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James M. Ferguson

Bioinformatician

I am a bioinformatician specialising in genomic technologies, real-time nanopore sequencing, signal analysis, machine learning, and associated hardware. I have a background in software development and more than a decade of pathology industry experience.

Research Interests

I am a Genomic Systems Analyst at the Garvan Institute with a background in clinical pathology testing, algorithms and software development. Leading computational development within the Centre for Population Genomics' Genomic Technologies Group, I apply my unique skills to develop new bioinformatic tools, as well as design and support nanopore sequencing infrastructure.

My research areas include:

  • Nanopore signal analysis

  • Clinical testing and method development

  • Short tandem repeat disorders

  • Viral genomics (HIV/SARS-Cov-2)

  • Single-cell sequencing

  • Direct RNA Sequencing

  • Genome assembly

  • Methylation detection

  • Machine/Deep learning

Contact

Publication Highlights

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Ferguson, J. M. and M. A. Smith (2019). "SquiggleKit: a toolkit for manipulating nanopore signal data." Bioinformatics 35(24): 5372-5373.

Smith, M. A., T. Ersavas, J. M. Ferguson, H. Liu, M. C. Lucas, O. Begik, L. Bojarski, K. Barton and E. M. Novoa (2020). "Molecular barcoding of native RNAs using nanopore sequencing and deep learning." Genome Res 30(9): 1345-1353.

Ferguson, J. M., H. Gamaarachchi, T. Nguyen, A. Gollon, S. Tong, C. Aquilina-Reid, R. Bowen-James and I. W. Deveson (2021). "InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses." Bioinformatics.

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