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Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
Much has changed since the inaugural ICGSE conference in 2006. Tools have improved, awareness of cultural differences is widespread, and developments such as the foregrounding of open source have all enhanced our ability to work across…
Machine learning (ML) is becoming increasingly crucial in many fields of engineering but has not yet played out its full potential in bioprocess engineering. While experimentation has been accelerated by increasing levels of lab automation,…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional methods frequently struggle with the inherent complexity,…
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…
Computing is an indispensable component of nearly all technologies and is ubiquitous for vast segments of society. It is also essential to discoveries and innovations in most disciplines. However, while past grand challenges in science have…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
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…
The vision of Organic Computing addresses challenges that arise in the design of future information systems that are comprised of numerous, heterogeneous, resource-constrained and error-prone components or devices. Here, the notion organic…
Generative Artificial Intelligence (GenAI) is taking the world by storm. It promises transformative opportunities for advancing and disrupting existing practices, including healthcare. From large language models (LLMs) for clinical note…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…