Christian Brueffer

@cbrueffer
265 Followers
451 Following
65 Posts

Bioinformatics and Data Science consultant at https://insilico.consulting and #LundUniversity in Sweden • dev at #FreeBSD • bits, bytes, and nucleotides.

#bioinformatics #cancer #oncology #genomics #transcriptomics #liquidbiopsy #personalizedmedicine #opensource

Personal Websitehttps://www.brueffer.io
Twitterhttps://twitter.com/cbrueffer
GitHubhttps://github.com/cbrueffer
ORCIDhttps://orcid.org/0000-0002-3826-0989
Christian BruefferAug 10, 2023
Warren Currie 🦠🦐Aug 9, 2023

[EDIT] FLIP is saved!
https://newatlas.com/marine/flipping-flip-ship-saved/
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Well it had to happen eventually. #Scripps is retiring FLIP (FLoating Instrument Platform). This is an amazing piece of engineering (and soooo weird on the inside - everything pivots, so walls become floors). The #ship to be towed out to a location, and it would literally flip, sinking most of the ship directly down to give a *very stable platform for #oceanography research. Launched in 1962.

https://maritime-executive.com/article/world-s-strangest-research-vessel-heads-for-scrapyard-after-51-years

Flipping FLIP ship saved from scrapyard at last minute

The US Navy and Scripps Institution of Oceanography's unique FLoating Instrument Platform (FLIP) has been saved at the last minute from the breaker's yard. Scheduled to be scrapped in Mexico, it was purchased by undersea design company DEEP.

New Atlas
Show threadChristian BruefferJun 19, 2023
@PhilippBayer bought two replacement sets on Amazon over the years (also for Sennheiser), were both completely fine. Can dig out the shop names if needed.
Christian BruefferJun 13, 2023

Recently I switched from a cancer #bioinformatics industry job to full time #freelance bioinformatics and data science #consulting/#contracting via my own Sweden-based limited company.

If you or your company need help tackling bioinformatics challenges, let's talk!

Christian BruefferApr 14, 2023
BioconductorApr 14, 2023

🌟#JobAlert: #Bioconductor 🧬is hiring a Cloud/DevOps Engineer!

Passionate about #opensource & have AWS experience? Apply now!

➡️ https://careers-dfci.icims.com/jobs/33592/cloud-devops-engineer%2c-bioconductor/job?mobile=false&width=888&height=500&bga=true&needsRedirect=false&jan1offset=0&jun1offset=60

Please boost to help spread the word! 🙏

#DevOps #CloudJobs #Bioinformatics #rstats

Cloud/DevOps Engineer, Bioconductor in Boston, Massachusetts | Careers at Longwood Medical Area

The Bioconductor Core Team's infrastructure comprises a complex, hybrid multi-cloud development, test, and publishing environment. This position is with the Department of Data Science.    The scope and depth of the Bioconductor code base have grown with the rapid advance of genomics. And this means ever-increasing demands for connectivity, performance, and technical features in our infrastructure.   Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate and comprehensive care to patients of all backgrounds, and design programs to promote public health particularly among high-risk and underserved populations. We conduct groundbreaking research that advances treatment, we educate tomorrow's physician/researchers, and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

careers
Christian BruefferApr 10, 2023

At #AACR23 and interested in #MultipleMyeloma?

Check out our SAGAdx/abbvie collaboration on monitoring t(11;14) translocations in PBMCs/plasma using WGS and #dPCR. #liquidbiopsy #precisionmedicine #oncology

