Harun Mustafa

Harun Mustafa

Assistant research scientist in the Salzberg Lab at the Center for Computational Biology

Research Experience

Assistant research scientist and postdoctoral fellow in biomedical engineering

Salzberg Lab, Center for Computational Biology, Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA

10.2026 – Present

  • PI: Prof. Steven Salzberg
  • Postdoctoral fellowship (10.2025 – 09.2026); Assistant research scientist (09.2026 – Present)
  • Improving microbiome analysis by computationally removing contaminants from reference sequence databases
  • Development of novel algorithms for whole-genome alignment of human genome assemblies

Established researcher and postdoctoral fellow in biomedical informatics

Biomedical Informatics Group, Department of Computer Science, ETH Zurich, Zürich, Switzerland

01.2023 – 08.2025

  • PI: Prof. Gunnar Rätsch
  • Co-Supervisor: Dr. André Kahles
  • Postdoctoral fellowship (01.2023 – 12.2024); Established researcher (01.2025 – 08.2025)
  • Development of scalable statistical methods for reference-free differential sequence marker assembly in association studies
  • Search and indexing methods for large-scale biological sequence data

Doctoral researcher in biomedical informatics

Biomedical Informatics Group, Department of Computer Science, ETH Zurich, Zürich, Switzerland

02.2017 – 12.2022

  • PI: Prof. Gunnar Rätsch
  • Co-Supervisor: Dr. André Kahles
  • Development of methods for efficient graph representations and analysis of biological sequence data

Master's researcher in computational biology

Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

10.2015 – 12.2016

  • PIs: Prof. Sven Panke, Prof. Jörg Stelling
  • Supervisors: Sabine Oesterle, Lukas Widmer
  • Computational prediction of sites in proteins permissive to internal tagging

Master's researcher in computational systems biology

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

04.2015 – 09.2015

  • Supervisors: Prof. Jörg Stelling, Prof. Sven Panke, Prof. Yaakov Benenson, Prof. Savas Tay
  • Member of the ETH Zurich team competing in the 2015 International Genetically Engineered Machine (iGEM) competition
  • 3D spatiotemporal reaction-diffusion modelling for the circulating tumour cell detection system MicroBeacon

Undergraduate researcher in computational biology

Computational Biology Lab, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

05.2012 – 08.2014

  • PI: Prof. Michael Brudno
  • Co-Supervisor: Dr. Matei David
  • Helped develop the novel Alu insert detection tool alu-detect
  • Assembly and analysis of novel Alu inserts from high-throughput sequencing reads

Undergraduate researcher in computational life sciences

Department of Chemical Informatics, University of Szeged, Szeged, Hungary

05.2011 – 05.2012

  • PI: Prof. Imre G. Csizmadia
  • Co-Supervisor: Prof. Béla Viskolcz
  • Title: “Conformational and thermodynamic analysis of tyrosyl dipeptide radicals generated by side chain-centred hydrogen abstraction: A computational study”

Undergraduate researcher in computational chemistry

Department of Chemistry, University of Toronto; Global Institute of Computational Molecular and Materials Science, Toronto, Ontario, Canada

09.2010 – 05.2012

  • PI: Prof. Imre G. Csizmadia
  • Co-Supervisor: Dr. Sinisa Vukovic
  • Title: “Selenium glycoside as a delivery vehicle for selenium supplements”