Welcome to Mike Miller's lab at UC Davis

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

Current Members

Ensieh Habibi - Doctoral Researcher - ehabibi@ucdavis.edu - July 2017
William Hemstrom - Doctoral Researcher - whemstrom@ucdavis.edu - October 2016
Connie Huang -
Undergraduate Researcher - conhuang@ucdavis.edu - January 2017
Melissa Jones - Doctoral Researcher - mlyjones@ucdavis.edu - April 2018
Samantha Kannry - Master's Researcher - shkannry@ucdavis.edu - October 2017
Michael Miller - Principal Investigator - micmiller@ucdavis.edu - October 2012
Sean O'Rourke - Research Associate - smorourke@ucdavis.edu - January 2013
Ryan Peek - Doctoral Researcher - rapeek@ucdavis.edu - October 2014
Michelle Pepping - Doctoral Researcher - mypepping@ucdavis.edu - October 2016
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
George Whitman - Research Technician - gewhitman@ucdavis.edu - July 2014

Former Members
Omar Ali - Master's Researcher - April 2013 through March 2016
Jason Baumsteiger - Postdoctoral Researcher - July 2015 through August 2017
Ricardo Castilho - Visiting Doctoral Researcher
Lucydalila Cedillo -
Undergraduate Researcher - April 2014 through June 2016
Vania Costa - Visiting Graduate Researcher
Corey Luna - Undergraduate Researcher - January 2017 through June 2017
Agusto Luzuriaga - Visiting Graduate Researcher
Fernanda Maciel - Visiting Doctoral Researcher - July 2017 through January 2018
Kayla Meza - Undergraduate Researcher - October 2014 through June 2016
Zach Norgaard - Master's Researcher - April 2014 through June 2015
Lucia Pardal - Visiting Postdoctoral Researcher
Daniel Prince - Doctoral Researcher - April 2013 through September 2017
Hiromi Uno - Visiting Postdoctoral Researcher - July 2016 through March 2017

Selected Publications (full publication list on Google Scholar)

Peek RA, O'Rourke SM, Miller MR. Flow regulation associated with decreased genetic health of a river-breeding frog species. bioRxiv. [Full Text]

Thompson TQ, Bellinger RM*, O'Rourke SM*, Prince DJ*, Stevenson AE, Rodrigues AT, Sloat MR, Speller CF, Yang DY, Butler VL, Banks MA, Miller MR. Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. bioRxiv. *Equal contribution [Full Text]

Prince DJ, O'Rourke SM*, Thompson TQ*, Ali OA, Lyman HS, Saglam IK, Hotaling TJ, Spidle AP, Miller MR. (2017) The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. Science Advances. 3(8):e1603198.
*Equal contribution [Full Text]

Welly BT, Miller MR, Stott JL, Blanchard MT, Islas-Trejo AD, O’Rourke SM, Young AE, Medrano JF, Van Eenennaam AL. (2017) Genome Report: 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]

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

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]

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]

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]

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]

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]

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

May 2018. A single gene is spawning a fierce debate in salmon conservation. Science. [Podcast]

May 2018. Spring Chinook restoration might be easier said than done. Science. [Full Text]

May 2018. A different animal. Science. [Full Text]

March 2018. College students passionate about North Umpqua River. The News-Review. [Full Text]

Winter 2018. GREB1L. Strong Runs. [PDF]

January 2018. On the Evolution and Conservation of Summer Steelhead and Spring Chinook. The Osprey.

October 2017. Scientists study steelhead genes in North Umpqua River. The News-Review.
[Full Text]

September 2017. Dams seen driving 'mass extinction' of salmon. E&E News. [Full Text]

September 2017. Evolutionary genomics informs salmon conservation. California WaterBlog. [Full Text]

September 2017. Tribe Calling For Spring Chinook To Be Listed As Endangered Species. Capital Public Radio. [Full Text]

August 2017. Evolutionary history can help conserve salmon. The Wildlife Society. [Full Text]

August 2017. Karuk Build A Case For Listing Klamath Spring Chinook. Jefferson Public Radio. [Full Text]

August 2017. Gene study prompts request to list spring Chinook as endangered. The Siskiyou Daily News. [Full Text]

August 2017. Karuk Tribe seeks to list Klamath River salmon as endangered. Herald and News. [Full Text]

August 2017. Yurok Tribe Hails New Science Showing Spring-Run Klamath Salmon as Genetically Distinct. Lost Coast Outpost. [Full Text]

August 2017. Study reveals new salmon species. YubaNet. [Full Text]

August 2017. One Fish, two fish. North Coast Journal. [Full Text]

August 2017. New genetic evidence could have major implications in the fight to save spring-run Chinook. Sacramento Bee. [Full Text]

August 2017. Study Reveals Evolutionary History of Imperiled Salmon Stocks. UC Davis News. [Full Text]

February 2017. The Turkish paradox: Can scientists thrive in a state of emergency? Nature. [Full Text]

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 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]