Biomedicine meets data science | Bioinformatician & Molecular biologist | Consulting, Research, Service
Aktualisiert am 30.10.2024
Profil
Freiberufler / Selbstständiger
Remote-Arbeit
Verfügbar ab: 01.11.2024
Verfügbar zu: 80%
davon vor Ort: 25%
Bioinformatics
Molecular Biology
Data Science
Bioinformatician
Next-generation sequencing
Transcriptomics
Epigenetics
Proteomics
R
Python
Bash
Biological Data Analysis
Computational Biology
Research
Data Analytics
Immunology
Neuroscience
Biology
Project management
Teamwork
Science
single cell
transcriptomics
English
Verhandlungssicher
German
Muttersprache
Dutch
Grundkenntnisse

Einsatzorte

Einsatzorte

Hamburg (+500km)
Deutschland
möglich

Projekte

Projekte

1 year 9 months
2023-02 - now

High-dimensional flow cytometry analysis pipeline

  • Developing a pipeline to analyse high-dimensional flow cytometry data in R using existing machine learning algorithms and Bioconductor tools
  • Expected outcome: user-friendly Bioconductor R package
Institute Medical Systems Biology, University Medical Center Hamburg-Eppendorf
2 years 5 months
2022-06 - now

Immune development in neonatal intestine

  • Project lead, collaborating with 3 scientists, implementing omics technologies
  • Managing a >250,000? budget for omics applications
  • Expected outcome: developmental atlas of human intestinal immune cells
multiomics (single-cell and bulk) high-dimensional flow cytometry
Leibniz-Institute of Virology
1 year 4 months
2022-06 - 2023-09

Sex differences in antiviral immunity

  • Supervising 3 scientists conducting bioinformatic analyses in 2 subprojects and developing a single-cell long read mRNA sequencing protocol & pipeline
  • Outcome: role of sex-specific genetics in antiviral response (scientific publication in iScience)
single-cell mRNA sequencing (long and short read)
Department of Immunology, University Medical Center Hamburg-Eppendorf
4 years 9 months
2016-09 - 2021-05

Negative immune checkpoints in multiple sclerosis

mRNA sequencing flow cytometry
  • Project lead managing multiple subprojects with (inter)national collaborations
  • Outcome: immune checkpoints VISTA is differentially regulated in multiple sclerosis and involved in microglia myelin phagocytosis (scientific publications in Glia, Journal of Molecular Medicine and Acta neuropathologica communications)
mRNA sequencing flow cytometry
Department of Neuroscience, University Medical Center Groningen
1 year 4 months
2019-03 - 2020-06

Microglia development in the fetal central nervous system

mRNA sequencing (bulk & single-cell) ATAC sequencing

  • Collaborating with 2 hospitals and next-generation sequencing company
  • Outcome: epigenetic and transcriptomic landscape of microglia during human fetal development (scientific publication in Science)

mRNA sequencing (bulk & single-cell) ATAC sequencing
Department of Neuroscience, University Medical Center Groningen

Aus- und Weiterbildung

Aus- und Weiterbildung

4 years 9 months
2016-09 - 2021-05

Neuroimmunology

Ph.D., cum laude, University of Groningen, Groningen, The Netherlands
Ph.D., cum laude
University of Groningen, Groningen, The Netherlands
1 year 11 months
2014-09 - 2016-07

Biomedical Sciences

M.Sc., cum laude, University of Groningen, Groningen, The Netherlands
M.Sc., cum laude
University of Groningen, Groningen, The Netherlands
1 year
2013-09 - 2014-08

Molecular Biology

B.Sc. (Hons), first class, University of Aberdeen, Aberdeen, Scotland, United Kingdom
B.Sc. (Hons), first class
University of Aberdeen, Aberdeen, Scotland, United Kingdom
2 years
2011-09 - 2013-08

Applied Biology

B.Sc., gpa 1.5, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany
B.Sc., gpa 1.5
University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany

Kompetenzen

Kompetenzen

Top-Skills

Bioinformatics Molecular Biology Data Science Bioinformatician Next-generation sequencing Transcriptomics Epigenetics Proteomics R Python Bash Biological Data Analysis Computational Biology Research Data Analytics Immunology Neuroscience Biology Project management Teamwork Science single cell transcriptomics

Schwerpunkte

Bioinformatics

Biomedical

  • Immunology, Neuroscience, Developmental biology, Molecular biology, Genetics


Technologies

  • Transcriptomics: Gene expression (spatial, single-cell, bulk), Non-coding RNA
  • Epigenomics: Chromatin accessibility (ATAC), DNA-protein interactions (ChIP)
  • Proteomics: Mass spectrometry, High-dimensional flow cytometry
  • Immunomics: T/B cell receptor repertoire, Cytokine profiling
  • Integration of multiple omics approaches on single-cell and bulk level


Computational

  • R: Bioconductor, EdgeR, DESeq2, Seurat, Slingshot, Monocle, SCENIC, and more
  • Python: Scanpy
  • Other: Nextflow, Docker, Git, Jupyter, Bash, Alignment tools (salmon, bowtie, and other command line tools)

Produkte / Standards / Erfahrungen / Methoden

Profile:

Data is the future of biomedicine, and I contribute to discovery and innovation with the analysis and interpretation of large biomedical datasets. My main focus is on omics technologies in immunology, neuroscience and developmental biology.

