Copenhagen, Capital Region of Denmark, Denmark
I am a molecular microbiologist and sequencing specialist with over 10 years’ experience in next-generation sequencing (NGS) and microbial genomics. My current work focuse on high-complexity samples as wastewater and clinical microbiome samples for metagenomic sequencing. I design and implement robust workflows from sample to sequence: extraction of low-input or host-rich material, library preparation (amplicon, metagenome, targeted panels), sequencing (short- and long-read platforms), and downstream bioinformatic analysis of microbial communities, pathogens, and resistomes. Highlights of my expertise include: • Deep proficiency in metagenomic/amplification/enrichment-based sequencing of complex, mixed microbial communities (e.g., wastewater, clinical samples). • Strong foundation in molecular microbiology (culture-independent pathogen and indicator detection, microbial ecology). • Workflow optimization: high-throughput sample processing, cutting corners for faster TAT, minimizing host-background, maximizing microbial yield and data quality, reduce cost. • Selection and implementation of appropriate sequencing technologies (short-read, long-read, hybrid approaches). • Bioinformatic interpretation: taxonomic, resistome/virulome analysis, microbial source‐tracking, diversity/stats reporting. • Collaboration track-record: supporting academic groups with sequencing service, protocol development, and data exchange. • I have experience training student, staff, developing SOPs, managing NGS operations, and ensuring quality control in a clinical setting or core facility setting. If you have an interest in me or some of the projects that I work with then feel free to contact me. This page is a good overview of my previous work but things are so much more easy to elaborate on and discuss in person. My publications are generally updated on https://scholar.google.com/citations?user=aDCvKGcAAAAJ&hl=en or ORCID (ID: https://orcid.org/0000-0003-3936-5499).
Developing metagenomic sequencing approaches for wastewater and clinical samples, long and short-read sequencing.
External censor on bachelor projects for Medical Laboratory Scientists within the subjects: Clinical Microbiology Molecular biology and genetic tests Elected for the period 2017/01/01 - 2020/12/31 and re-elected until 2024/12/31
Main task is to get sequencing implemented in a feasible way to obtain a rapid and actionable result for the patient. Responsible for: The surveillance of virus variants at Rigshospitalet. Virus outbreak investigations at the hospital. Virus resistance analysis for difficult to treat patients. Development of new methods, all the way from the sample to getting the answer into LIMS. Training and teaching of staff.
Teacher in Next Generation Sequencing in the course (A-kursus i Molekylærbiologi 2021, nr. 212901) for Medical Doctors specializing in Clinical Microbiology.
I was responsible for the Next Generation Sequencing Wet-Lab Workflows at the Department of Clinical Microbiology and the development of new assays and executing research projects. Both Illumina and Oxford Nanopore sequencing approaches were applied. Projects included: RNA/DNA virus sequencing, bacterial sequencing, RNA/DNA metagenomic sequencing of microbiomes from skin, vaginal, nasal, rectal and feces samples. Routine tasks included: development, implementation and support of the hepatitis C virus genotyping and resistance assay, surveillance of internal/external quality controls, ring trials, training of lab personel and students. The position was also a collaboration with Professor Jens Bukh and his CO-HEP group to continue the research that was initiated during my PhD. My Hospital website: https://research.regionh.dk/hvidovre/da/persons/martin-schou-pedersen(e0402cb5-1a12-4af3-a8df-5185bfec06a1)/publications.html
I worked on development of a Next Generation Sequencing assay for screening of hepatitis C virus in infected patients at Hvidovre Hospital in order to genotype the viral quasispecies without prior information on the samples at baseline before initiation of treatment. This is performed at the Department of Clinical Microbiology (supervisor Kristian Schønning) and at the Copenhagen Hepatitis C Program (CO-HEP)(supervisor Jens Bukh), both located at Hvidovre Hospital, together with Roskilde University (supervisor Håvard Jenssen). The project bridges the basic research performed at the University and at the CO-HEP group with their developed cell culture systems for HCV and the applied research that are conducted at the Microbiology Department. Look under organization and honour & awards to see my teaching experience during the PhD, scientific presentations and funding bodies.
Working on my Ph.d. project before the official start.