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Chongyuan Luo, Ph.D. - Publications

Affiliations: 
2006-2012 Plant Biology Rutgers University, New Brunswick, New Brunswick, NJ, United States 
 2012-2019 Genomic Analysis Laboratory Salk Institute for Biological Studies, La Jolla, CA, United States 
 2019- Human Genetics University of California Los Angeles School of Medicine 
Area:
Epigenomics, Neuroscience
Website:
https://luogenomics.github.io/
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia. Biorxiv : the Preprint Server For Biology. PMID 38328094 DOI: 10.1101/2024.01.25.577200  0.583
2023 Flint J, Heffel MG, Chen Z, Mefford J, Marcus E, Chen PB, Ernst J, Luo C. Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription. Cell Genomics. 3: 100454. PMID 38116123 DOI: 10.1016/j.xgen.2023.100454  0.366
2023 Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Luo C, et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 624: 366-377. PMID 38092913 DOI: 10.1038/s41586-023-06805-y  0.76
2023 Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, et al. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genomics. 3: 100342. PMID 37492103 DOI: 10.1016/j.xgen.2023.100342  0.729
2023 Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Luo C, et al. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. Biorxiv : the Preprint Server For Biology. PMID 37131654 DOI: 10.1101/2023.04.16.536509  0.759
2022 Gandal MJ, Haney JR, Wamsley B, Yap CX, Parhami S, Emani PS, Chang N, Chen GT, Hoftman GD, de Alba D, Ramaswami G, Hartl CL, Bhattacharya A, Luo C, Jin T, et al. Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Nature. PMID 36323788 DOI: 10.1038/s41586-022-05377-7  0.302
2022 Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, et al. knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. Elife. 11. PMID 35604009 DOI: 10.7554/eLife.66909  0.782
2022 Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genomics. 2. PMID 35419551 DOI: 10.1016/j.xgen.2022.100107  0.759
2022 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Luo C, et al. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. PMID 35319013 DOI: 10.1038/s41586-022-04562-y  0.641
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Luo C, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8  0.73
2021 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Luo C, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 598: 111-119. PMID 34616062 DOI: 10.1038/s41586-021-03465-8  0.752
2021 Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8  0.833
2021 Gao C, Liu J, Kriebel AR, Preissl S, Luo C, Castanon R, Sandoval J, Rivkin A, Nery JR, Behrens MM, Ecker JR, Ren B, Welch JD. Iterative single-cell multi-omic integration using online learning. Nature Biotechnology. PMID 33875866 DOI: 10.1038/s41587-021-00867-x  0.559
2021 Evrony GD, Hinch AG, Luo C. Applications of Single-Cell DNA Sequencing. Annual Review of Genomics and Human Genetics. PMID 33722077 DOI: 10.1146/annurev-genom-111320-090436  0.363
2021 Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron. 109: 11-26. PMID 33412093 DOI: 10.1016/j.neuron.2020.12.010  0.399
2020 He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 583: 752-759. PMID 32728242 DOI: 10.1038/S41586-020-2119-X  0.768
2020 Lavery LA, Ure K, Wan YW, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, et al. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. Elife. 9. PMID 32159514 DOI: 10.7554/Elife.52981  0.632
2020 Lavery LA, Ure K, Wan Y, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, et al. Author response: Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome Elife. DOI: 10.7554/Elife.52981.Sa2  0.544
2020 Behrens M, Lai C, Pinto-Duarte A, Li J, Luo C, Powell S, Ecker J, Mukamel E. Using the Power of Single-Nucleus Epigenomics to Map the Molecular Complexity of the Adult Brain Biological Psychiatry. 87: S61-S62. DOI: 10.1016/J.Biopsych.2020.02.179  0.532
2019 Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature Methods. PMID 31501549 DOI: 10.1038/S41592-019-0547-Z  0.837
2019 Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. Elife. 8. PMID 30644360 DOI: 10.7554/Elife.40197  0.641
2018 Luo C, Hajkova P, Ecker JR. Dynamic DNA methylation: In the right place at the right time. Science (New York, N.Y.). 361: 1336-1340. PMID 30262495 DOI: 10.1126/Science.Aat6806  0.663
