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 bioinformatics, data science, and IT for several years at a cancer diagnostics company, working on precision medicine, genomics, and liquid biopsies. 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

Consulting

I’m available for consulting opportunities in industry and academia. 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

  • Computational pipeline/workflow development
  • Data processing, cleaning, and visualization
  • Statistical analysis and modeling
  • Machine learning
  • Software development

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

See all publications

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

See all publications

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

Contact