Arabidopsis

The paper characterizes glucosinolate chemodiversity in Cardamine hirsuta accessions and wild-collected material, identifying genetic sources of variation in glucosinolate composition across organs and accessions.

This study shows that GSNOR-dependent nitric oxide homeostasis affects methylome persistence in Arabidopsis after multi-generational environmental stress exposure.

The paper identifies gene regulatory networks governing seed size in Brassica napus through transcriptomic analysis of developmental stages and seed organs.

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

This study identifies surface proteins in Asgard archaea using visual surfaceomics, revealing a peptidophilic cell surface involved in peptide capture and symbiotic interactions.

This paper simulates Arabidopsis root tip development from a genome, showing emergent cell identities and zones without pre-defined structures, but with limitations in niche maintenance and regeneration.

Earl Grey ParTEA annotates transposable elements across multiple genomes, revealing shared and private TE families and improving annotation consistency.

The paper models genotype-specific photosynthetic trait trajectories using functional data analysis to predict biomass, finding that early growth period traits most strongly influence final dry weight.

This study examines how genetic architecture of flowering time in Arabidopsis thaliana changes between overwintering environments and growth chambers, finding extensive gene-by-environment interaction and environment-specific genetic effects.

This study shows that NMD deficiency in Arabidopsis leads to biphasic heat tolerance, with initial tolerance due to transcriptome priming and later sensitivity linked to reduced HsfA2 function and altered gene expression.

This study identifies DCP5 as a key regulator of circadian RNA stability in Arabidopsis by modulating the decay of high-amplitude clock-controlled genes.

The paper introduces DIFFRACT, a framework that uses local fractal dimension changes in protein interaction networks to detect functional reorganization, showing its utility in identifying novel biological roles in RAVER1-deficient cells.

This study identifies a polar targeting peptide in plants and reveals its evolutionary conservation and diversification within the SOSEKI protein family.

This study identifies spatial developmental reprogramming in roots of Schrenkiella parvula under salinity, revealing distinct zones and regulatory programs that enable continued growth.

This study shows that ROS1-induced DNA demethylation leads to distinct epigenetic changes in chromosome arms and pericentromeres during plant immune memory formation and erasure.

The paper shows that cell cycle progression in Arabidopsis stem cells maintains pluripotency by resetting epigenetic marks and silencing fate-determining genes through PRC2 recruitment.

The paper identifies candidate eukaryote homologs of Asgard archaea by analyzing structural clusters, revealing shared expansions of solenoid proteins.

This study shows fungal volatiles promote lateral root formation and enhance plant tolerance to osmotic stress by modulating auxin signaling and nutrient transport.

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

This study identifies WRKY transcription factors as mediators of NPR1-regulated SA/JA crosstalk in Arabidopsis, showing nuclear NPR1 controls JA repression through these factors.

This study identifies RAP2.6 as a negative regulator of submergence tolerance in Arabidopsis, showing its interaction with GSNOR1-dependent redox and hormonal signaling.

The paper compares gene expression in freshly induced and repeatedly subcultured peanut embryogenic calli to identify candidate developmental regulators.

This study shows that the fruitless gene in male Aedes aegypti mosquitoes is essential for swarming and attraction to female flight sounds, with its disruption causing loss of these behaviors.

The study reanalyzes mosquito flight data to show DEET's transient repellent effect is not influenced by ambient light color.

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

The paper identifies molecular mechanisms that integrate environmental cues to trigger diapause exit in killifish embryos using transcriptomics and chemical screening.

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

The paper identifies cytoplasmic effects on allelic expression in Arabidopsis thaliana, showing cytoplasmic-genome interactions with nuclear genes and independence from genomic imprinting.

This study shows that Pantoea ananatis triggers systemic resistance in Arabidopsis through root sensing via the LORE receptor kinase, using HAAs and 3-OH-C10 as MAMPs.

This study shows that the plant heat shock regulatory network controls both the magnitude and distribution of stress-responsive gene expression across cells.