Publications

2025

Mi X, Chen AB, Duarte D, Carey E, Taylor CR, Braaker PN, Bright M, Almeida RG, Lim JX, Ruetten VMS, Wang Y, Wang M, Zhang W, Zheng W, Reitman ME, Huang Y, Wang X, Li L, Deng H, Shi SH, Poskanzer KE, Lyons DA, Nimmerjahn A, Ahrens MB, Yu G. Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals. Cell. 2025 May 15;188(10):2794-2809.e21. doi: 10.1016/j.cell.2025.03.012. Epub 2025 Apr 8. PMID: 40203826.

Wang Y, Fu Y, Lu Y, Zhang Z, Clarke R, Parker SJ, Herrington DM, Yu G, Wang Y. iDDN: determining trans-omics network structure and rewiring with integrative differential dependency networks. Bioinform Adv. 2025 May 8;5(1):vbaf086. doi: 10.1093/bioadv/vbaf086. PMID: 40365110; PMCID: PMC12070392.

Gazit Shimoni N, Tose AJ, Seng C, Jin Y, Lukacsovich T, Yang H, Verharen JPH, Liu C, Tanios M, Hu E, Read J, Tang LW, Lim BK, Tian L, Földy C, Lammel S. Changes in neurotensin signalling drive hedonic devaluation in obesity. Nature. 2025 May;641(8065):1238-1247. doi: 10.1038/s41586-025-08748-y. Epub 2025 Mar 26. PMID: 40140571.

Lyu B, Wang J, Risher WC, Yu G. VSOT: volume-surface optimization for accurate ultrastructure analysis of dendritic spines. Bioinformatics. 2025 May 6;41(5):btaf220. doi: 10.1093/bioinformatics/btaf220. PMID: 40272896.

Zhang SX, Kim A, Madara JC, Zhu PK, Christenson LF, Lutas A, Kalugin PN, Sunkavalli PS, Jin Y, Pal A, Tian L, Lowell BB, Andermann ML. Stochastic neuropeptide signals compete to calibrate the rate of satiation. Nature. 2025 Jan;637(8044):137-144. doi: 10.1038/s41586-024-08164-8. Epub 2024 Nov 6. PMID: 39506113; PMCID: PMC11981016.

2024

Séjourné G, Eroglu C. Astrocyte-neuron crosstalk in neurodevelopmental disorders. Curr Opin Neurobiol. 2024 Dec;89:102925. doi: 10.1016/j.conb.2024.102925. Epub 2024 Oct 1. PMID: 39357429.

Du D, Bhardwaj S, Lu Y, Wang Y, Parker SJ, Zhang Z, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y. Embracing the informative missingness and silent gene in analyzing biologically diverse samples. Sci Rep. 2024 Nov 16;14(1):28265. doi: 10.1038/s41598-024-78076-0. PMID: 39550430; PMCID: PMC11569126.

Muir J, Lin S, Aarrestad IK, Daniels HR, Ma J, Tian L, Olson DE, Kim CK. Isolation of psychedelic-responsive neurons underlying anxiolytic behavioral states. Science. 2024 Nov 15;386(6723):802-810. doi: 10.1126/science.adl0666. Epub 2024 Nov 14. PMID: 39541450; PMCID: PMC11588385.

Salazar MPR, Kolanukuduru S, Ramirez V, Lyu B, Sejourne G, Sesaki H, Yu G, Eroglu C. Mitochondrial fission controls astrocyte morphogenesis and organization in the cortex.
bioRxiv 2024.10.22.619706; doi: https://doi.org/10.1101/2024.10.22.619706

Bindu DS, Savage JT, Brose N, Bradley L, Dimond K, Tan CX, Eroglu C. GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes. bioRxiv [Preprint]. 2024 Oct 10:2023.01.17.524433. doi: 10.1101/2023.01.17.524433. PMID: 36711516; PMCID: PMC9884502.

Schottdorf M, Yu G, Walker EY. Data science and its future in large neuroscience collaborations. Neuron. 2024 Sep 25;112(18):3007-3012. doi: 10.1016/j.neuron.2024.08.017

Savage JT, Ramirez JJ, Risher WC, Wang Y, Irala D, Eroglu C. SynBot is an open-source image analysis software for automated quantification of synapses. Cell Rep Methods. 2024 Sep 16;4(9):100861. doi: 10.1016/j.crmeth.2024.100861. Epub 2024 Sep 9. PMID: 39255792.

