Related papers: Key challenges facing data-driven multicellular sy…

Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…

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…

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…

Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…

Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…

Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…

In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…

Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…

A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…

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…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome,…

Across biological subdisciplines, the last decade has seen an explosion of high-dimensional datasets, including datasets for cells, species, immune systems, neurons and behaviour. At the ICTS workshop 'Unifying Theories in High-Dimensional…

The field of single-cell biology is growing rapidly and is generating large amounts of data from a variety of species, disease conditions, tissues, and organs. Coordinated efforts such as CZI CELLxGENE, HuBMAP, Broad Institute Single Cell…

Data is a precious resource in today's society, and is generated at an unprecedented and constantly growing pace. The need to store, analyze, and make data promptly available to a multitude of users introduces formidable challenges in…

Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…

Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…

The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…