Research Publications and Conferences

Computer Science

  • Alnasir, J. (2021). Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster. PLOS Computational Biology, Cambridge. [ Read ]

  • Alnasir, J., Heinis, T., Sokolovskii, R (2023). Survey of Information Encoding Techniques for DNA. Computing Surveys, ACM (Association for Computing Machinery), iss: 0360-0300. [ ACM Comp. Surveys ]

  • Alnasir, J. (2020). Distributed Computing in a Pandemic: A Review of Technologies available for Tackling COVID-19. ADCAIJ (Advances in Distributed Computing and Artificial Intelligence Journal), 11(1) (recently accepted). [ ADCAIJ ]

  • Alnasir, J (2021). Encoding information into DNA. Mathematical Foundations in Bioinformatics (MatBio '21), King's College London. [ MatBio '21 ]

  • Alnasir, J. (2023). DNA Storage Error Simulator: A Tool for Simulating Errors in Synthesis, Storage, PCR and Sequencing. JCB: Journal of Computational Biology, New York, 30(2), 131-148. [ preprint ]

  • Alnasir, J. & Shanahan, H. P. (2020). Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq. bioRxiv, Cold Spring Harbor Laboratory. [ Journal. Comp. Bio. ]

  • Alnasir, J (2019). Fostering Reproducibility, Standardisation, Fault-tolerance and Deployability in Computational Pipelines using Nextflow Workflow Language - Adoption and Training at the ICR. Mathematical Foundations in Bioinformatics (MatBio '19), King's College London. [ MatBio '19 ]

  • Alnasir, J. & Shanahan, H. P. (2018). The application of Hadoop in Structural Bioinformatics. Oxford University Press: Briefings in Bioinformatics, pp1-10. [ Read ]

  • Alnasir, J. & Shanahan, H. P. (2017). Transcriptomics: Quantifying non-uniform read distribution using MapReduce.. International Journal of Foundations of Computer Science, 29(8). [ Read ]

  • Alnasir, J., & Shanahan, H. (2017). A novel method to detect bias in Short Read NGS RNA-seq data. Journal of Integrative Bioinformatics, 14(3). [ Read ]

  • Alnasir, J., & Shanahan, H. P. (2015). Transcriptomics on Spark Workshop ? Introducing Hercules ? an Apache Spark MapReduce algorithm for quantifying non-uniform gene expression. CloudTech'16, Marrakech, Morocco. [ Read]

  • Alnasir, J., & Shanahan, H. P. (2015). Investigation into the annotation of protocol sequencing steps in the sequence read archive. GigaScience, 4(1), 23. [ Read ]

  • Alnasir, J. & Shanahan, H., (2015). PDB-Hadoop: Parallelising user applications on the protein databank using Apache Hadoop. Poster session presented at 3DSig Structural Bioinformatics and Computational Biophysics 2015, Dublin, Ireland. [ Read ]

  • Alnasir, J (2015). Applying Apache Hadoop, Hive and Map Reduce to Legacy Systems and Applications. 1hr Conference talk at MSTI (Mediterranean Space of Technology and Innovation) Innovation week 2015. ENSIAS (École nationale supérieure d'informatique et d'analyse des systèmes), Rabat, Morocco. 
    [ Programme ]

    Royal Holloway, Computer Science department's annual research colloquium abstracts:

    2016 - Hercules/MapReduce/Transcriptomics [ I was Editor/co-organiser ]
    [ Read ]
    2015 - PDB-Hadoop/Legacy applications on the PDB [ Read ]
    2014 - Illumina/SRA meta-data annotation [ I was co-organiser ] [ Read ]

Chemistry and Pharmacology

  • Austen B, Duberly K, Alnasir J, Dabhi S, Wijesiriwardana N (2019) Cyclisation of Cell-Penetrating PDZ-Binding Peptides Directed to PSD95, American Journals of Chemistry; 3(1), pp1-11
    [ Read ]

  • Alnasir, J. & Austen, B. (2011). Characterisation of cyclic neuroprotective PDZ binding ligands. Poster session presented at Royal Society of Chemistry (RSC): Protein and Peptide Science Group Early Stage Researcher Meeting, London, United Kingdom and subsequently at St. Georges research day.
    [ Read , Abstract #10 ]

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