Jovana Maksimovic

This study uses scRNA-seq on amniotic fluid to create a cell atlas of healthy fetal cells, revealing gestational age-related changes in cell composition and gene expression.

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

The paper introduces a probe-based workflow to detect oncogenic gene fusions in single-cell RNA-seq, validated in cancer cell lines and pediatric B-ALL cohorts.

barbieQ is an R package for analysing barcode count data from clonal tracking experiments, providing statistical tests for differential barcode proportion and occurrence.

This study benchmarks seven HTO demultiplexing tools using datasets with genetic variant-based ground truth, finding similar performance on high-quality data but poor performance on lower quality data for bimodal distribution methods.

The paper uses scRNA-seq and flow cytometry to identify novel immune and epithelial cell populations in preschool CF patients' bronchoalveolar lavage.

The paper introduces two new methods for gene set testing in DNA methylation data and shows they outperform existing approaches.

The paper provides a Bioconductor workflow for analysing methylation array data, covering quality control, normalization, differential methylation analysis, and visualization.

The paper presents a 2-stage approach using RUV-inverse to remove unwanted variation in differential methylation analysis of Illumina HumanMethylation450 array data, showing improved performance over existing methods.