Stuart C. Sealfon

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

The paper analyzes multi-omic, multi-tissue molecular responses to acute exercise in sedentary adults, identifying key pathways and exerkines involved in exercise effects.

The paper uses single-nucleus multiomics to study pituitary cell changes during the mouse estrous cycle, finding stage-dependent gene regulatory circuits and validated ETS2-driven gene expression patterns.

This study generates twelve SARS-CoV-2 viruses with mutations in individual proteins and shows that many have interferon-antagonizing activity and immunosuppressive effects in human cells and mice, with NSP1 and NSP15 having the greatest impact.

This study identifies tissue-specific lncRNA responses to endurance exercise in rats, revealing sex differences and potential therapeutic implications.

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

This study examines how acute endurance and resistance exercise alter alternative splicing in human skeletal muscle, adipose tissue, and blood, identifying 5102 differential splicing events and their regulatory mechanisms.

The paper identifies four activin-sensitive enhancers upstream of the murine Fshb gene, showing differential regulation by SMAD2/3 and FOXL2 in gonadotropes.

This study identifies how genetic and environmental factors shape the human immune cell epigenome through differential methylation and chromatin accessibility changes.

The paper creates a large-scale Consensus Pituitary Atlas to improve reproducibility and enable marker discovery and analysis in pituitary research.

The paper analyzes the epigenomic changes in innate immune cells after influenza virus infection and finds coordinated rewiring of the epigenetic landscape.

The paper uses single-nucleus multiome sequencing to analyze gene regulatory changes in human skeletal muscle after endurance exercise, identifying fiber-type specific regulatory programs and transcription factor networks.

This paper provides a comprehensive guide for quality control metrics and mitigation strategies for 11 epigenetics and transcriptomics assays to improve exposure signature discovery.

SPEEDI automates single-cell multi-omics analysis by integrating data, inferring batches, and labeling cell types without user input, improving reproducibility and accessibility.

This study examines how endurance exercise training affects rat subcutaneous white adipose tissue, revealing sex-specific molecular responses and differences in adiposity and metabolism.

The paper introduces CREMA, a framework for mapping cis-regulatory circuits using single-cell multiome data without peak-calling, and validates it using mouse pituitary data.

The paper identifies lipidomic biomarkers and therapeutic targets in sepsis patients, including those with COVID-19, and develops an interactive network analysis tool for multiomic data exploration.

This study profiles multi-omic changes in multiple tissues of rats during endurance exercise training, identifying molecular adaptations and sex-specific responses across time.

This study compares host module activation patterns and temporal dynamics across four influenza H1N1 viruses to identify conserved and differentially regulated immune responses.

The paper introduces SAIL, a machine learning tool to predict and analyze combinatorial stimulus interactions, revealing context-dependent functions and probabilistic algebra of cellular responses.

PLIER improves pathway inference and cell proportion analysis in gene expression data, enhancing replicability and biological insight in trans-eQTL studies.

This study improves zebrafish transcriptome annotation using long-read sequencing, identifying novel transcripts and isoforms, and validating them through computational and experimental methods.

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.