Teleoperation of robotic systems for precise and delicate object grasping requires high-fidelity haptic feedback to obtain comprehensive real-time information about the grasp. In such cases, the most common approach is to use kinesthetic…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…
The Imaging Computational Microscope (ICM) is a suite of computational tools for automated analysis of functional imaging data that runs under the cross-platform MATLAB environment (The Mathworks, Inc.). ICM uses a semi-supervised…
Large language models (LLMs) are increasingly envisioned as decision-support tools in clinical practice, yet safe clinical reasoning demands integrating heterogeneous knowledge bases -- trials, primary studies, regulatory documents, and…
Computational experiments have become essential for scientific discovery, allowing researchers to test hypotheses, analyze complex datasets, and validate findings. However, as computational experiments grow in scale and complexity, ensuring…
Clinical decision-making is inherently complex, often influenced by cognitive biases, incomplete information, and case ambiguity. Large Language Models (LLMs) have shown promise as tools for supporting clinical decision-making, yet their…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
High-throughput technologies to collect field data have made observations possible at scale in several branches of life sciences. The data collected can range from the molecular level (genotypes) to physiological (phenotypic traits) and…