PhD in Computational Biology with expertise in Data Analysis and Machine Learning, and with academic, industry and hobby experience

In short

Education

  • PhD: Computational Biology
  • Master’s degree: Bioinformatics
  • Bachelor’s degree: Cognitive Science

Research interests

  • Connectomics
  • Spatial transcriptomics
  • Systems Neuroscience
  • Genetics and epigenetics
  • Gene regulatory elements
  • Machine learning
  • Artificial Life

Development experience

  • Machine learning methods
  • Data analysis tools
  • Bioinformatics
  • Artificial life simulations
  • Graphical User Interface software
  • Videogame development

Programming languages

  • Python/Cython
  • C/C++
  • R
  • Rust
  • x86 assembly
  • C#
  • … and more

Past project showcase (not a comprehensive list)

Software/research article

Gnocis

Gnocis is a Python package for interactive and reproducible analysis and machine learning of DNA sequences.

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Github

Publication

Software/research article

MOCCA suite

Motif Occurrence Combinatorics Classification Algorithms (MOCCA) is a suite of tools for machine learning of DNA cis-regulatory elements. Published in BMC Bioinformatics, Bjørn Bredesen and Marc Rehmsmeier, 2021.

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Github

Publication

Research article

DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements

Published in Nucleic Acids Research, Bjørn Bredesen and Marc Rehmsmeier, 2019.

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Publication

PhD thesis

Modelling the structure, function and evolution of Polycomb/Trithorax Response Elements

Doctoral thesis. Successfully defended on 20.11.2020. Published on-line in Bergen Open Research Archive, Bjørn Bredesen, 2020.

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Publication

Software

Katachi3D

Multi-platform voxel-graphics editor, implemented in Python with OpenGL and wxPython. With parts optimized in Cython. Features include layers and fast normal-based mesh-smoothing.

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Github

Software

AMP12x0

AMP12x0 is a minimalistic DJ program for the Microsoft Windows operating system, sporting two artificial turntables and a mixer, with natural user interaction.

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Software

Akvarie

Akvarie is simple artificial life model, with asexually reproducing artificial swimmers controlled by genetically determined machine code.

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Software

Model Studio 2

ModelStudio 2 is a minimalistic polygonal 3D model editor.

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Software

PRESVM

Software for modelling Polycomb/Trithorax Response Element sequences using Support Vector Machines. Implemented in C++, for GNU/Linux. Developed for my master's project.

Page coming soon

Software

Titanium Motion

Video editing program for Microsoft Windows. Features include an intuitive, DAW-like GUI, with a flexible plugin interface and variety of plugins.

Page coming soon

My story

Photo
I was born and raised in rainy Bergen, Norway. Since early childhood, I have been passionate about science and software development. I dabbled with video game development throughout my teens and transitioned into GUI software and scientific software in my 20s. Growing interests in biological and artificial intelligence led me to pursue a bachelor's degree in Cognitive Science. After my bachelor's, I did a master's degree in Bioinformatics, where I applied Machine Learning to the study of fruit fly Polycomb Response Elements, a class of cis-regulatory elements in DNA that maintain epigenetic memories. To round off my education, I had the great fortune to do a PhD, where I developed and applied new methods and tools to the study of the Polycomb system, in greater detail and in more organisms. For the final two years of my PhD, I was employed in the software development and data science industries, where I gained experience with commercial software development and industrial machine learning. Over the past decade, I became increasingly fascinated with biological intelligence and my latest pursuit is within the fields of Systems Neuroscience and Neuroinformatics. On the side, I have a variety of technical and creative hobbies, including personal software development and music production.

In memory of Dr. Marc Rehmsmeier

It is with great sadness that I share that my dear PhD supervisor and collaborator Dr. Marc Rehmsmeier passed away in April 2022. I will always remain deeply grateful for having had the great fortune and privilege to work with and learn from Marc. An orbituary written by Prof. Dr. Leonie Ringrose can be found at the following page: http://www.ringroselab.com/marc.
Copyright Bjørn Bredesen-Aa, 2022 - E-mail: bjorn at bjornbredesen dot no