Full-Stack Engineer · Palo Alto, California

Furkan M. Torun

I'm a Full-Stack Engineer at Arc Institute with a background in molecular biology and genetics. My career spans every side of life sciences engineering across big pharma at Abbott, market-leading cancer diagnostics at Exact Sciences, a biotech startup, and a research lab.

I integrate cloud architecture, AI/ML and bioinformatics to build scalable platforms for large-scale biological data. — debugging DNA software.

Get in Touch
Furkan M. Torun

Career

Experience

My professional journey

10/2026 — Present

Full-Stack Engineer

Arc Institute — Palo Alto, CA, United States

  • Own and evolve the Virtual Cell Challenge backend, engineering robust authentication, metrics pipelines, and participant analytics.
  • Build and maintain internal genomics platforms, automating NGS sample tracking, submission workflows, and quality control (QC) pipelines.
AI-Driven DevelopmentPythonGoogle CloudData ModelingREST APISSQL
04/2026 — 09/2026

Data Engineer

Abbott — Munich, Germany

  • Led cloud migration for 3 major products from legacy and on-prem environments to a unified AWS setup, enhancing pipeline orchestration, scalability, and reliability.
  • Reduced AWS costs by approximately 60% and cut deployment time ~75% through CI/CD, accelerating data delivery by decommissioning hybrid environments.
AWSTerraformPythonSQLCI/CDBashPackerDataOps
11/2022 — 03/2026

Data Engineer

Exact Sciences — Munich, Germany

  • Designed, implemented, and optimized data pipelines and a web application, reducing pipeline errors by 45% and increasing processing speed by 2.5×.
  • Built and deployed an AWS-based web dashboard that eliminated manual overhead and optimized the usability, tracking, and efficiency of Nextflow bioinformatics workflows.
  • Developed a scalable multi-omics data platform and integrated machine learning models to identify key biological patterns and predictive biomarkers for cancer diagnosis.
PythonAWSTerraformAirflowPackerMLDjangoBiomarker 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

Languages

Python Bash SQL 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

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

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.

Contact

Let's Work Together

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

Email

furkanmtorun[at]gmail[dot]com

Connect

LinkedIn Google Scholar GitHub YouTube X/Twitter
© 2026 Furkan M. Torun. All rights reserved. Palo Alto, CA, US

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