José Sergio Hleap

SCALLOPS improves processing of optical pooled screens by enabling efficient alignment and analysis of large-scale image data, demonstrating superior performance over existing methods.

PerturbView enables highly multiplexed optical pooled screens in primary cells and tissues by improving barcode amplification, revealing regulators of NFκB signaling and enabling spatial transcriptomics integration.

This study compares metagenomics and total RNA-Seq for microbial identification accuracy using 768 workflows, finding total RNA-Seq more accurate at lower sequencing depths and suggesting its potential for cost-effective freshwater assessments.

This study evaluates seven taxonomic assignment methods for metabarcoding eukaryotes using mock communities, finding that BLAST top hit performs competitively when optimized and that reference database quality impacts accuracy.

A2G2 improves alignment accuracy for large sequence sets in conserved regions using MAFFT and a reference-based strategy.

The paper uses structural analysis to refine the classification of Glycoside Hydrolase Family 13 and identifies structurally variable sites that are functionally important.

This paper applies geometric morphometrics to protein structures to analyze shape variation and demonstrate its utility in understanding structure-function relationships and simulation trajectories.