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Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue.
Chen ZJ, Das SS, Kar A, Lee SHT, Abuhanna KD, Alvarez M, Sukhatme MG, Gelev KZ, Heffel MG, Zhang Y, Avram O, Rahmani E, Sankararaman S, Heinonen S, Peltoniemi H, Halperin E, Pietiläinen KH, Luo C, Pajukanta P. Chen ZJ, et al. Among authors: luo c. bioRxiv [Preprint]. 2024 Nov 3:2024.11.02.621694. doi: 10.1101/2024.11.02.621694. bioRxiv. 2024. PMID: 39554055 Free PMC article. Preprint.
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain.
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, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O'Connor C, Yao Z, Smith KA, Tasic B, Zeng H, Luo C, Dixon JR, Ren B, Behrens MM, Ecker JR. Liu H, et al. Among authors: luo c. bioRxiv [Preprint]. 2023 Apr 18:2023.04.16.536509. doi: 10.1101/2023.04.16.536509. bioRxiv. 2023. Update in: Nature. 2023 Dec;624(7991):366-377. doi: 10.1038/s41586-023-06805-y. PMID: 37131654 Free PMC article. Updated. Preprint.
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.
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, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O'Connor C, Wu Z, Stoica I, Yao Z, Smith KA, Tasic B, Luo C, Dixon JR, Zeng H, Ren B, Behrens MM, Ecker JR. Liu H, et al. Among authors: luo c. Nature. 2023 Dec;624(7991):366-377. doi: 10.1038/s41586-023-06805-y. Epub 2023 Dec 13. Nature. 2023. PMID: 38092913 Free PMC article.
scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia.
Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. Zhou J, et al. Among authors: luo c. bioRxiv [Preprint]. 2024 Jan 25:2024.01.25.577200. doi: 10.1101/2024.01.25.577200. bioRxiv. 2024. Update in: Cell Genom. 2025 Mar 12;5(3):100774. doi: 10.1016/j.xgen.2025.100774. PMID: 38328094 Free PMC article. Updated. Preprint.
Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics.
Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ. Yap CX, et al. Among authors: luo c. Sci Adv. 2024 May 24;10(21):eadn7655. doi: 10.1126/sciadv.adn7655. Epub 2024 May 23. Sci Adv. 2024. PMID: 38781333 Free PMC article.
Temporally distinct 3D multi-omic dynamics in the developing human brain.
Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. Heffel MG, et al. Among authors: luo c. Nature. 2024 Nov;635(8038):481-489. doi: 10.1038/s41586-024-08030-7. Epub 2024 Oct 9. Nature. 2024. PMID: 39385032 Free PMC article.
Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation.
Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O'Connor C, Chen S, Luo C, Dixon JR, Ecker JR. Zhou J, et al. Among authors: luo c. bioRxiv [Preprint]. 2025 Mar 24:2025.03.23.644697. doi: 10.1101/2025.03.23.644697. bioRxiv. 2025. PMID: 40196612 Free PMC article. Preprint.
Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing.
Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Bloom JS, et al. Among authors: luo c. medRxiv [Preprint]. 2021 Mar 9:2020.08.04.20167874. doi: 10.1101/2020.08.04.20167874. medRxiv. 2021. Update in: Nat Biomed Eng. 2021 Jul;5(7):657-665. doi: 10.1038/s41551-021-00754-5. PMID: 32909008 Free PMC article. Updated. Preprint.
9,078 results