Christian Brueffer

Christian Brueffer

Biomedical Data Scientist and Bioinformatician

SAGA Diagnostics

Lund University

About Me

I am a Biomedical Data Scientist currently working as Senior Bioinformatician within cancer diagnostics at SAGA Diagnostics. Additionally I conduct research in affiliation with Lund University in Sweden.

My main interest is in using computational methods and biological/medical data to improve our understanding and treatment of diseases. Many of my projects, including my doctoral thesis, have been focused on cancer in humans. 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. A rough overview can be found on GitHub and OpenHub.

Interests
  • Data Science and Bioinformatics
  • Disease Biology and Diagnostics
  • Open Source Software
  • Software Engineering
Education

  • PhD in Medical Science (Bioinformatics and Cancer Genomics)

    Lund University, Sweden

  • MSc in Bioinformatics

    Lund University, Sweden

  • BSc in Scientific Programming

    Aachen University of Applied Sciences, Germany

Recent Posts

Snakemake on AWS ParallelCluster using Slurm
AWS ParallelCluster is a quick way to bring a Snakemake workflow to the cloud, but there are some issues to be aware of.
Christian Brueffer
Jul 19, 2022 7 min read Snakemake, Amazon AWS, Cloud Computing, Open Source Software
Snakemake on AWS ParallelCluster using Slurm

Projects

Dec 18, 2020
PhD Project: RNA Sequencing-based Tools for Breast Cancer Diagnostics
PhD Project: RNA Sequencing-based Tools for Breast Cancer Diagnostics

My PhD work in developing RNA sequencing-based diagnostic tools for breast cancer.
Feb 4, 2020
SCAN-B MutationExplorer
SCAN-B MutationExplorer

A web-based application for exploring tumor somatic mutations.
Aug 16, 2019
FreeBSD
FreeBSD

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

Recent & Upcoming Talks

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Swedish Bioinformatics Workshop 2021: SAGA Diagnostics Sponsor Presentation
SAGA Diagnostics sponsor presentation.
Oct 20, 2021 12:00 — 12:30 LTH E-huset, Lund, Sweden
Swedish Bioinformatics Workshop 2021 SAGA Diagnostics Website
Defining the Mutational Landscape of the Primary Breast Cancer Transcriptome through large-scale RNA-seq in the SCAN-B Project
May 29, 2020 08:00 — 11:00 McCormick Place, Chicago, IL, USA
PhD Project MutationExplorer Project
Defining the Mutational Landscape of the Primary Breast Cancer Transcriptome through large-scale RNA-seq in the SCAN-B Project
Nov 4, 2019 10:45 — 11:05 Folkets Hus, Umeå, Sweden
PhD Project MutationExplorer Project
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Featured Publications

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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. The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.
EMBO Molecular Medicine, 2020. 12(10):e12118

DOI PDF bioRxiv Preprint Code Dataset Press Release PhD Project

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Devon Ryan, Anthony Bretaudeau, Gildas Le Corguillé, Christian Brueffer, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nature Methods, 2018. 15(7):475–476

DOI bioRxiv Preprint Project Code

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. 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.
JCO Precision Oncology, 2018. 2:1–18

DOI PDF Dataset PhD Project

Recent Publications

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Quickly discover relevant content by filtering publications.
Arturas Dobilas, Yilun Chen, Miguel Alcaide, Christian Brueffer, Pia Leandersson, Lao H. Saal, Christer Borgfeldt. Preoperative circulating tumor DNA level is associated to poor overall survival in patients with ovarian cancer.
ResearchSquare, 2022 (Preprint)

DOI PDF

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 Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz Barrera, Luis A. Rubio-Rodríguez, 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, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, 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, Mian 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. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Cell Genomics, 2022. 2(5): 100129

DOI PDF bioRxiv Preprint Project

Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, Jesse G. Meyer, Ariel I. Mundo, Dimitri Perrin, David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene. Molecular and Serologic Diagnostic Technologies for SARS-CoV-2.
arXiv, 2022

DOI arXiv Preprint Project

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Popular Topics

Amazon AWS Bioconda Bioinformatics Biopython Breast Cancer Cancer Cloud Computing Computer Security COVID-19 FreeBSD Genome in a Bottle Kidney Cancer Liquid Biopsy Machine Learning Open Source Software PhD RNA Sequencing SARS-CoV-2 SCAN-B Structural Variants

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