Christopher (Chris) Hempel

Christopher (Chris) Hempel

Bioinformatics Contractor and Consultant

Currently under contract for:

Prof. Carlos Duarte

Red Sea Research Center

King Abdullah University of Science and Technology (KAUST)

Welcome to my homepage!

I’m Chris, a dedicated Bioinformatics Contractor and Consultant. I’m passionate about unlocking the secrets hidden in biological data. With my expertise in data analysis, genomics, and programming, I specialize in finding innovative solutions to complex bioinformatical problems. This homepage is a short introduction to myself and my work. Enjoy scrolling!

Interests
  • Bioinformatics
  • Metagenomics
  • Metatranscriptomics
  • Metabarcoding
  • Machine learning
  • Molecular ecology
Education

  • Ph.D. in Integrative Biology, 2022

    University of Guelph, Canada

  • M.Sc. in Biodiversity, 2018

    Ruhr University Bochum, Germany

  • B.Sc. in Biology, 2016

    University of Duisburg-Essen, Germany

Skills

Bioinformatics

Metagenomics, Metatranscriptomics & Metabarcoding

Data Analysis & Statistics

Uncovering data patterns and trends

Molecular ecology

DNA- & RNA-based biodiversity assessments

Python

For data processing, analysis, and visualization as well as statistics & machine learning

Shell

For data processing, bioinformatics programs & pipelines

R

For statistics

Github

Project management & version control

Molecular laboratory

DNA + RNA extraction, PCR & HTS

Field sampling

Microbes, plankton, eDNA, eRNA & macroinvertebrates

Publications

Reconstruction of small subunit ribosomal RNA from high-throughput sequencing data: A comparative study of metagenomics and total RNA sequencing
PDF Cite DOI
Reconstruction of small subunit ribosomal RNA from high-throughput sequencing data: A comparative study of metagenomics and total RNA sequencing
Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data
PDF Cite DOI
Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data
Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments
PDF Cite DOI
Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments
Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae)
PDF Cite DOI
Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae)
Using Environmental DNA to Monitor the Reintroduction Success of the Rhine Sculpin (Cottus rhenanus) in a Restored Stream
PDF Cite DOI
Using Environmental DNA to Monitor the Reintroduction Success of the Rhine Sculpin (Cottus rhenanus) in a Restored Stream
Geographic distance and mountain ranges structure freshwater protist communities on a European scalе
PDF Cite DOI
Geographic distance and mountain ranges structure freshwater protist communities on a European scalе

Coding projects

Simply click on a project to access its GitHub repository.

Metagenomics vs. total RNA-Seq for SSU assembly
My second PhD chapter. Comparing metagenomics vs. total RNA-Seq data, including data-processing pipelines, for SSU assembly.
Metagenomics vs. total RNA-Seq for SSU assembly
Predicting environmental stressor levels with machine learning
My third PhD chapter. Predicting environmental stressor levels with machine learning, including a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.
Predicting environmental stressor levels with machine learning
European lakes biodiversity assessments
My Bachelor thesis. Analyzing the biodiversity of 21 European lakes; part of a bigger project to analyze the biodiversity of lakes across Europe, which led to a publication.
European lakes biodiversity assessments
Mitogenome assembly evaluation
Comparing mitochondrial genome assembly and annotation tools as part of a publication on the mitogenomes of biting midges.
Mitogenome assembly evaluation
Metagenomics vs. total RNA-Seq for microbial community analysis
My first PhD chapter. Comparing metagenomics vs. total RNA-Seq data, including data-processing pipelines, for microbial abundance estimations. Involves testing 1,536 combinations of data-processing tools.
Metagenomics vs. total RNA-Seq for microbial community analysis
Super Mario reinforcement learning NN
Training a NN to beat super mario levels using reinforcement learning.
Super Mario reinforcement learning NN
Boxing jab detector - pose estimation
Estimating poses of people in videos or the webcam by detecting joints using a Neural Network. The joints and their connections are then used to predict if a person is doing a boxing jab.
Boxing jab detector - pose estimation
Sentimental analysis GME tweets
Testing if the emotions of GameStop stock (GME)-related tweets were correlated to the GME value during the GME boom on 28th January 2021, based on NLP and part of a Hackathon.
Sentimental analysis GME tweets

Experience

 
 
 
 
 
Bioinformatics Contractor and Consultant
King Abdullah University of Science and Technology (KAUST)
May 2023 – Present Remotely
Processing and analysis of metabarcoding and metagenomics datasets from the Red Sea.
 
 
 
 
 
Scientific Editor
Textcheck Inc.
May 2021 – April 2023 Remotely
Editing the grammar and structure of scientific manuscripts.
 
 
 
 
 
Teaching Coordinator
University of Guelph
February 2021 – March 2021 Guelph, ON Canada
Coordinating a team of Graduate Teaching Assistants.
 
 
 
 
 
Ph.D. in Integrative Biology
Steinke Lab - University of Guelph
January 2019 – December 2022 Guelph, ON Canada
Thesis: Comparing Metagenomics and Total RNA Sequencing for Microbial Identification and Environmental Assessments.
 
 
 
 
 
Laboratory Manager
University of Guelph - Steinke Lab
May 2019 – September 2021 Guelph, ON Canada

Responsibilities included:

  • General laboratory organization
  • Safety supervision
  • Orders
  • Remote server management
 
 
 
 
 
M.Sc. in Biodiversity
Ruhr University Bochum
October 2016 – October 2018 Bochum, Germany
Thesis: Development of an eDNA-based monitoring assay to investigate the dispersal potential of the Rhine sculpin (Cottus rhenanus).
 
 
 
 
 
B.Sc. in Biology
University of Duisburg-Essen
October 2013 – September 2016 Essen, Germany
Thesis: Development of analytical tools for molecular biodiversity assessments.

Contact