Senior Bioinformatician / PhD Candidate

SAGA Diagnostics

Lund University

Biography

I work as a Senior Bioinformatician at the cancer diagnostics company SAGA Diagnostics and am completing a PhD in cancer genomics at Lund University in Sweden.

My research focuses on the development of diagnostics based on tumor DNA/RNA deep sequencing (also known as next generation sequencing) to improve breast cancer treatment and survival. Most of my projects are embedded in the Sweden Cancerome Analysis Network–Breast (SCAN-B) study. Additionally I work on improving open source bioinformatics and reproducible research infrastructure by contributing to projects such as conda-forge, Bioconda, and Biopython.

Over the past 20 years I have contributed to a number of open source software projects, most notably the FreeBSD computer operating system. An overview can be found on OpenHub.

Interests

  • Bioinformatics
  • Cancer Biology and Diagnostics
  • Open Source Software
  • Software Engineering

Education

  • MSc in Bioinformatics

    Lund University

  • BSc in Scientific Programming

    Aachen University of Applied Sciences

Projects

SCAN-B MutationExplorer

A web-based application for exploring tumor somatic mutations.

RNA Sequencing for Breast Cancer Diagnostics

My PhD work in developing RNA sequencing-based diagnostic tools for breast cancer.

FreeBSD

I have been a developer with the FreeBSD operating system project since 2003. This page collates some related links.

Recent & Upcoming Talks

2020-05-29 08:00 — 11:00 McCormick Place, Chicago, Illinois, USA (Virtual due to COVID-19)

Defining the Mutational Landscape of 3,217 Primary Breast Cancer Transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)

Project Project
2019-11-04 10:45 — 11:05 Folkets Hus, Umeå, Sweden

Defining the Mutational Landscape of the Primary Breast Cancer Transcriptome through large-scale RNA-seq in the Sweden Cancerome Analysis Network–Breast (SCAN-B) Project

Project Project
2019-05-23 09:10 — 09:35 Ekologihuset, Lund, Sweden

Towards Better Breast Cancer Diagnostics: Large-scale Profiling of Tumor Transcriptomes

Project Project
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Recent Publications

Quickly discover relevant content by filtering publications.

A crowdsourced set of curated structural variants for the human genome

Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook
Preprint PDF Code DOI

The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome

Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
Preprint Code Project DOI

Detection of circulating tumor cells and circulating tumor DNA before and after mammographic breast compression in a cohort of breast cancer patients scheduled for neoadjuvant treatment

Daniel Förnvik, Kristina E. Aaltonen, Yilun Chen, Anthony M. George, Christian Brueffer, Robert Rigo, Niklas Loman, Lao H. Saal, Lisa Rydén
PDF DOI

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch C, Valieris R, Caprez A, Batut B, Haudgaard M, Cokelaer T, Beauchamp KA, Pedersen BS, Hoogstrate Y, Ryan D, Bretaudeau A, Le Corguillé G, Brueffer C, …, Köster J
Preprint Project DOI

Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative

Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal
PDF Dataset Project DOI
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Contact