Eduardo da Veiga Beltrame

This study benchmarks VAE-based methods for scRNA-seq batch integration, finding dataset-dependent performance trade-offs and recommending hyperparameter settings for optimal results.

This study uses single-nucleus RNA-seq to map the adult C. elegans transcriptome and assess inter- and trans-generational effects of alcohol exposure at cell type resolution.

scvi-tools provides a Python package for probabilistic analysis of single-cell omics data, offering standardized interfaces and extensible tools for various analysis tasks.

The paper introduces two web apps for analyzing single-cell RNA sequencing data with C. elegans datasets from WormBase.

The paper presents a modular and efficient workflow for single-cell RNA-seq pre-processing using kallisto and bustools, demonstrating its flexibility for RNA velocity analyses.

The paper curates a database of single-cell transcriptomics studies to analyze trends in the field and provides insights into cell type identification.

The paper quantifies the tradeoff between sequencing depth and cell number in single-cell RNA-seq, finding that deeper sequencing per cell provides greater benefits than increasing cell numbers beyond 15,000 reads per cell.

The paper introduces the Poseidon syringe pump system as an open-source alternative to commercial systems, highlighting design principles for open-source bioinstrumentation.