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Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…
This research paper discusses the advances made in the past decade in biomedicine and Large Language Models. To understand how the advances have been made hand-in-hand with one another, the paper also discusses the integration of Natural…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
In this Chapter, we ask questions (1) What is the right way to measure the quality of information processing in a biological system? and (2) What can real-life organisms do in order to improve their performance in information-processing…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
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…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have…
We introduced a methodology to efficiently exploit natural-language expressed biomedical knowledge for repurposing existing drugs towards diseases for which they were not initially intended. Leveraging on developments in Computational…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…