Department of Statistics, UCLA

A brief overview of the papers and commentaries in this special edition.

Ambulance response times in Santa Barbara County for 2006 are analyzed using point process techniques, including kernel intensity estimates and K-functions. Clusters of calls result in significantly higher response times, and this effect is quantified. In particular, calls preceded by other calls within 20 km and within the previous hour are significantly more likely to result in violations. This effect appears to be especially pronounced within semi-rural neighborhoods.

[WestJEM. 2009;10:42-47.]

Introductory remarks

The manuscript considers multivariate functional data analysis with a known graphical model among the functional variables representing their conditional relationships (e.g., brain region-level fMRI data with a prespecified connectivity graph among brain regions). Functional Gaussian graphical models (GGM) used for analyzing multivariate functional data customarily estimate an unknown graphical model, and cannot preserve knowledge of a given graph. We propose a method for multivariate functional analysis that exactly conforms to a given inter-variable graph. We first show the equivalence between partially separable functional GGM and graphical Gaussian processes (GP), proposed recently for constructing optimal multivariate covariance functions that retain a given graphical model. The theoretical connection helps to design a new algorithm that leverages Dempster's covariance selection for obtaining the maximum likelihood estimate of the covariance function for multivariate functional data under graphical constraints. We also show that the finite term truncation of functional GGM basis expansion used in practice is equivalent to a low-rank graphical GP, which is known to oversmooth marginal distributions. To remedy this, we extend our algorithm to better preserve marginal distributions while respecting the graph and retaining computational scalability. The benefits of the proposed algorithms are illustrated using empirical experiments and a neuroimaging application.

Scientific collaboration networks are a form of unequally distributed social capital that shapes both researcher job placement and long-term research productivity and prominence. However, the role of collaboration networks in shaping the gender and racial diversity of the scientific workforce remains unclear. Here we propose a computational null model to investigate the degree to which early-career scientific collaborators with representationally diverse cohorts of scholars are associated with forming or participating in more diverse research groups as established researchers. When testing this hypothesis using two large-scale, longitudinal datasets on scientific collaborations, we find that the gender and racial diversity in a researcher's early-career collaboration environment is strongly associated with the diversity of their collaborators in their established period. This diversity-association effect is particularly prominent for men. Coupled with gender and racial homophily between advisors and advisees, collaborator diversity represents a generational effect that partly explains why changes in representation within the scientific workforce tend to happen very slowly.

Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype-Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.

This repository contains the R source code and derived data products to reproduce analyses in the paper: ‘A Twenty-First Century Structural Change in Antarctica’s Sea ice System’ by Marilyn N. Raphael, Thomas J. Maierhofer, Ryan L. Fogt, William R. Hobbs, and Mark S. Handcock. It appears in Nature-Communications Earth & Environment, 6, 131 (2025), under DOI: 10.1038/s43247-025-02107-5. There is also a detailed support site on GitHub: https://github.com/RaphaelLab/StructuralChangeInAntarcticSeaIceSystem

Understanding how cells respond differently to perturbation is crucial in cell biology, but existing methods often fail to accurately quantify and interpret heterogeneous single-cell responses. Here we introduce the perturbation-response score (PS), a method to quantify diverse perturbation responses at a single-cell level. Applied to single-cell perturbation datasets such as Perturb-seq, PS outperforms existing methods in quantifying partial gene perturbations. PS further enables single-cell dosage analysis without needing to titrate perturbations, and identifies buffered and sensitive response patterns of essential genes, depending on whether their moderate perturbations lead to strong downstream effects. PS reveals differential cellular responses on perturbing key genes in contexts such as T cell stimulation, latent HIV-1 expression and pancreatic differentiation. Notably, we identified a previously unknown role for the coiled-coil domain containing 6 (CCDC6) in regulating liver and pancreatic cell fate decisions. PS provides a powerful method for dose-to-function analysis, offering deeper insights from single-cell perturbation data.