As self-employed software engineer and bioinformatics consultant with 15 years of experience, I provide services to international biotechnology firms.
Aktualisiert am 24.05.2024
Profil
Freiberufler / Selbstständiger
Remote-Arbeit
Verfügbar ab: 01.06.2024
Verfügbar zu: 50%
davon vor Ort: 30%
bioinformatics
Software-Entwicklung
data a
DevOps
Cloud Computing
AWS
SQL
Linux
R programming
R/Shiny
Dashboard
Java
MATLAB
Jupyter Notebook
Cluster analysis
Netzwerkanalyse
metabolism
omics data
Machine Learning
statistical data analysis
gene expression analysis
gene enrichment
full-stack developer
German
Muttersprache
English
Proficient
Spanish
Proficient
French
Intermediate
Portuguese
Beginner

Einsatzorte

Einsatzorte

Deutschland, Schweiz, Österreich
Remote work possible
möglich

Projekte

Projekte

2 years 4 months
2022-09 - now

Software development for DNA chromatogram analysis

Software engineer and bioinformatics consultant AWS R Shiny ...
Software engineer and bioinformatics consultant
For Ansa Biotechnologies Inc., I develop and maintain a software application for screening and analyzing DNA chromatograms. I am the sole responsible for the software, which involves cloud computing, software engineering, DevOps, CI/CD, data visualization, user support, and bioinformatics analyses.
AWS R Shiny DevOps Webapplication Continu
Ansa Biotechnologies Inc.
Remote
3 years
2020-07 - 2023-06

Human cell type gene expression data

Bioinformatics Consultant R Bioinformatics Databases
Bioinformatics Consultant
For BitBio Ltd., I collected and integrated gene expression datasets from the literature and public databases. I conducted statistical analysis and annotated human cell type expression data with various physiological and developmental features using controlled vocabularies and ontologies.
R Bioinformatics Databases
BitBio Ltd.
2 years 4 months
2019-12 - 2022-03

In Silico Liver

R Shiny SQLit ...
I was the sole responsible for the cloud-based infrastructure of Ochre Bio Ltd. for 2 years during its fast growth as a scale-up. The project required scientific data curation, large-scale data integration, statistical testing, relational database engineering, algorithm development, machine learning, interactive visualizations, gene and pathway enrichment. The custom algorithms I developed led to the discovery of the company?s main lead gene for the treatment of liver disease.
R Shiny SQLit MySQ bioinformatics data visualization Machine Learning statisti Algori high-perfor
Ochre Bio Ltd.
Remote
2 months
2019-09 - 2019-10

Microglial clustering in neurodegenerative disease

Bioinformatics consultant machine le R Matlab ...
Bioinformatics consultant
Clustering of microglia cells using gene expression data sets from the public studies. Annotation of data sets using demographic information and differential gene expression. Identification of microglial cell types and target genes associated with neurodegenerative diseases.
   
machine le R Matlab bioinformatics health
MD Anderson Cancer Center
Remote
2 years
2017-03 - 2019-02

Unravelling the contribution of soil biodiversity to maize

Research Associate Java MATLAB R ...
Research Associate

  • RECONSTRUCT: Unravelling the contribution of soil biodiversity to maize growth and fitness through combined omics-based in silico modeling and reconstruction biology
  • At the Max Planck Institute, I applied statistical modelling to multi-omics data (metabolomics, proteomics, fluxomics), and used high-performance computing, graph modelling, hypothesis testing, and bioinformatics analysis. I was also involved in University teaching.

Java MATLAB R statistical modeling omics data data visualization data analysis
Max Planck Institute for Molecular Plant Physiology
Potsdam

Aus- und Weiterbildung

Aus- und Weiterbildung

2008 ? 2012
Max Planck Institute and University of Potsdam (Germany)
PhD in Bioinformatics

Focus:

  • metabolic
  • network analysis, complex network
  • randomization

2000 ? 2007
Humboldt University (Germany)
BSc & MSc in Computer Science

Selection of certificates
  • AWS: Cloud Technical Essentials
  • AWS: DevOps on AWS: Code, Build, and Test
  • Duke University: MLOps Platforms: Amazon SageMaker and Azure ML
  • Google Cloud: Introduction to Large Language Models
  • European Patent Office: Intellectual Property Rights for Marie Curie Fellows
  • Biosystems Engineering: Bioreactors and Cell Factories
  • Evidence-Based Teaching (University of California, Berkeley)
  • Cloud Technical Essentials (AWS)
  • DevOps on AWS: Code, Build, and Test (AWS)
  • MLOps Platforms: Amazon SageMaker and Azure ML (Duke University)
  • Introduction to Large Language Models (Google Cloud)
  • Intellectual Property Rights for Marie Curie Fellows (European Patent Office)

