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
Master’s
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/rnafusionpipeline - 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
Bachelor’s
- urbis: Municipality survey iOS app hackathon
- sign-academy: Learn alphabet sign language hackathon
- baa-ios-exam: Movie iOS application written in Swift
- baa-timetable: CLI for Timetable at BAA
- livecoding-phonebook: Phone book written in c++
- java-cv-generator: Web Java application for generating CV using LateX