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2025
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Molecular Biology
USA
2026

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Best Scientists

D-Index
178
Citations
138728
World Ranking
646
National Ranking
404

Molecular Biology

D-Index
183
Citations
147021
World Ranking
31
National Ranking
22

Research.com Recognitions

  • 2026 - Research.com Molecular Biology in United States Leader Award
  • 2025 - Research.com Best Scientists Award
  • 2025 - Research.com Molecular Biology in United States Leader Award
  • 2024 - Research.com Genetics and Molecular Biology in United States Leader Award
  • 2023 - Research.com Genetics in United States Leader Award
  • 2015 - Fellow of the American Academy of Arts and Sciences
  • 2012 - Fellow of the American Association for the Advancement of Science (AAAS)
  • 2006 - Member of the National Academy of Sciences

Overview

Joseph R. Ecker is affiliated with the Salk Institute for Biological Studies in the United States. Their research primarily focuses on the field of Biochemistry, Genetics, and Molecular Biology, with significant contributions in Molecular Biology, Plant Science, Neurology, Genetics, and Biophysics. Several specific research topics are prominent in their work, including Single-cell and spatial transcriptomics, Epigenetics and DNA Methylation, Genomics and Chromatin Dynamics, Plant Molecular Biology Research, RNA Research and Splicing, Neuroinflammation and Neurodegeneration Mechanisms, and Cell Image Analysis Techniques.

The scientist has authored numerous publications, with recent notable papers including:

  • Expanded encyclopaedias of DNA elements in the human and mouse genomes (2020, Nature)
  • A multimodal cell census and atlas of the mammalian primary motor cortex (2021, Nature)
  • Comprehensive analysis of single cell ATAC-seq data with SnapATAC (2021, Nature Communications)
  • An atlas of dynamic chromatin landscapes in mouse fetal development (2020, Nature)
  • A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex (2021, Nature)

Ecker collaborates frequently with several co-authors, including Joseph R. Nery, Hanqing Liu, Bing Ren, M. Margarita Behrens, and Rosa Castanon. Publication venues commonly featuring their work include bioRxiv (Cold Spring Harbor Laboratory), Nature, ENCODE Datasets, eLife, and Nature Communications.

Their academic recognition includes election as a Fellow of the American Academy of Arts and Sciences in 2015, Fellow of the American Association for the Advancement of Science (AAAS) in 2012, and membership in the National Academy of Sciences since 2006.

Best Publications

  • Integrative analysis of 111 reference human epigenomes

    Anshul Kundaje;Wouter Meuleman;Wouter Meuleman;Jason Ernst

  • Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

    José M. Alonso;Anna N. Stepanova;Thomas J. Leisse;Christopher J. Kim

  • Human DNA methylomes at base resolution show widespread epigenomic differences

    Ryan Lister;Mattia Pelizzola;Robert H. Dowen;R. David Hawkins

  • Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

    Ryan Lister;Ronan C. O'Malley;Julian Tonti-Filippini;Brian D. Gregory

  • Expanded encyclopaedias of DNA elements in the human and mouse genomes

    Jill E. Moore;Michael J. Purcaro;Henry E. Pratt;Charles B. Epstein

  • HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots

    Astrid R.W. Schröder;Paul Shinn;Huaming Chen;Charles Berry

  • CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases

    Joseph J. Kieber;Madge Rothenberg;Gregg Roman;Kenneth A. Feldmann

  • Ethylene biosynthesis and signaling networks.

    Kevin L.-C. Wang;Hai Li;Joseph R. Ecker

  • Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

    Xiaoyu Zhang;Junshi Yazaki;Ambika Sundaresan;Shawn Cokus

  • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

    Susanna Atwell;Yu S. Huang;Bjarni J. Vilhjálmsson;Glenda Willems

  • Phased diploid genome assembly with single-molecule real-time sequencing

    Chen-Shan Chin;Paul Peluso;Fritz J Sedlazeck;Maria Nattestad

  • Global Epigenomic Reconfiguration During Mammalian Brain Development

    Ryan Lister;Ryan Lister;Eran A. Mukamel;Joseph R. Nery;Mark Urich

  • The NIH Roadmap Epigenomics Mapping Consortium

    Bradley E Bernstein;John A Stamatoyannopoulos;Joseph F Costello;Bing Ren

  • Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

    Matthew T. Weirauch;Matthew T. Weirauch;Ally Yang;Mihai Albu;Atina G. Cote

  • Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

    Ryan Lister;Mattia Pelizzola;Yasuyuki S. Kida;R. David Hawkins

  • Chromatin architecture reorganization during stem cell differentiation

    Jesse R. Dixon;Inkyung Jung;Siddarth Selvaraj;Yin Shen

  • EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis.

    Jose M. Alonso;Takashi Hirayama;Gregg Roman;Saeid Nourizadeh

  • Exploiting the triple response of Arabidopsis to identify ethylene-related mutants.

    Plinio Guzman;Joseph R. Ecker

  • Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1

    Roberto Solano;Anna Stepanova;Qimin Chao;Joseph R. Ecker

  • Assignment of 30 Microsatellite Loci to the Linkage Map of Arabidopsis

    Callum J. Bell;Joseph R. Ecker

Frequent Co-Authors

Joseph R. Nery
Joseph R. Nery Salk Institute for Biological Studies
Jose M. Alonso
Jose M. Alonso North Carolina State University
Bing Ren
Bing Ren New York Genome Center
Ryan Lister
Ryan Lister University of Western Australia
Joanne Chory
Joanne Chory Salk Institute for Biological Studies
Robert J. Schmitz
Robert J. Schmitz University of Georgia
M. Margarita Behrens
M. Margarita Behrens Salk Institute for Biological Studies
Detlef Weigel
Detlef Weigel Max Planck Institute for Developmental Biology
Axel Visel
Axel Visel Lawrence Berkeley National Laboratory
Len A. Pennacchio
Len A. Pennacchio Lawrence Berkeley National Laboratory

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