I have 5+ years of experience in bioinformatics, biomedical research and experimental generation of omics data. As a result of my mixed background in computational- and molecular biology, I know where the data comes from and what it means.


EXPERIENCE

Biomedical

  • Immunology, Neuroscience, Developmental biology, Molecular biology, Genetics


Technologies

  • Transcriptomics: Gene expression (spatial, single-cell, bulk), Non-coding RNA
  • Epigenomics: Chromatin accessibility (ATAC), DNA-protein interactions (ChIP)
  • Proteomics: Mass spectrometry, High-dimensional flow cytometry
  • Immunomics: T/B cell receptor repertoire, Cytokine profiling
  • Integration of multiple omics approaches on single-cell and bulk level


Computational

  • R: Bioconductor, EdgeR, DESeq2, Seurat, Slingshot, Monocle, SCENIC, and more
  • Python: Scanpy
  • Other: Nextflow, Docker, Git, Jupyter, Bash, Alignment tools (salmon, bowtie, and other command line tools)


Employment History

06/2022 - today

Role: Postdoctoral Research Associate

Customer: Leibniz-Institute of Virology & University Medical Center Hamburg-Eppendorf, Germany


Tasks:

  • Teaching a bioinformatics course
  • Implementing next-generation sequencing protocols and pipelines
  • Developing novel computational pipelines for proteomic data analysis
  • Analysing and interpreting various omics datasets


09/2016 - 05/2021

Role: Doctoral Researcher

Customer: University Medical Center Groningen, The Netherlands


Tasks:

  • Generating next-generation sequencing libraries
  • Applying computational algorithms for omics data analysis
  • Supervising 4 Master and 1 Doctoral student
  • Presenting results at (inter)national conferences and in publications


03/2017 ? 05/2017

Role: Visiting Scientist

Customer: Dartmouth Hitchcock Medical Center, Dartmouth College, USA


Tasks:

  • Implementing molecular biology technologies in the laboratory
  • Conducting immunological assays and experiments


Internship

01/2016 ? 06/2016

Role: M.Sc. Research Intern 

Customer: University Medical Center Groningen, The Netherlands


11/2014 ? 06/2015

Role: M.Sc. Research Intern 

Customer: University Medical Center Groningen, The Netherlands


01/2014 ? 03/2014

B.Sc. Research Intern

University of Aberdeen, Scotland, United Kingdom

Einsatzorte

Einsatzorte

Hamburg (+500km)
Deutschland
möglich

Projekte

Projekte

1 year 9 months
2023-02 - now

High-dimensional flow cytometry analysis pipeline

  • Developing a pipeline to analyse high-dimensional flow cytometry data in R using existing machine learning algorithms and Bioconductor tools
  • Expected outcome: user-friendly Bioconductor R package
Institute Medical Systems Biology, University Medical Center Hamburg-Eppendorf
2 years 5 months
2022-06 - now

Immune development in neonatal intestine

  • Project lead, collaborating with 3 scientists, implementing omics technologies
  • Managing a >250,000? budget for omics applications
  • Expected outcome: developmental atlas of human intestinal immune cells
multiomics (single-cell and bulk) high-dimensional flow cytometry
Leibniz-Institute of Virology
1 year 4 months
2022-06 - 2023-09

Sex differences in antiviral immunity

  • Supervising 3 scientists conducting bioinformatic analyses in 2 subprojects and developing a single-cell long read mRNA sequencing protocol & pipeline
  • Outcome: role of sex-specific genetics in antiviral response (scientific publication in iScience)
single-cell mRNA sequencing (long and short read)
Department of Immunology, University Medical Center Hamburg-Eppendorf
4 years 9 months
2016-09 - 2021-05

Negative immune checkpoints in multiple sclerosis

mRNA sequencing flow cytometry
  • Project lead managing multiple subprojects with (inter)national collaborations
  • Outcome: immune checkpoints VISTA is differentially regulated in multiple sclerosis and involved in microglia myelin phagocytosis (scientific publications in Glia, Journal of Molecular Medicine and Acta neuropathologica communications)
mRNA sequencing flow cytometry
Department of Neuroscience, University Medical Center Groningen
1 year 4 months
2019-03 - 2020-06

Microglia development in the fetal central nervous system

mRNA sequencing (bulk & single-cell) ATAC sequencing

  • Collaborating with 2 hospitals and next-generation sequencing company
  • Outcome: epigenetic and transcriptomic landscape of microglia during human fetal development (scientific publication in Science)

mRNA sequencing (bulk & single-cell) ATAC sequencing
Department of Neuroscience, University Medical Center Groningen

