W. Brad Barbazuk

Exposure Duration Shapes the Hepatic Response to GenX: Divergent Acute and Chronic Transcriptomic Profiles Reveal Non-Monotonic Dose Effects and Increased Sensitivity in Human Liver Spheroids

simCRISPR: Modeling experimental complexity in pooled CRISPR screens

The paper develops simCRISPR, a simulation framework for pooled CRISPR screens, evaluates normalization strategies for detecting gene-by-environment interactions, and shows improved results with safe-harbor normalization.

Physiologically Relevant 3D CRISPR Screening Enhances Mechanistic Insight into Chemical Toxicity Compared to 2D Screening

This paper develops a 3D CRISPR screening system using HepG2/C3A spheroids to improve the identification of genetic determinants of chemical toxicity compared to traditional 2D methods.

Identification of Functional Genetic Components Modulating Toxicity Response to PFOS using Genome-wide CRISPR Screens in HepG2/C3A cells

This study identifies 340 genes modulating PFOS-induced cytotoxicity in liver cells using CRISPR screens and validates two genes, SLC6A9 and CPSF2, with functional and molecular evidence.

Genome-wide CRISPR screens identified C18orf32 as a novel regulator of lipid metabolism that mediates PFOA-induced toxicity

The paper identifies C18orf32 as a novel regulator of lipid metabolism involved in PFOA-induced toxicity through CRISPR screening and transcriptomic analysis.

Characterizing common loss-of-function genes and their potential utility in assessing population variability and chemical susceptibility

The paper identifies common loss-of-function genes and develops a method to integrate them into cell-based models to assess population variability in chemical susceptibility.

The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant

This study provides a genome and epigenomic analysis of the invasive fern Lygodium microphyllum, revealing differences between its gametophyte and sporophyte life phases and their responses to freezing stress.

A Circadian Light Regulator Controls a Core CAM Gene in the Ice Plant's C3-to-CAM Transition

The paper identifies McHY5 as a transcription factor that activates PPCK1, a key CAM enzyme, during the C3-to-CAM transition in ice plant, revealing regulatory divergence between CAM and C3 species.

Genetic Analysis of Human RNA Binding Motif Protein 48 (RBM48) Reveals an Essential Role in U12-Type Intron Splicing

This study shows that RBM48 mutations cause U12-type intron retention in human cells and identifies conserved genes affected in both human and maize RBM48 mutants.

miTAR: a hybrid deep learning-based approach for predicting miRNA targets

The paper introduces miTAR, a hybrid deep learning model for miRNA target prediction, achieving higher accuracy than existing methods on two datasets.

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Long-read assemblies of an inbred cannabis trio plus whole-genome sequencing of 40 cultivars link cannabinoid synthase gene deletions to chemotype and associate CsTLP1 loss with powdery mildew susceptibility.

The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation

This paper presents the avocado genome, revealing its phylogenetic position, introgressive hybridization, and pathogen-driven gene space adaptation.

Evolutionarily Conserved Alternative Splicing Across Monocots

The paper identifies evolutionarily conserved alternative splicing events across nine plant species and finds they are enriched in signaling pathway-related genes.