About

This is the web site of Manuel Holtgrewe, computer scientist, bioinformatician (focus on medical genetics), scientist, engineer, technologist, nerd – not necessarily in this order.

All thoughts and opinions expressed on this website are my own and are not necessarily shared by my employer.

“What exactly are you doing” you ask?

DNA + CPU + Hospital + Collaboration

I’m working with DNA in computers in a clinical setting with wonderful collaborators!

Bioinformatics Staff Scientist, Beule Lab, BIH

Since 2022, I am migrating to my role as a staff scientist at Dieter Beule’s lab at Berlin Institute of Health. Here, I’m continuing my research

Core Unit Bioinformatics (CUBI), BIH

In my third life, I joined the then newly founded Berlin Institute of Health (BIH) in Core Unit Bioinformatics (CUBI). Together with group leader Dieter Beule and my colleagues, I was fortunate enough being able to shape this world-class group that provides service-oriented scientific collaborations to groups at Berlin Institute of Health, Charité – Universitätsmedizin Berlin, and Max Delbrück Center Berlin. Thanks to the excellent project from our wonderful collaborators my publications are too numerous to list here. Some highlights:

  • Holtgrewe M, Stolpe O, Nieminen M, …, Beule D. “VarFish: comprehensive DNA variant analysis for diagnostics and research”. NAR, 2020. [paper]
  • Weiner J, Suwalski P, Holtgrewe M, …, Heidecker B. “Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01”. EClinicalMedicine, 2021. [paper]
  • Holtgrewe M, Knaus A, Hildebrand G, …, Krawitz PM. “Multisite de novo mutations in human offspring after paternal exposure to ionizing radiation”. Scientific reports, 2018. [paper]
  • Seidel F, Holtgrewe M, …, Klasasen S. “Pathogenic Variants Associated With Dilated Cardiomyopathy Predict Outcome in Pediatric Myocarditis”. Circulation, 2021. [paper]
  • Melo US, Schöpflin R, Acuna-Hidalgo R, Mensah MA, Fischer-Zirnsak B, Holtgrewe M, …, Mundlos S. “Hi-C identifies complex genomic rearrangements and TAD-shuffling in developmental diseases”. AJHG, 2020. [paper]

You can find the full list of my publications on Google Scholar and more information on the CUBI Website.

BIH HPC Team Lead

Further, I have been the technical lead of the BIH HPC team since 2017. Me and a team of 2-3 others have been planning and operating a cluster of 200-300 nodes, 10k+ cores, 40/100GbE interconnect and 2PB+ of high-performance storage. You can find more information on the BIH HPC Website and the documentation that I primarly created at docs.hpc.bihealth.org.

PhD Studies

I then became an algorithmic bioinformatician for my second life in 2009 and worked with Knut Reinert at Freie Universität Berlin for my doctoral studies. I completed my PhD in bioinformatics working on efficient algorithms for next-generation data processing, read mapping, and structural variant analysis. During this time, I was one of the main contributors to the SeqAn library. Some publications from this time.

  • Holtgrewe M, Ehmke, A-K, Weese D, Reinert K. “A novel and well-defined benchmarking method for second generation read mapping”. BMC Bioinformatics, 2010. [paper]
  • Weese D, Holtgrewe M, Reinert K. “RazerS 3: faster, fully sensitive read mapping”. Bioinformatics, 2012. [paper]
  • Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H. “Fiona: a parallel and automatic strategy for read error correction”. Bioinformatics, 2014. [paper]
  • Kehr B, Trappe K, Holtgrewe M, Reinert K. “Genome alignment with graph data structures: a comparison”. BMC Bioinformatics, 2014. [paper]
  • Holtgrewe M, Kuchenber L, Reinert K. “Methods for the detection and assembly of novel sequence in high-throughput sequencing data”. Bioinformatics, 2015. [paper]
  • Holtgrewe M. “Engineering Algorithms for Personal Genome Pipelines”. Freie Universität Berlin, PhD Thesis, 2015. [PDF]

Undergraduate and Graduate Studies

In my first life, I was a computer scientist trained at KIT-Fakultät für Informatik, Karlsruhe. During my studies, I specialized in algorithmics and parallel processing, you can find my diploma thesis (German Dipl.-Inform.) “A Scalable Coarsening Phase for a Multi-Level Graph Partitioning Algorithm” on Zenodo. Here are some publications from this time:

  • Birn M, Holtgrewe M, Sanders P, Singler J. “Simple and fast nearest neighbor search”. ALENEX, 2010. [paper].
  • Holtgrewe M, Sanders P, Schulz C. “Engineering a scalable high quality graph partitioner”. IPDPS, 2020. [[paper]]](https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=5470485)
  • Holtgrewe M. “A scalable coarsening phase for a multi-level graph partitioning algorithm”. Master’s Thesis. Universität Karlsruhe, 2009. [PDF]

The Small Print

Contact

Manuel Holtgrewe
Charité – Universitätsmedizin Berlin
Charitéplatz 1
10117 Berlin
Germany