Aus- und Weiterbildung

Aus- und Weiterbildung

4 years 9 months
2016-09 - 2021-05

Neuroimmunology

Ph.D., cum laude, University of Groningen, Groningen, The Netherlands
Ph.D., cum laude
University of Groningen, Groningen, The Netherlands
1 year 11 months
2014-09 - 2016-07

Biomedical Sciences

M.Sc., cum laude, University of Groningen, Groningen, The Netherlands
M.Sc., cum laude
University of Groningen, Groningen, The Netherlands
1 year
2013-09 - 2014-08

Molecular Biology

B.Sc. (Hons), first class, University of Aberdeen, Aberdeen, Scotland, United Kingdom
B.Sc. (Hons), first class
University of Aberdeen, Aberdeen, Scotland, United Kingdom
2 years
2011-09 - 2013-08

Applied Biology

B.Sc., gpa 1.5, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany
B.Sc., gpa 1.5
University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany

Kompetenzen

Kompetenzen

Top-Skills

Bioinformatics Molecular Biology Data Science Bioinformatician Next-generation sequencing Transcriptomics Epigenetics Proteomics R Python Bash Biological Data Analysis Computational Biology Research Data Analytics Immunology Neuroscience Biology Project management Teamwork Science single cell transcriptomics

Schwerpunkte

Bioinformatics

Biomedical

  • Immunology, Neuroscience, Developmental biology, Molecular biology, Genetics


Technologies

  • Transcriptomics: Gene expression (spatial, single-cell, bulk), Non-coding RNA
  • Epigenomics: Chromatin accessibility (ATAC), DNA-protein interactions (ChIP)
  • Proteomics: Mass spectrometry, High-dimensional flow cytometry
  • Immunomics: T/B cell receptor repertoire, Cytokine profiling
  • Integration of multiple omics approaches on single-cell and bulk level


Computational

  • R: Bioconductor, EdgeR, DESeq2, Seurat, Slingshot, Monocle, SCENIC, and more
  • Python: Scanpy
  • Other: Nextflow, Docker, Git, Jupyter, Bash, Alignment tools (salmon, bowtie, and other command line tools)

Produkte / Standards / Erfahrungen / Methoden

Profile:

Data is the future of biomedicine, and I contribute to discovery and innovation with the analysis and interpretation of large biomedical datasets. My main focus is on omics technologies in immunology, neuroscience and developmental biology.

I have 5+ years of experience in bioinformatics, biomedical research and experimental generation of omics data. As a result of my mixed background in computational- and molecular biology, I know where the data comes from and what it means.


EXPERIENCE

Biomedical

  • Immunology, Neuroscience, Developmental biology, Molecular biology, Genetics


Technologies

  • Transcriptomics: Gene expression (spatial, single-cell, bulk), Non-coding RNA
  • Epigenomics: Chromatin accessibility (ATAC), DNA-protein interactions (ChIP)
  • Proteomics: Mass spectrometry, High-dimensional flow cytometry
  • Immunomics: T/B cell receptor repertoire, Cytokine profiling
  • Integration of multiple omics approaches on single-cell and bulk level


Computational

  • R: Bioconductor, EdgeR, DESeq2, Seurat, Slingshot, Monocle, SCENIC, and more
  • Python: Scanpy
  • Other: Nextflow, Docker, Git, Jupyter, Bash, Alignment tools (salmon, bowtie, and other command line tools)


Employment History

06/2022 - today

Role: Postdoctoral Research Associate

Customer: Leibniz-Institute of Virology & University Medical Center Hamburg-Eppendorf, Germany


Tasks:

  • Teaching a bioinformatics course
  • Implementing next-generation sequencing protocols and pipelines
  • Developing novel computational pipelines for proteomic data analysis
  • Analysing and interpreting various omics datasets


09/2016 - 05/2021

Role: Doctoral Researcher

Customer: University Medical Center Groningen, The Netherlands


Tasks:

  • Generating next-generation sequencing libraries
  • Applying computational algorithms for omics data analysis
  • Supervising 4 Master and 1 Doctoral student
  • Presenting results at (inter)national conferences and in publications


03/2017 ? 05/2017

Role: Visiting Scientist

Customer: Dartmouth Hitchcock Medical Center, Dartmouth College, USA


Tasks:

  • Implementing molecular biology technologies in the laboratory
  • Conducting immunological assays and experiments


Internship

01/2016 ? 06/2016

Role: M.Sc. Research Intern 

Customer: University Medical Center Groningen, The Netherlands


11/2014 ? 06/2015

Role: M.Sc. Research Intern 

Customer: University Medical Center Groningen, The Netherlands


01/2014 ? 03/2014

B.Sc. Research Intern

University of Aberdeen, Scotland, United Kingdom

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