Dr. Aaron Golden


Research interests

  • Microbiome, Microbial & Pathogen Genomics
  • Development/Application of Data Science Methodologies in Genomics
  • Applied Computational Homology & Topological Data Analysis

Research overview

I have been working in the genomics field since 2002, when I agreed to supervise a final year project on characterizing codon usage patterns in the first complete microbe genomes. The student in question, Shaun Mahony, went on to be subsequently awarded the first bioinformatics Doctorate at NUI Galway, and now runs his own successful lab at Penn State University in the United States.

The work pioneered by Shaun has formed the basis for many of my subsequent research activities, essentially one of discerning patterns or clusters within complex and high dimensional ‘omic’ datasets, and in fully characterizing the nature and meaning of these distinct entities in the biological context under scrutiny. This blends mathematical methods and computational techniques applied to specific problems in the life sciences.

Between 2011 and 2016 I was fortunate to be Senior Faculty at the Albert Einstein College of Medicine’s Genetics Department, as well as at the Department of Mathematical Sciences at Yeshiva University, both located in New York City. This time gave me a unique opportunity to participate in cutting edge clinical and basic research projects, ranging from therapeutics (e.g. aptamer design using NGS-SELEX), diagnostics (e.g. robust identification of HPV insertion sites in tissue biopsies) and systems level analysis of complex biomedical datasets (e.g. semantic computing based elucidation of pathogen virulence in the apicomplexan Toxoplasma gondii, using toxoMine http://toxomine.org).

My group also supported the development of genomics support resources for the International 22q11.2 Brain Behavior Consortium http://22q11-ibbc.org/, which aims to integrate clinical information on neurological conditions with whole genome sequencing of 1000 individuals possessing 22q11 Deletion Syndrome.

Back at NUI Galway I am particularly interested in further exploring the richly diverse and dynamic environment of the various symbiotic microbiomes essential to our existence, using underutilized and ‘unorthodox’ analytical techniques. Another area of focus will be a return to the problem of characterizing the unknown regions of fully sequenced individual microbes – ranging from genome annotation to deconvolution of regulatory networks from transcription data. Potential solutions to these problems lie in the intersection of the domains of topology and dynamical systems.

Selected publications

  • Rhee, D.B., Croken, M.M., Shieh, K.R., Sullivan, J., Micklem, G., Kim, K., Golden, A. (2015). toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. Database (Oxford), 2015:bav066.
  • Delio, M., Patel, K., Maslov, A., Marion, R.W., McDonald, T.V., Cadoff, E.M., Golden, A., Greally, J.M., Vijg, J., Morrow, B., Montagna, C. (2015). Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants. PLoS ONE, 10, 7:e0133742.
  • Wijetunga, N.A., Delahaye, F., Zhao, Y.M., Golden, A., Mar, J.C., Einstein, F.H., Greally, J.M. (2014). The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. Nat Commun, 5:5195.
  • Golden, A., Djorgovski, S., Greally, J.M. (2013). Astrogenomics: big data, old problems, old solutions?. Genome Biol., 14, 8:129.
  • Agoni, L., Golden, A., Guha, C., Lenz, J. (2012). Neandertal and Denisovan retroviruses. Curr. Biol., 22, 11:R437-8.