Andrew C. Adey, Ph.D.

  • Professor of Molecular and Medical Genetics, School of Medicine
  • Member, CEDAR, OHSU Knight Cancer Institute, School of Medicine
  • Molecular and Medical Genetics Graduate Program, School of Medicine
  • Program in Molecular and Cellular Biosciences, School of Medicine
  • Cancer Biology Graduate Program, School of Medicine

Biography

Dr. Adey started out in biotechnology development at the University of Texas where he researched alternative applications of microarrays in the lab of Andrew D. Ellington, Ph.D. He later served as interim director of the UT microarray core facility and then helped set up the UT genome sequencing and analysis facility in the early days of next generation sequencing. He then completed his doctoral studies in the Molecular and Cellular Biology Program at the University of Washington in the lab of Jay Shendure, M.D., Ph.D. in the Genome Sciences Department.

Previous research highlights include pioneering a novel transposase-based method for rapid, low-input DNA sequencing library construction, which I extended to the genome-wide analysis of DNA methylation. I also applied long-range sequencing methods to produce the first haplotype resolved genome and epigenome of an aneuploid cell line, HeLa, where I investigated the role of haplotype and copy number on the epigenetic and transcriptional landscape. I plan to continue my focus on the development and implementation of novel strategies to investigate the epigenome with high precision. This includes single cell approaches to disambiguate epigenetic and transcriptional heterogeneity within populations of cells which is typically obscured by bulk preparation methods. This work will provide insight into the dynamic regulatory landscape of cells and may reveal functional and targetable subpopulations in the context of disease intervention.

Education and training

  • Degrees

    • B.S., 2008, University of Texas
    • Ph.D., 2014, University of Washington

Memberships and associations:

  • Member, American Society of Human Genetics
  • SAB, Phase Genomics

Areas of interest

  • Quantitative Oncology Program, OHSU Knight Cancer Institute
  • Programmatic Theme: Omics, OHSU Knight Cancer Institute
  • Single Cell
  • Epigenetics
  • Development
  • Sequencing
  • Biotechnology

Additional information

Honors and awards

  • University of Washington Distinguished Dissertation Award 2014
  • Harold M. Weintraub Graduate Student Award 2014

Publications

Publications

  • Atlas-scale single-cell DNA methylation profiling with sciMETv3

    Cell Genomics
    1. Ruth V. Nichols
    2. Lauren E. Rylaarsdam
    3. Brendan L. O'Connell
    4. Zohar Shipony
    5. Nika Iremadze
    6. Sonia N. Acharya
    7. Andrew C. Adey

  • Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer

    Nature Cancer
    1. Jason M. Link
    2. Jennifer R. Eng
    3. Carl Pelz
    4. Kevin MacPherson-Hawthorne
    5. Patrick J. Worth
    6. Shamaline Sivagnanam
    7. Dove J. Keith
    8. Sydney Owen
    9. Ellen M. Langer
    10. Alison Grossblatt-Wait
    11. Gustavo Salgado-Garza
    12. Allison L. Creason
    13. Sara Protzek
    14. Julian Egger
    15. Hannah Holly
    16. Michael B. Heskett
    17. Koei Chin
    18. Nell Kirchberger
    19. Konjit Betre
    20. Elmar Bucher
    21. David Kilburn
    22. Zhi Hu
    23. Michael W. Munks
    24. Isabel A. English
    25. Motoyuki Tsuda
    26. Jeremy Goecks
    27. Emek Demir
    28. Andrew C. Adey
    29. Adel Kardosh
    30. Charles D. Lopez
    31. Brett C. Sheppard
    32. Alex Guimaraes
    33. Brian Brinkerhoff
    34. Terry K. Morgan
    35. Gordon B. Mills
    36. Lisa M. Coussens
    37. Jonathan R. Brody
    38. Rosalie C. Sears

  • Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment

    iScience
    1. Çiğdem Ak
    2. Zeynep Sayar
    3. Guillaume Thibault
    4. Erik A. Burlingame
    5. M. J. Kuykendall
    6. Jennifer Eng
    7. Alex Chitsazan
    8. Koei Chin
    9. Andrew C. Adey
    10. Christopher Boniface
    11. Paul T. Spellman
    12. George V. Thomas
    13. Ryan P. Kopp
    14. Emek Demir
    15. Young Hwan Chang
    16. Vasilis Stavrinides
    17. Sebnem Ece Eksi

  • Novel recruitment approaches and operational results for a statewide population Cohort for cancer research

    Journal of Clinical and Translational Science
    1. Zhenzhen Zhang
    2. Autumn Shafer
    3. Katie Johnson-Camacho
    4. Andrew Adey
    5. Pavana Anur
    6. Kim A. Brown
    7. Casey Conrad
    8. Rachel Crist
    9. Paige E. Farris
    10. Christina A. Harrington
    11. Lisa K. Marriott
    12. Asia Mitchell
    13. Brian O'Roak
    14. Vanessa Serrato
    15. C. Sue Richards
    16. Paul T. Spellman
    17. Jackilen Shannon

