Publications
2025
Kirk RW, Sun L, Xiao R, Clark EA, Nelson SB. Multiplexed CRISPRi Reveals a Transcriptional Switch Between KLF Activators and Repressors in the Maturing Neocortex. (2025) bioRxiv 636951 [Preprint] doi: 10.1101/2025.02.07.636951v3. In revision ELife.
2024
Wise DL, Greene SB, Escobedo-Lozoya Y, Van Hooser SD and Nelson SB (2024) Progressive circuit hyperexcitability in mouse neocortical slice cultures with increasing duration of activity silencing. ENeuro doi: 10.1523/ENEURO.0362-23.2024.
Wise DL, Escobedo-Lozoya Y, Valakh V, Gao EY, Bhonsle A, Lei QL, Cheng X., Greene SB, Van Hooser SD and Nelson SB (2024) Prolonged activity deprivation causes pre- and postsynaptic compensatory plasticity at neocortical excitatory synapses. ENeuro doi: 10.1523/ENEURO.0362-23.2024.
2023
Valakh V, Wise D, Zhu XA, Sha M, Fok J, Van Hooser SD, Schectman R, Cepeda I, Kirk R, O'Toole S and Nelson SB (2023) A transcriptional constraint mechanism limits the homeostatic response to activity deprivation in mammalian neocortex. Elife. 12:e74899. doi: 10.7554/eLife.74899. PMID: 36749029
2021
Nanu RD, Murdy TJ, Levitan D, Nelson SB, Katz DB (2021) Loss of Stk11 in basolateral amygdalar projection neurons impairs taste aversion learning by altering the temporal pattern of taste response plasticity in gustatory cortex bioRxiv 2021.05.31.446460 [Preprint]; doi: https://doi.org/10.1101/2021.05.31.446460.
Valakh V, Zhu XA, Wise D, Van Hooser SD, Schectman R, Cepeda I, Kirk R, O'Toole S and Nelson SB (2021) A transcriptional constraint mechanism limits the homeostatic response to activity deprivation in mammalian neocortex. bioRxiv 2021.10.20.465163 [Preprint]; doi: https://doi.org/10.1101/2021.10.20.465163.
Slutsky I., Schratt G., Stan G.B., Nelson S., and Bruggeman F.J. (2021) Homeostasis. Cell Syst. 12:1124-1126 doi: 10.1016/j.cels.2021.11.002.
2020
Clark EA, Rutlin M, Capano L, Aviles S, Saadon JR, Taneja P, Zhang Q, Bullis J, Lauer T, Myers E, Schulmann A, Forrest D, Nelson SB (2020) Cortical RORb is required for layer 4 transcriptional identity and barrel integrity. Elife. 9:e52370. doi: 10.7554/eLife.52370.
Levitan D, Liu C, Yang T, Shima Y, Lin JY, Wachutka J, Marrero Y, Ali Marandi Ghoddousi R, Veiga Beltrame ED, Richter TA, Katz DB, Nelson SB (2020) Deletion of Stk11 and Fos in BLA projection neurons alters their intrinsic excitability and impairs formation of long-term aversive memory. Elife. 9:e61036. doi: 10.7554/eLife.61036.PDF
2019
Clark EA, Rutlin M, Capano L, Aviles S, Saadon JR, Taneja P, Zhang Q, Bullis J, Lauer T, Myers E, Schulmann A, Forrest D, Nelson SB (2019) Cortical RORb is required for layer 4 transcriptional identity and barrel integrity. bioRxiv 782995 [Preprint]. doi: https://doi.org/10.1101/782995.
Levitan D, Liu C, Lin J-Y, Wachutka J, Marrero Y, Beltrame E, Shima Y, Ghoddousi AR, Yang T, Katz DB and Nelson SB (2019) Deletion of Stk11 and Fos in BLA projection neurons alters their intrinsic excitability and impairs formation of long-term aversive memory. bioRxiv 787325v1 [Preprint]. doi: https://doi.org/10.1101/787325.
Phillips JW, Schulmann A, Hara E, Winnubst J, Liu C, Valakh V, Wang L, Shields B, Korff W, Chandrashekar J, Lemire A, Mensh B, Dudman J, Nelson SB, Hantman A (2019) A defining spectrum of neuronal identities across thalamic pathways. Nature Neurosci. doi: 10.1038/s41593-019-0483-3. *Corresponding authors.
