Andrey D. Prjibelski

The paper introduces a spatial long-read sequencing method to study developmental splicing and polyadenylation changes in cortical layers and cell types, finding layer-specific and age-related regulatory patterns.

The paper develops a high-resolution spatial long-read sequencing method and software to analyze isoform variability in brain cell types, revealing both region-specific and cell-type-specific patterns.

This paper introduces flowtigs, a characterization of safe walks for flow decompositions in general graphs, and demonstrates their application to improve metagenomic assembly contiguity.

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

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.

The paper identifies brain-region specific splicing patterns at single-cell and spatial resolution in postnatal mice, revealing cell-type specific and region-specific isoform expression.

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

The paper introduces CycloNovo, a de novo cyclopeptide sequencing algorithm, revealing a vast hidden cyclopeptidome in the human gut and other environments.

The paper introduces rnaSPAdes, a de novo transcriptome assembler, and evaluates its performance against other tools using RNA-Seq datasets.