Barykina NV, Carey EM, Oliinyk OS., Nimmerjahn A, Verkhusha VV. Destabilized near-infrared fluorescent nanobodies enable background-free targeting of GFP-based biosensors for imaging and manipulation. Nat Commun. 2024 Sep 6;15(1):7788. doi: 10.1038/s41467-024-51857-x. PMID: 39242569; PMCID: PMC11379940.

Chen YY, Evavold CL, Mann M, Davenport ER, McFall-Ngai M, Bienko M, Ueda HR, Tian L, Tjahjono N, Anikeeva P, Liu JG, Deans TL, Shen X. What tool or method do you wish existed? Cell. 2024 Aug 22;187(17):4433-4438. doi: 10.1016/j.cell.2024.07.043. PMID: 39178826.

Dong C, Gowrishankar R, Jin Y, He XJ, Gupta A, Wang H, Sayar-Atasoy N, Flores RJ, Mahe K, Tjahjono N, Liang R, Marley A, Or Mizuno G, Lo DK, Sun Q, Whistler JL, Li B, Gomes I, Von Zastrow M, Tejeda HA, Atasoy D, Devi LA, Bruchas MR, Banghart MR, Tian L. Unlocking opioid neuropeptide dynamics with genetically encoded biosensors. Nat Neurosci. 2024 Sep;27(9):1844-1857. doi: 10.1038/s41593-024-01697-1. Epub 2024 Jul 15. PMID: 39009835; PMCID: PMC11374718.

Fu Y, Lu Y, Wang Y, Zhang B, Zhang Z, Yu G, Liu C, Clarke R, Herrington DM, Wang Y. DDN3.0: determining significant rewiring of biological network structure with differential dependency networks. Bioinformatics. 2024 Jun 3;40(6):btae376. doi: 10.1093/bioinformatics/btae376. PMID: 38902940; PMCID: PMC11199198.

Irala D, Wang S, Sakers K, Nagendren L, Ulloa Severino FP, Bindu DS, Savage JT, Eroglu C. Astrocyte-secreted neurocan controls inhibitory synapse formation and function. Neuron. 2024 May 15;112(10):1657-1675.e10. doi: 10.1016/j.neuron.2024.03.007. Epub 2024 Apr 3. PMID: 38574730; PMCID: PMC11098688.

Mi X, Chen ABY, Duarte D, Carey E, Taylor CR, Braaker PN, Bright M, Almeida RG, Lim JX, Rutten VM, Zheng W, Wang M, Reitman ME, Wang Y, Poskanzer KE, Lyons DA, Nimmerjahn A, Misha Ahrens MB, Yu G. Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals. bioRxiv 2024.05.02.592259; doi: https://doi.org/10.1101/2024.05.02.592259

Cheng Z, Wei S, Wang Y, Wang Y, Lu R, Wang Y, Yu G. An Efficient and Principled Model to Jointly Learn the Agnostic and Multifactorial Effect in Large-Scale Biological Data. bioRxiv. 2024:2024-04. doi: https://doi.org/10.1101/2024.04.12.589306

Wu CT, Du D, Chen L, Dai R, Liu C, Yu G, Bhardwaj S, Parker SJ, Zhang Z, Clarke R, Herrington DM, Wang Y. CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. Bioinformatics. 2024 Mar 4;40(3):btae107. doi: 10.1093/bioinformatics/btae107. PMID: 38407991; PMCID: PMC10924278.

Lawal OO, Ulloa Severino FP, Wang S, Bindu DS, Sakers K, Johnson SA, Yin HH, Eroglu C. Astrocytic thrombospondins 1 and 2 are required for cortical synapse development controlling instrumental performance. bioRxiv 2024.03.01.582935; doi: https://doi.org/10.1101/2024.03.01.582935\

2023

Barclay KM, Abduljawad N, Cheng Z, Kim MW, Zhou L, Yang J, Rustenhoven J, Perez JM, Smyth L, Beatty W, Hou J, Saligrama N, Colonna M, Yu G, Kipnis J, Li Q. An inducible genetic tool for tracking and manipulating specific microglial states in development and disease. bioRxiv [Preprint]. 2023 Dec 4:2023.12.01.569597. doi: 10.1101/2023.12.01.569597. PMID: 38106187; PMCID: PMC10723357.

Tan CX, Bindu DS, Hardin EJ, Sakers K, Baumert R, Ramirez JJ, Savage JT, Eroglu C. delta -Catenin controls astrocyte morphogenesis via layer-specific astrocyte-neuron cadherin interactions. J Cell Biol. 2023 Nov 6;222(11):e202303138. doi: 10.1083/jcb.202303138. Epub 2023 Sep 14. PMID: 37707499; PMCID: PMC10501387.