https://doi.org/10.1158/1538-7445.AM2023-5710

Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens

Abstract. Venetoclax (Ven) is a selective B-cell lymphoma 2 inhibitor being studied in t(11;14)+ relapsed/refractory multiple myeloma (MM) Detection of t(11;14) in MM requires bone marrow (BM) aspiration and evaluation of CD138+ plasma cells by fluorescence in situ hybridization (FISH) Innovative techniques may provide less invasive detection of t(11;14) in liquid biopsies Here we present results of the SAGAsign® integrated approach combining low-coverage whole-genome sequencing (WGS) to characterize t(11;14) breakpoints together with personalized digital polymerase chain reaction (dPCR) assays to efficiently detect and monitor the genomic rearrangements in circulating tumor DNA (ctDNA) Baseline BM aspirates were collected from 270 patients (pts) from Ven clinical trials (NCT02755597, NCT01794520, NCT03314181, NCT02899052) Previously generated WGS to an average coverage ~22 × was used Paired samples of peripheral blood mononuclear cell (PBMC) DNA and plasma circulating cell-free DNA (cfDNA) were analyzed by dPCR at timepoints after Ven-based treatment Of the 90 t(11;14)+ pts by FISH, 160 t(11;14) breakpoints were identified by WGS in 74 pts (concordance in Table) At the time of data cutoff, dPCR assays were designed and evaluated in 8 t(11;14)+ pts; 7/8 (88%) and 6/8 (75%) pts had detectable t(11;14) in cfDNA or PBMCs, respectively Higher levels of t(11;14) mutant allele frequency (MAF) were observed in cfDNA compared with PBMCs After Ven-based treatment, t(11;14) MAF in cfDNA became undetectable in pts with a complete response In conclusion, this approach has the capability to reconstruct t(11;14) breakpoints from WGS data that is highly concordant with FISH; translocations appear more readily detectable in cfDNA than PBMC samples from pts with MM SAGAsign assays detected and monitored t(11;14) in liquid biopsies thus highlighting its potential utility for identifying pts with t(11;14) for targeted therapiesConcordance between WGS and FISH testing for t(11;14)Samples, nFISH+FISH−TotalWGS+741183WGS−16169187Total90180270Concordance, %n/N95% CIt(11;14) positive82.274/9072.7-89.5t(11;14) negative93.9169/18089.3-96.9Overall testing90.0243/27085.8-93.3Citation Format: Xiaotong Li, Lao H. Saal, Christian Brueffer, Yilun Chen, Johanna Asklin, Saman Alvi, Srinivas Venkatram, Jeremy A. Ross. Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5710.

American Association for Cancer Research
Christian BruefferMar 15, 2023
Daniel S. KatzMar 15, 2023

It's great to get compliments on @joss

"The JOSS process is absolutely brilliant, and the tooling around it is impressive. This is the first publishing framework that actually makes the paper better with very tight and continuous reviewer/editor feedback."

https://github.com/openjournals/joss-reviews/issues/5072#issuecomment-1469930303

"Thanks for your time and effort. This has been the best experience I've ever had in submitting a paper due to the tooling you're using and the very open and friendly review process."

https://github.com/openjournals/joss-reviews/issues/5040#issuecomment-1469744999

[REVIEW]: Universal Numbers Library: Multi-format Variable Precision Arithmetic Library · Issue #5072 · openjournals/joss-reviews

Submitting author: @Ravenwater (E. Theodore L. Omtzigt) Repository: https://github.com/stillwater-sc/universal Branch with paper.md (empty if default branch): main Version: 3.68 Editor: @danielskat...

GitHub
Christian BruefferJan 23, 2023
Johannes KösterJan 23, 2023
#Snakemake 7.20.0 is released. It contains many little bug fixes (thanks a lot dear users and devs!). In addition authentication to TES, Github and Gitlab has been improved. Finally, it is now possible to define memory and runtime requirements of jobs with units (e.g. mem="5GB" or runtime="1d"). https://snakemake.github.io
Snakemake

Christian BruefferJan 15, 2023
Ella KayeJan 15, 2023

I generally hold Posit in very high esteem, particularly for their open source work and their contributions to building an inclusive data science community, but the news about their partnership with Palantir stinks.

@Posit, how does going into business with Palantir (and hence Thiel) fit with you being a Public Benefit Company and Certified B Corp, and your inclusivity values?

https://en.wikipedia.org/wiki/Palantir_Technologies#Controversies

Palantir Technologies - Wikipedia

Christian BruefferJan 12, 2023
Benjamin S-B Jan 5, 2023

Please RT: the Ludwig Institute for Cancer Research in Oxford is looking for a *Senior Data Processing Engineer*. Your job will be to ensure our genomic data is processed using automated, state-of-the-art workflows. This is a critical post within the institute as we scale up the generation of clinical data. If you want to help cancer research and have an idea or two about bioinformatics and data, you should apply:

https://bit.ly/licrdpe2

#job #jobs #bioinformatics #datascience #career

Job Details

Christian BruefferDec 21, 2022
Show threadDoug RabsonDec 19, 2022

I just merged support for nullfs file mounts into FreeBSD-current. It was a little more than 40 lines of code after code review...

I plan to merge this to the stable/13 branch soon so this feature will be available in #FreeBSD 13.2 and later. An upcoming release of my ocijail #container runtime will use file mounts for #podman and #buildah containers when available.