Biology subjects

Boza, G.

Publications and source records attributed to Boza, G..

3 recordsLinked to original sources

bioRxiv2025

Multi-omics time-series analysis in microbiome research: a systematic review

Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. Thus, we performed a systematic literature review on data science methods for longitudinal multi-omics, with a particular focus on microbiome research.

bioinformatics↗

bioRxiv2023

Moderate Diversity of activation thresholds promotes cooperation in the Threshold Public Good Games

Societies face various collective actions which posits social dilemmas, in which a certain number of group members must act cooperatively in order to reach a collective goal. Such social dilemmas are often modelled as Threshold Public Good Games, in which the collective goal is reached successfully if the number of cooperative decisions reaches a threshold. Because cooperation is often a costly act, to coordinate such actions actors can attempt to communicate, to ensure that cooperative decisions are only made once the chances of reaching the goal, thus meeting the threshold is secured. Here we focus on the distribution of activation thresholds in societies, which captures the dynamics of peer pressure and the interaction between different levels of selfish and cooperative behaviours. Here we show that moderate diversity of activation thresholds favours cooperation under wide range of parameters.

ecology↗

bioRxiv2018

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability

Understanding the mechanisms promoting the assembly and maintenance of host-beneficial microbiomes is an open problem. An increasing amount of evidence supports the idea that animal and plant hosts can use private resources and the ecological phenomenon known as community bistability to favour some microbial strains over others. We briefly review empirical evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotic compounds to suppress non-beneficial, competitor strains, and (iii) provide resources (for a limited time) that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. By explicitly modelling localized microbial interactions and diffusion dynamics, we further show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that that there is a wide range of conditions under which hosts can promote the assembly of a self-sustaining defensive microbiome. This, in turn, supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.

microbiology↗