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Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
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…
Over the past decade, researchers have focused increasing levels of attention on the use of survey and non-survey data to inform decision-making by multiple stakeholders. Work with such data generally requires extensive exploration before a…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
1. Joint Species Distribution models (JSDMs) explain spatial variation in community composition by contributions of the environment, biotic associations, and possibly spatially structured residual covariance. They show great promise as a…
The recognition of multi-class cell nuclei can significantly facilitate the process of histopathological diagnosis. Numerous pathological datasets are currently available, but their annotations are inconsistent. Most existing methods…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
Microbial ecology serves as a foundation for a wide range of scientific and biomedical studies. Rapidly-evolving high-throughput sequencing technology enables the comprehensive search for microbial biomarkers using longitudinal experiments.…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Phenomics is an emerging branch of modern biology that uses high throughput phenotyping tools to capture multiple environmental and phenotypic traits, often at massive spatial and temporal scales. The resulting high dimensional data…
We would like to congratulate Lee, Nadler and Wasserman on their contribution to clustering and data reduction methods for high $p$ and low $n$ situations. A composite of clustering and traditional principal components analysis, treelets is…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
Seismic data often contain gaps due to various obstacles in the investigated area and recording instrument failures. Deep learning techniques offer promising solutions for reconstructing missing data parts by leveraging existing…
Multimodal Foundation Models (FMs) offer a path to learn general-purpose representations from heterogeneous ecological data, easily transferable to downstream tasks. However, practical biodiversity modelling remains fragmented; separate…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Metagenomic taxonomic annotation aims to identify the microbial origins of DNA fragments in environmental samples. Traditional methods that rely on sequence similarity are often constrained by the high microbial diversity and the…