Alex El-Shaikh
Technical CV Academic CV

Software Architect & Senior Software Engineer

Dr. Alex El-Shaikh

I design and build scalable backend systems from architecture to delivery, combining Java/Spring Boot engineering, AWS cloud services, database systems, and technical project coordination.

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7+ years Scalable, data-intensive systems
Java / Spring Boot Production backend architecture
AWS + databases Cognito, S3, Aurora, PostgreSQL, MariaDB
5 publications DNA storage and database systems

Engineering Focus

Architecture, data, and delivery with research depth.

A practical backend profile shaped by production systems, academic database research, and repeated coordination across requirements, implementation, testing, and release.

Backend architecture visual with cloud, service stack, and API endpoint Systems

Scalable backend architecture

Java/Spring Boot services, REST APIs, cloud integrations, batch processing, and maintainable modular design.

Database visual with central data store and pipeline elements Data

Database-heavy applications

Relational and NoSQL systems, ETL pipelines, query optimization, indexing, and TB-scale research data.

Delivery coordination visual with blueprint and task tiles Delivery

Technical coordination

Requirements analysis, architecture decisions, code reviews, mentoring, and Scrum/Kanban collaboration.

DNA data storage visual with helix and data cube Research

Product-minded research depth

DNA data storage, distributed systems, scientific software, and translating complex domains into usable systems.

Career

Selected experience

Apr 2026 - present

Senior Software Engineer

Frankfurt am Main, Germany

  • Design scalable Java/Spring Boot backends in AWS environments.
  • Integrate Cognito, S3, Aurora, PostgreSQL, and MariaDB into production systems.
  • Drive architecture decisions, performance improvements, code reviews, and testing quality.
Modern backend and cloud architecture workspace visual
Feb 2025 - Mar 2026

Postdoctoral Researcher

Imperial College London, Department of Computing

  • Led scalable database and distributed-system architecture work.
  • Improved performance by up to 50% through query, architecture, and concurrency tuning.
  • Worked with TB-scale data, containerized services, teaching, and student supervision.
Modern academic campus scene representing Imperial College London
2019 - 2024

Research Fellow & PhD Candidate

Philipps University Marburg

  • Completed PhD research on random access for DNA data storage systems, grade 1.0.
  • Built REST services with Spring Boot and FastAPI for international research partners.
  • Worked on NFDI4Biodiversity, ETL pipelines, S3-compatible APIs, and database systems.
Modern university town campus scene representing the University of Marburg
Mar 2014 - Oct 2019

Teaching & Research Assistant

Philipps University Marburg

  • Supported programming labs, software engineering practicals, and student groups.
  • Tutored Java, OOP, algorithms, logic, mathematics, and database systems.
University programming lab with students and tutoring support

Academic Foundation

Education

2019 - 2024

PhD in Computer Science

Philipps University Marburg

  • Dr. rer. nat., grade 1.0.
  • Dissertation: Implementing random access on DNA data storage systems.
2016 - 2019

M.Sc. Computer Science

Philipps University Marburg

  • Thesis: Lightweight Indexing on Data Streams, grade 1.3.
  • Minor in economics and ERASMUS semester at Aalto University in Helsinki.
2012 - 2015

B.Sc. Computer Science

Philipps University Marburg

  • Thesis: Android game with interactive water simulation, grade 1.3.
  • Minor in business administration.

Research

Publications

2026
Under Review

An Economic Analysis of DNA-based Data Storage Systems

Alex El-Shaikh, Bernhard Seeger, Thomas Heinis

BibTeX 
@article{El-Shaikh2026economic,
  author={El-Shaikh, Alex and Seeger, Bernhard and Heinis, Thomas},
  title={An Economic Analysis of DNA-based Data Storage Systems},
  year={2026},
  note={Under Review}
}
2023
Scientific Reports

Content-based filter queries on DNA data storage systems

Alex El-Shaikh, Bernhard Seeger

DOI PDF
BibTeX 
@article{El-Shaikh2023query,
  author={El-Shaikh, Alex and Seeger, Bernhard},
  title={Content-based filter queries on DNA data storage systems},
  journal={Scientific Reports},
  year={2023},
  volume={13},
  number={1},
  pages={7053},
  doi={10.1038/s41598-023-34160-5},
  url={https://doi.org/10.1038/s41598-023-34160-5}
}
2023
BTW 2023

