Biology subjects

Lima, H.

Publications and source records attributed to Lima, H..

3 recordsLinked to original sources

bioRxiv2025

sabinaHSBM: An R package for link prediction network reconstruction using Hierarchical Stochastic Block Models

O_LINetwork analysis is a powerful framework for investigating complex systems across disciplines, including ecology, where it helps uncover patterns in predator-prey, host- parasite, or plant-pollinator interactions. However, ecological network data are often incomplete or error-prone due to sampling limitations, detection failures, and taxonomic uncertainty--leading to missing (false negative) and spurious (false positive) links that obscure structure and hinder inference. The hierarchical stochastic block model (HSBM), particularly in its degree-corrected form, is among the most effective tools for reconstructing networks under such uncertainty. Despite its robustness, the primary implementation of HSBM in the Python-based graph-tool library has remained largely inaccessible to ecologists. C_LIO_LIHere, we introduce sabinaHSBM, the first R package that makes degree-corrected HSBM broadly available through a user-friendly, flexible workflow. By bridging a gap between advanced network modeling and widely used ecological analysis platforms, sabinaHSBM facilitates network reconstruction and link prediction from binary bipartite data. The workflow involves three main steps: (1) preparing input data, (2) estimating posterior link probabilities, and (3) reconstructing the network. The package supports detection of undocumented and spurious links, exploration of hierarchical structure, and propagation of uncertainty throughout. Key features include cross-validation, flexible thresholding, probabilistic evaluation metrics, and two link prediction modes: estimating all link probabilities or identifying undocumented ones. C_LIO_LIWe illustrate the packages functionality through a case study using a published global dataset of carnivore-parasite associations, showing that inferred groupings are phylogenetically clustered. To assess predictive accuracy, we examined the top 10 highest-probability links identified by the model and found published evidence for 8, despite their absence from the original dataset. This highlights the models ability to recover biologically meaningful but underreported interactions. C_LIO_LIBy integrating all components of HSBM-based reconstruction into an accessible R package, sabinaHSBM empowers researchers to improve relational data quality and uncover overlooked patterns in complex ecological networks and beyond. C_LI

ecology↗

bioRxiv2022

randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

O_LIThe increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the worlds biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. C_LIO_LIThis prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. C_LIO_LIHere, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package randtip, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. C_LIO_LIAlthough randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the blind expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. C_LIO_LIPhylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses. C_LI

evolutionary biology↗

bioRxiv2019

BCR analysis of single-sorted, putative IgE+ memory B cells in food allergy: an ephemeral existence?

Immunoglobulin (Ig) E is the critical effector molecule in allergic reactions. Consequently, research efforts to understand the biology of IgE-expressing cells is of paramount importance. In particular, the role of IgE+ memory B cells (MBCs) in the perpetuation of allergic reactivity has been the subject of intense research. Studies in mice have convincingly established that IgE+ B cells are rare and transient and, therefore, an unlikely candidate to maintain allergic disease. In contrast, IgE+ MBCs have been detected by flow cytometry in the sputum and peripheral blood of humans and have been proposed as a clinical marker of allergic disease. We established a method to genetically validate, at the single-cell level, the putative IgE+ MBCs identified by flow cytometry from humans. We, then used this information to develop an enhanced flow cytometry protocol that more accurately identifies bona fide IgE+ MBCs. We found that IgE+ MBCs were detected in some patients with atopic dermatitis, but at a frequency that was ~100 times lower than previously reported. We also found that IgE+ MBCs were undetectable in PBMCs from peanut allergic patients. These findings provide tools to identify bona fide IgE+ MBCs, demonstrate their extreme rarity in circulation and are consistent with the lack of a central role for IgE+ MBCs in the maintenance of allergic sensitivity.\n\nOne Sentence SummaryThe frequency of IgE+ MBCs in the peripheral circulation of humans is orders of magnitude lower than previously reported and comparable between allergic and healthy donors, which cautions about the clinical utility of their assessment.

immunology↗