- Working across single-cell genomics projects, with a focus on computational processing, quality control, and reproducible workflow execution.
- Building, running, and improving workflows for large-scale single-cell data, including contributions to nf-scautoqc.
- Helping research teams turn complex sequencing datasets into reliable outputs for downstream biological interpretation.
Batuhan Çakır
Senior Bioinformatician and PhD Candidate
I work across single-cell genomics projects, building and running reproducible analysis workflows while exploring lineage tracing and cell-state dynamics.
About Me.
I’ve been interested in computers from an early age, and I always knew they would shape my future. My interest in coding began during my undergraduate studies, when a MATLAB course made me realise how much I enjoyed solving problems through programming.
That interest became a clear path when I started my MSc in Bioinformatics and Systems Biology in 2017. During that time, I built my foundations in Python and R and was introduced to bioinformatics in a way that immediately clicked with me. Working on single-cell RNA-seq and trajectory-focused projects showed me that I had found the field I wanted to grow in.
Since then, my work has focused on the space between coding and biology, with particular interests in single-cell genomics, lineage tracing, and reproducible analysis workflows. My path has taken me from academic research in Turkey to the Wellcome Sanger Institute, where I now work as a Senior Bioinformatician while continuing my PhD. Across these roles, what has stayed constant is my enjoyment of building useful computational tools and continuing to grow through the work I do.
Experience.
2024 — Present
Senior Bioinformatician
Wellcome Sanger Institute
2021 — 2024
Bioinformatician
Wellcome Sanger Institute
- Supported the curation of datasets for the CZ CELLxGENE Discover portal and contributed to project-specific resources for data access and visualisation.
- Contributed to collaborative single-cell projects across data analysis, curation, and workflow support.
2021 — Present
PhD at Bioinformatics & Systems Biology
Gebze Technical University
- Studying lineage-tracing data with a focus on computational analysis, clonal dynamics, and LARRY barcoding.
- Developing workflows including nf-larry and nf-cellsnplite as part of ongoing thesis work.
2019 — 2021
Research Assistant
Gebze Technical University
- Contributed to research projects in bioinformatics and structural biology.
- Supported teaching in courses including Biostatistics and Heat and Mass Transfer, helping with coursework assessment, quizzes, and student support.
2019
Visiting Scientist
Wellcome Sanger Institute
- Benchmarked single-cell RNA-seq visualisation tools during an internship with the Cellular Genetics Informatics team.
2017 — 2021
MSc at Bioinformatics & Systems Biology
Gebze Technical University
- Worked on single-cell RNA-seq analysis in stem cell differentiation.
- Thesis: Mathematical Modelling of Molecular Trajectories in Stem Cell Transformation Processes via Bioinformatic Analysis of Single Cell Omics Data (manuscript in review)
- Completed a research internship at the Wellcome Sanger Institute during the MSc, focusing on single-cell RNA-seq visualisation tools.
2012 — 2016
BSc at Bioengineering
Yildiz Technical University
- Built an interdisciplinary foundation through coursework spanning molecular biology, genetics, engineering, and bioengineering, with additional exposure to areas such as virology and immunology.
Selected Work.
PIPELINE / NEXTFLOW
nf-scautoqc
A reproducible Nextflow pipeline for automated quality control, doublet detection, and the integration of single-cell RNA-seq datasets.
View Repository →PIPELINE / NEXTFLOW
nf-larry
A reproducible Nextflow pipeline for LARRY barcoding experiments, assigning barcode evidence to cells and generating clone-aware AnnData outputs for downstream analysis.
View Repository →PIPELINE / NEXTFLOW
nf-cellsnplite
A Nextflow pipeline for running cellsnp-lite on aligned sequencing reads, supporting single-cell genotyping and downstream demultiplexing workflows.
View Repository →RESOURCE
CELLxGENE Discover Curation
Contributed to the curation of COVID-19 Cell Atlas datasets for the CELLxGENE Discover portal, helping make single-cell resources easier to access, explore, and reuse.
BENCHMARKING
Benchmarking scRNA-seq Visualisation Tools
Benchmarked single-cell RNA-seq visualisation tools to evaluate their usability, performance, and suitability for exploring large single-cell datasets. Published in NARGAB.
Read Paper →Say Hello
Whether it’s about computational biology, reproducible workflows, single-cell analysis, a shared project idea, or just saying hello, I’m always happy to hear from you.