Hey, I'm Furkan 👋

I'm a Data Engineer at Exact Sciences, with a background in molecular biology and genetics, and I have previously worked at a research lab and a biotech startup.

My work integrates data science, machine learning, and cloud computing to analyze large-scale omics datasets and deliver actionable biological insights — view my publications.

I also develop open-source tools for bioinformatics and build scalable, cloud-native data products — explore my projects.

So, let's continue 🧬 debugging DNA software!

Munich, Bavaria, Germany
Furkan M. Torun
Furkan M. Torun
Get in Touch

Experience

My professional journey

Data Engineer

11/2022 — Present • 2+ years
Exact Sciences — Munich, Germany
  • Design, implement, and optimize scalable data pipelines on AWS for advanced proteomics data analysis and governance.
  • Create cloud-based web dashboards on AWS to streamline experimental workflows.
  • Implement and fine-tune machine learning models for large-scale omics data analysis.
  • Develop omics data platform to drive biomarker discovery and advance cancer research.
Python AWS Terraform Packer Airflow ML Django Bash Biomarker Discovery

Data Scientist

06/2020 — 05/2022 • 2 years
OmicEra Diagnostics — Munich, Germany
  • Built a comprehensive real-time quality control pipeline and monitoring dashboard for mass spectrometry-based proteomics.
  • Developed OmicLearn, an open-access, user-friendly ML platform for omics data.
  • Applied machine learning and deep learning techniques to proteomics data for biomarker discovery.
  • Published two scientific papers, including one as the first author.
Python Machine and Deep Learning Statistics Docker Flask REST APIs SQL CI/CD

Computational Biologist

02/2018 — 01/2020 • 2 years
Rare Disease Lab — Kayseri, Turkey
  • Created end-to-end bioinformatics pipelines for comparative genomics analysis.
  • Built ConVarT, a search engine for missense variants across humans and other organisms.
  • Developed MSABrowser, a JavaScript library for visualizing sequence alignments.
  • Published two scientific papers, including one as the first author.
Bioinformatics/Computational Biology JavaScript PHP SQL Bash HTML/CSS Git

Talks

Conference presentations and speaking engagements

View Recordings on YouTube
21 May 2024

Become a Data Storyteller with Streamlit →

PyMunich Meetup — Munich, Germany

20 November 2023

Become a Data Storyteller with Streamlit →

PyData Meetup — Prague, Czech Republic

16 September 2023

How to Build an Open-Source ML Platform in Biology? →

PyCon CZ — Prague, Czech Republic

26 July 2023

Organizer & Moderator: Bits in Bio | July Edition →

Bits in Bio — Munich, Germany

22 June 2023

Application of machine learning on biological datasets →

Munich DataGeeks Meetup — Munich, Germany

7 June 2023

Application of machine learning on biological datasets →

PyLadies Meetup — Munich, Germany

28 May 2023

How to Build an Open-Source ML Platform in Biology? →

PyCon IT — Florence, Italy

15-18 June 2019

ConVarT poster presentation at ESHG →

52nd European Human Genetics Conf. — Gothenburg, Sweden

Publications

Research contributions and scientific publications

View Publications on Google Scholar

Transparent exploration of machine learning for biomarker discovery from proteomics and omics data →

Torun, F.M., Winter, S.V., Doll, S., Riese, F.M., Vorobyev, A., Mueller-Reif, J.B., Geyer, P.E., & Strauss, M.T.

Journal of Proteome Research • DOI: 10.1021/acs.jproteome.2c00473

2022 First Author Featured on the cover of the February 2023 issue of the journal →

ConVarT: a search engine for matching human genetic variants with variants from non-human species →

Pir, M.S., Bilgin, H.I., Sayici, A., Coskun, F., Torun, F.M., Zhao, P., Kang, Y., Cevik, S., Kaplan, O.I.

Nucleic Acids Research • DOI: 10.1093/nar/gkab939

2022

High‐resolution serum proteome trajectories in COVID‐19 reveal patient‐specific seroconversion →

Geyer, P., Arend, F., Doll, S., Louiset, M., Virreira Winter, S., Mueller-Reif, J. & Torun, F.M. et al.

EMBO Molecular Medicine • DOI: 10.15252/emmm.202114167

2021

MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations →

Torun, F.M., Bilgin, H.I. and Kaplan, O.I.

Bioinformatics Advances • DOI: 10.1093/bioadv/vbab009

2021 First Author

Honors

Recognition and achievements

February 2023

Journal Cover Feature

My first-authored paper OmicLearn is featured on the cover of Journal of Proteome Research.

June 2022

Academic Excellence

Graduated with a high honor degree (3.63/4.00) and 1st ranked in Faculty of Life and Natural Sciences.

May 2022

Researcher Travel Fellowship

Received the Travel Fellowship by Open Bioinformatics Foundation (OBF).

Tech Stack

Technologies and tools I work with

Core Skills
Data Science / Engineering, Amazon Web Services (AWS),
Machine Learning, Omics, Bioinformatics / Computational Biology
Programming Languages
Python, Bash, JavaScript
Web Development
Flask, Django, HTML/CSS, jQuery
Cloud and IaC
AWS, Terraform, Packer
Machine/Deep Learning
Scikit-learn, XGBoost/LGBM, PyTorch
Others
Docker, REST and GraphQL APIs, SQL/NoSQL Databases, Airflow, Celery,
CI/CD (Github Actions/GitLab Pipelines), DVC, BDD, Agile/Scrum Methodology
Bioinformatics
Genetics/Genomics, Biomarker discovery, Variant calling & annotation,
RNA-Seq, CLI/GUI tool and database/platform development

Volunteering

Community involvement and leadership

Organizer

04/2023 — 07/2024 • 1+ year
Bits in Bio — Munich, Germany

Brought everyone interested in biotechnology, management, bioinformatics, or software in life sciences together with regular in-person events and sponsored meetups.

Co-founder

08/2018 — 01/2020 • 1.5 years
Rare Diseases — Kayseri, Turkey

Established the platform and led the team for an open-access database about rare diseases in Turkish and creating public awareness.

Let's Work Together

I'm always interested in new opportunities, exciting projects and
giving talks in conferences/events.

Email

furkanmtorun@gmail.com

Connect


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