相关论文: Bugs as Features (Part II): A Perspective on Enric…

Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…

The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the…

Combining clinical and omics data can improve both daily clinical routines and research to gain more insights into complex medical procedures. We present the results of our first phase in a multi-year collaboration with analysts and…

The human gastrointestinal tract is an environment that hosts an ecosystem of microorganisms essential to human health. Vital biological processes emerge from fundamental inter- and intra-species molecular interactions that influence the…

In this paper we describe our experience in developing curriculum courses aimed at graduate students in emerging computational fields, including biology and medical science. We focus primarily on computational data analysis and statistical…

Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…

Interactive segmentation is a crucial research area in medical image analysis aiming to boost the efficiency of costly annotations by incorporating human feedback. This feedback takes the form of clicks, scribbles, or masks and allows for…

The global surge in the cases of gastric cancer has prompted an investigation into the potential of gut microbiota as a predictive marker for the disease. The alterations in gut diversity are suspected to be associated with an elevated risk…

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of…

Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…

The emerging field at the intersection of quantitative biology, network modeling, and control theory has enjoyed significant progress in recent years. This Special Issue brings together a selection of papers on complementary approaches to…

High dimensional and heterogeneous count data are collected in various applied fields. In this paper, we look closely at high-resolution sequencing data on the microbiome, which have enabled researchers to study the genomes of entire…

Artificial Intelligence has an important place in the scientific community as a result of its successful outputs in terms of different fields. In time, the field of Artificial Intelligence has been divided into many sub-fields because of…

We analyzed Medical Subject Headings (MeSH) from 21.6 million research articles indexed by PubMed to map this vast space of entities and their relations, providing insights into the origins and future of biomedical convergence. Detailed…

The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of functions and behaviors. Understanding patterns of these complex interactions and how they are…

By retracing my scientific journey that began 20 years ago, I highlight in this thesis the need to consider the organization of the brain, which is certainly globally hierarchical, but also highly distributed and mixed in the neuronal…

Cognitive engineering is a multi-disciplinary field and hence it is difficult to find a review article consolidating the leading developments in the field. The in-credible pace at which technology is advancing pushes the boundaries of what…

Associative learning is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was early recognized to be a general trait of complex multicellular organisms but also found in "simpler"…

The network architecture of the human brain has become a feature of increasing interest to the neuroscientific community, largely because of its potential to illuminate human cognition, its variation over development and aging, and its…

Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…