Mike Covington

CTO and Co-Founder

Amaryllis Nucleics

Former Assistant Project Scientist

Research Interests

Biologists need computational tools that are easily scalable, customizable and modular. I am moved by the concept of creating and accumulating all of the data gathering, formatting and analysis modules that a particular lab might need such that the even less computer-savvy researchers can easily customize their own workflows to do exactly what they want. Therefore, one of my main research interests is the development of robust, easy-to-use, open-source bioinformatic software.

Personal Interests

My hobbies include such pastimes as:

  • Learning new programming languages and techniques while hanging out with my four cats.
  • Trying to answer questions in StackExchange communities.
  • Riding on a snowboard, kayak, or motorcycle.
  • Finding and consuming the best vegan junk food.
  • Playing cards with my mom.
  • Experimenting with musical instruments (especially the ukulele, stylophone, and melodica).


Degree Field Institution Year(s) Advisor
Chronobiology The Scripps Research Institute 2000 - 2002 Steve Kay
Ph.D. Molecular Biology University of Oregon 1997 - 2002 Ry Wagner
B.A. Biochemistry Lewis & Clark College 1993 - 1997 Gary Reiness


Position Field Institution Year(s) Advisor
CTO and Co-Founder Bioinformatics Amaryllis Nucleics 2016 - Present
Assistant Project Scientist Bioinformatics University of California, Davis 2011 - 2016 Julin Maloof
Assistant Professor Plant-Insect Interactions Rice University 2008 - 2011
Postdoctoral Researcher Functional Genomics University of California, Davis 2002 - 2008 Stacey Harmer


  • Song YH, Kubota A, Kwon MS, Covington MF, Lee N, et al. (2018). Molecular basis of flowering under natural long-day conditions in Arabidopsis. Nat Plants 4(10): 824-835. PubMed Nat Plants

  • Markelz RJC, Covington MF, Brock MT, Devisetty UK, Kliebenstein DJ, et al. (2017). Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3 (Bethesda) 7(7): 2259-2270. PubMed G3 (Bethesda)

  • Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, et al. (2016). A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (Bethesda). PubMed G3 (Bethesda)

  • Brock MT, Lucas LK, Anderson NA, Rubin MJ, Markelz RJ, et al. (2016). Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Mol Ecol 25(5): 1122-40. PubMed Mol Ecol

  • Müller-Moulé P, Nozue K, Pytlak ML, Palmer CM, Covington MF, et al. (2016). YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ 4: e2574. PubMed PeerJ PDF

  • Baker RL, Leong WF, Brock MT, Markelz RJ, Covington MF, et al. (2015). Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytol. PubMed New Phytol PDF

  • Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR (2015). BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front Plant Sci 6: 366. PubMed Front Plant Sci PDF

  • Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN (2014). Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. G3 (Bethesda) 4(11): 2065-78. PubMed G3 (Bethesda) PDF

  • Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, et al. (2014). A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol 164(1): 259-72. PubMed Plant Physiol PDF

  • Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, et al. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A 110(28): E2655-62. PubMed Proc Natl Acad Sci U S A PDF

  • Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, et al. (2013). A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell 25(7): 2465-81. PubMed Plant Cell PDF

  • Goodspeed D, Chehab EW, Covington MF, Braam J (2013). Circadian control of jasmonates and salicylates: the clock role in plant defense. Plant Signal Behav 8(2): e23123. PubMed Plant Signal Behav PDF

  • Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF (2012). Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior. Proc Natl Acad Sci U S A 109(12): 4674-7. PubMed Proc Natl Acad Sci U S A PDF

  • Jones MA, Covington MF, DiTacchio L, Vollmers C, Panda S, et al. (2010). Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci U S A 107(50): 21623-8. PubMed Proc Natl Acad Sci U S A PDF

  • Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M, et al. (2008). The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant 1(1): 27-41. PubMed Mol Plant PDF

  • Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9(8): R130. PubMed Genome Biol PDF

  • Covington MF, Harmer SL (2007). The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5(8): e222. PubMed PLoS Biol PDF

  • Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, et al. (2007). Rhythmic growth explained by coincidence between internal and external cues. Nature 448(7151): 358-61. PubMed Nature PDF

  • Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, et al. (2007). Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet 3(10): 1800-12. PubMed PLoS Genet PDF

  • Covington MF, Panda S, Liu XL, Strayer CA, Wagner DR, et al. (2001). ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 13(6): 1305-15. PubMed Plant Cell PDF

  • Liu XL, Covington MF, Fankhauser C, Chory J, Wagner DR (2001). ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell 13(6): 1293-304. PubMed Plant Cell PDF