Alla Mikheenko

The paper identifies cryptic splicing events (CEs) sensitive to TDP-43 loss and develops a composite score to detect TDP-43 pathology across tissues.

This study identifies sex-dependent motor neuron dysfunction and cargo-specific axonal transport impairments in FUS-ALS mice, linking endosomal transport defects to denervation in ALS.

The paper identifies reduced PUFA levels in FTD/ALS models and shows neuronal PUFA supplementation improves survival and reduces neuronal death.

This study demonstrates that CRISPR-CasRx reduces C9orf72 repeat RNAs and DPRs in vitro and in vivo, suggesting its therapeutic potential for ALS/FTD.

This study investigates how knocking down RNA binding proteins affects mRNA transport and local translation in neurons, revealing distinct impacts on neuritic proteome and transcriptome.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper identifies novel cryptic polyadenylation events induced by TDP-43 loss in ALS/FTD using bioinformatic methods and shows their potential disease relevance and impact on protein translation.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper generates C9orf72 DPR knock-in mice and identifies an extracellular matrix signature in C9ALS/FTD that is conserved across species and protected by TGF-β1 and COL6A1.

The paper compares error patterns in long-read transcriptomics using Pacific Biosciences and Oxford Nanopore by analyzing cDNA copies of individual RNA molecules.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The paper introduces SnISOr-Seq, a method for single-nuclei isoform RNA sequencing, and finds distinct combination patterns of transcript elements in human brain cell types.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

The paper extends rnaSPAdes to perform hybrid transcriptome assembly using short and long RNA reads, improving gene and isoform reconstruction.

The paper introduces tandemMapper and tandemQUAST to map long reads to extra-long tandem repeats and improve their assembly quality.

MetaRiPPquest identifies RiPPs by combining genome/metagenome mining with mass spectrometry analysis, discovering 5 novel natural products from 6 datasets.