Maria D. Logacheva

Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing

The paper optimizes gene editing tools for Capsella bursa-pastoris, creating a homoeolog-aware gRNA database and demonstrating successful in vivo editing of homoeologous genes.

The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known

This study examines the plastid genome of Rhopalocnemis phalloides, finding exceptionally high intraspecific polymorphism and identifying misclassified plastid genomes in NCBI databases.

Inheritance bias of deletion-harbouring mtDNA in yeast: the role of copy number and intracellular selection

The paper investigates how mtDNA deletion variants (rho-) outcompete wild-type mtDNA (rho+) in yeast, finding higher copy numbers and intracellular fitness advantage contribute to biased inheritance.

Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis

Trans2express is a de novo transcriptome assembly pipeline that produces high-quality assemblies suitable for gene expression analysis in non-model plants.

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite the absence of recent whole-genome duplications

This study reports the chromosome-scale genome of Heracleum sosnowskyi, revealing an unusually high number of genes without recent whole-genome duplications, and identifies genes involved in furanocoumarin biosynthesis.

Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads

FLIC reconstructs full-length isoforms from long-read data, outperforming existing tools and matching CAGE accuracy while being more efficient.

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives.

The paper compares the nuclear genomes of non-photosynthetic Balanophoraceae plants with their photosynthetic relatives, finding higher substitution rates and gene loss in Balanophoraceae.

Accurate Fetal Variant Calling in the Presence of Maternal Cell Contamination

The paper presents methods to improve fetal variant calling accuracy in the presence of maternal cell contamination using Bayesian models and learned genotype-correction models.

Studying RNA#8211;DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics

The paper introduces Red-C, a method to study RNA-DNA interactions, identifies ncRNAs associated with repressed chromatin, and traces mRNA production kinetics in K562 cells.

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

This paper describes the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, highlighting its extreme reduction and high AT content.

RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of holo-mycoheterotrophic plants

The paper compares transcriptomes of mycoheterotrophic plants to show lineage-specific genomic changes and substitution rates in nuclear genes related to photosynthesis.

Coat color allele and mtDNA haplotype distributions in Russian cat populations: a citizen-science research

The paper analyzes coat color alleles and mtDNA haplotypes in Russian cats to study population genetics and phylogeography, finding genetic homogeneity and unique mitotypes.