Jacob Hughey

LimoRhyde2: genomic analysis of biological rhythms based on effect sizes

LimoRhyde2 analyzes genomic data to identify rhythmic genes by focusing on effect sizes rather than statistical significance, revealing genes with high-amplitude rhythms.

The Phenotype-Genotype Reference Map: Improving biobank data science through replication.

The paper introduces a phenotype-genotype reference map for replicating GWAS results in biobank data and demonstrates its utility in detecting data corruption and assessing reproducibility.

Sex inclusion in transcriptome studies of daily rhythms

The paper examines sex inclusion in transcriptome studies of daily rhythms and finds strong underrepresentation of females across species and tissues.

The seeker R package: simplified fetching and processing of transcriptome data

The seeker R package simplifies fetching and processing of RNA-seq and microarray data by wrapping existing tools and providing a unified interface for analysis.

The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants

The paper introduces the phers R package, which enables PheRS-based analysis of linked EHR and genetic data to study Mendelian disease and rare variants.

Automated quality control and cell identification of droplet-based single-cell data using dropkick

dropkick improves scRNA-seq quality control by automatically distinguishing real cells from ambient barcodes, outperforming existing methods in recovering rare cell types and excluding noise.

Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic changes in the mammalian circadian clock

The paper shows that optogenetic activation of VIPergic SCN neurons mimics the effects of extended photoperiod on circadian rhythms and behavior.

pmparser and PMDB: resources for large-scale, open studies of the biomedical literature

The paper introduces pmparser and PMDB, tools for converting and storing PubMed data to enable large-scale biomedical literature analysis.

The risks of using the chi-square periodogram to estimate the period of biological rhythms

This study shows the chi-square periodogram (CSP) underestimates biological rhythm periods, especially in short time-courses, and recommends using alternative methods like the Lomb-Scargle periodogram.

Distinct components of photoperiodic light are differentially encoded by the mammalian circadian clock

The paper investigates how different components of photoperiodic light influence circadian clock properties through behavioral and SCN measurements.

Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record

This study shows Cox regression improves power to detect genotype-phenotype associations in EHR-linked genomic studies compared to logistic regression.

Simphony: simulating large-scale, rhythmic data

Simphony simulates large-scale rhythmic data for benchmarking methods, allowing users to specify experimental designs and feature properties.

LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data

LimoRhyde provides a flexible framework for analyzing rhythmic transcriptome data, enabling detection of differential rhythmicity and expression in circadian systems.

Population level rhythms in human skin: implications for circadian medicine

The paper identifies robust circadian rhythms in human skin at the population level and develops single-sample biomarkers for circadian phase.

Pulling the covers in electronic health records for an association study with self-reported sleep behaviors

This study uses EHR data to analyze sleep behaviors and their associations with health outcomes, finding links between weekend sleep patterns and mental health.

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells

MetaCyto enables meta-analysis of flow and mass cytometry data, revealing racial differences in immune cell populations across 2926 samples.