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
See all talks

Recent Publications

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precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jaspez, Jose M. Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A. Rubio-Rodriguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian MA, LinQi Tang, YuanPing DU, ShaoWei Zhang, Jordi Morata, Raul Tonda, Genis Parra, Jean-Remi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Ozem Kalay, Gungor Budak, Kubra Narci, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook
Preprint Project 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 PDF Code Dataset Project DOI

Features of increased malignancy in eosinophilic clear cell renal cell carcinoma

Helén Nilsson, David Lindgren, Håkan Axelson, Christian Brueffer, Lao H. Saal, Jaana Lundgren, Martin Johansson
PDF DOI

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

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
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