Publications

• The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour.Yoshida TM, Nguyen M, Zhang L, Lu BY, Zhu B, Murray KN, Mineur YS, Zhang C, Xu D, Lin E, Luchsinger J, Bhatta S, Waizman DA, Coden ME, Ma Y, Israni-Winger K, Russo A, Wang H, Song W, Al Souz J, Zhao H, Craft JE, Picciotto MR, Grutzendler J, Distasio M, Palm NW, Hafler DA, Wang A. Nature. 2025 Jul; 2025 May 28. PMID: 40437096.
• Transcriptomic profiling after B cell depletion reveals central and peripheral immune cell changes in multiple sclerosis.Wei J, Moon J, Yasumizu Y, Zhang L, Radassi K, Buitrago-Pocasangre N, Deerhake ME, Strauli N, Chen CW, Herman A, Pedotti R, Raposo C, Yim I, Pappalardo J, Longbrake EE, Sumida TS, Axisa PP, Hafler DA. J Clin Invest. 2025 Jun 2; 2025 Mar 11. PMID: 40067358.
• The single-cell opioid responses in the context of HIV (SCORCH) consortium.Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. Mol Psychiatry. 2024 Dec; 2024 Jun 15. PMID: 38879719.
• CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.Liu T, Long W, Cao Z, Wang Y, He CH, Zhang L, Strittmatter SM, Zhao H. Brief Bioinform. 2024 Nov 22. PMID: 39592241.
• Single-cell transcriptomic and proteomic analysis of Parkinson's disease brains.Zhu B, Park JM, Coffey SR, Russo A, Hsu IU, Wang J, Su C, Chang R, Lam TT, Gopal PP, Ginsberg SD, Zhao H, Hafler DA, Chandra SS, Zhang L. Sci Transl Med. 2024 Oct 30; 2024 Oct 30. PMID: 39475571.
• Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE).Hanin A, Zhang L, Huttner AJ, Plu I, Mathon B, Bielle F, Navarro V, Hirsch LJ, Hafler DA. Neurol Neuroimmunol Neuroinflamm. 2024 Jul; 2024 May 29. PMID: 38810181.
• scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles.Zhu B, Wang Y, Ku LT, van Dijk D, Zhang L, Hafler DA, Zhao H. Genome Biol. 2023 Dec 18; 2023 Dec 18. PMID: 38111007.
• Single-cell analysis reveals inflammatory interactions driving macular degeneration.Kuchroo M, DiStasio M, Song E, Calapkulu E, Zhang L, Ige M, Sheth AH, Majdoubi A, Menon M, Tong A, Godavarthi A, Xing Y, Gigante S, Steach H, Huang J, Huguet G, Narain J, You K, Mourgkos G, Dhodapkar RM, Hirn MJ, Rieck B, Wolf G, Krishnaswamy S, Hafler BP. Nat Commun. 2023 May 5; 2023 May 5. PMID: 37147305.
• A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data.Zhu B, Li H, Zhang L, Chandra SS, Zhao H. Brief Bioinform. 2022 Sep 20. PMID: 35514182.
• The immunology of Parkinson's disease.Zhu B, Yin D, Zhao H, Zhang L. Semin Immunopathol. 2022 Sep; 2022 Jun 8. PMID: 35674826.
• Reversal of synapse loss in Alzheimer mouse models by targeting mGluR5 to prevent synaptic tagging by C1Q.Spurrier J, Nicholson L, Fang XT, Stoner AJ, Toyonaga T, Holden D, Siegert TR, Laird W, Allnutt MA, Chiasseu M, Brody AH, Takahashi H, Nies SH, Pérez-Cañamás A, Sadasivam P, Lee S, Li S, Zhang L, Huang YH, Carson RE, Cai Z, Strittmatter SM. Sci Transl Med. 2022 Jun; 2022 Jun 1. PMID: 35648810.
• A multidimensional coding architecture of the vagal interoceptive system.Zhao Q, Yu CD, Wang R, Xu QJ, Dai Pra R, Zhang L, Chang RB. Nature. 2022 Mar; 2022 Mar 16. PMID: 35296859.
• Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells.Franjic D, Skarica M, Ma S, Arellano JI, Tebbenkamp ATN, Choi J, Xu C, Li Q, Morozov YM, Andrijevic D, Vrselja Z, Spajic A, Santpere G, Li M, Zhang S, Liu Y, Spurrier J, Zhang L, Gudelj I, Rapan L, Takahashi H, Huttner A, Fan R, Strittmatter SM, Sousa AMM, Rakic P, Sestan N. Neuron. 2022 Feb 2; 2021 Nov 18. PMID: 34798047.
• Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells.Lucca LE, Axisa PP, Lu B, Harnett B, Jessel S, Zhang L, Raddassi K, Zhang L, Olino K, Clune J, Singer M, Kluger HM, Hafler DA. J Exp Med. 2021 Apr 5. PMID: 33651881.
• Transcriptomic and clonal characterization of T cells in the human central nervous system.Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Sci Immunol. 2020 Sep 18. PMID: 32948672.
• EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells.Zhang L, Ettou S, Khalid M, Taglienti M, Jain D, Jung YL, Seager C, Liu Y, Ng KH, Park PJ, Kreidberg JA. Development. 2018 Jul 18; 2018 Jul 18. PMID: 29945864.
• Depleting the methyltransferase Suv39h1 improves DNA repair and extends lifespan in a progeria mouse model.Liu B, Wang Z, Zhang L, Ghosh S, Zheng H, Zhou Z. Nat Commun. 2013. PMID: 23695662.
• Rett syndrome mutation MeCP2 T158A disrupts DNA binding, protein stability and ERP responses.Goffin D, Allen M, Zhang L, Amorim M, Wang IT, Reyes AR, Mercado-Berton A, Ong C, Cohen S, Hu L, Blendy JA, Carlson GC, Siegel SJ, Greenberg ME, Zhou Z. Nat Neurosci. 2011 Nov 27; 2011 Nov 27. PMID: 22119903.
• Histone H4 lysine 16 hypoacetylation is associated with defective DNA repair and premature senescence in Zmpste24-deficient mice.Krishnan V, Chow MZ, Wang Z, Zhang L, Liu B, Liu X, Zhou Z. Proc Natl Acad Sci U S A. 2011 Jul 26; 2011 Jul 11. PMID: 21746928.