Zheng W, Peng JC, Hou Z, Lyu B, Wang M, Mi X, Qiao S, Wan Y, Yu G. NIS3D: A Completely Annotated Benchmark for Dense 3D Nuclei Image Segmentation. 37th Conference on Neural Information Processing Systems (NeurIPS 2023)

Ulloa Severino FP, Lawal OO, Sakers K, Wang S, Kim N, Friedman AD, Johnson SA, Sriworarat C, Hughes RH, Soderling SH, Kim IH, Yin HH, Eroglu C. Training-induced circuit-specific excitatory synaptogenesis in mice is required for effort control. Nat Commun. 2023 Sep 8;14(1):5522. doi: 10.1038/s41467-023-41078-z. PMID: 37684234; PMCID: PMC10491649.

Zhang SX, Kim A, Madara JC, Zhu PK, Christenson LF, Lutas A, Kalugin PN, Jin Y, Pal A, Tian L, Lowell BB, Andermann ML. Competition between stochastic neuropeptide signals calibrates the rate of satiation.
Res Sq [Preprint]. 2023 Jul 26:rs.3.rs-3185572. doi: 10.21203/rs.3.rs-3185572/v1. PMID: 37546985; PMCID: PMC10402269.

Du D, Bhardwaj S, Parker SJ, Cheng Z, Zhang Z, Lu Y, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y.
ABDS: tool suite for analyzing biologically diverse samples. bioRxiv [Preprint]. 2023 Jul 5:2023.07.05.547797. doi: 10.1101/2023. 07.05.547797. PMID: 37461566; PMCID: PMC10349978.

Andreoni A, Tian L. Lighting up action potentials with fast and bright voltage sensors. Nat Methods. 2023 Jul;20(7):990-992. doi: 10.1038/s41592-023-01928-6. PMID:37429963.

Chuapoco MR, Flytzanis NC, Goeden N, Christopher Octeau J, Roxas KM, Chan KY,Scherrer J, Winchester J, Blackburn RJ, Campos LJ, Man KNM, Sun J, Chen X, LefevreA, Singh VP, Arokiaraj CM, Shay TF, VendemiattiJ, Jang MJ, Mich JK, Bishaw Y, GoreBB, Omstead V, Taskin N, Weed N, Levi BP, Ting JT, Miller CT, Deverman BE, Pickel J,Tian L, Fox AS, Gradinaru V. Adeno-associated viral vectors forfunctional intravenousgene transfer throughout the non-human primate brain. Nat Nanotechnol. 2023 Jul 10.doi: 10.1038/s41565-023-01419-x. Epub ahead of print. PMID: 37430038.

Lin Tian, Chunyang Dong, Raajaram Gowrishankar et al. Unlocking opioidneuropeptide dynamics with genetically-encoded biosensors, 30 May 2023,PREPRINT (Version 1) available at Research Square[https://doi.org/10.21203/rs.3.rs-2871083/v1]

Savage JT, Ramirez J, Risher WC, Irala D, Eroglu C. SynBot: An open-source imageanalysis software for automated quantification of synapses. bioRxiv [Preprint]. 2023Jun 28:2023.06.26.546578. doi: 10.1101/2023.06.26.546578. PMID: 37425715; PMCID:PMC10327002.

Left: An immune brain cell (microglia) in a human brain. Right: Microglia in the novel organoid model with a human-brain-like environment. The cells are almost indistinguishable. Schafer ST, Mansour AA, Schlachetzki JCM, Pena M, Ghassemzadeh S, Mitchell L, Mar A, Quang D, Stumpf S, Ortiz IS, Lana AJ, Baek C, Zaghal R, Glass CK, Nimmerjahn A, Gage FH. An in vivo neuroimmune organoid model to study human microglia phenotypes. Cell. 2023 May 11;186(10):2111-2126.e20. doi: 10.1016/j.cell.2023.04.022. PMID: 37172564.

Irala D, Wang S, Sakers K, Nagendren L, Ulloa-Severino FP, Bindu DS, Eroglu C. Astrocyte-Secreted Neurocan Controls Inhibitory Synapse Formation and Function. bioRxiv [Preprint]. 2023 Apr 3:2023.04.03.535448. doi: 10.1101/2023.04.03.535448. PMID: 37066164; PMCID: PMC10104008.

