Christian Brueffer

Christian Brueffer

Bioinformatician and Data Scientist

InSilico Consulting AB

Lund University

About Me

I am a freelance Bioinformatician and Data Scientist providing consulting services to clients in industry and academia to help them make sense of their data. Previously, I lead the bioinformatics and data science team at SAGA Diagnostics, a company developing personalized cancer diagnostics based on genomics and liquid biopsy. 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
  • Bioinformatics and Data Science
  • 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

Consulting

I provide bioinformatics and data science consulting services to clients in industry and academia through my company InSilico Consulting AB. With a decade of experience in bioinformatics, biomedical data science, genomics, and diagnostics, as well as over two decades in IT to draw from I can help you make sense of your data. For more details on my experience, please see About Me and my publications and public talks.

Areas I can help you with include, but are not limited to

  • Genomics, Transcriptomics, and other Omics analyses
  • Clinical data analysis
  • Cancer/oncology-related applications, such as somatic mutation profiling and liquid biopsy
  • Computational pipeline/workflow development
  • Data processing, cleaning, integration, and visualization
  • Machine learning
  • Software development

See https://insilico.consulting for more details.

Get in touch

For consulting inquiries, please contact me via email or LinkedIn.

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 Publications

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Sontosh K Deb, Divya Kalra, Jędrzej Kubica, Erik Stricker, Van Q. Truong, Qiandong Zeng, Christopher J. Fiscus, Daniel Paiva Agustinho, Adam Alexander, Marlon Arciniega-Sanchez, Lorianne Bosseau, Christian Brueffer, Astrid Canal, Joyjit Daw, David Enoma, Alison Diaz-Cuevas, Colin Diesh, Janet M. Doolittle-Hall, Luis Fernandez-Luna, Tina Han, Wolfram Höps, Peiming Peter Huang, Tony Huang, Michal Bogumil Izydorczyk, Farhang Jaryani, Rupesh K. Kesharwani, Shaheerah Khan, Sina Majidian, Ayan Malakar, Tania Girão Mangolini, Sejal Modha, Mauricio Moldes, Rajarshi Mondal, Abdullah Al Nahid, Chi-Lam Poon, Sagayamary Sagayaradj, Philippe Sanio, Tania Sepulveda-Morales, Muhammad Shahzaib, Muhammad Sohail Raza, Trinh Tat, Ishaan Thota, Umran Yaman, Jason Yeung, Qiyi Yu, Xinchang Zheng, Medhat Mahmoud, Fritz J. Sedlazeck, Ben Busby. The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics.
F1000Research, 2024. 13:708

DOI PDF Code

Lao H. Saal, Niklas Loman, Yilun Chen, Miguel Alcaide, Christian Brueffer, Sergii Gladchuk, Hina Dalal, Pei Meng, Anthony M. George, Sofia Birkeälv, Hani Saghir, Siker Kimbung, Daniel Förnvik, Lina Zander, Gabriella Honeth, Karen Howarth, Åke Borg, Anna Ehinger, Martin Malmberg, Lisa Rydén. Monitoring ctDNA dynamics in early breast cancer using a novel ultra-sensitive tumor-informed structural variant approach combining whole-genome sequencing and multiplex dPCR.
Journal of Clinical Oncology, 2024. 42:16_suppl

DOI PDF

Valentina Paspalj, Christoph Grimm, Magdalena Postl, Christina Viktoria Tauber, Nuria Segui, Christian Brueffer, Miguel Alcaide, Lucia Oton, Yilun Chen, Lao H. Saal, Gerda Hofstetter, Leonhard Muellauer, Mirjana Kessler, Fabian Trillsch. Tumor-informed ctDNA as an objective marker for postoperative residual disease in epithelial ovarian cancer.
Journal of Clinical Oncology, 2024. 42:16_suppl

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Popular Topics

Bioinformatics Biopython Breast Cancer Cancer Computer Security COVID-19 ctDNA Digital PCR FreeBSD Genome in a Bottle Liquid Biopsy Open Source Software Ovarian Cancer PhD RNA Sequencing SARS-CoV-2 SCAN-B Structural Variants Targeted Sequencing Whole Genome Sequencing

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