Ecker, Joseph R.
Salk Institute for Biological Studies · Howard Hughes Medical Institute
44 papers on CoChatORCID 0000-0001-5799-5895
Most cited papers
- Verified
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature
Genomics and Chromatin DynamicsEpigenetics and DNA Methylation
Cited by 6,368
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Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 4,673
- Verified
The NIH Roadmap Epigenomics Mapping Consortium
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 1,892
- Verified
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Schröder, A. R. W., Shinn, P., Chen, H., Berry, C., Ecker, J. R., & Bushman, F. (2002) · Cell
HIV Research and TreatmentVirus-based gene therapy research
Cited by 1,832
- Verified
Global epigenomic reconfiguration during mammalian brain development
Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science
Epigenetics and DNA MethylationGenetic Syndromes and Imprinting
Cited by 1,830
- Verified
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., et al. (2010) · Nature
Genetic Mapping and Diversity in Plants and AnimalsGenetic Associations and Epidemiology
Cited by 1,780
- Verified
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature
Genomics and Chromatin DynamicsEpigenetics and DNA Methylation
Cited by 1,646
- Verified
Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues
Zhang, X., Odom, D. T., Koo, S.-H., Conkright, M. D., Canettieri, G., Best, J., Chen, H., Jenner, R., Herbolsheimer, E., Jacobsen, E., et al. (2005) · Proceedings of the National Academy of Sciences
Genomics and Chromatin DynamicsChromatin Remodeling and Cancer
Cited by 992
- Verified
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2021) · Nature
Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research
Cited by 812
- Verified
Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2020) · Nature
Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research
Cited by 809
- Verified
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell
Epigenetics and DNA MethylationPluripotent Stem Cells Research
Cited by 806
- Verified
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 804
- Verified
Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., et al. (2015) · Neuron
Genomics and Chromatin DynamicsEpigenetics and DNA Methylation
Cited by 739
- Verified
Human body epigenome maps reveal noncanonical DNA methylation variation
Schultz, M. D., He, Y., Whitaker, J. W., Hariharan, M., Mukamel, E. A., Leung, D., Rajagopal, N., Nery, J. R., Urich, M. A., Chen, H., et al. (2015) · Nature
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 690
- Verified
Dynamic DNA methylation: In the right place at the right time
Luo, C., Hajkova, P., & Ecker, J. R. (2018) · Science
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 668
- Verified
A role for LEDGF/p75 in targeting HIV DNA integration
Ciuffi, A., Llano, M., Poeschla, E., Hoffmann, C., Leipzig, J., Shinn, P., Ecker, J. R., & Bushman, F. (2005) · Nature Medicine
HIV Research and TreatmentVirus-based gene therapy research
Cited by 658
- Verified
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
Hon, G. C., Hawkins, R. D., Caballero, O. L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L. E., et al. (2012) · Genome Research
Epigenetics and DNA MethylationGenomics and Chromatin Dynamics
Cited by 583
- Verified
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Luo, C., Keown, C. L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J. R., Sandoval, J. P., et al. (2017) · Science
Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics
Cited by 545
- Verified
A multimodal cell census and atlas of the mammalian primary motor cortex
BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature
Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics
Cited by 522
- Verified
Phototropin-related NPL1 controls chloroplast relocation induced by blue light
Jarillo, J. A., Gabrys, H., Capel, J., Alonso, J. M., Ecker, J. R., & Cashmore, A. R. (2001) · Nature
Light effects on plantsPhotosynthetic Processes and Mechanisms
Cited by 476
- Verified
Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Fang, R., Preissl, S., Li, Y., Hou, X., Lucero, J., Wang, X., Motamedi, A., Shiau, A. K., Zhou, X., Xie, F., et al. (2021) · Nature Communications
Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics
Cited by 455
- Verified
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature
Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics
Cited by 398
- Verified
An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature
Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics
Cited by 397
- Verified
Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain
Luo, C., Lancaster, M. A., Castanon, R., Nery, J. R., Knoblich, J. A., & Ecker, J. R. (2016) · Cell Reports
Epigenetics and DNA MethylationPluripotent Stem Cells Research
Cited by 370
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