  • sciMET-cap

    Genome biology
    1. Sonia N. Acharya
    2. Ruth V. Nichols
    3. Lauren E. Rylaarsdam
    4. Brendan L. O’Connell
    5. Theodore P. Braun
    6. Andrew C. Adey

  • Systematic benchmarking of single-cell ATAC-sequencing protocols

    Nature biotechnology
    1. Florian V. De Rop
    2. Gert Hulselmans
    3. Chris Flerin
    4. Paula Soler-Vila
    5. Albert Rafels
    6. Valerie Christiaens
    7. Carmen Bravo González-Blas
    8. Domenica Marchese
    9. Ginevra Caratù
    10. Suresh Poovathingal
    11. Orit Rozenblatt-Rosen
    12. Michael Slyper
    13. Wendy Luo
    14. Christoph Muus
    15. Fabiana Duarte
    16. Rojesh Shrestha
    17. S. Tansu Bagdatli
    18. M. Ryan Corces
    19. Lira Mamanova
    20. Andrew Knights
    21. Kerstin B. Meyer
    22. Ryan Mulqueen
    23. Akram Taherinasab
    24. Patrick Maschmeyer
    25. Jörn Pezoldt
    26. Camille Lucie Germaine Lambert
    27. Marta Iglesias
    28. Sebastián R. Najle
    29. Zain Y. Dossani
    30. Luciano G. Martelotto
    31. Zach Burkett
    32. Ronald Lebofsky
    33. José Ignacio Martin-Subero
    34. Satish Pillai
    35. Arnau Sebé-Pedrós
    36. Bart Deplancke
    37. Sarah A. Teichmann
    38. Leif S. Ludwig
    39. Theodore P. Braun
    40. Andrew C. Adey
    41. William J. Greenleaf
    42. Jason D. Buenrostro
    43. Aviv Regev
    44. Stein Aerts
    45. Holger Heyn

  • The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1β–mediated AML progression

    Blood
    1. Hsin Yun Lin
    2. Mona Mohammadhosseini
    3. John McClatchy
    4. Marina Villamor-Payà
    5. Sophia Jeng
    6. Daniel Bottomly
    7. Chia Feng Tsai
    8. Camilo Posso
    9. Jeremy Jacobson
    10. Andrew Adey
    11. Sara Gosline
    12. Tao Liu
    13. Shannon McWeeney
    14. Travis H. Stracker
    15. Anupriya Agarwal

  • txci-ATAC-seq

    Genome biology
    1. Hao Zhang
    2. Ryan M. Mulqueen
    3. Natalie Iannuzo
    4. Dominique O. Farrera
    5. Francesca Polverino
    6. James J. Galligan
    7. Julie G. Ledford
    8. Andrew C. Adey
    9. Darren A. Cusanovich

  • Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility

    Cell Reports Methods
    1. Konstantin Queitsch
    2. Travis W. Moore
    3. Brendan L. O'Connell
    4. Ruth V. Nichols
    5. John L. Muschler
    6. Dove Keith
    7. Charles Lopez
    8. Rosalie C. Sears
    9. Gordon B. Mills
    10. Galip Gürkan Yardımcı
    11. Andrew C. Adey

  • Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

    Genome Research
    1. Brendan L. O’Connell
    2. Ruth V. Nichols
    3. Dmitry Pokholok
    4. Jerushah Thomas
    5. Sonia N. Acharya
    6. Andrew Nishida
    7. Casey A. Thornton
    8. Marissa Co
    9. Andrew J. Fields
    10. Frank J. Steemers
    11. Andrew C. Adey

  • BET inhibitors rescue anti-PD1 resistance by enhancing TCF7 accessibility in leukemia-derived terminally exhausted CD8+ T cells

    Leukemia
    1. Kyle A. Romine
    2. Kevin MacPherson
    3. Hyun jun Cho
    4. Yoko Kosaka
    5. Patrick A. Flynn
    6. Kaelan H. Byrd
    7. Jesse L. Coy
    8. Matthew T. Newman
    9. Ravina Pandita
    10. Christopher P. Loo
    11. Jaime Scott
    12. Andrew C. Adey
    13. Evan F. Lind

  • Meet the author

    Cell Reports Methods
    1. Andrew C. Adey

  • Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon

    American Journal of Human Genetics
    1. Timothy D. O'Brien
    2. Amiee B. Potter
    3. Catherine C. Driscoll
    4. Gregory Goh
    5. John H. Letaw
    6. Sarah McCabe
    7. Jane Thanner
    8. Arpita Kulkarni
    9. Rossana Wong
    10. Samuel Medica
    11. Tiana Week
    12. Jacob Buitrago
    13. Aaron Larson
    14. Katie Johnson Camacho
    15. Kim Brown
    16. Rachel Crist
    17. Casey Conrad
    18. Sara Evans-Dutson
    19. Ryan Lutz
    20. Asia Mitchell
    21. Pavana Anur
    22. Vanessa Serrato
    23. Autumn Shafer
    24. Lisa K. Marriott
    25. K. J. Hamman
    26. Amelia Mulford
    27. Wojciech Wiszniewski
    28. Jone E. Sampson
    29. Andrew Adey
    30. Brian J. O'Roak
    31. Christina A. Harrington
    32. Jackilen Shannon
    33. Paul T. Spellman
    34. C. Sue Richards

