Michael Miller, Ph.D.

Michael Miller

Position Title

2251 Meyer Hall


  • B.S., Biology, University of Oregon, 2006.
  • Ph.D., Biology, University of Oregon, 2011.

Research Interests

Animal genetics and genomics; conservation and ecological genetics and genomics; genomics and bioinformatics technology development; salmonid fishes.

Graduate Groups


Current Graduate Students

  • Razib Khan, PhD Program, Integrative Genetics and Genomics Graduate Group. Expected Graduation Date: Summer 2017.
  • Ryan Peek, PhD Program, Ecology Graduate Group. Expected Graduation Date: Summer 2018.
  • Michelle Pepping, MS Program, Animal Biology Graduate Group. Expected Graduation Date: Summer 2018.
  • Daniel Prince, PhD Program, Integrative Genetics and Genomics Graduate Group. Expected Graduation Date: Summer 2018.
  • Tasha Thompson, PhD Program, Integrative Genetics and Genomics Graduate Group. Expected Graduation Date: Summer 2019.


  • Omar Ali, MS Integrative Genetics and Genomics, Winter 2016.
  • Zach Norgaard, MS Intergrative Genetics and Genomics, Spring 2015.

Selected Publications

Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B. Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon. Submitted.

Saglam IK, Baumsteiger J, Smith MJ, Linares-Casenave J, Nichols AL, O'Rourke SM, Miller MR,. Phylogenetics suggests the common origin of two scientific icons: Devils Hole and Devils Hole pupfish. Submitted.

Saglam IK, Miller MR, O'Rourke SM, Caglar SS. Phylo-comparative analysis from RAD sequence data reveal the dual role of drift and selection in reproductive character displacement. Submitted.

Arraiano-Castilho R, Saglam IK, O'Rourke SM, Miller MR, Beja-Pereira A. Cryptic speciation challenges conservation and management of mycological resources. Submitted.

Bernardi G, Azzurro E, Golani D, Miller MR,. Genomic signatures of pre-adaptation and post-invasion rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader. Submitted.

Norgaard ZK, Ali OA, Amish SJ, O'Rourke SM, Prince DJ, Luikart G, Muhlfeld CC, Miller MR,. Caution and skepticism are critical when analyzing massively parallel sequencing data. Submitted.

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics. In press. [Full Text]

Ali OA, O'Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR,. RAD Capture (Rapture): Flexible and efficient sequence-based genotyping. Genetics. In press. [Full Text]

Arciniega M, Clemento AJ, Miller MR, Peterson M, Garza JC, Pearse DE. (2015) Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California.Conservation Genetics. 1-11. [Full Text]

Hand BK, Hether TD, Kovach RP, Muhlfeld CC, Amish SJ, Boyer MC, O’Rourke SM, Miller MR, Lowe WH, Hohenlohe PA, Luikart G. (2015) Genomics and introgression: discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing. Current Zoology. 61(1):146-154.

Palti Y, Gao G, Liu S, Kent MP, Lien S, Miller MR, Rexroad CE 3rd, Moen T. (2015) The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout. Molecular Ecology Resources. 15(3):662–672. [Full Text]

Welly BT, Miller MR, Blanchard MT, Islas-Trejo AD, O’Rourke SM, Young AE, Stott JL, Medrano JF, Van Eenennaam AL. (2014) Genome assembly of the putative etiologic agent of epizootic bovine abortion. Proceedings, Western Section, American Society of Animal Science. 65(1):8-12.

Andrews KR, Hohenlohe PA, Miller MR, Seeb JE, Luikart G. (2014) Trade-offs and utility of alternative RADseq methods. Molecular Ecology. 23(24):5943–5946. [Full Text]

Pearse DE, Miller MR, Abadía-Cardoso A, Garza JC. (2014) Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout.Proceedings of the Royal Society B: Biological Sciences. 281(1783):20140012. [Full Text]

Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet E, Yao J, Thorgaard GH, Salem M, Rexroad CE 3rd. (2014) A resource of single-nucleotide polymorphisms for rainbow trout generated by RAD sequencing of doubled haploids. Molecular Ecology Resources. 14(3):588–596. [Full Text]

