Dr Jamie Alnasir M.Pharm (Hons) Ph.D. - Research Publications and Conference Contributions

Research Publications and Scholarly Outputs

Recently-Accepted Journal Articles

Alnasir, J. J. (2026). “Twelve Quick Tips for Designing AI-driven HPC Workflows.” PLOS Computational Biology. Accepted for publication. Preprint: arXiv:2606.07491.

Peer-Reviewed Journal Articles

Alnasir, J. J., Heinis, T., and Sokolovskii, R. (2023). “Survey of Information Encoding Techniques for DNA.” ACM Computing Surveys. doi: 10.1145/3626233.
Alnasir, J. J. and Shanahan, H. P. (2023). “Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq.” Journal of Computational Biology, 30(2), 131–148. doi: 10.1089/cmb.2021.0476.
Alnasir, J. J. (2022). “Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19.” Advances in Distributed Computing and Artificial Intelligence Journal, 11(1), 9–43. doi: 10.14201/adcaij.27337.
Alnasir, J. J. (2021). “Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster.” PLOS Computational Biology, 17(8), e1009207. doi: 10.1371/journal.pcbi.1009207.
Austen, B., Duberly, K., Alnasir, J. J., Dabhi, S., and Wijesiriwardana, N. (2019). “Cyclisation of Cell-Penetrating PDZ-Binding Peptides Directed to PSD95.” American Research Journals of Chemistry, 3(1), 1–11.
Alnasir, J. J. and Shanahan, H. P. (2018). “The Application of Hadoop in Structural Bioinformatics.” Briefings in Bioinformatics, bby106. doi: 10.1093/bib/bby106. [ Read ]
Alnasir, J. J. and Shanahan, H. P. (2018). “Transcriptomics: Quantifying non-uniform read distribution using MapReduce.” International Journal of Foundations of Computer Science, 29(8), 1355–1372. [ Read ]
Alnasir, J. J. and Shanahan, H. P. (2017). “A Novel Method to Detect Bias in Short Read NGS Data.” Journal of Integrative Bioinformatics, 14(3). [ Read ]
Alnasir, J. J. and Shanahan, H. P. (2015). “Investigation into the Annotation of Protocol Sequencing Steps in the Sequence Read Archive.” GigaScience, 4(1), Article 23. [ Read ]

Preprints and Working Papers

Alnasir, J. J. (2025). “Reimagining the Traditional Flight Computer: E6BJA as a Modern, Multi-Platform Tool for Flight Calculations and Training.” arXiv preprint, arXiv:2512.23055.
Alnasir, J. J. and Heinis, T. (2022). “DNA Storage Error Simulator: A Tool for Simulating Errors in Synthesis, Storage, PCR and Sequencing.” arXiv preprint, arXiv:2205.14437.

Conference Presentations, Abstracts and Posters

Alnasir, J. J. (2021). “Encoding Information into DNA.” Conference presentation at Mathematical Foundations in Bioinformatics (MatBio '21), King's College London, London, United Kingdom.
Alnasir, J. J. (2019). “Fostering Reproducibility, Standardisation, Fault-tolerance and Deployability in Computational Pipelines using Nextflow Workflow Language – Adoption and Training at the ICR.” Conference presentation at Mathematical Foundations in Bioinformatics (MatBio '19), King's College London, London, United Kingdom.
Alnasir, J. J. and Shanahan, H. P. (2016). “Transcriptomics: Leveraging a MapReduce algorithm and Python for gene-expression analysis on Apache Spark.” Conference presentation at Mathematical Foundations in Bioinformatics (MatBio '16), London, United Kingdom.
Alnasir, J. J. and Shanahan, H. P. (2016). “Transcriptomics on Spark Workshop – Introducing Hercules – an Apache Spark MapReduce algorithm for quantifying non-uniform gene expression.” Workshop contribution at CloudTech '16, Marrakech, Morocco.
Alnasir, J. J. (2016). “Hercules / MapReduce / Transcriptomics.” Abstract presented at the Royal Holloway Computer Science Annual Research Colloquium. Editor and co-organiser.
Alnasir, J. J. (2015). “Applying Apache Hadoop, Hive and Map Reduce to Legacy Systems and Applications.” Invited one-hour conference talk at Mediterranean Space of Technology and Innovation (MSTI) Innovation Week 2015, ENSIAS, Rabat, Morocco.
Alnasir, J. J. and Shanahan, H. P. (2015). “PDB-Hadoop: Parallelising user applications on the Protein Data Bank using Apache Hadoop.” Poster presented at 3DSig Structural Bioinformatics and Computational Biophysics 2015, Dublin, Ireland.
Alnasir, J. J. (2015). “PDB-Hadoop / Legacy Applications on the PDB.” Abstract presented at the Royal Holloway Computer Science Annual Research Colloquium.
Alnasir, J. J. (2014). “Illumina / SRA Meta-data Annotation.” Abstract presented at the Royal Holloway Computer Science Annual Research Colloquium. Co-organiser.
Alnasir, J. J. and Austen, B. (2011). “Characterisation of Cyclic Neuroprotective PDZ-binding Ligands.” Poster presented at the Royal Society of Chemistry Protein and Peptide Science Group Early Stage Researcher Meeting, London, United Kingdom; subsequently presented at St George's Research Day.

Theses

Alnasir, J. J. (2018). “The Analysis of High-throughput Biological Datasets Utilising Cloud Computing.” Ph.D. thesis, Royal Holloway, University of London. Supervisors: Prof. Hugh Shanahan and Prof. Gregory Gutin.
Alnasir, J. J. (2011). “Characterisation of Cyclic Neuroprotective PDZ-binding Ligands.” M.Pharm thesis, Kingston University and St George's Hospital Medical School. Supervisor: Prof. Brian Austen.

Software, Computational Tools and Digital Platforms

E6BJA / Jamie's Flight Computer. Multi-platform aviation computation and training software conceived and developed by Dr Alnasir, with approximately 20,000 active users, including pilots and professional flight planners, across iOS/iPadOS, Android and Windows, and a further approximately 8,000 users of the Lite edition. This Comprehensive Flight Computer demonstrates sustained translation of computational methods into a safety-conscious operational domain.
AirWeatherNOTAM. Aviation weather and NOTAM information platform developed for pilot flight-planning and operational information workflows. Approximately 2,500 users. Distributed through Google Play for Android.
CliniCompute. Educational medical calculation software developed for clinical and healthcare education contexts. Approximately 1,000 users across iOS/iPadOS and Android. Distributed through the Apple App Store and Google Play.
Zeus Molecular Visualiser. Molecular visualisation software for Android supporting structural and computational biology applications. The current release has approximately 100 users; an earlier release reached approximately 1,000 users before being replaced by a new app-store version. Distributed through Google Play.
Choose-Survey. Research software platform developed at Royal Holloway, University of London, supporting academic research and participant engagement. The platform integrated institutional identity, data-management and engagement functionality within university governance and data-protection requirements.
Athena. Scientific molecular visualisation and computational biology software developed to support molecular analysis, biological visualisation and research use. Implemented in Java/Sun Java3D and deployed across Linux and Solaris/SPARC environments.