Position

Position

  • Senior bioinformatics scientist
  • software engineer
  • data scientist

Kompetenzen

Kompetenzen

Top-Skills

bioinformatics Software-Entwicklung data a DevOps Cloud Computing AWS SQL Linux R programming R/Shiny Dashboard Java MATLAB Jupyter Notebook Cluster analysis Netzwerkanalyse metabolism omics data Machine Learning statistical data analysis gene expression analysis gene enrichment full-stack developer

Produkte / Standards / Erfahrungen / Methoden

Profile
Bioinformatics scientist and software engineer with more than 15 years of experience. Research positions at the Max Planck Society (Germany), University of California, Berkeley, and Lawrence Berkeley National Laboratory (USA). 17 publications and one book chapter. Consultant since 2019, offering services to over 20 international startups and biotechnology companies. Special interest in software engineering, bioinformatics, cloud computing, machine learning, gene expression, network analysis, and data visualization.


Software engineering

  • full stack software development
  • cloud computing
  • DevOps
  • container services
  • database engineering
  • CI/CD
  • SaaS & IaaS
  • high-performance computing
  • R, Shiny, Java, Matlab, Python, Jupyter, C, SQL

Machine Learning
  • supervised & unsupervised
  • linear & multivariate regression
  • cluster algorithms & analysis

Bioinformatics
  • genomics
  • transcriptomics
  • metabolomics
  • fluxomics
  • linear optimization
  • differential expression analysis
  • enrichment analysis
  • pathway analysis
  • mammalian cell types & tissues
  • statistical modeling
  • data visualization


Laboratory Experience
  • Genome editing
  • Molecular cloning
  • Membrane engineering
  • GC-FID
  • Flow cytometry
  • Fluorescence microscopy
  • DNA extraction
  • Protein quantification

Work history

2022 - today

Role: Steering Committee
Customer: Independent Data Lab

2019 - today

Role: Self-employed bioinformatics consultant (remote)

2017 - 2019 
Role: Research Associate Research Associate: multi-omics data, statistical modelling, University teaching
Customer: Max Planck Institute (Germany)

2004 - 2007
Role: Software programmer 

Customer: Mercedes-Benz R&D, Germany

Teaching

  • Master?s course ?Constraint-based Modeling of Cellular Networks? (2018), University of Potsdam
  • Master?s course ?Profile Data and Network Analysis? (2017), University of Potsdam
  • Tutorial ?Introduction to theoretical systems biology? (2009), University of Potsdam


Peer-Reviews (total: 22)
Scientific Reports, Plant Physiology, Bioinformatics, MDPI Metabolites, MDPI Algorithms, MDPI Molecules, Microbial Cell Factories, Journal of Molecular Engineering & Systems Biology, Frontiers in Genetics

Betriebssysteme

Windows
Linux

Programmiersprachen

R
Shiny
Java
Matlab
Python
Jupyter Notebook
C
SQL

Einsatzorte

Einsatzorte

Deutschland, Schweiz, Österreich
Remote work possible
möglich

Projekte

Projekte

2 years 4 months
2022-09 - now

Software development for DNA chromatogram analysis

Software engineer and bioinformatics consultant AWS R Shiny ...
Software engineer and bioinformatics consultant
For Ansa Biotechnologies Inc., I develop and maintain a software application for screening and analyzing DNA chromatograms. I am the sole responsible for the software, which involves cloud computing, software engineering, DevOps, CI/CD, data visualization, user support, and bioinformatics analyses.
AWS R Shiny DevOps Webapplication Continu
Ansa Biotechnologies Inc.
Remote
3 years
2020-07 - 2023-06

Human cell type gene expression data

Bioinformatics Consultant R Bioinformatics Databases
Bioinformatics Consultant
For BitBio Ltd., I collected and integrated gene expression datasets from the literature and public databases. I conducted statistical analysis and annotated human cell type expression data with various physiological and developmental features using controlled vocabularies and ontologies.
R Bioinformatics Databases
BitBio Ltd.
2 years 4 months
2019-12 - 2022-03

In Silico Liver

R Shiny SQLit ...
I was the sole responsible for the cloud-based infrastructure of Ochre Bio Ltd. for 2 years during its fast growth as a scale-up. The project required scientific data curation, large-scale data integration, statistical testing, relational database engineering, algorithm development, machine learning, interactive visualizations, gene and pathway enrichment. The custom algorithms I developed led to the discovery of the company?s main lead gene for the treatment of liver disease.
R Shiny SQLit MySQ bioinformatics data visualization Machine Learning statisti Algori high-perfor
Ochre Bio Ltd.
Remote
2 months
2019-09 - 2019-10

Microglial clustering in neurodegenerative disease

Bioinformatics consultant machine le R Matlab ...
Bioinformatics consultant
Clustering of microglia cells using gene expression data sets from the public studies. Annotation of data sets using demographic information and differential gene expression. Identification of microglial cell types and target genes associated with neurodegenerative diseases.
   
machine le R Matlab bioinformatics health
MD Anderson Cancer Center
Remote
2 years
2017-03 - 2019-02

Unravelling the contribution of soil biodiversity to maize

Research Associate Java MATLAB R ...
Research Associate

  • RECONSTRUCT: Unravelling the contribution of soil biodiversity to maize growth and fitness through combined omics-based in silico modeling and reconstruction biology
  • At the Max Planck Institute, I applied statistical modelling to multi-omics data (metabolomics, proteomics, fluxomics), and used high-performance computing, graph modelling, hypothesis testing, and bioinformatics analysis. I was also involved in University teaching.

