Thomas G. Brooks

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.

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.

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.

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.