Jeremy Miller, Ph.D.

Scientist, Sr.

Brain Science Human Cell Types

Bio:

Dr. Miller joined the Allen Institute in 2011 to help with computational data analysis of the Allen Human Brain Atlas project. He is first author on several major manuscripts describing the Allen Institute’s large-scale transcriptomic resources on the adult and developing human and non-human primate brain, including the Aging, Dementia, and Traumatic Brain Injury Study. Miller received his Ph.D. in neuroscience from UCLA, where he studied gene expression changes in the brain in Alzheimer's disease and normal aging in the lab of Dr. Daniel Geschwind.

Research Focus:

Miller's current work focuses in three general areas: (1) characterizing cell types of the mammalian brain and their underlying features, including molecular pathways unique to human; (2) understanding how features of these cell types change with disease in human; and (3) developing tools for standardizing cell type taxonomies and for communicating cell type findings to the general scientific community.

Publications

Annals of Neurology

Ferroptosis of Microglia in Aging Human White Matter Injury

Aug 21, 2023

Philip A. Adeniyi, Xi Gong, Ellie MacGregor, Kiera Degener-O'Brien, Evelyn McClendon, Mariel Garcia, Oscar Romero, Joshua Russell, Taasin Srivastava, Jeremy Miller, C. Dirk Keene, Stephen A. Back

Cell Reports

Multi-modal characterization and simulation of human epileptic circuitry

Dec 27, 2022

Anatoly Buchin, Rebecca de Frates, Anirban Nandi, Rusty Mann, Peter Chong, Lindsay Ng, Jeremy Miller, Rebecca Hodge, Brian Kalmbach, Soumita Bose, Ueli Rutishauser, Stephen McConoughey, Ed Lein, Jim Berg, Staci Sorensen, Ryder Gwinn, Christof Koch, Jonathan Ting, Costas A. Anastassiou

Genome Research

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

Oct 01, 2021

Brian Aevermann, Yun Zhang, Mark Novotny, Mohamed Keshk, Trygve Bakken, Jeremy Miller, Rebecca Hodge, Boudewijn Lelieveldt, Ed Lein, Richard H. Scheuermann

Nature Computational Science

Consistent cross-modal identification of cortical neurons with coupled autoencoders

Feb 01, 2021

Rohan Gala, Agata Budzillo, Fahimeh Baftizadeh, Jeremy Miller, Nathan Gouwens, Anton Arkhipov, Gabe Murphy, Bosiljka Tasic, Hongkui Zeng, Michael Hawrylycz, Uygar Sümbül

Nature

Shared and distinct transcriptomic cell types across neocortical areas

Nov 01, 2018

Bosiljka Tasic, Zizhen Yao, Lucas T. Graybuck, Kimberly A. Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N. Economo, Sarada Viswanathan, Osnat Penn, Trygve Bakken, Vilas Menon, Jeremy Miller, Olivia Fong, Karla E. Hirokawa, Kanan Lathia, Christine Rimorin, Michael Tieu, Rachael Larsen, Tamara Casper, Eliza Barkan, Matthew Kroll, Sheana Parry, Nadiya V. Shapovalova, Daniel Hirschstein, Julie Pendergraft, Heather A. Sullivan, Tae Kyung Kim, Aaron Szafer, Nick Dee, Peter Groblewski, Ian Wickersham, Ali Cetin, Julie A. Harris, Boaz P. Levi, Susan M. Sunkin, Linda Madisen, Tanya L. Daigle, Loren Looger, Amy Bernard, John Phillips, Ed Lein, Michael Hawrylycz, Karel Svoboda, Allan R. Jones, Christof Koch, Hongkui Zeng

Science (New York, N.Y.)

An anatomic transcriptional atlas of human glioblastoma

May 11, 2018

Ralph B. Puchalski, Nameeta Shah, Jeremy Miller, Rachel Dalley, Steve R. Nomura, Jae-Guen Yoon, Kimberly A. Smith, Michael Lankerovich, Darren Bertagnolli, Kris Bickley, Andrew F. Boe, Krissy Brouner, Stephanie Butler, Shiella Caldejon, Mike Chapin, Suvro Datta, Nick Dee, Tsega Desta, Tim Dolbeare, Nadezhda Dotson, Amanda Ebbert, David Feng, Xu Feng, Michael Fisher, Garrett Gee, Jeff Goldy, Lindsey Gourley, Benjamin W. Gregor, Guangyu Gu, Nika Hejazinia, John Hohmann, Parvinder Hothi, Robert Howard, Kevin Joines, Ali Kriedberg, Leonard Kuan, Chris Lau, Felix Lee, Hwahyung Lee, Tracy Lemon, Fuhui Long, Naveed Mastan, Erika Mott, Chantal Murthy, Kiet Ngo, Eric Olson, Melissa Reding, Zack Riley, David Rosen, David Sandman, Nadiya Shapovalova, Clifford R. Slaughterbeck, Andrew Sodt, Graham Stockdale, Aaron Szafer, Wayne Wakeman, Paul E. Wohnoutka, Steven J. White, Don Marsh, Robert C. Rostomily, Lydia Ng, Chinh Dang, Allan Jones, Bart Keogh, Haley R. Gittleman, Jill S. Barnholtz-Sloan, Patrick J. Cimino, Megha S. Uppin, C. Dirk Keene, Farrokh R. Farrokhi, Justin D. Lathia, Michael E. Berens, Antonio Iavarone, Amy Bernard, Ed Lein, John W. Phillips, Steven W. Rostad, Charles Cobbs, Michael J. Hawrylycz, Greg D. Foltz

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX

Jan 01, 2017

Brian Aevermann, Jamison McCorrison, Pratap Venepally, Rebecca Hodge, Trygve Bakken, Jeremy Miller, Mark Novotny, Danny N. Tran, Francisco Diezfuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S. Lasken, E. D. Lein, Nicholas Schork, Richard H. Scheuermann

Neuron

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain

Jul 16, 2014

Carol L. Thompson, Lydia Ng, Vilas Menon, Salvador Martinez, Chang-Kyu Lee, Katie Glattfelder, Susan M. Sunkin, Alex Henry, Christopher Lau, Chinh Dang, Raquel Garcia-Lopez, Almudena Martinez-Ferre, Ana Pombero, John L. R. Rubenstein, Wayne B. Wakeman, John Hohmann, Nick Dee, Andrew J. Sodt, Rob Young, Kimberly Smith, Thuc-Nghi Nguyen, Jolene Kidney, Leonard Kuan, Andreas Jeromin, Ajamete Kaykas, Jeremy Miller, Damon Page, Geri Orta, Amy Bernard, Zackery Riley, Simon Smith, Paul Wohnoutka, Michael J. Hawrylycz, Luis Puelles, Allan R. Jones

Jeremy Miller, Ph.D.

Publications

Science Programs at Allen Institute