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Joseph R. Ecker, Ph.D.

Affiliations: 
HHMI-The Salk Institute for Biological Studies 
Area:
epigenetics, molecular genetics
Website:
http://www.salk.edu/faculty/ecker.html
Google:
"Joseph Ecker"
Bio:

http://www.hhmi.org/research/hhmi-gbmf/ecker_bio.html

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Parents

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Richard W. Hyman grad student 1978-1982 Penn State College of Medicine (Chemistry Tree)
Ronald W. Davis post-doc 1983-1986 Stanford Medical School (Evolution Tree)

Children

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Ammar Naqvi research assistant 2006-2008 (Chemistry Tree)
Stephen F Gonzalez research assistant 2019-2022 Salk Institute
Peter Berube grad student UCSD Bioinformatics
Katherine N. Chang grad student Alliances and Partnerships Manager, Illumina
Christopher Kim grad student
Ramlah B. Nehring grad student Vice President of Corporate Development at Foundation Medicine
Jeffrey Nelson grad student UW Madison
Qian Peng grad student Assistant Professor of MCN, Scripps Resarch (Neurotree)
Gregg Roman grad student Associate Professor, University of Houston (Neurotree)
Matt Schultz grad student Team Lead, INVITAE
Anna Stepanova grad student NCSU
Ambika Sundaresan grad student Sr. Bioinformatics Scientist, Illumina
Pengcheng Tan grad student UCLA Bioinformatics Program
Shelly Trigg grad student Research Scientist, Gloucester Marine Genomics Institute
Sung Yeon grad student Yale
Jingtian Zhou grad student UCSD Bioinformatics
May Wu grad student 2022-
Kaushik Komandur grad student 2024- UCSD Biomedical Sciences
Hanqing Liu grad student 2017-2022 UCSD Biology
post-doc Sr. Associate Vice Provost for Technology Management, Drexel Applied Innovation
José Alonso post-doc Williams Neal Reynolds Distinguished Professor of Plant Biology and Genetics, North Carolina State University
Justin Borevitz post-doc Professor, Australian National University
Qimin Chao post-doc Director, Morphotek, Inc.
Ken Dewar post-doc Associate Professor, Department of Human Genetics, McGill University
Robert H. Dowen post-doc Assistant Professor, Biology Department, University of North Carolina (Chemistry Tree)
Patrick Dunn post-doc Staff Scientist, Celera Genomics
Shuai Fu post-doc
Mary Galli post-doc Research Assistant, Waksman Institute, Rutgers University
Renee M. Garza post-doc HHMI-The Salk Institute for Biological Studies (Chemistry Tree)
Brian Gregory post-doc Associate Professor, Department of Biology, University of Pennsylvania
Hongwei Guo post-doc Assistant Professor, Peking University, CHINA (Cell Biology Tree)
Yupeng He post-doc Manager, Bioinformatics, Guardant Health
Robert Henley post-doc 10X Genomics
Takashi Hirayama post-doc IPSR, Okayama University
Elizabeth Howell post-doc
Shao-Shan Carol Huang post-doc Assistant Professor, New York University
Natanella Illouz-Eliaz post-doc HHMI-The Salk Institute for Biological Studies
Sumie Ishiguro post-doc Assistant Professor, Nagoya University
Florian Jupe post-doc Bayer Crop Science
Taji Kawakatsu post-doc Principal Researcher, National Institute of Agrobiological Sciences, Japan
Joseph John Kieber post-doc UNC Chapel Hill
Yukio Kurihara post-doc RIKEN
Travis Lee post-doc Salk Institute (Chemistry Tree)
Mathew G. Lewsey post-doc Associate Professor, La Trobe University, Australia
Hai Li post-doc Associate Research Scientist, Columbia University
Sarah J. Liljegren post-doc Associate Professor, Department of Biology, University of Mississippi
Jun Lim post-doc Assistant Professor, Department of Bioscience and Biotechnology, Konkuk University, South Korea
Ryan Lister post-doc Winthrop Professor, The University of Western Australia
Chongyuan Luo post-doc Assistant Professor, Department of Human Genetics, UCLA
Tatsuya Nobori post-doc HHMI-The Salk Institute for Biological Studies
Ronan O'Malley post-doc Director of Sequencing Operations, JGI
Mattia Pelizzola post-doc
Hong Qiao post-doc UT Austin
Robert J. Schmitz post-doc Associate Professor, University of Georgia
Tatjana Singer post-doc Manager of Collaborations, Omniome, Inc.
Liang Song post-doc Assistant Professor, University of British Columbia
Joseph Swift post-doc HHMI-The Salk Institute for Biological Studies
Wei Tian post-doc HHMI-The Salk Institute for Biological Studies
Wenliang Wang post-doc HHMI-The Salk Institute for Biological Studies
Bang-An Wang post-doc HHMI-The Salk Institute for Biological Studies
Kevin Wang post-doc Assistant Professor, Academia Sinica, Taiwan
Mingtian Xie post-doc CIBUS
Junshi Yazaki post-doc
Hitoshi Yoshida post-doc NARO, Japan
Mark Zander post-doc Assistant Professor, Waksman Institute, Rutgers University
Zhuzhu Zhang post-doc HHMI-The Salk Institute for Biological Studies
James Walker post-doc 2022-
Wubin Ding post-doc 2023-
Roberto Solano post-doc 1996-1999
Hiroshi Shiba post-doc 2005-2006 Nara Institute of Science and Technology
Robert J. Schmitz post-doc 2008-2013
Manoj Hariharan research scientist 2012-

Collaborators

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Antonio Pinto-Duarte collaborator (Neurotree)
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Publications

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Zhou J, Wu Y, Liu H, et al. (2025) Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. Biorxiv : the Preprint Server For Biology
Zhou J, Luo C, Liu H, et al. (2025) Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia. Cell Genomics. 100774
Miller CN, Jarrell-Hurtado S, Haag MV, et al. (2025) A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation. Developmental Cell
Nobori T, Monell A, Lee TA, et al. (2025) A rare PRIMER cell state in plant immunity. Nature
Swift J, Luginbuehl LH, Hua L, et al. (2024) Exaptation of ancestral cell-identity networks enables C photosynthesis. Nature
Heffel MG, Zhou J, Zhang Y, et al. (2024) Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature
Denyer T, Wu PJ, Colt K, et al. (2024) Streamlined spatial and environmental expression signatures characterize the minimalist duckweed . Genome Research
Tian W, Ding W, Shen J, et al. (2024) BAllC and BAllCools: Efficient formatting and operating for Single-Cell DNA methylation data. Bioinformatics (Oxford, England)
Gonzalez S, Swift J, Yaaran A, et al. (2024) transcriptome responses to low water potential using high-throughput plate assays. Elife. 12
Chien JF, Liu H, Wang BA, et al. (2024) Cell-type-specific effects of age and sex on human cortical neurons. Neuron
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