Bioinformatics · Computational biology · Biostatistics

Bartosz Czech, PhD, Eng.

Bioinformatician and computational biologist

Assistant Professor at Wrocław University of Environmental and Life Sciences · Senior Bioinformatician in pharmaceutical R&D · Founder of GeneStat

Wrocław, Poland

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14 peer-reviewed articles

134 citations

7 h-index

7 years in pharma R&D

Citation counts from OpenAlex, updated 2026-11-06. Google Scholar counts are usually higher.

About

I am a bioinformatician and computational biologist. I analyse sequencing, mass spectrometry and drug screening data, build statistical models that answer biological questions, and write R packages and pipelines that make these analyses repeatable. My methods do not depend on the organism: I have worked with data from human cancer cell lines, cattle, chickens, cats, dog cells infected with influenza virus, and gut bacteria.

Current roles

Since May 2026

Assistant Professor

Department of Genetics, Wrocław University of Environmental and Life Sciences. Research in bioinformatics and computational biology; teaching bioinformatics and biostatistics.

Since July 2019

Senior Bioinformatician

Pharmaceutical R&D, contracted through 7N. Drug response screens, NGS and phosphoproteomics data, R/Shiny applications and WDL pipelines.

Since 2019 · own company

Founder, GeneStat

Bioinformatics and statistics services for research groups and companies: sequencing and spatial transcriptomics data, statistical analysis of experiments, written reports.

Research

Sequencing data analysis

Whole-genome and targeted sequencing, variant calling, bulk and single-cell RNA-seq, small RNA-seq and 16S rRNA. I take the data from raw reads through quality control and alignment to statistical tests.

Multi-omics integration

Combining data types to explain one biological process, for example host gene expression with gut microbiome profiles. I also analyse mass spectrometry phosphoproteomics.

Statistical modelling and machine learning

Dose-response models for drug screens and drug combinations, mixed models and association studies, and supervised and unsupervised learning.

All publications →

Selected work

R package

ggwas

ggplot2 plots for GWAS summary statistics: Manhattan, QQ, Miami, locus zoom, PheWAS and more. Submitted to Bioconductor.

Nature Communications · 2025

Resistance to TEAD inhibitors

Joint activation of the Hippo and MAPK pathways makes cancer cells resistant to TEAD inhibition. I processed the drug screen data with the gDR package.

Frontiers in Microbiology · 2022 · first author

Host transcriptome and microbiome integration

Co-expression networks connect host RNA-seq with 16S rRNA profiles of gut bacteria to describe the response to heat stress.

Skills

Sequencing and omics data

WGS and WESVariant callingStructural variants and gene fusionsBulk RNA-seqSingle-cell RNA-seqSpatial transcriptomics (Visium HD)Small RNA-seqChIP-seqATAC-seq and scATAC-seqEpigenomics16S rRNA and metagenomicsGenome annotationComparative and population genomics

Drug discovery and proteomics

Dose-response modellingDrug combinations and synergyHigh-throughput screensCRISPR screensMS phosphoproteomicsKinase activity (KSEA)Pathway and enrichment analysisNetwork biologyStructural biology

Statistics and machine learning

Linear and mixed modelsGWAS and statistical geneticsStudy design and power analysisMulti-omics integrationExploratory data analysisSupervised and unsupervised learningDeep learningFeature engineeringscikit-learncaretTensorFlow and KerasPyTorch

Programming and visualisation

RR packages (Bioconductor)ShinyPythonBash, sed, AWKSQLGit, GitHub, GitLabggplot2PlotlySeabornDashR Markdown and QuartoJupyterLaTeXREST APIs

Pipelines, infrastructure and data

WDL pipelinesHPC and SlurmLinuxAWSDockerKubernetesCondaSnowflakeMySQL and SQLiteDatabase designFAIR dataMetadata management

Collaboration and delivery

ScrumProduct ownershipJiraTrelloReports for non-specialistsScientific writingTechnical documentationTeaching and training

Path

1. 2014BSc in BioinformaticsWrocław University of Environmental and Life Sciences
2. 2017MSc in BioinformaticsBiostatistics and bioinformatics programming
3. 2018NGS internshipAarhus University, Denmark
4. 2019Pharma R&D, GeneStat, PhDSenior bioinformatician via 7N; own company; doctoral studies
5. 2024PhD in Biological SciencesWrocław University of Environmental and Life Sciences
6. 2025MBA in Healthcare ManagementPoznan University of Medical Sciences, in progress
7. 2026Assistant ProfessorDepartment of Genetics, Wrocław University of Environmental and Life Sciences

Teaching

I teach bioinformatics and biostatistics to bioinformatics and biology students at Wrocław University of Environmental and Life Sciences. Slides, worksheets and datasets are public (course pages in Polish; Coding Lab in English).

Biostatistics

Statistical thinking and tests for biologists, with R.

Data Analysis

Machine learning in R and Python for bioinformatics students.

Computer Lab

The Unix command line and shell tools for biological data.

Coding Lab

Erasmus+ course in English: Linux, Bash, AWK, Conda and Docker.

Contact and collaboration

I am open to collaboration on sequencing and multi-omics projects. Academic projects run through the university, commercial analyses through GeneStat. Write to me with a short description of your data and the question you want to answer.

bartosz.w.czech@gmail.com bartosz.czech@upwr.edu.pl

Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland