Feb 16th, 2012

My research interest mainly includes gene network, analyzing microarray data and evolution (e.g.phylogenetic). In my research, I quite often use Perl, R, Cytoscape and some other command line and shell scripts. I am listing my current activities about my research.

Published Applications

  • TAIR BLAST: A module to gather automated BLAST result from TAIR.
  • TAIR GeneDescriptions: Automatically download gene descriptions using locus identifiers (AGI codes) or gene names.
  • Graph::Writer::Cytoscape: Write a directed graph out as Cytoscape competible input file
  • SNP Toolset Various scripts for SNP table convertion, modification and processing etc..


  • Suren, H., Hodgins, K.A., Yeaman, S., Nurkowski, K.A., Smets, P., Rieseberg, L.H., Aitken, S.N., and Holliday, J.A. (2016). Exome capture from the spruce and pine giga-genomes. Mol Ecol Resour 16, 1136-1146.
  • Yeaman, S., Hodgins, K.A., Lotterhos, K.E., Suren, H., Nadeau, S., Degner, J.C., Nurkowski, K.A., Smets, P., Wang, T., Gray, L.K., Liepe, K.J., Hamann, A., Holliday, J.A., Whitlock, M.C., Rieseberg, L.H., and Aitken, S.N. (2016). Convergent local adaptation to climate in distantly related conifers. Science 353, 1431-1433.
  • Zhang, M., Zhou, L., Bawa, R., Suren, H., and Holliday, J.A. (2016). Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar. Mol Biol Evol 33, 2899-2910.
  • Yeaman, S., Hodgins, K.A., Suren, H., Nurkowski, K.A., Rieseberg, L.H., Holliday, J.A., and Aitken, S.N. (2014). Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glaucaxPicea engelmannii). New Phytol 203, 578-591.
  • Collakova, E., Klumas, C., Suren, H., Myers, E., Heath, L.S., Holliday, J.A., and Grene, R. (2013). Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biol 13, 72.
  • Grene, R., Klumas, C., Suren, H., Yang, K., Collakova, E., Myers, E., Heath, L.S., and Holliday, J.A. (2012). Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front Plant Sci 3, 241.
  • Holliday, J.A., Suren, H., and Aitken, S.N. (2012). Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proc Biol Sci 279, 1675-1683.