Ecker, Joseph R.
Salk Institute for Biological Studies · Howard Hughes Medical Institute
44 papers on CoChatORCID 0000-0001-5799-5895
Most cited papers
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Retroviral DNA integration: viral and cellular determinants of target-site selection
Lewinski, M. K., Yamashita, M., Emerman, M., Ciuffi, A., Marshall, H., Crawford, G., Collins, F., Shinn, P., Leipzig, J., Hannenhalli, S., et al. (2006) · PLoS Pathogens
HIV Research and TreatmentVirus-based gene therapy research
Cited by 364
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Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Lee, D.-S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J. R., Fitzpatrick, C., O’Connor, C., Dixon, J. R., et al. (2019) · Nature Methods
Genomics and Chromatin DynamicsEpigenetics and DNA Methylation
Cited by 340
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Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels
Salehin, M., Li, B., Tang, M., Katz, E., Song, L., Ecker, J. R., Kliebenstein, D. J., & Estelle, M. (2019) · Nature Communications
Plant Stress Responses and TolerancePlant Molecular Biology Research
Cited by 311
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A Combinatorial Interplay Among the 1-Aminocyclopropane-1-Carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana
Tsuchisaka, A., Yu, G., Jin, H., Alonso, J. M., Ecker, J. R., Zhang, X., Gao, S., & Theologis, A. (2009) · Genetics
Postharvest Quality and Shelf Life ManagementPlant Molecular Biology Research
Cited by 309
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DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution
Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2020) · Nature
Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation
Cited by 290
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DNA methylation atlas of the mouse brain at single-cell resolution
Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2021) · Nature
Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation
Cited by 289
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Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
Lister, R., Gregory, B. D., & Ecker, J. R. (2009) · Current Opinion in Plant Biology
Genomics and Phylogenetic StudiesChromosomal and Genetic Variations
Cited by 274
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Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Sabbagh, M. F., Heng, J. S., Luo, C., Castanon, R. G., Nery, J. R., Rattner, A., Goff, L. A., Ecker, J. R., & Nathans, J. (2018) · eLife
Barrier Structure and Function StudiesGenomics and Chromatin Dynamics
Cited by 245
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PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism
Lariguet, P., Schepens, I., Hodgson, D., Pedmale, U. V., Trevisan, M., Kami, C., de Carbonnel, M., Alonso, J. M., Ecker, J. R., Liscum, E., et al. (2006) · Proceedings of the National Academy of Sciences
Light effects on plantsPlant Molecular Biology Research
Cited by 190
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Robust single-cell DNA methylome profiling with snmC-seq2
Luo, C., Rivkin, A., Zhou, J., Sandoval, J. P., Kurihara, L., Lucero, J., Castanon, R., Nery, J. R., Pinto-Duarte, A., Bui, B., et al. (2018) · Nature Communications
Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics
Cited by 189
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An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Fang, R., Qiu, Y., Poirion, O., Li, B., Liu, H., et al. (2020) · Nature
Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics
Cited by 187
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An atlas of gene regulatory elements in adult mouse cerebrum
Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., et al. (2021) · Nature
Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics
Cited by 185
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Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation
Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T. J., Dixon, J. R., & Ecker, J. R. (2019) · Proceedings of the National Academy of Sciences
Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics
Cited by 180
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A comparative atlas of single-cell chromatin accessibility in the human brain
Li, Y. E., Preissl, S., Miller, M., Johnson, N. D., Wang, Z., Jiao, H., Zhu, C., Wang, Z., Xie, Y., Poirion, O., et al. (2023) · Science
Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics
Cited by 173
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The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection
Buganim, Y., Markoulaki, S., van Wietmarschen, N., Hoke, H., Wu, T., Ganz, K., Akhtar-Zaidi, B., He, Y., Abraham, B. J., Porubsky, D., et al. (2014) · Cell Stem Cell
Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation
Cited by 163
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Single-cell DNA methylation and 3D genome architecture in the human brain
Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R. G., Kenworthy, M., Altshul, J., Valadon, C., Aldridge, A., et al. (2023) · Science
Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics
Cited by 154
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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.-A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J. R., et al. (2023) · Nature
Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics
Cited by 139
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Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population
Kim, E. J., Zhang, Z., Huang, L., Ito-Cole, T., Jacobs, M. W., Juavinett, A. L., Senturk, G., Hu, M., Ku, M., Ecker, J. R., et al. (2020) · Neuron
Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research
Cited by 103
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Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Luo, C., Lee, Q. Y., Wapinski, O., Castanon, R., Nery, J. R., Mall, M., Kareta, M. S., Cullen, S. M., Goodell, M. A., Chang, H. Y., et al. (2019) · eLife
Epigenetics and DNA MethylationPluripotent Stem Cells Research
Cited by 76
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Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain
Zhang, Z., Zhou, J., Tan, P., Pang, Y., Rivkin, A., Kirchgessner, M. A., Williams, E., Lee, C.-T., Liu, H., Franklin, A. D., et al. (2020) · Nature
Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation
Cited by 75
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