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Harmful algal blooms (HABs) are episodes of high concentrations of algae that are potentially toxic for human consumption. Mollusc farming can be affected by HABs because, as filter feeders, they can accumulate high concentrations of marine…
This work presents twelve fine-tuned deep learning architectures to solve the bacterial classification problem over the Digital Image of Bacterial Species Dataset. The base architectures were mainly published as mobile or efficient…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), linked with CRISPR associated (CAS) genes, play a profound role in the interactions between phage and their bacterial hosts. It is now well understood that CRISPR-CAS…
Rapid identification of bacteria is essential to prevent the spread of infectious disease, help combat antimicrobial resistance, and improve patient outcomes. Raman optical spectroscopy promises to combine bacterial detection,…
Seed formation is part of the reproductive cycle, leading to the accumulation of resistance stages that can withstand harsh environmental conditions for long periods of time. At the community level, multiple species with such long-lasting…
A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Traditionally, diagnosis and treatment of fungal infections in humans depend heavily on face-to-face consultations or examinations made by specialized laboratory scientists known as mycologists. In many cases, such as the recent…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Predicting non-covalent host-guest recognition remains challenging due to the complex interplay of electrostatics, dispersion, and steric effects, and the limited transferability of existing docking approaches to synthetic supramolecular…
The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated…
We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs.…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…