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The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
In nature, biological organisms jointly evolve both their morphology and their neurological capabilities to improve their chances for survival. Consequently, task information is encoded in both their brains and their bodies. In robotics,…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…
Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…
Biodiversity loss is a critical planetary boundary, yet its connection to computing remains largely unexamined. Prior sustainability efforts in computing have focused on carbon and water, overlooking biodiversity due to the lack of…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
This study here suggests a classification of technologies based on taxonomic characteristics of interaction between technologies in complex systems that is not a studied research field in economics of technical change. The proposed taxonomy…
The complexity of human biology and its intricate systems holds immense potential for advancing human health, disease treatment, and scientific discovery. However, traditional manual methods for studying biological interactions are often…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Bio-hybrid systems---close couplings of natural organisms with technology---are high potential and still underexplored. In existing work, robots have mostly influenced group behaviors of animals. We explore the possibilities of mixing…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
The convergence of artificial intelligence (AI) and synthetic biology is rapidly accelerating the pace of biological discovery and engineering. AI techniques, such as large language models and biological design tools, are enabling the…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…