Harun Mustafa

Harun Mustafa

Postdoctoral fellow in the Salzberg Lab at the Center for Computational Biology

Research Experience

Postdoctoral fellow in biomedical engineering

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

10.2025 – Present

  • PI: Prof. Steven Salzberg
  • Improving microbiome analysis by computationally detecting and removing contaminants from microbial sequence databases.
  • Development of novel algorithms for whole-genome alignments of human genome assemblies

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
  • 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.

Dr. sc. candidate 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.

Postgraduate 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
  • 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”