Reitman ME, Tse V, Mi X, Willoughby DD, Peinado A, Aivazidis A, Myagmar BE, Simpson PC, Bayraktar OA, Yu G, Poskanzer KE. Norepinephrine links astrocytic activity to regulation of cortical state. Nat Neurosci. 2023 Apr;26(4):579-593. doi: 10.1038/s41593-023-01284-w. Epub 2023 Mar 30. PMID: 36997759; PMCID: PMC10089924.

wearable microscope Shekhtmeyster P, Carey EM, Duarte D, Ngo A, Gao G, Nelson NA, Clark CL, Nimmerjahn A. Multiplex translaminar imaging in the spinal cord of behaving mice. Nat Commun. 2023 Mar 21;14(1):1427. doi: 10.1038/s41467-023-36959-2. PMID: 36944637; PMCID: PMC10030868.

Shekhtmeyster P, Duarte D, Carey EM, Ngo A, Gao G, Olmstead JA, Nelson NA, Nimmerjahn A. Trans-segmental imaging in the spinal cord of behaving mice. Nat Biotechnol. 2023 Mar 6. doi: 10.1038/s41587-023-01700-3. Epub ahead of print. PMID: 36879007.

mouse gene editing Bindu DS, Tan CX, Savage JT, Eroglu C. GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes. bioRxiv [Preprint]. 2023 Jan 19:2023.01.17.524433. doi: 10.1101/2023.01.17.524433. PMID: 36711516; PMCID: PMC9884502.

Chen X, Wolfe DA, Sivadasan Bindu D et al. Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates. bioRxiv [Preprint]. 2023 Jan 13:2023.01.12.523844. doi: 10.1101/2023.01.12.523844. PMID: 36711773; PMCID: PMC9882234.

2022

Chen G, Xu J, Luo H, Luo X, Singh SK, Ramirez JJ, James ML, Mathew JP, Berger M, Eroglu C, Ji RR. Hevin/Sparcl1 drives pathological pain through spinal cord astrocyte and NMDA receptor signaling. JCI Insight. 2022 Dec 8;7(23):e161028. doi: 10.1172/jci.insight.161028. PMID: 36256481; PMCID: PMC9746899.

Mi X, Wang M, Chen ABY, Lim JX, Wang Y, Ahrens M, Yu G. BILCO: An Efficient Algorithm for Joint Alignment of Time Series. 36th Conference on Neural Information Processing Systems (NeurIPS 2022).

GLIA cover Nimmerjahn A, Hirrlinger J. Astrocyte regulation of neural circuit function and animal behavior. Glia. 2022 Aug;70(8):1554-1580. doi: 10.1002/glia.24168. Epub 2022 Mar 17. PMID: 35297525; PMCID: PMC9291267.

Hirrlinger J, Nimmerjahn A. A perspective on astrocyte regulation of neural circuit function and animal behavior. Glia. 2022 Aug;70(8):1554-1580. doi: 10.1002/glia.24168. Epub 2022 Mar 17. PMID: 35297525; PMCID: PMC9291267.

Lawal O, Ulloa Severino FP, Eroglu C. The role of astrocyte structural plasticity in regulating neural circuit function and behavior. Glia. 2022 Aug;70(8):1467-1483. doi: 10.1002/glia.24191. Epub 2022 May 10. PMID: 35535566; PMCID: PMC9233050.

neurophotonics cover Abdelfattah AS, Ahuja S, Akkin T, et al. Neurophotonic tools for microscopic measurements and manipulation: status report. Neurophotonics. 2022 Jan;9(Suppl 1):013001. doi: 10.1117/1.NPh.9.S1.013001. Epub 2022 Apr 27. PMID: 35493335; PMCID: PMC9047450.

2021

Shekhtmeyster P, Duarte D, Carey EM, Ngo A, Gao G, Olmstead JA, Nelson NA, Nimmerjahn A. Trans-segmental imaging in the spinal cord of behaving mice. bioRxiv 2021.12.23.474042; doi: https://doi.org/10.1101/2021.12.23.474042

Shekhtmeyster P, Carey EM, Duarte D, Ngo A, Grace Gao, Nelson NA, Clark CL, Nimmerjahn A. Multiplex, translaminar imaging in the spinal cord of behaving mice. bioRxiv 2021.12.23.474039; doi: https://doi.org/10.1101/2021.12.23.474039

Merten K, Folk RW, Duarte D, Nimmerjahn A. Astrocytes encode complex behaviorally relevant information. bioRxiv 2021.10.09.463784; doi: https://doi.org/10.1101/2021.10.09.463784?