Welcome to Mike Miller's lab at UC Davis

Department of Animal Science
University of California
1 Shields Ave
Davis, CA 95616

Current Members

Jason Baumsteiger - Postdoctoral Researcher - jbaumsteiger@ucdavis.edu - July 2015
Michael Miller - Principal Investigator - micmiller@ucdavis.edu - November 2012
Sean O'Rourke - Research Associate - smorourke@ucdavis.edu - January 2013
Ryan Peek - Doctoral Researcher - rapeek@ucdavis.edu - October 2014
Michelle Pepping - Master's Researcher - mypepping@ucdavis.edu - October 2016
Daniel Prince - Doctoral Researcher - djprince@ucdavis.edu - July 2013
Ismail Saglam - Postdoctoral Researcher - iksaglam@ucdavis.edu - January 2014
Anna Sturrock - Postdoctoral Researcher - asturrock@ucdavis.edu - October 2016
Tasha Thompson - Doctoral Researcher - tthompson@ucdavis.edu - April 2015
Hiromi Uno - Visiting Postdoctoral Researcher - hiromiuno1@gmail.com - July 2016
George Whitman - Research Technician - gewhitman@ucdavis.edu - July 2014

Former Members
Omar Ali - Master's Researcher - April 2013 through March 2016
Ricardo Castilho - Visiting Doctoral Researcher
Lucydalila Cedillo -
Undergraduate Researcher - April 2014 through June 2016
Vania Costa - Visiting Graduate Researcher
Agusto Luzuriaga - Visiting Graduate Researcher
Kayla Meza - Undergraduate Researcher - October 2014 through June 2016
Zach Norgaard - Master's Researcher - April 2014 through June 2015
Lucia Pardal - Visiting Postdoctoral Researcher


Arraiano-Castilho R, Saglam IK, O'Rourke SM, Miller MR, Beja-Pereira A. RAD sequencing reveals cryptic speciation in Amanita (Basidiomycota, Amanitaceae). Submitted.

Hotaling S, Muhlfeld CC, Giersch JJ, Ali OA, Jordan S, Miller MR, Luikart G, Weisrock DW. Demographic model testing reveals a history of divergence with gene flow for a glacially-tied stonefly in a changing post-Pleistocene landscape. 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.

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.

Owen JR, Noyes N, Young AE, Prince DJ, Blanchard PC, Lehenbauer TW, Aly SS, Davis JH, O’Rourke SM, Abdo Z, Belk K, Miller MR, Morley P, Van Eenennaam AL. Whole-genome sequencing and concordance between antimicrobial susceptibility genotypes and phenotypes of bacterial isolates associated with bovine respiratory disease. G3: Genes, Genomes, Genetics. In revision.

Prince DJ, O'Rourke SM*, Thompson TQ*, Ali OA, Lyman HS, Saglam IK, Hotaling TJ, Spidle AP, Miller MR. The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. bioRxiv. *Equal contribution [Full Text]

Saglam IK, Baumsteiger J, Miller MR. Failure to differentiate between divergence of species and their genes can result in over-estimation of mutation rates in recently diverged species. Proceedings of the Royal Society B: Biological Sciences. In press.

Luzuriaga-Neira A, Villacís-Rivas G, Cueva-Castillo F, Escudero-Sanchez G, Ulloa-Nuñez A, Rubilar-Quezada M, Monteiro R, Miller MR, Beja-Pereira A. (2017) On the origins and genetic diversity of South American chickens: One step closer. Animal Genetics. In press. [Full Text]

Welly BT, Miller MR, Stott JL, Blanchard MT, Islas-Trejo AD, O’Rourke SM, Young AE, Medrano JF, Van Eenennaam AL. (2017) Identification and validation of antigenic proteins from Pajaroellobacter abortibovis using de novo genome sequence assembly and reverse vaccinology. G3: Genes, Genomes, Genetics. 7(2):321-331. [Full Text]

Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B. (2016) Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon. Ecology and Evolution. 6:7706–7716. [Full Text]

