Waitt Advanced Biophotonics Center

Geeven, G., Zhu, Y., Kim, B.J., Bartholdy, B.A., Yang, S.M., Macfarlan, T.S., Gifford, W.D., Pfaff, S.L., Verstegen, M.J., Pinto, H., Vermunt, M.W., Creyghton, M.P., Wijchers, P.J., Stamatoyannopoulos, J.A., Skoultchi, A.I., de Laat, W. Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. (2015) Genome Biology. 16:289. DOI: 10.1186/s13059-015-0857-0

Harrison, B.J., Venkat, G., Hutson, T., Rau, K.K., Bunge, M.B., Mendell, L.M., Gage, F.H., Johnson, R.D., Hill, C., Rouchka, E.C., Moon, L., Petruska, J.C. Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model. (2015) Genomics Data. 6:249-52. DOI: 10.1016/j.gdata.2015.10.005

Amin, N.D., Bai, G., Klug, J.R., Bonanomi, D., Pankratz, M.T., Gifford, W.D., Hinckley, C.A., Sternfeld, M.J., Driscoll, S.P., Dominguez, B., Lee, K.F., Jin, X., Pfaff, S.L. Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure. (2015) Wissenschaft. 350(6267):1525-9. DOI: 10.1126/science.aad2509

Kim, E.J., Juavinett, A.L., Kyubwa, E.M., Jacobs, M.W., Callaway, E.M. Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function. (2015) Neuron. 88(6):1253-1267. DOI: 10.1016/j.neuron.2015.11.002

Brennand, K.J., Marchetto, M.C., Benvenisty, N., Brüstle, O., Ebert, A., Izpisua Belmonte, J.C., Kaykas, A., Lancaster, M.A., Livesey, F.J., McConnell, M.J., McKay, R.D., Morrow, E.M., Muotri, A.R., Panchision, D.M., Rubin, L.L., Sawa, A., Soldner, F., Song, H., Studer, L., Temple, S., Vaccarino, F.M., Wu, J., Vanderhaeghen, P., Gage, F.H., Jaenisch, R. Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. (2015) Stem Cell Reports. 5(6):933-45. DOI: 10.1016/j.stemcr.2015.10.011

Veltz, R., Sejnowski, T.J. Periodic Forcing of Inhibition-Stabilized Networks: Nonlinear Resonances and Phase-Amplitude Coupling. (2015) Neural Computation. 27(12):2477-509. DOI: 10.1162/NECO_a_00786

Mertens, J., Paquola, A.C., Ku, M., Hatch, E., Böhnke, L., Ladjevardi, S., McGrath, S., Campbell, B., Lee, H., Herdy, J.R., Gonçalves, J.T., Toda, T., Kim, Y., Winkler, J., Yao, J., Hetzer, M.W., Gage, F.H. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. (2015) Cell Stem Cell. 17(6):705-18. DOI: 10.1016/j.stem.2015.09.001

Bartol, T.M., Bromer, C., Kinney, J., Chirillo, M.A., Bourne, J.N., Harris, K.M., Sejnowski, T.J. Nanoconnectomic upper bound on the variability of synaptic plasticity. (2015) Elife. 4:e10778. DOI: 10.7554/eLife.10778

Kim, H.J., Denli, A.M., Wright, R., Baul, T.D., Clemenson, G.D., Morcos, A.S., Zhao, C., Schafer, S.T., Gage, F.H., Kagalwala, M.N. REST Regulates Non-Cell-Autonomous Neuronal Differentiation and Maturation of Neural Progenitor Cells via Secretogranin II. (2015) Journal of Neuroscience. 35(44):14872-84. DOI: 10.1523/JNEUROSCI.4286-14.2015

Pan, F.C., Brissova, M., Powers, A.C., Pfaff, S., Wright, C.V. Inactivating the permanent neonatal diabetes gene Mnx1 switches insulin-producing β-cells to a δ-like fate and reveals a facultative proliferative capacity in aged β-cells. (2015) Entwicklung. 142(21):3637-48. DOI: 10.1242/dev.126011

Mertens, J., Wang, Q.W., Kim, Y., Yu, D.X., Pham, S., Yang, B., Zheng, Y., Diffenderfer, K.E., Zhang, J., Soltani, S., Eames, T., Schafer, S.T., Boyer, L., Marchetto, M.C., Nurnberger, J.I., Calabrese, J.R., Ødegaard, K.J., McCarthy, M.J., Zandi, P.P., Alda, M., Alba, M., Nievergelt, C.M., , Mi, S., Brennand, K.J., Kelsoe, J.R., Gage, F.H., Yao, J. Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder. (2015) Natur. 527(7576):95-9. DOI: 10.1038/nature15526

Bourane, S., Duan, B., Koch, S.C., Dalet, A., Britz, O., Garcia-Campmany, L., Kim, E., Cheng, L., Ghosh, A., Ma, Q., Goulding, M. Gate control of mechanical itch by a subpopulation of spinal cord interneurons. (2015) Wissenschaft. 350(6260):550-4. DOI: 10.1126/science.aac8653

