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Diako Ebrahimi




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Assistant Professor of Quantitative Biology with an academic career producing broad and cross-disciplinary research and learning opportunities. I am a versatile and effective investigator and educator with proven cross-disciplinary leadership expertise. Over the course of my career I have merged data and information from multiple experimental and quantitative fields of science (e.g. quantitative biology, bioinformatics, evolution, virology, cancer, and analytical chemistry) to identify key problems, develop novel hypotheses and lead cross-disciplinary projects. My current research focuses on quantitative biology approaches to study viral and cancer immunity. Throughout my professional and academic careers, I have consistently driven myself to meet challenges and achieve goals. As a highly motivated, results-driven individual, I offer my organization decisive leadership, dedication, and a commitment to excellence.

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Research Experience

Field of Study

Biological/biomedical sciences

Research Interests

Assistant Professor of Quantitative Biology at the Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, and Institute for Molecular Virology, 2015 – Present
• Develop computational biology approaches to uncover the molecular mechanisms of viral/cancer mutagenesis and evolution (e.g. methylation, APOBEC).
• Employ translational bioinformatic methods to discover the link between genomic and transcriptomic variations in human immune genes and determinants of viral control.
• Develop computational pipelines to quantify tumor and tumor microenvironment gene expression profiles.
• Apply quantitative genomics to reveal the role of endogenous retroelements in human evolution and cancer.

Fellow of the Australian National Health and Medical Research Council, 2009 – 2014
• Developed interdisciplinary research directions involving computational analysis of host/pathogen interactions.
> Hypermutation signature: Role of RNA/DNA editing by APOBEC and ADAR in the evolution and inactivation of exogenous retroviruses (HIV, SIV, and HBV) and endogenous elements (ERV, LINE, and SINE)
> MHC signature: Role of major histocompatibility complex alleles in viral escape
> CpG depletion signature: Role of CpG methylation, host mimicry and TLR recognition in CpG depletion
• Developed two open access bioinformatic tools:
> HYPERSIGN: Comparison and classification of mutated sequences without alignment.
> G2A3: Analysis of multiple alignments containing complicating indels.

Postdoctoral Fellow at the Chemometrics and Metrology Research Group, 2007 – 2009
• Developed a new research direction involving analysis of high dimensional and complex data using techniques such as principal component analysis (PCA), partial least squares (PLS) and parallel factor analysis (PARAFAC).


– Current Research (Quantitative Biology)

2019 36- M. Bayati, H. Rabiee, M. Mehrbod, F. Vafaee, D. Ebrahimi, A. Forrest, H. Alinejad-Rokny, CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes, bioRxiv, doi:
2019 35- A. Z. Cheng, J. Yockteng-Melgar, M. C. Jarvis, N. Malik-Soni, I. Borozan, M. A. Carpenter, J. L. McCann, D. Ebrahimi, N. M. Shaban, E. Marcon, J. Greenblatt, W. L. Brown, L. Frappier, R. S. Harris, Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity Nature Microbiology, 4, 78-88.
2018 34- D. Ebrahimi, C. Richards, M. Carpenter, J. Wang, T. Ikeda, J. T. Becker, A. Z. Cheng, J. L. McCann, N. M. Shaban, D. J. Salamango, G. J. Starrett, J. R. Lingappa, J. Yong, W. L. Brown, R. S. Harris, Genetic and mechanistic basis for APOBEC3H alternative splicing, retroviral restriction, and counteraction by HIV-1 protease. Nature Communications, 9:4137.

2018 33- M. Jarvis, A. N. Temiz, D. Ebrahimi, R. S. Harris, Mutation signatures including APOBEC in cancer cell lines, Journal of the National Cancer Institute Cancer Spectrum, 2(1), pky002.

2017 32- Y. Nakano, N. Misawa, G. Juarez-Fernandez, M. Moriwaki, S. Nakaoka, T. Funo, E. Yamada, A. Soper, R. Yoshikawa, D. Ebrahimi, Y. Tachiki, S. Iwami, R. S. Harris, Y. Koyanagi, K. Sato, HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation, PLoS Pathogens, 13(5), e1006348.