  • Supervised learning of high-confidence phenotypic subpopulations from single-cell data

    Nature Machine Intelligence
    1. Tao Ren
    2. Canping Chen
    3. Alexey V. Danilov
    4. Susan Liu
    5. Xiangnan Guan
    6. Shunyi Du
    7. Xiwei Wu
    8. Mara H. Sherman
    9. Paul T. Spellman
    10. Lisa M. Coussens
    11. Andrew C. Adey
    12. Gordon B. Mills
    13. Ling Yun Wu
    14. Zheng Xia

  • Cas12a-Capture

    CRISPR Journal
    1. Taylor L. Mighell
    2. Andrew Nishida
    3. Brendan L. O'connell
    4. Caitlin V. Miller
    5. Sally Grindstaff
    6. Casey A. Thornton
    7. Andrew C. Adey
    8. Daniel Doherty
    9. Brian J. O'roak

  • High-throughput robust single-cell DNA methylation profiling with sciMETv2

    Nature communications
    1. Ruth V. Nichols
    2. Brendan L. O’Connell
    3. Ryan M. Mulqueen
    4. Jerushah Thomas
    5. Ashley R. Woodfin
    6. Sonia Acharya
    7. Gail Mandel
    8. Dmitry Pokholok
    9. Frank J. Steemers
    10. Andrew C. Adey

  • Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

    Nature biotechnology
    1. Duanchen Sun
    2. Xiangnan Guan
    3. Amy E. Moran
    4. Ling Yun Wu
    5. David Z. Qian
    6. Pepper Schedin
    7. Mu Shui Dai
    8. Alexey V. Danilov
    9. Joshi J. Alumkal
    10. Andrew C. Adey
    11. Paul T. Spellman
    12. Zheng Xia

  • Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development

    Journal of Neuroscience
    1. Marissa Co
    2. Rebecca A. Barnard
    3. Jennifer N. Jahncke
    4. Sally Grindstaff
    5. Lev M. Fedorov
    6. Andrew C. Adey
    7. Kevin M. Wright
    8. Brian J. O’Roak

  • Age-dependent transcriptional alterations in cardiac endothelial cells

    Physiological genomics
    1. Uchenna Emechebe
    2. Jonathan W. Nelson
    3. Nabil J. Alkayed
    4. Sanjiv Kaul
    5. Andrew C. Adey
    6. Anthony P. Barnes

  • Epigenetic loss of heterogeneity from low to high grade localized prostate tumours

    Nature communications
    1. Sebnem Ece Eksi
    2. Alex Chitsazan
    3. Zeynep Sayar
    4. George V. Thomas
    5. Andrew J. Fields
    6. Ryan P. Kopp
    7. Paul T. Spellman
    8. Andrew C. Adey

  • High-content single-cell combinatorial indexing

    Nature biotechnology
    1. Ryan M. Mulqueen
    2. Dmitry Pokholok
    3. Brendan L. O’Connell
    4. Casey A. Thornton
    5. Fan Zhang
    6. Brian J. O’Roak
    7. Jason Link
    8. Galip Gürkan Yardımcı
    9. Rosalie C. Sears
    10. Frank J. Steemers
    11. Andrew C. Adey

  • Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum

    Nature communications
    1. Timothy A. Bates
    2. Hans C. Leier
    3. Zoe L. Lyski
    4. Savannah K. McBride
    5. Felicity J. Coulter
    6. Jules B. Weinstein
    7. James R. Goodman
    8. Zhengchun Lu
    9. Sarah A.R. Siegel
    10. Peter Sullivan
    11. Matt Strnad
    12. Amanda E. Brunton
    13. David X. Lee
    14. Andrew C. Adey
    15. Benjamin N. Bimber
    16. Brian J. O’Roak
    17. Marcel E. Curlin
    18. William B. Messer
    19. Fikadu G. Tafesse

  • Single-cell multiomics to probe relationships between histone modifications and transcription

    Nature Methods
    1. Andrew C. Adey

  • Spatially mapped single-cell chromatin accessibility

    Nature communications
    1. Casey A. Thornton
    2. Ryan M. Mulqueen
    3. Kristof A. Torkenczy
    4. Andrew Nishida
    5. Eve G. Lowenstein
    6. Andrew J. Fields
    7. Frank J. Steemers
    8. Wenri Zhang
    9. Heather L. McConnell
    10. Randy L. Woltjer
    11. Anusha Mishra
    12. Kevin M. Wright
    13. Andrew C. Adey

  • High-Throughput Single-Cell Sequencing with Linear Amplification

    Molecular Cell
    1. Yi Yin
    2. Yue Jiang
    3. Kwan Wood Gabriel Lam
    4. Joel B. Berletch
    5. Christine M. Disteche
    6. William S. Noble
    7. Frank J. Steemers
    8. R. Daniel Camerini-Otero
    9. Andrew C. Adey
    10. Jay Shendure