Saglam IK, Baumsteiger J, Smith MJ, Linares-Casenave J, Nichols AL, O'Rourke SM, Miller MR. (2016) Phylogenetics suggests the common origin of two scientific icons: Devils Hole and Devils Hole pupfish. Molecular Ecology. 25(16):3962–3973. [Full Text]

Bernardi G, Azzurro E, Golani D, Miller MR. (2016) Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader. Molecular Ecology. 25(14):3384–3396.
[Full Text]

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics. 17(2):81-92. [Full Text]

Ali OA, O'Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR. (2016) RAD Capture (Rapture): Flexible and efficient sequence-based genotyping. Genetics. 202(2):389-400. [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. 17(1):165-175.
[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.
[Full Text]

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-sequencing in ecological and conservation genomics. Molecular Ecology. 22(11):2841-2847. [Full Text] [Cover]

Kohwi M, Lupton JR, Lai SL, Miller MR, Doe CQ. (2013) Developmentally regulated subnuclear genome reorganization restricts neural progenitor competence 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 reveals that Sox9 is required for retinal differentiation. Developmental Biology. 329(1):1-15.
*Equal contribution [Full Text]

Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU. (2007) High density detection of restriction site associated DNA (RAD) markers for rapid mapping of mutated loci in Neurospora. Genetics. 177(2):1163-1171. [Full Text]

Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, Postlethwait JH, Johnson EA. (2007) RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biology. 8(6):R105. [Full Text]

Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research. 17(2):240-248. [Full Text]

Research Highlights and Other Press

June 2016. We know where the world’s loneliest species came from. BBC Earth. [Full Text]

June 2016. Evolution: When pupfish got to Devils Hole. Nature. [Full Text]

June 2016. Devils Hole pupfish. George and Nina Moreas Email. [PDF]

June 2016. UC Davis Student Takes Father’s Lessons to Heart, Named Top Graduate. UC Davis University News. [Full Text]

February 2016. Rapture sequencing: fast, low-cost, large-scale genotyping. Genes to Genomes.
[Full Text]

February 2016. Welcome to the Rapture. The Molecular Ecologist. [Full Text]

June 2013.
Evaluation of Gay et al., 2013 Genes Dev. Faculty of 1000. [Full Text]

January 2013. Evaluation of Gay et al., 2013 Genes Dev. Faculty of 1000. [Full Text]

January 2013. Progenitor Competence: Genes Switching Places. Cell.
[Full Text]

March 2012. Evaluation of Miller et al., 2012 Mol Ecol. Faculty of 1000. [Full Text]

January 2012. Non-model organisms. Nature Methods. [Full Text]

January 2012. Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout. Molecular Ecology. [Full Text]

November 2011. Genetic buzzer-beater genes may save fish.
UO Media Relations. [Full Text]

November 2011. Graduate Student Spotlight - Mike Miller. UO Department of Biology Newsletter. [PDF]

October 2011. Evaluation of Liu et al., 2011 Cell. Faculty of 1000. [Full Text]

October 2011. Michael R. Miller - 2010 Peter von Hippel Graduate Scholar Recipient. UO Institute of Molecular Biology Newsletter.

September 2011. Tumorigenesis: The origins of glioma. Nature Reviews Cancer.
[Full Text]

August 2011. Fast-Forwarding Mendel. Oregon Quarterly.
[Full Text] [PDF]

July 2011. Glioma Development: Where Did It All Go Wrong? Cell.
[Full Text]

July 2011. Scientists Claim Oligodendrocyte Precursor Cells Are the Cell of Origin in Glioma. Genetic Engineering & Biotechnology News.
[Full Text]

July 2011. Cellular origin of deadly brain cancer is identified. UO Media Relations.
[Full Text]

December 2010. Breakthrough of the Year - Areas to Watch. Science.
[Full Text]

August 2009. Evaluation of Miller et al., 2009 Nat Methods. Faculty of 1000. [Full Text]

August 2009. Tech News - Microarrays. BioTechniques.
[Full Text]

May 2009. New tool isolates RNA within specific cells. UO Media Relations.
[Full Text]

October 2007. Evaluation of Lewis et al., 2007 Genetics. Faculty of 1000. [Full Text]

March 2007. Evaluation of Miller et al., 2007 Genome Res. Faculty of 1000. [Full Text]