2017 31- T. Ikeda, M. Shimoda, D. Ebrahimi, J. L. VandeBerg, R.S. Harris, A. Koito, K. Maeda, Opossum APOBEC1 is a DNA mutator with retrovirus and retroelements restriction activity, Scientific Reports, 7:46719.

2016 30- H. Alinejad-Rokny, F. Anwar, Sh. Waters, M. P. Davenport, D. Ebrahimi*, Source of CpG depletion in the HIV-1 genome, Molecular Biology and Evolution, 33(12): 3205-3212.

2016 29- G. Starrett, E. M. Luengas, N. A. Temiz, D. Ebrahimi, et al., The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis, Nature Communications, 7:12918.

2015 28- H. Alinejad-Rokny, D. Ebrahimi*, A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods, Journal of Biomedical Informatics, 58, 220-225.

2014 27- D. Ebrahimi, H. Alinejad-Rokny, M. P. Davenport, Insight into the motif preference of APOBEC3, PLoS One, 9(1), e87679.

2014 26- S. L. Goonerante, H. Alinejad-Rokny, D. Ebrahimi, et al., Linking pig-tailed macaque major histocompatibility complex class I haplotypes and cytotoxic T lymphocyte escape mutations in SIV infection, Journal of Virology, 88(24), 14310-14325.

2013 25- F. Anwar, M. P. Davenport, D. Ebrahimi*, Footprint of APOBEC3 on the genome of human retroelements, Journal of Virology, 87(14), 8195-8204.

2012 24- D. Ebrahimi, F. Anwar, M. P. Davenport, APOBEC3G and APOBEC3F rarely co-mutate the same HIV genome. Retrovirology, 9:113.

2011 23- D. Ebrahimi, M. P. Davenport, APOBEC3 has not left an evolutionary footprint on the HIV-1 genome, Journal of Virology, 85, 9139-9146.

– Previous Research (Analytical and Environmental Chemistry/Chemometrics)

2015 22- L. Hejazi, M. Guilhaus, D. B. Hibbert, D. Ebrahimi, Gas chromatography with parallel hard and soft ionization mass spectrometry, Rapid Communications in Mass Spectrometry, 29(1), 91-99.

2014 21- R. R. Khoury, G. J. Sutton, D. Ebrahimi, D. B. Hibbert, Formation constants of copper (II) complexes with tripeptides containing Glu, Gly and His: Potentiometric measurements and modelling by generalized analysis of variance, Inorganic Chemistry, 53, 1278-1287.

2013 20- R. R. Khoury, G. J. Sutton, D. B. Hibbert, D. Ebrahimi*, Measurement and modelling of acid dissociation constants of tri-peptides containing Glu, Gly, and His using potentiometry and generalized multiplicative analysis of variance, Dalton Transactions, 42, 2940-2947.

2011 19- M. Sh. Sharifi, D. Ebrahimi, D.B. Hibbert, et al., Bio-Activity of Natural Polymers from the Genus Pistacia: A Validated Model for Their Antimicrobial Action, Global Journal of Health Science, 4(1), 149-161.

2011 18- L. Hejazi, J. W. Wong, D. Cheng, N. Proschogo, D. Ebrahimi, et al., Mass and relative elution time profiling: two-dimensional analysis of sphingolipids in Alzheimer’s disease brains, Biochemical Journal, 438, 65-175.

2011 17- R. R. Khoury, D. Ebrahimi, L. Hejazi, M. P. Bucknall, R. Pickford, D. B. Hibbert, Degradation of fatty acid methyl esters in biodiesels exposed to sunlight and seawater, Fuel, 90(8), 2677-2683.

2011 16- L. Hejazi, D. B. Hibbert, D. Ebrahimi*, Identification of the geometrical isomers of alpha-linolenic acid using GC/MS with a binary decision tree, Talanta, 83, 1233-1238.

2010 15- D. B. Hibbert, D. Blackmore, J. Li, D. Ebrahimi, M. Collins, S. Vujic, P. Gavoyannis, A probabilistic approach to heroin signatures, Analytical and Bioanalytical Chemistry, 396(2), 765-773.

2009 14- L. Hejazi, D. Ebrahimi*, M. Guilhaus, D. B. Hibbert, Discrimination among geometrical isomers of α-linolenic acid methyl ester using low energy electron ionization mass spectrometry, Journal of the American Society for Mass Spectrometry, 20, 1272-1280.

