Ksenia V. Krasileva

The Annotated Blueprint: Integrated Functional Genomic Resources for a Model Tetraploid Wheat Triticum turgidum cv. Kronos

The paper presents a chromosome-scale reference genome for Triticum turgidum cv. Kronos, enhancing functional genomic resources through improved annotations and re-analysis of existing datasets.

Tracking Transgenes with Color: RUBY as a Visual Marker in CRISPR-Edited Mutant Plants in Two Triticum Species

The paper develops a RUBY reporter system linked to CRISPR-Cas9 for non-destructive transgene tracking in wheat, enabling rapid identification of edited plants and reducing screening costs.

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes

The paper introduces K-PROB, a Bayesian method to identify cis-regulatory elements in plant pan-genomes by linking sequence variation with gene expression.

mamp-ml: A deep learning approach to epitope immunogenicity in plants

The paper introduces mamp-ml, a deep learning model predicting plant receptor-ligand interactions using sequence data and ESM-2, achieving 73% accuracy without experimental structures.

Molecular Insights into Fungal Innate Immunity Using the Neurospora crassa - Pseudomonas syringae Model

This study investigates fungal immune responses using Neurospora crassa and Pseudomonas syringae, identifying genes involved in bacterial resistance and susceptibility.

Structure-Aware Annotation of Leucine-rich Repeat Domains

The paper develops a structure-aware method to annotate Leucine-rich Repeat (LRR) domains by integrating geometric properties of protein structures, improving accuracy over sequence-based approaches.

Pathogen-inducible expression of autoactive NLRs confers multi-pathogen resistance in tomato

This study develops a synthetic strategy using pathogen-inducible promoters paired with autoactive NLRs to confer multi-pathogen resistance in tomato without growth impairment.

Resurrection of the Plant Immune Receptor Sr50 to Overcome Pathogen Immune Evasion

This study engineers the plant immune receptor Sr50 to recognize a pathogen effector variant, restoring immune responses against stem rust.

Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust

The paper identifies 16 wheat mutants with enhanced resistance to stripe rust and other fungal pathogens through forward genetic screening and maps their mutations to a long-read genome.

Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes

The paper examines TE variation in Magnaporthe oryzae pathotypes, revealing differences in TE expansion dynamics and evolutionary history across host-specific lineages.

Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen

The paper identifies genomic and epigenomic features associated with gene presence-absence variation in fungal plant pathogens and shows that these features differ between pathotypes.

The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors

This study characterizes the circularome of Magnaporthe oryzae, revealing diverse LTR retrotransposons, genes, and effectors on extrachromosomal circular DNAs.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire

The paper develops NLR-Annotator to identify NLR genes in wheat genomes and characterizes their structure, phylogeny, and expression, finding 3,400 NLR loci with 88% low basal expression.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.