What I offer
I support all your needs around data analysis, statistical evaluation and bioinformatic analysis.
My particular expertise is the analysis of “omics” data such as genomics and transcriptomics originating from all kinds of instruments. My special interest is in bacterial genomics.
If you want to hire me for a project please reach out to: sebastian.duemcke@sam-d.com
How to work with me
I like to start each project with a conversation to make sure I understand the goals, and most importantly, the underlying data and how it was acquired.
I will then develop a project plan. The details of this plan depends on how well defined the project and goals are at this stage.
Usually, when I have the impression that the project is still in an exploratory phase, I will suggest a smaller scale, proof-of-concept project that can help better understand the challenges ahead and start a deeper discussion on the required analyses.
My portfolio
Design and Deploy a cloud platform to pre-process public sequencing datasets into VCF files
The platform was developed on AWS as an AWS Batch pipeline. Downloads of specific samples by their ID are triggered by an AWS SNS message with the ID that download the fastq files into an AWS S3 bucket. The AWS Batch pipeline kicks off when the sequencing files have been downloaded. A containerized worflow is run (potentially on AWS ECS spot instances to save on costs) and the final VCF files provided in a result S3 bucket. Using this approach a total of over 14 000 samples were processed in just a few days.
Client: redacted
Development of algorithms for improving tuberculosis diagnosis
I have created and implemented algorithms for the following:
- to detect antibiotic resistance in tuberculosis sequencing data.
- to identify the tuberculosis species present in the sample
- to trace back infection chains by differentiating between a patient-to-patient transmission and an independent infection
Client: Clemedi AG
Co-development of in-vitro diagnostic medical device software
I was responsible for overseeing the development of medical device software following IEC 62304 practives, including writing the technical documentation.
Client: Clemedi AG
Design pipeline for detecting somatic mutations in targeted cancer sequencing
After trimming, PCR duplicate removal and quality filtering, sequencing data are aligned against the human reference genome and mutations called. Resulting variant calls are filtered against a database of known mutations. Additionally copy-number variants and long range variants are called using specialised tools
Client: redacted
Publications
I have co-authored many scientific publications which you can find here: https://www.ncbi.nlm.nih.gov/pubmed/?term=“Dümcke+S”