// Twitter Cards // Prexisting Head The Biologist Is In: Publish or Perish

Monday, February 23, 2015

Publish or Perish

Most of my biology-focused posts have been about topics related to garden projects I've done or have been thinking about. The subject of gardening does account for much of the biology I spend my free-time thinking about, especially now in the middle of a winter-bound Minnesota. It is also far easier to examine the growth and interactions of living things in the garden than it is to go on expeditions or develop lab protocols to explore the diversity of biological topics.

I've avoided talking in detail about the biology I do at work because the work is on-going and to publicize it here might detract from the process of publishing the work in more formal contexts once the projects reach usable conclusions. Sometimes a key result can be quickly replicated once the idea behind it has been developed, so talking about results too early can be asking for some competitor to beat you to publication. I've defended my thesis and dealt with graduate school bureaucracy sufficiently to be awarded my PhD. I can now refer to myself as "Darren Abbey, PhD" in professional contexts. (I can also refer to myself as "The Doctor" (Dr. Who?) in certain social contexts.)

Along the way, I've written or contributed to several research publications. The following list is the publications I've been received name credit for my contributions, from oldest to most recent.

  1. Gale CA, Leonard MD, Finley KR, Christensen L, McClellan M, Abbey D, Kurischko C, Bensen E, Tzafrir I, Kauffman S, Becker J, Berman J. (2009) SLA2 mutations cause SWE1-mediated cell cycle phenotypes in Candida albicans and Saccharomyces cerevisiae. Microbiology. 155(Pt 12):3847-59. [PMID: 19778960]
  2. Forche A, Abbey D, Pisithkul T, Weinzierl MA, Ringstrom T, Bruck D, Petersen K, Berman J. (2011) Stress alters rates and types of loss of heterozygosity in Candida albicans. MBio. 2(4). [PMID: 21791579]
  3. Abbey D, Hickman M, Gresham D, Berman J. (2012) High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda). 1(7):523-30. Erratum in: G3 (Bethesda). 2(11):1473. [PMID: 22384363]
  4. Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang YM, Su CH, Bennett RJ, Wang Y, Berman J. (2013) The 'obligate diploid' Candida albicans forms mating-competent haploids. Nature. 494(7435):55-9. [PMID: 23364695]
  5. Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J. (2014) YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Med. 6(11):100. [PMID: 25505934]
  6. Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A. (2015) The evolution of drug resistance in clinical isolates of Candida albicans. Elife. 4. [PMID: 25646566]
I've also got a couple others in the pipeline. For one I'm looking for a target journal, for the other I'm still deciding exactly how to present the results. I'll let you know more details once they're further along the way to publication.

The projects a grad student works on depends on a mix of the lab they end up in and their personal style of problem solving. I ended up in a Candida albicans lab and brought to it a heavy computational approach. The mix between the two is the realm of computational biology, the topic I find myself most connected to.

The academic life can readily be described as, "Publish or Perish". With six name papers from my time in grad school, I've done alright. Now I just have to figure out the next step.