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  • šŸ‘‹ Hi, Iā€™m @bayjan
  • šŸ‘€ Iā€™m interested in using machine learning algorithms to find patterns from data, especially, biomedical multi-omics data.
    • Iā€™m interested in comparative genomics analysis and do irregular DevOps tasks as well.
  • šŸŒ± Iā€™m currently learning a deep learning framework and its application to several data types.
  • šŸ“« How to reach me: at GitLab https://gitlab.com/bayjan, at twitter @bayjan and at Google Scholar https://scholar.google.com/citations?user=UOg0jLgAAAAJ&hl=en

Bioinformatician turned Data Scientist

I am a data scientist with a background in bioinformatics and expertise in machine learning, statistics, and programming in Python and R.

Skills

Programming

Python (Biopython)
R
SQL (MySQL, PostgreSQL)
Bash scripting
Grid/Cloud computing
NoSQL (MongoDB)
Probabilistic programming (Stan/PyStan)

Essential bioinformatics skills

Comparative genomics tools
Orthology prediction
NGS data analysis (assembly, SNP/InDel analysis, annotation)
Phylodynamic analysis (e.g. BEAST tool)
Galaxy (workflow management and tool integration framework)
Analysis of large metagenomics data sets (Qiime)
MLST profiling (e.g.: SeqSphere)

Knowledge in statistics and machine learning

Linear models
Multivariate statistics
Machine learning algorithms (e.g. Random Forest, SVM) and libraries (e.g. scikit-learn, WEKA, H2GO)
Deep learning with PyTorch (fast.ai)

Other relevant skills

Linux
HPC
Snakemake
Docker
Git
Elasticsearch
Web programming (mostly using Python)
Apache Spark
Kubernetes

jb's Projects

bayjan icon bayjan

Config files for my GitHub profile.

notebooks icon notebooks

A collection of Jupyter and Squonk notebooks developed for OpenRiskNet

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