# 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. ## Contact & Links - **Email:** bc8@sanger.ac.uk - **X (Twitter):** [https://x.com/cakirb_](https://x.com/cakirb_) - **LinkedIn:** [https://linkedin.com/in/batuhancakir](https://linkedin.com/in/batuhancakir) - **Bluesky:** [https://bsky.app/profile/cakirb.bsky.social](https://bsky.app/profile/cakirb.bsky.social) - **GitHub:** [https://github.com/cakirb](https://github.com/cakirb) - **Google Scholar:** [https://scholar.google.com/citations?user=iGaYmB4AAAAJ&hl=en](https://scholar.google.com/citations?user=iGaYmB4AAAAJ&hl=en) - **ORCID:** [https://orcid.org/0000-0003-4513-606X](https://orcid.org/0000-0003-4513-606X) 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. ## 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 ### Career - **Senior Bioinformatician** @ Wellcome Sanger Institute (2024 — Present) - 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. - **Bioinformatician** @ Wellcome Sanger Institute (2021 — 2024) - 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. - **Research Assistant** @ Gebze Technical University (2019 — 2021) - 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. - **Visiting Scientist** @ Wellcome Sanger Institute (2019) - Benchmarked single-cell RNA-seq visualisation tools during an internship with the Cellular Genetics Informatics team. ### Education - **PhD at Bioinformatics & Systems Biology** @ Gebze Technical University (2021 — Present) - 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. - **MSc at Bioinformatics & Systems Biology** @ Gebze Technical University (2017 — 2021) - 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. - Completed a research internship at the Wellcome Sanger Institute during the MSc, focusing on single-cell RNA-seq visualisation tools. - **BSc at Bioengineering** @ Yildiz Technical University (2012 — 2016) - 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 ### nf-scautoqc (Pipeline / Nextflow) A reproducible Nextflow pipeline for automated quality control, doublet detection, and the integration of single-cell RNA-seq datasets. - Repository: [https://github.com/cellgeni/nf-scautoqc](https://github.com/cellgeni/nf-scautoqc) ### nf-larry (Pipeline / Nextflow) A reproducible Nextflow pipeline for LARRY barcoding experiments, assigning barcode evidence to cells and generating clone-aware AnnData outputs for downstream analysis. - Repository: [https://github.com/cellgeni/nf-larry](https://github.com/cellgeni/nf-larry) ### nf-cellsnplite (Pipeline / Nextflow) A Nextflow pipeline for running cellsnp-lite on aligned sequencing reads, supporting single-cell genotyping and downstream demultiplexing workflows. - Repository: [https://github.com/cellgeni/nf-cellsnplite/](https://github.com/cellgeni/nf-cellsnplite/) ### CELLxGENE Discover Curation (Resource) 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. - Portal: [https://cellxgene.cziscience.com/](https://cellxgene.cziscience.com/) - Paper: [https://doi.org/10.1093/nar/gkae1142](https://doi.org/10.1093/nar/gkae1142) ### Benchmarking scRNA-seq Visualisation Tools (Benchmarking) Benchmarked single-cell RNA-seq visualisation tools to evaluate their usability, performance, and suitability for exploring large single-cell datasets. Published in NARGAB. - Paper: [https://academic.oup.com/nargab/article/2/3/lqaa052/5877814](https://academic.oup.com/nargab/article/2/3/lqaa052/5877814) ## AI Usage This website was designed and developed with AI assistance under my direction. - **Gemini 3.1 Pro:** Main implementation and iteration support. - **Claude Opus 4.7:** Frontend refinement and visual polish. - **GPT-5.5:** Analytics additions, copy refinement, and final content review.