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For many conditions, it is of clinical importance to know not just the ability of a test to distinguish between those with and without the disease, but also the sensitivity to detect disease at different stages: in particular, the test's…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…
The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
Machine learning methods in healthcare have traditionally focused on using data from a single modality, limiting their ability to effectively replicate the clinical practice of integrating multiple sources of information for improved…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
In biomedical applications it is often necessary to estimate a physiological response to a treatment consisting of multiple components, and learn the separate effects of the components in addition to the joint effect. Here, we extend…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new…
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…
Effective dietary monitoring is critical for managing Type 2 diabetes, yet accurately estimating caloric intake remains a major challenge. While continuous glucose monitors (CGMs) offer valuable physiological data, they often fall short in…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
Multimodal medical imaging plays a pivotal role in clinical diagnosis and research, as it combines information from various imaging modalities to provide a more comprehensive understanding of the underlying pathology. Recently, deep…