Sebastian's personal website

Bioinformatic consulting

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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

What my clients say

Our collaboration with Dr Dümcke has been exceptional and has exceeded all our expectations. From the very beginning, the partnership was characterised by professionalism, reliability and a high level of expertise. We were particularly impressed by the clear communication, which was always solution-oriented and constructive. Challenges were tackled efficiently and creatively. In addition, Dr Dümcke’s excellent preparation and structured approach ensured a smooth and productive process throughout. The results speak for themselves: high quality, delivered on time and perfectly tailored to our needs. We highly value our collaboration with Dr Dümcke and have no hesitation in recommending him. We look forward to working with him on future projects. — Dr. Stefanie Buchheister, MH Hannover

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

Detect pathogenic bacteria in sequencing data and microbiome profiling of mice feces and exhaust filter dust of laboratory animal facility

I have developed a custom detection method for a set of pathogenic species from shotgun sequencing of exhaust filter dust samples. Prediction was compared to performance on qPCR analyses. I also evaluated meta-genomic species composition of exhaust filter dust samples and mice feces (alpha and beta diversity) and compared with diversity obtained from 16S targeted sequencing.

Client: Medizinische Hochschule Hannover

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 practices 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”