Lary, C. | Search bioRxiv

bioRxiv2025

BifurcatoR: A Framework for Revealing Clinically Actionable Signal in Variance Masquerading as Noise

BackgroundDisease heterogeneity is a persistent challenge in medicine, complicating both research and treatment. Standard analytical pipelines often assume patient populations are homogeneous, overlooking variance patterns that may signal biologically distinct subgroups. Variance heterogeneity (VH)--including skewness, outliers, and multimodal distributions--offers a powerful but underused lens for detecting latent etiological structures relevant to prognosis and therapeutic response. MethodsA major barrier to VH analysis is the fragmented landscape of available methods, many of which rely on normality assumptions that biological data frequently violate. In addition, existing tools often require programming expertise, and clear guidance on study design considerations--such as sample size and method selection--is lacking. To address these issues, we developed BifurcatoR, an open-source software platform that simplifies the detection, modeling, and interpretation of VH. BifurcatoR integrates simulation-based method evaluation, study design recommendations, and a user-friendly web interface to support VH analysis across a range of data distributions. We benchmarked VH methods through simulation and applied BifurcatoR to two clinical datasets: acute myeloid leukemia (AML) and obesity. ResultsSimulation studies revealed that VH method performance is highly context-specific, varying with distribution shape, mean-variance coupling, and underlying subgroup structure. In AML, BifurcatoR identified two molecularly distinct subgroups with different treatment responses, including an EVI1-high group with significantly poorer prognosis (p < 0.005) among KMT2A-rearranged cases. In a separate study, VH analysis uncovered immunophenotypic subgroups in obesity based on gene-level discordance across monozygotic twin pairs, highlighting latent variation in adipose immune cell composition. ConclusionsVH is not "noise", biological variation without clinical relevance. Instead, VH is a structured signal that can reveal latent and clinically meaningful subtypes. BifurcatoR offers a practical, accessible framework for incorporating VH into biomedical research, with implications for biomarker discovery, patient stratification, and precision medicine.

bioinformatics↗

bioRxiv2024

Thermoneutral Housing has Limited Effects on Social Isolation-Induced Bone Loss in Male C57BL/6J Mice

Social isolation stress has numerous known negative health effects, including increased risk for cardiovascular disease, dementia, as well as overall mortality. The impacts of social isolation on skeletal health, however, have not been thoroughly investigated. We previously found that four weeks of social isolation through single housing led to a significant reduction in trabecular and cortical bone in male, but not female, mice. One possible explanation for these changes in male mice is thermal stress due to sub-thermoneutral housing. Single housing at room temperature ([~]20-25{degrees}C)--below the thermoneutral range of mice ([~]26-34{degrees}C)--may lead to cold stress, which has known negative effects on bone. Therefore, the aim of this study was to test the hypothesis that housing mice near thermoneutrality, thereby ameliorating cold-stress, will prevent social isolation-induced bone loss in male C57BL/6J mice. 16-week-old mice were randomized into social isolation (1 mouse/cage) or grouped housing (4 mice/cage) at either room temperature ([~]23{degrees}C) or in a warm temperature incubator ([~]28{degrees}C) for four weeks (N=8/group). As seen in our previous studies, isolated mice at room temperature had significantly reduced bone parameters, including femoral bone volume fraction (BV/TV), bone mineral density (BMD), and cortical thickness. Contrary to our hypothesis, these negative effects on bone were not ameliorated by thermoneutral housing. Social isolation increased glucocorticoid-related gene expression in bone and Ucp1 and Pdk4 expression in BAT across temperatures, while thermoneutral housing increased percent lipid area and decreased Ucp1 and Pdk4 expression in BAT across housing conditions. Overall, our data suggest social isolation-induced bone loss is not a result of thermal stress from single housing and provides a key insight into the mechanism mediating the effects of isolation on skeletal health. Lay SummarySocial isolation is a major public health concern and is known to increase the risk for many diseases, including heart disease and dementia. The impact of social isolation on bone health, however, has not been well-studied. We previously found that four weeks of social isolation reduces bone in male mice. Isolated mice may experience more cold stress than mice housed in groups, as we commonly keep laboratory mice at temperatures below their ideal range, which could lead to bone loss. The aim of our study was therefore to test if housing mice at warmer temperatures, within their ideal temperature range, prevents isolation-induced bone loss in male mice. We found that housing mice at warmer temperatures did not fully prevent isolation-induced bone loss. We also found social isolation increased the expression of genes related to glucocorticoid signaling in bone across temperatures, as well as genes associated with mitochondrial metabolism within fat tissue. Overall, our results show that social isolation-induced bone loss is likely not a result of cold stress from single housing and provide insight into the mechanisms by which isolation causes bone loss.

physiology↗