Alexandru Ioan Tomescu

The paper introduces a linear-time algorithm to compute ultrabubbles in bidirected pangenome graphs, achieving significant speedups over existing methods.

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.

This paper introduces an Integer Linear Programming formulation for accurate flow decomposition in the presence of errors, showing improved accuracy over previous methods.

cloudrnaSPAdes assembles full-length isoforms from barcoded RNA-seq linked-read data, accurately handling high isoform diversity in simulated and real human data.

GraphChainer improves alignment of erroneous long reads to acyclic variation graphs, aligning more reads and total read length than existing tools.

The paper introduces EMERALD, a tool to infer alignment-safe intervals from protein sequence clusters, enhancing the analysis of biodiversity at a tree-of-life scale.

GGCAT constructs and queries compacted and colored de Bruijn graphs faster than existing tools.

The paper improves genome assembly contiguity by integrating the omnitig framework into existing assemblers using simplified algorithms, showing better alignment-based contiguity with minimal computational cost.

The paper introduces Matchtigs, a method to compress kmer sets with a polynomial algorithm and greedy heuristic, achieving significant size reduction and performance improvements in downstream applications.