Java MATLAB R statistical modeling omics data data visualization data analysis
Max Planck Institute for Molecular Plant Physiology
Potsdam

Aus- und Weiterbildung

Aus- und Weiterbildung

2008 ? 2012
Max Planck Institute and University of Potsdam (Germany)
PhD in Bioinformatics

Focus:

  • metabolic
  • network analysis, complex network
  • randomization

2000 ? 2007
Humboldt University (Germany)
BSc & MSc in Computer Science

Selection of certificates
  • AWS: Cloud Technical Essentials
  • AWS: DevOps on AWS: Code, Build, and Test
  • Duke University: MLOps Platforms: Amazon SageMaker and Azure ML
  • Google Cloud: Introduction to Large Language Models
  • European Patent Office: Intellectual Property Rights for Marie Curie Fellows
  • Biosystems Engineering: Bioreactors and Cell Factories
  • Evidence-Based Teaching (University of California, Berkeley)
  • Cloud Technical Essentials (AWS)
  • DevOps on AWS: Code, Build, and Test (AWS)
  • MLOps Platforms: Amazon SageMaker and Azure ML (Duke University)
  • Introduction to Large Language Models (Google Cloud)
  • Intellectual Property Rights for Marie Curie Fellows (European Patent Office)

Position

Position

  • Senior bioinformatics scientist
  • software engineer
  • data scientist

Kompetenzen

Kompetenzen

Top-Skills

bioinformatics Software-Entwicklung data a DevOps Cloud Computing AWS SQL Linux R programming R/Shiny Dashboard Java MATLAB Jupyter Notebook Cluster analysis Netzwerkanalyse metabolism omics data Machine Learning statistical data analysis gene expression analysis gene enrichment full-stack developer

Produkte / Standards / Erfahrungen / Methoden

Profile
Bioinformatics scientist and software engineer with more than 15 years of experience. Research positions at the Max Planck Society (Germany), University of California, Berkeley, and Lawrence Berkeley National Laboratory (USA). 17 publications and one book chapter. Consultant since 2019, offering services to over 20 international startups and biotechnology companies. Special interest in software engineering, bioinformatics, cloud computing, machine learning, gene expression, network analysis, and data visualization.


Software engineering

  • full stack software development
  • cloud computing
  • DevOps
  • container services
  • database engineering
  • CI/CD
  • SaaS & IaaS
  • high-performance computing
  • R, Shiny, Java, Matlab, Python, Jupyter, C, SQL

Machine Learning
  • supervised & unsupervised
  • linear & multivariate regression
  • cluster algorithms & analysis

Bioinformatics
  • genomics
  • transcriptomics
  • metabolomics
  • fluxomics
  • linear optimization
  • differential expression analysis
  • enrichment analysis
  • pathway analysis
  • mammalian cell types & tissues
  • statistical modeling
  • data visualization


Laboratory Experience
  • Genome editing
  • Molecular cloning
  • Membrane engineering
  • GC-FID
  • Flow cytometry
  • Fluorescence microscopy
  • DNA extraction
  • Protein quantification

Work history

2022 - today

Role: Steering Committee
Customer: Independent Data Lab

2019 - today

Role: Self-employed bioinformatics consultant (remote)

2017 - 2019 
Role: Research Associate Research Associate: multi-omics data, statistical modelling, University teaching
Customer: Max Planck Institute (Germany)

2004 - 2007
Role: Software programmer 

Customer: Mercedes-Benz R&D, Germany

Teaching

  • Master?s course ?Constraint-based Modeling of Cellular Networks? (2018), University of Potsdam
  • Master?s course ?Profile Data and Network Analysis? (2017), University of Potsdam
  • Tutorial ?Introduction to theoretical systems biology? (2009), University of Potsdam


Peer-Reviews (total: 22)
Scientific Reports, Plant Physiology, Bioinformatics, MDPI Metabolites, MDPI Algorithms, MDPI Molecules, Microbial Cell Factories, Journal of Molecular Engineering & Systems Biology, Frontiers in Genetics

Betriebssysteme

Windows
Linux

Programmiersprachen

R
Shiny
Java
Matlab
Python
Jupyter Notebook
C
SQL

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