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All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…
Genomics, especially multi-omics, has made precision medicine feasible. The completion and publicly accessible multi-omics resource with clinical outcome, such as The Cancer Genome Atlas (TCGA) is a great test bed for developing…
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information…
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.…
In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to the dawn of Sumerian…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of…
The rapid advancement of high-throughput sequencing and other assay technologies has resulted in the generation of large and complex multi-omics datasets, offering unprecedented opportunities for advancing precision medicine strategies.…
To address the requirement of enabling a comprehensive perspective of life-sciences data, Semantic Web technologies have been adopted for standardized representations of data and linkages between data. This has resulted in data warehouses…
Our growing ability to tailor healthcare to the needs of individuals has the potential to transform clinical treatment. However, the measurement of multiple biomarkers to inform clinical decisions requires rapid, effective, and affordable…
Research in the Life Sciences depends on the integration of large, distributed and heterogeneous data sources and web services. The discovery of which of these resources are the most appropriate to solve a given task is a complex research…
Information retrieval from distributed heterogeneous data sources remains a challenging issue. As the number of data sources increases more intelligent retrieval techniques, focusing on information content and semantics, are required.…
Multimodal clinical data are characterized by high dimensionality, heterogeneous representations, and structured missingness, posing significant challenges for predictive modeling, data integration, and interpretability. We propose BIONIC…
The dynamics of systems biological processes are usually modeled by a system of ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we introduce…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel…
Human life expectancy has dramatically improved over the course of the last century. Although this reflects a global improvement in sanitation and medical care, this also implies that more people suffer from diseases that typically manifest…