Gregory R. Grant

A Benchmark of Unsupervised Circadian Phase Inference Methods for Bulk Transcriptomic Data

This study benchmarks unsupervised circadian phase inference methods on bulk transcriptomic data, finding CHIRAL performs best with lower error than other methods.

Gut-derived serine protease reduces sleep but extends lifespan

This study identifies a gut-derived serine protease that reduces sleep but extends lifespan in Drosophila by increasing peripheral ROS, suggesting a link between sleep reduction and stress adaptation.

Role of IL10 signaling in the circadian control of host response to Influenza infection

The paper investigates how IL-10 signaling interacts with circadian rhythms to influence the host response to influenza infection, finding that blocking IL-10 signaling abolishes time-of-day-specific protection.

Effect of external cues on clock-driven protection from Influenza A infection

The paper shows that disrupting light cycles during a critical window reduces time-of-day protection from influenza, but rhythmic meal timing can compensate, highlighting the role of environmental cues in immune response.

Generating Correlated Data for Omics Simulation

The paper introduces methods to generate correlated omics data for benchmarking, showing improved performance in DESeq2 and CYCLOPS when dependencies are included.

MAJIQ-CLIN: A novel tool for the identification of Mendelian disease-causing variants from RNA-Seq data

MAJIQ-CLIN improves the detection of Mendelian disease-causing variants from RNA-Seq by addressing splicing aberrations, showing better accuracy and efficiency than existing tools.

Sources of non-uniform coverage in short-read RNA-Seq data

This study investigates sources of non-uniform coverage in RNA-Seq data and finds that no single factor explains the issue, contradicting prior claims.

Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms

This study shows that age-related blood-borne factors alter circadian gene expression in cultured fibroblasts, affecting oxidative phosphorylation and cholesterol biosynthesis pathways.

Disruption of the PGE2 synthesis / response pathway restrains atherogenesis in programmed cell death-1 (Pd-1) deficient hyperlipidemic mice

This study shows that disrupting the PGE2 synthesis or response pathway reduces atherogenesis in PD-1 deficient hyperlipidemic mice through different immune mechanisms.

BEERS2: RNA-Seq simulation through high fidelity in silico modeling

BEERS2 simulates RNA-seq reads with high fidelity, incorporating detailed library preparation and sequencing steps, and evaluates its impact on the Salmon pseudoalignment algorithm.

Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver

This paper performs a meta-analysis of mouse liver transcriptomics data to assess consistency of biological rhythms across studies, finding high concordance for core clock genes but low overlap for other rhythmic genes.

Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis

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.

RNA splicing analysis using heterogeneous and large RNA-seq datasets

The paper introduces MAJIQ v2, a tool for analyzing RNA splicing in large and heterogeneous RNA-seq datasets, showing improved performance over existing methods and applying it to brain subregion-specific splicing analysis.

The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans

This study maps expression and splicing QTLs in East Africans and finds population-specific genetic variation related to immunity, metabolism, and pigmentation.

MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

MOCCASIN corrects known and unknown confounders in RNA splicing analysis using synthetic and real data from TARGET and ENCODE.

Comparative evaluation of full-length isoform quantification from RNA-Seq

This study evaluates isoform quantification methods using simulated data, finding that no method significantly outperforms a simple approach on realistic data.

Distinct vascular genomic response of proton and gamma radiation.

This study compares the genomic response of mouse aorta to proton and gamma radiation, finding differences in gene responsiveness and pathway activation.

Iso-relevance Functions - A Systematic Approach to Ranking Genomic Features by Differential Effect Size

The paper introduces a framework to rank genomic features by differential effect size, showing that pseudocounts optimize the balance between fold-change and difference sorting.

Variability in the Analgesic Response to Ibuprofen Following Third-Molar Extraction is Associated with Differences in Activation of the Cyclooxygenase Pathway

This study identifies differences in cyclooxygenase pathway activation and inflammatory biomarker levels as factors associated with variability in ibuprofen analgesic response following third-molar extraction.

Complete Transcriptome Profiling Of Normal And Age-Related Macular Degeneration Eye Tissues Reveals Changes In Regulation Of Non-Coding RNA And Extreme Disregulation Of Anti-Sense Transcription

The paper uses RNA sequencing to analyze transcriptome changes in AMD and normal tissues, finding extreme anti-sense transcription and non-coding RNA regulation changes.

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates

The paper develops a probability model to detect outlier RNA-Seq samples for improved differential splicing analysis, showing it outperforms existing tools in identifying inconsistent replicates.