Sugino K, Clark E, Schulmann A, Shima Y, Wang L, Hunt DL, Hooks BM, Trankner D, Chandrashekar J, Picard S, Lemire A, Spruston N, Hantman A, and Nelson SB (2019) Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. ELife. 8. pii: e38619. doi: 10.7554/eLife.38619. *Corresponding authors.
Levitan D, Lin J-Y, Wachutka J, Mukherjee N, Nelson SB, and Katz DB (2019) Single and population coding of taste in the gustatory cortex of awake mice. J. Neurophysiol. 122(4):1342-1356. doi: 10.1152/jn.00357.2019.
Clark EA, Shima Y, Nelson SB (2019) ATAC-seq on Sorted Adult Mouse Neurons. Bio-protocol. 10.21769/BioProtoc.3382.
Hobert O. and Nelson S.B. (2019) Neuronal Identity. Curr. Op. Neurobiol. 56:iii-iv.
2018
Flores VL, Parmet T, Mukherjee N, Nelson SB, Katz DB, and Levitan D (2018) The role of the gustatory cortex in experience-evoked enhancement of learning. bioRxiv 369520 [Preprint]. doi: https://doi.org/10.1101/369520. Now published. Learning and Memory. 25(11):587-600. doi: 10.1101/lm.048181.118.
Phillips JW, Schulmann A, Hara E, Liu C, Shields B, Korff W, Lemire A, Dudman J, Nelson SB, and Hantman A. A topographic axis of transcriptional identity in thalamus. bioRxiv 241315 [Preprint]. doi: https://doi.org/10.1101/241315.
2017
Moreno-Juan V, Filipchuk A, Antón-Bolaños N, Mezzera C, Gezelius H, Andrés B, Rodríguez-Malmierca L, Susín R, Schaad O, Iwasato T, Schuele R, Rutlin M, Nelson SB, Ducret S, Valdeolmillos M, Rijli FM, and López-Bendito G (2017) Prenatal thalamic waves regulate cortical area size prior to sensory processing. Nature Comm. Feb 3;8:14172. PMC5296753. doi: 10.1038/ncomms14172.
O'Toole SM, Ferrer MM, Mekonnen J, Zhang H, Shima Y, Ladle DR, and Nelson SB (2017) Dicer maintains the identity and function of proprioceptive sensory neurons. J Neurophysiol. 117:1057-1069. PMC5338617 doi: 10.1152/jn.00763.2016
Choy J.M., Suzuki N., Shima Y., Budisantoso T., Nelson S.B., and Bekkers J.M. (2017) Optogenetic Mapping of Intracortical Circuits Originating from Semilunar Cells in the Piriform Cortex. Cereb Cortex. 27:589-601. PMC5939214.
2016
Abraira VE, Kuehn ED, Chirila AM, Springel MW, Toliver AA, Zimmerman AL, Orefice LL, Boyle KA, Bai L, Song BJ, Bashista KA, O'Neill TG, Zhuo J, Tsan C, Hoynoski J, Rutlin M, Kus L, Niederkofler V., Watanabe M., Dymecki SM, Nelson SB, Heintz N, Hughes DI, and Ginty DD (2016) The Cellular and synaptic architecture of the mechanosensory dorsal horn. Cell. 168(1-2):295-310. doi: 10.1016/j.cell.2016.12.010. PMC5236062.
Crittenden JR, Tillberg PW, Riad MH, Shima Y, Gerfen CR, Curry J, Housman DE, Nelson SB, Boyden ES, and Graybiel AM (2016) Striosome-dendron bouquets highlight a unique striatonigral circuit targeting dopamine-containing neurons. Proc. Natl. Acad. Sci. USA 113(40):11318-11323. PMC5056098
Steinmetz CC, Tatavarty V, Sugino K, Shima Y, Joseph A, Line H, Rutlin M, Lambo M, Hempel CM, Okaty BW, Paradis S, *Nelson SB, and *Turrigiano GG (2016) Upregulation of µ3A drives homeostatic plasticity by rerouting AMPAR into the recycling endosomal pathway. Cell Reports. 16(10):2711-22. PMC5226429 *Corresponding authors
Shima Y, Hempel CM, Bullis J, Taneja P, Mehta S, Sugino K, Lois C, and Nelson SB (2016) A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types. Elife 5. pii: e13503. doi: 10.7554/eLife.13503. PMC4846381