Joaquin Reyna

An Open Benchmark for Systems Vaccinology: Insights from the CMI-PB Challenges

The paper benchmarks computational models predicting B. pertussis booster vaccine responses using multi-omics data from three cohorts, identifying key predictors of immunity and establishing a community resource for systems vaccinology.

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

Loop Catalog compiles HiChIP data from 1000+ human and mouse samples to provide a resource for analyzing chromatin loops and their regulatory roles.

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

The paper benchmarks 49 algorithms for predicting B. pertussis vaccination outcomes, finding that purpose-built models outperform literature-based ones due to better handling of nonlinearities and data preprocessing.

Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares

The paper introduces nipalsMCIA, a tool for multi-omics dimensionality reduction that improves speed and flexibility over existing methods for single-cell data.

Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations

The paper identifies regulatory network modules in human stem cells, showing epigenetic and genetic factors influence pluripotency state differences.

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

The paper maps eQTLs in fetal-like pancreatic progenitor cells, identifying regulatory variants that influence diabetes risk by affecting gene expression and splicing in early development.

A systems vaccinology resource to develop and test computational models of immunity

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

This study identifies causal genetic variants for cardiac traits by integrating spatiotemporal eQTL analysis with GWAS data, showing stage- and tissue-specific effects.

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease

This study systematically analyzes the MHC region to uncover genetic associations between HLA types, gene expression, and disease, revealing novel insights into disease mechanisms.