Selected Publications

Heffel, M.G.*, Zhou, J.*, Zhang, Y.*, Lee, D-S.*, Hou, K.*, et al. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature (2024)

Luo, C.*, Liu, H.*, Xie, F.*, et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genomics (2022)

Lee, D.*, Luo, C.*, Zhou, J.*, et al. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature Methods (2019)

Luo, C. et al. Robust single-cell DNA methylome profiling with snmC-seq2. Nature Communications. (2018)

Luo, C.*, Keown, C.L.*, et al. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science. (2017)

BRAIN Initiative Cell Census Network

Liu, H.*, et al. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. Nature (2023)

BRAIN Initiative Cell Census Network (BICCN). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature (2021)

Liu, H.*, Zhou, J.*, et al. DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution. Nature (2021)

Bakken, T.E., et al. Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse. Nature (2021)

Yao, Z.*, Liu, H.*, Xie, F.*, Fischer, S.*, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature (2021)

Mammalian Epigenomics

IGVF Consortium Deciphering the impact of genomic variation on function. Nature. (2024)

Chien, J-F.*, et al., Cell-type-specific effects of age and sex on human cortical neurons. Neuron (2024)

Gandal, M.J.*, et al., Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Nature (2022)

Li, J.*, Pinto-Duarte, A.*, et al. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. Elife. (2022)

Gao. C., et al. Iterative single-cell multi-omic integration using online learning. Nat Biotechnol. (2021)

Evrony, G.D.*, Hinch, A.G.*, Luo, C.*, et al. Applications of Single-Cell DNA Sequencing. Annu Rev Genomics Hum Genet. (2021)

Armand, E.J.*, Li, J.*, Xie, F.*, et al. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron. (2021)

He, Y., et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. (2020)

Lavery, L.A., et al. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. Elife. (2020)

Luo, C.*, Lee, Q.Y.*, et al. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. Elife. (2019)

Luo, C.*, Hajkova, P.*, Ecker, J.R. Dynamic DNA methylation: In the right place at the right time. Science. (2018)

Sabbagh, M.F., et al. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. Elife. (2018)

Luo, C.*, Lancaster, M.A.*, et al. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. Cell Reports. (2016)

Mo, A., et al. Epigenomic landscapes of retinal rods and cones. Elife. (2016)

Wu, J.*, Okamura, D.*, et al. An alternative pluripotent state confers interspecies chimaeric competency. Nature. (2015)

Mo, A.*, Mukamel, E.A.*, Davis, F.P.*, Luo, C.*, et al. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. (2015)

Luo, C., Ecker, J.R. Exceptional epigenetics in the brain. Science. (2015)

COVID-19

Bloom, J.S., et al., Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng (2021)

Guo, L., et al., Rapid cost-effective viral genome sequencing by V-seq. bioRxiv (2020)

Guo, L.*, Boocock, J.*, et al., Genomic epidemiology of the Los Angeles COVID-19 outbreak. medRxiv (2020)

Plant Epigenomics

Widiez, T.*, Symeonidi, A.*, et al. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress.Plant J. (2014)

Luo, C.*, Dong, J.*, et al., Decoding the role of chromatin architecture in development: coming closer to the end of the tunnel.Front. Plant Sci. (2014)

Luo, C., Lam, E. Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using ChIP-seq.Methods Mol Biol. (2014)

Luo, C., et al. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for Natural Antisense Transcript production.Plant J. (2012)

Vaquero-Sedas, M.I., et al. Analysis of the epigenetic status of telomeres by using ChIP-seq data.Nucleic Acids Res. (2012)

Amini, A., et al. Chromatin Beacons: Global sampling of chromatin physical properties using chromatin charting lines.Methods Mol Biol. (2011)

Luo, C., Lam, E. ANCORP: a high resolution approach that generated distinct chromatin state model from multiple genome-wide datasets.Plant J. (2010)

Lam, E., et al. Charting functional and physical properties of chromatin in living cells.Curr Opin Genet Dev. (2009)

Luo, C.*, Durgin, B.G.*, Watanabe, N.*, and Lam, E. Defining the Functional Network of Epigenetic Regulators in Arabidopsis thaliana.Mol. Plant. (2009)

Luo, C., Lam, E. Chromatin Charting: Global mapping of epigenetic effects.Methods Mol Biol. (2009)

Other Publications

Chin, C.S.*, Peluso, P.*, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. (2016)

Rotter, D., Bharti, A.K., Li, H.M., Luo, C., Bonos, S.A., Bughrara, S., Jung, G., Messing, J., Meyer, W.A., Rudd, S., Warnke, S.E., and Belanger, F.C. Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses. (2007) Mol Genet Genomics. 278, 197-209.