2018 Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, et al. Robust single-cell DNA methylome profiling with snmC-seq2. Nature Communications. 9: 3824. PMID 30237449 DOI: 10.1038/S41467-018-06355-2  0.785
2018 Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. Elife. 7. PMID 30188322 DOI: 10.7554/Elife.36187  0.633
2018 Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. Author response: Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons Elife. DOI: 10.7554/Elife.40197.020  0.608
2018 Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Author response: Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells Elife. DOI: 10.7554/Elife.36187.042  0.513
2017 Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, et al. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science (New York, N.Y.). 357: 600-604. PMID 28798132 DOI: 10.1126/Science.Aan3351  0.813
2016 Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker JR. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. Cell Reports. 17: 3369-3384. PMID 28009303 DOI: 10.1016/J.Celrep.2016.12.001  0.646
2016 Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. PMID 27749838 DOI: 10.1038/Nmeth.4035  0.698
2016 Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Epigenomic landscapes of retinal rods and cones. Elife. 5. PMID 26949250 DOI: 10.7554/Elife.11613  0.769
2015 Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 86: 1369-84. PMID 26087164 DOI: 10.1016/J.Neuron.2015.05.018  0.775
2015 Luo C, Ecker JR. Exceptional epigenetics in the brain Science. 348: 1094-1095. PMID 26045424 DOI: 10.1126/Science.Aac5832  0.667
2015 Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, et al. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 521: 316-21. PMID 25945737 DOI: 10.1038/Nature14413  0.776
2015 Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Author response: Epigenomic landscapes of retinal rods and cones Elife. DOI: 10.7554/Elife.11613.056  0.62
2014 Luo C, Dong J, Zhang Y, Lam E. Decoding the role of chromatin architecture in development: coming closer to the end of the tunnel. Frontiers in Plant Science. 5: 374. PMID 25191327 DOI: 10.3389/Fpls.2014.00374  0.599
2014 Widiez T, Symeonidi A, Luo C, Lam E, Lawton M, Rensing SA. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. The Plant Journal : For Cell and Molecular Biology. 79: 67-81. PMID 24779858 DOI: 10.1111/Tpj.12542  0.561
2014 Luo C, Lam E. Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using ChIP-seq. Methods in Molecular Biology (Clifton, N.J.). 1112: 177-93. PMID 24478015 DOI: 10.1007/978-1-62703-773-0_12  0.597
2013 Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. The Plant Journal : For Cell and Molecular Biology. 73: 77-90. PMID 22962860 DOI: 10.1111/Tpj.12017  0.613
2012 Vaquero-Sedas MI, Luo C, Vega-Palas MA. Analysis of the epigenetic status of telomeres by using ChIP-seq data. Nucleic Acids Research. 40: e163. PMID 22855559 DOI: 10.1093/Nar/Gks730  0.417
2011 Amini A, Luo C, Lam E. Chromatin beacons: global sampling of chromatin physical properties using chromatin charting lines. Methods in Molecular Biology (Clifton, N.J.). 701: 301-14. PMID 21181538 DOI: 10.1007/978-1-61737-957-4_17  0.581
2010 Luo C, Lam E. ANCORP: a high-resolution approach that generates distinct chromatin state models from multiple genome-wide datasets. The Plant Journal : For Cell and Molecular Biology. 63: 339-51. PMID 20444227 DOI: 10.1111/J.1365-313X.2010.04236.X  0.622
2009 Luo C, Durgin BG, Watanabe N, Lam E. Defining the functional network of epigenetic regulators in Arabidopsis thaliana. Molecular Plant. 2: 661-74. PMID 19825647 DOI: 10.1093/Mp/Ssp017  0.607
2009 Luo C, Lam E. Chromatin charting: global mapping of epigenetic effects. Methods in Molecular Biology (Clifton, N.J.). 553: 127-39. PMID 19588104 DOI: 10.1007/978-1-60327-563-7_7  0.564
2009 Lam E, Luo C, Watanabe N. Charting functional and physical properties of chromatin in living cells. Current Opinion in Genetics & Development. 19: 135-41. PMID 19327981 DOI: 10.1016/J.Gde.2009.02.004  0.613
2007 Rotter D, Bharti AK, Li HM, Luo C, Bonos SA, Bughrara S, Jung G, Messing J, Meyer WA, Rudd S, Warnke SE, Belanger FC. Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses. Molecular Genetics and Genomics : Mgg. 278: 197-209. PMID 17497174 DOI: 10.1007/S00438-007-0240-2  0.348
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