2009 13- L. Hejazi, D. Ebrahimi*, D. B. Hibbert, M. Guilhaus, Compatibility of electron ionization and soft ionization methods in gas chromatography/orthogonal time of flight mass spectrometry, Rapid Communications in Mass Spectrometry, 23, 2181-2189.

2009 12- L. Hejazi, D. Ebrahimi*, M. Guilhaus, D. B. Hibbert, Determination of the composition of fatty acid mixtures using GCXFI-MS: a comprehensive two dimensional separation approach, Analytical Chemistry, 81, 1450-1458.

2008 11- D. Ebrahimi*, D. B. Hibbert, et al., Generalized multiplicative analysis of variance of kill kinetics data of antibacterial agents, Chemometrics and Intelligent Laboratory Systems, 92, 101-109.

2008 10- D. Ebrahimi, D. B. Hibbert, Identification of sources of diesel oil spills using parallel factor analysis: A bridge between American society for testing and materials and Nordtest methods, Journal of Chromatography A, 1198-1199, 181-187.

2008 9- D. Ebrahimi, E. Chow, et al., Multi-analyte sensing: a chemometrics approach to understanding the merits of electrode arrays versus single electrodes, The Analyst, 133, 1090-1096.

2008 8- D. Ebrahimi, D. B. Hibbert, D. Kennedy, B. Messerle, High throughput screening arrays of rhodium and iridium complexes as catalysts for intramolecular hydroamination using parallel factor analysis. The Analyst, 133, 817–822.

2007 7- D. Ebrahimi, J. Li, D. B. Hibbert, Classification of weathered petroleum oils by multi-way analysis of gas chromatography-mass spectrometry data using PARAFAC2 parallel factor analysis, Journal of Chromatography A, 1166, 163-170.

2007 6- J. Ghasemi, D. Ebrahimi, L. Hejazi, R. Leardi, A. Niazi, Simultaneous kinetic-spectrophotometric determination of sulfide and sulfite by partial least squares and genetic algorithm variable selection. Journal of Analytical Chemistry, 62(4), 348–354.

2006 5- E. Chow, D. Ebrahimi, et al., Application of N-PLS calibration to the simultaneous determination of Cu2+, Cd2+ and Pb2+ using peptide modified electrochemical sensors, The Analyst, 131, 1051-1057.

2004 4- L. Hejazi, D. Ebrahimi, Y. Yamini, R. G. Brereton, Solid phase extraction and simultaneous spectrophotometric determination of trace amounts of Co, Ni and Cu using partial least squares regression. Talanta, 62(1), 185-191.

2003 3- Y. Yamini, L. Hejazi, D. Ebrahimi, Solid phase extraction and simultaneous determination of trace amounts of Copper and Iron using mixture of ligands, Microchimica Acta, 142, 21-25.

2003 2- J. Ghasemi, D. Ebrahimi, Kinetic spectrophotometric determination of sulfite using a full curve (PLS) and a fixed time method, Analytical Letters 2003, 36(10), 2243-2254.

2002 1- J. Ghasemi, D. Ebrahimi, Kinetic spectrophotometric determination of sulfide using whole kinetic curve and a fixed time method. Microchemical journal, 71, 1-8.

* Senior author (Corresponding author)

Awards & Honors

– Reviewers’ Choice award, American Society for Human Genetics (ASHG), San Diego, USA. 2018
– New Investigator Scholarship, Conference on Retroviruses and Opportunistic Infections (CROI), Boston, USA. 2018
– Charles J. Epstein Trainee Award for Excellence in Human Genetics Research, Semi-finalist and Reviewers’ Choice awards, American Society for Human Genetics (ASHG), Baltimore, USA. 2015
– Australian National Health and Medical Research Council (NHMRC) Fellowship, AU. 2009 – 2013
– International Postgraduate Research Scholarship, School of Chemistry, UNSW, AU. 2004 – 2007
– Carl Storm International Diversity Fellowship, Gordon Research Conference, Statistics in Chemistry and Chemical Engineering, Boston, USA. 2005
Teaching Fellowship, School of Chemistry, University of New South Wales, AU. 2006 – 2009



San Antonio, TX, USA