DNAContainer: An object-based storage architecture on DNA

Alex El-Shaikh, Bernhard Seeger

DOI PDF
BibTeX 
@incollection{El-Shaikh2023container,
  author={El-Shaikh, Alex and Seeger, Bernhard},
  title={DNAContainer: An object-based storage architecture on DNA},
  year={2023},
  booktitle={BTW 2023},
  publisher={Gesellschaft fuer Informatik e.V.},
  address={Bonn},
  pages={773--795},
  doi={10.18420/BTW2023-50}
}
2023
Datenbank-Spektrum

An Extension of DNAContainer with a Small Memory Footprint

Alex El-Shaikh, Bernhard Seeger

DOI PDF
BibTeX 
@article{El-Shaikh2023smf,
  author={El-Shaikh, Alex and Seeger, Bernhard},
  title={An Extension of DNAContainer with a Small Memory Footprint},
  journal={Datenbank-Spektrum},
  year={2023},
  doi={10.1007/s13222-023-00460-3}
}
2022
NAR Genomics and Bioinformatics

High-scale random access on DNA storage systems

Alex El-Shaikh, Marius Welzel, Dominik Heider, Bernhard Seeger

DOI PDF
BibTeX 
@article{El-Shaikh2022random,
  author={El-Shaikh, Alex and Welzel, Marius and Heider, Dominik and Seeger, Bernhard},
  title={High-scale random access on DNA storage systems},
  journal={NAR Genomics and Bioinformatics},
  year={2022},
  doi={10.1093/nargab/lqab126}
}

Academic Work

Talks, awards, and service

Academic work connecting database architecture, random access, query processing, and biochemical constraints for DNA-based storage systems.

Talks

Invited and conference presentations

Ain Shams University, Cairo

Invited talk on DNA as an alternative medium for data storage, including cost and long-term viability.

BTW 2023, TU Dresden

Presented DNAContainer and received the Best Workshop Paper Award at the NoDMC Workshop.

DSMM 2022, University of Marburg

Presented high-scale random access for emerging DNA data storage systems.

Awards

Research recognition

Best Paper

NoDMC Workshop, BTW 2023 for DNAContainer: an object-based storage architecture on DNA.

Editor's Choice

NAR Genomics and Bioinformatics selection for high-scale random access on DNA storage systems.

Service

Reviewing, supervision, and academic support

Peer Review

Trends in Biotechnology Nature Communications Scientific Reports Briefings in Bioinformatics BMC Bioinformatics npj Microgravity Archives of Computational Methods in Engineering Egyptian Journal of Forensic Sciences Computational and Structural Biotechnology Journal

Supervision

Bachelor projects Master projects Graduation projects Programming projects Exercise classes Tutorials

Mentoring

Teaching

Lectures

  • Relational Database Systems - University of Marburg
  • NoSQL Databases - University of Marburg
  • Geo Databases - University of Marburg
  • Implementing Database Systems - University of Marburg
  • Efficient Algorithms - University of Marburg
  • NoSQL Databases: MongoDB - Imperial College London
  • NoSQL Databases: Neo4j - Imperial College London

Exercise Sessions

Database Systems NoSQL Software Engineering Algorithms OOP Programming internships Logic Linear Algebra Analysis Geo-databases
University lecture room with a lecturer facing a database architecture diagram
I enjoy breaking down complex topics into understandable concepts and seeing students grow through engagement and collaboration.

Technical Range

Skills

Programming Languages

JavaPythonSQLRustC#C++RKotlinScalaJavaScriptLuaPrologJuliaHaskell

Frameworks & Tools

Spring BootAWSAmazon CognitoS3MavenDockerKubernetesGitLinuxJUnitPandasFastAPIREST APIsJDBCjOOQJPAKafkaCI/CD

Database Systems

PostgreSQLAmazon AuroraMariaDBMongoDBElasticsearchNeo4jRedisSparkHBase

Engineering Focus

Software architectureBackend systemsREST APIsData processingETL pipelinesPerformance tuningConcurrencyRefactoringClean CodeTesting

Methods & Coordination

Requirements engineeringSystem analysisTechnical project coordinationArchitecture decisionsScrumKanbanMentoringCode reviews

Spoken & Written Languages

German - nativeArabic - nativeEnglish - C1