Data Engineer · Munich, Germany

Furkan M. Torun

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

My work integrates cloud computing, data science, bioinformatics and machine learning to build scalable and cloud-native products to analyze large-scale omics datasets. — debugging DNA software.

Get in Touch

Career

Experience

My professional journey

11/2022 — Present

Data Engineer

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.

PythonAWSTerraformPackerAirflowMLDjangoBashBiomarker Discovery

06/2020 — 05/2022

Data Scientist

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.

PythonMachine and Deep LearningStatisticsDockerFlaskREST APIsSQLCI/CD

02/2018 — 01/2020

Computational Biologist

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.

BioinformaticsGenomicsJavaScriptPHPSQLBashHTML/CSSGit

Speaking

Talks

Conference presentations and meetup talks

View Recordings on YouTube

21 May 2024

Become a Data Storyteller with Streamlit

PyMunich Meetup — Munich, Germany

20 Nov 2023

Become a Data Storyteller with Streamlit

PyData Meetup — Prague, Czech Republic

16 Sep 2023

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

PyCon CZ — Prague, Czech Republic

26 Jul 2023

Organizer & Moderator: Bits in Bio | July Edition

Bits in Bio — Munich, Germany

22 Jun 2023

Application of machine learning on biological datasets

Munich DataGeeks Meetup — Munich, Germany

7 Jun 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 Jun 2019

ConVarT poster presentation at ESHG

52nd European Human Genetics Conference (ESHG'19) — Gothenburg, Sweden

Research

Publications

Research contributions and scientific publications

Google Scholar

2022 1st Author

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 | Featured on the cover of the February 2023 issue.

2022

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

2021

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

2021 1st Author

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

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

Bioinformatics Advances

Recognition

Honors & Awards

Academic and professional achievements

February 2023

Paper Featured on Journal Cover

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).

Tools

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

Cloud & Infrastructure

AWS Terraform Packer Docker CI/CD

Bioinformatics

Genetics/Genomics Biomarker Discovery Variant Calling & Annotation RNA-Seq CLI/GUI Tool & Platform Development

Web Development

Flask Django HTML/CSS jQuery

DevOps & Tools

REST & GraphQL APIs SQL/NoSQL Databases Airflow Celery DVC BDD Git Agile/Scrum

Machine / Deep Learning

Scikit-learn XGBoost/LGBM PyTorch

Community

Volunteering

Community involvement and leadership

Organizer

04/2023 — 07/2024