Gay L, Karfilis K, Miller MR, Doe CQ, Stankunas K. (2014) Applying thiouracil (TU)-tagging for mouse transcriptome analysis. Nature Protocols. 9(2):410–420. [Full Text]

Hale MC, Thrower FP, Berntson EA, Miller MR, Nichols K. (2013) Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss. G3: Genes, Genomes, Genetics. 2(9):1113-1127. [Full Text]

Narum SR, Campbell NR, Meyer K, Miller MR, Hardy R. (2013) Thermal adaptation and acclimation of ectotherms in differing aquatic climates. Molecular Ecology . 22(11):3090-3097. [Full Text]

Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. (2013) Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology. 22(11):3002-3013. [Full Text]

Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. (2013) Genotyping-by- s equencing in e cological and c onservation g enomics. Molecular Ecology. 22(11):2841-2847. [Full Text] [Cover]

Kohwi M, Lupton JR, Lai SL, Miller MR, Doe CQ. (2013) Developmentally r egulated s ubnuclear g enome r eorganization r estricts n eural p rogenitor c ompetence in Drosophila. Cell. 152(1):97–108. [Full Text] [Graphical Abstract]

Gay L, Miller MR, Ventura PB, Devasthali V, Vue Z, Thompson HL, Temple S, Zong H, Cleary MD, Stankunas K, Doe CQ. (2013) Mouse TU-tagging: a chemical/genetic intersectional method for purifying cell type - specific nascent RNA. Genes and Development. 27(1):98-115. [Full Text]

Lai SL, Miller MR, Robinson KJ, Doe CQ. (2012) The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation. Developmental Cell. 23(4):849-57. [Full Text]

Everett MV, Miller MR, Seeb JE. (2012) Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics. 13:521. [Full Text]

Hecht BC, Thrower FP, Hale MC, Miller MR, Nichols KM. (2012) The genetic architecture of migration related traits in rainbow and steelhead trout, Oncorhynchus mykiss. G3: Genes, Genomes, Genetics. 2(9):1113-1127. [Full Text]

Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, Haussler D, O'Brien SJ, Ryder OA, Venkatesh B. (2012) The fishes of Genome 10K. Marine Genomics. 7(9):3-6. [Full Text]

Miller MR, Brunelli JP, Wheeler PA, Liu S, Rexroad CE 3rd, Palti Y, Doe CQ, Thorgaard GH. (2012) A conserved haplotype controls parallel adaptation in geographically distant salmonid populations.Molecular Ecology. 21(2):237–249. [Full Text]

Carney TD, Miller MR, Robinson KJ, Bayraktar OA, Osterhout JA, Doe CQ. (2012) Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis.Developmental Biology. 361(1):137-142. [Full Text] [Cover]

O'Rourke SM, Yochem J, Connolly AA, Price MH, Carter L, Lowry JB, Turnbull DW, Kamps-Hughes N, Stiffler N, Miller MR, Johnson EA, Bowerman B. (2011) Rapid mapping and identification of mutations in Caenorhabditis elegans by RAD mapping and genomic interval pull-down sequencing. Genetics. 189(3):767-778. [Full Text]

Liu C, Sage JC*, Miller MR *, Verhaak RGW*, Hippenmeyer S, Vogel H, Forman O, Bronson RT, Nishiyama A, Luo L, Zong H. (2011) Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 146(2):209-221. *Equal contribution [Full Text] [Graphical Abstract]

Tran KD, Miller MR, Doe CQ. (2010) Recombineering Hunchback identifies two conserved domains required to maintain neuroblast competence and specify early-born neuronal identity. Development. 137(9):1421-1430. [Full Text] [Cover]

Miller MR, Robinson KJ, Cleary MD, Doe CQ. (2009) TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nature Methods. 6(6):439-441. [Full Text] [Cover]

Yokoi H*, Yan YL*, Miller MR, BreMiller RA, Catchen JM, Johnson EA, Postlethwait JH. (2009) Expression profiling of zebrafish sox9 mutants


Johnson EA*, Liu G*, Miller MR*. (2006) Methods of mapping polymorphisms and polymorphism microarrays. Patent Pub. No. WO/2006/122215. *Listed alphabetically [Full Text]