Leandro Lima

gene2fish arranges 53,595 Thisse in situ hybridization images of 8,263 zebrafish genes into a gene-by-stage grid, with anatomy-term search for validating scRNA-seq markers.

Amira detects AMR genes directly from long reads using gene-space de Bruijn graphs, achieving high recall and accuracy compared to assembly-based methods.

This paper introduces phylogenetic compression to efficiently search large microbial genome collections, achieving significant compression improvements and enabling fast BLAST-like searches on desktop computers.

This paper introduces pling, a tool that uses rearrangement distances to cluster plasmids more accurately by accounting for structural changes and avoiding over-clustering caused by transposable elements.

The paper compares plasmids from pre-antibiotic era bacteria with modern plasmids to show how resistance genes evolved and spread over time.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

This paper develops DrPRG, a tool for predicting drug resistance in Mycobacterium tuberculosis using reference graphs, showing improved sensitivity and specificity compared to existing methods.

CALDERA improves bacterial GWAS by testing subgraphs of De Bruijn graphs, enhancing power and interpretability while managing computational complexity.

Minos integrates variant calls from multiple tools to adjudicate discrepancies and jointly genotype bacterial cohorts, improving accuracy in detecting SNPs and indels.

This paper introduces a pan-genome graph structure and software tool, pandora, to analyze bacterial genomic variation across multiple isolates with higher SNP recovery and lower error rates than existing methods.

This paper benchmarks long-read error-correction tools on RNA-sequencing data, finding they improve base-pair accuracy but affect gene family sizes and isoform diversity.

DBGWAS is a fast, alignment-free method for bacterial GWAS that identifies interpretable genetic variants associated with phenotypes by analyzing kmer-based subgraphs.

This paper introduces an alignment-free GWAS method using compacted De Bruijn graphs to detect variable-length haplotypes associated with antimicrobial resistance in bacterial genomes.

This study compares mapping-first and assembly-first approaches for annotating and differentially analyzing alternative splicing from RNAseq data, showing complementary strengths and advocating their combined use.