Projects

This is a short list of projects I’ve been working on over the past few years.

PhD

Thesis: From high dimensionality to developmental biology - understanding the evolution of cell identity in the early embryo
- ccmnet: Detection of causal interactions from scRNA-seq datasets
- Preimplantation DL models: DL models for predicting cell types in early mouse and human development (web portal, datasets, models)
- nf-core/marsseq: Preprocessing pipeline for single-cell MARS-seq experiments
- cat-python: Estimates similarity between clusters from different single-cell sequencing techniques
Small tools and utilities are available at github.com/brickmanlab
- brickmanlab/scanvi-explainer: SCANVI explainer
- brickmanlab/primeseq: PRIME-seq preprocessing nf-core pipeline

Thesis: Genomic Profiling of a Comprehensive Nation-wide Collection of Childhood Solid Tumors
- nf-core/rnafusion: Preprocessing pipeline for identification of fusion genes from RNA-seq
- fusion-report: Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline
DM855-classification: Testing various supervised techniques (doesn’t work correctly on a chosen dataset)
DM843-project: Testing different clustering methods on protein similarity matrix generated by BLAST
DM847: Detecting candy flavour from breath analyzer using Random Forest Classification