Below are links to recent statOmics methods papers. A list with all my papers can be retrieved at Google Scholar or the Ghent University Archive.
- Genomics
- Model-Based Classification for Digital PCR: Your Umbrella for Rain (Analytical Chemistry 2017)
- ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering (BMC Bioinformatics 2015)
- VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering (Bioinformatics 2015)
- Impact of variance components on reliability of absolute quantification using digital PCR (BMC Bioinformatics 2014)
- Transcriptomics
- Trajectory-based differential expression analysis for single-cell sequencing data (Bioarvix 2019)
- Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications (Genome Biology 2018)
- stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage (Genome Biology 2017)
- Proteomics
- Robust summarization and inference in proteome-wide label-free quantification (Bioarvix 2019)
- Mass spectrometrists should search for all peptides, but assess only the ones they care about (Nature Methods 2017)
- Experimental design and data-analysis in label-free quantitative LC/MS proteomics: A tutorial with MSqRob (Journal of Proteomics 2018)
- MSqRob: Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics, (MCP 2016)
- Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines (JPR 2015)