He, W., Bai, G., Zhou, H., Wei, N., White, N.M., Lauer, J., Liu, H., Shi, Y., Dumitru, C.D., Lettieri, K., Shubayev, V., Jordanova, A., Guergueltcheva, V., Griffin, P.R., Burgess, R.W., Pfaff, S.L., Yang, X.L. CMT2D neuropathy is linked to the neomorphic binding activity of glycyl-tRNA synthetase. (2015) Natur. 526(7575):710-4. DOI: 10.1038/nature15510

Bartol, T.M., Keller, D.X., Kinney, J.P., Bajaj, C.L., Harris, K.M., Sejnowski, T.J., Kennedy, M.B. Computational reconstitution of spine calcium transients from individual proteins. (2015) Front Synaptic Neurosci. 7:17. DOI: 10.3389/fnsyn.2015.00017

Denli, A.M., Narvaiza, I., Kerman, B.E., Pena, M., Benner, C., Marchetto, M.C., Diedrich, J.K., Aslanian, A., Ma, J., Moresco, J.J., Moore, L., Hunter, T., Saghatelian, A., Gage, F.H. Primaten-spezifischer ORF0 trägt zur retrotranspon-vermittelten Vielfalt bei. (2015) Zelle. 163(3):583–93. DOI: 10.1016/j.cell.2015.09.025

Mu, Y., Zhao, C., Toni, N., Yao, J., Gage, F.H. Distinct roles of NMDA receptors at different stages of granule cell development in the adult brain. (2015) Elife. 4:e07871. DOI: 10.7554/eLife.07871

Britz, O., Zhang, J., Grossmann, K.S., Dyck, J., Kim, J.C., Dymecki, S., Gosgnach, S., Goulding, M. A genetically defined asymmetry underlies the inhibitory control of flexor-extensor locomotor movements. (2015) Elife. 4. DOI: 10.7554/eLife.04718

Wang, X., Pinto-Duarte, A., Behrens, M.M., Zhou, X., Sejnowski, T.J. Characterization of spatio-temporal epidural event-related potentials for mouse models of psychiatric disorders. (2015) Wissenschaftliche Berichte. 5:14964. DOI: 10.1038/srep14964

Barnes, S.A., Pinto-Duarte, A., Kappe, A., Zembrzycki, A., Metzler, A., Mukamel, E.A., Lucero, J., Wang, X., Sejnowski, T.J., Markou, A.*, Behrens, M.M.* Disruption of mGluR5 in parvalbumin-positive interneurons induces core features of neurodevelopmental disorders. (2015) Molekulare Psychiatrie. 20(10):1161-72. DOI: 10.1038/mp.2015.113

Pawar, K., Cummings, B.J., Thomas, A., Shea, L.D., Levine, A., Pfaff, S., Anderson, A.J. Biomaterial bridges enable regeneration and re-entry of corticospinal tract axons into the caudal spinal cord after SCI: Association with recovery of forelimb function. (2015) Biomaterials. 65:1-12. DOI: 10.1016/j.biomaterials.2015.05.032

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Preparation and Use of Retroviral Vectors for Labeling, Imaging, and Genetically Manipulating Cells. (2015) Cold Spring Harbor Protocols. 2015(10):883-8. DOI: 10.1101/pdb.top086363

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Analysis of Spine Motility of Newborn Granule Cells in Acute Brain Slices. (2015) Cold Spring Harbor Protocols. 2015(10):934-6. DOI: 10.1101/pdb.prot086397

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Imaging Newborn Granule Cells in Fixed Sections. (2015) Cold Spring Harbor Protocols. 2015(10):932-3. DOI: 10.1101/pdb.prot086389

Tashiro, A., Zhao, C., Suh, H., Gage, F.H. Purification and Injection of Retroviral Vectors. (2015) Cold Spring Harbor Protocols. 2015(10):925-31. DOI: 10.1101/pdb.prot086371

González, O.C., Krishnan, G.P., Chauvette, S., Timofeev, I., Sejnowski, T., Bazhenov, M. Modeling of Age-Dependent Epileptogenesis by Differential Homeostatic Synaptic Scaling. (2015) Journal of Neuroscience. 35(39):13448-62. DOI: 10.1523/JNEUROSCI.5038-14.2015

Prescott, S.L., Srinivasan, R., Marchetto, M.C., Grishina, I., Narvaiza, I., Selleri, L., Gage, F.H., Swigut, T., Wysocka, J. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. (2015) Zelle. 163(1):68-83. DOI: 10.1016/j.cell.2015.08.036

Hinckley, C.A., Alaynick, W.A., Gallarda, B.W., Hayashi, M., Hilde, K.L., Driscoll, S.P., Dekker, J.D., Tucker, H.O., Sharpee, T.O., Pfaff, S.L. Spinal Locomotor Circuits Develop Using Hierarchical Rules Based on Motorneuron Position and Identity. (2015) Neuron. 87(5):1008-21. DOI: 10.1016/j.neuron.2015.08.005

Kempermann, G., Song, H., Gage, F.H. Neurogenesis in the Adult Hippocampus. (2015) Cold Spring Harbor Perspectives in Biology. 7(9):a018812. DOI: 10.1101/cshperspect.a018812

Jovičić, A., Mertens, J., Boeynaems, S., Bogaert, E., Chai, N., Yamada, S.B., Paul, J.W., Sun, S., Herdy, J.R., Bieri, G., Kramer, N.J., Gage, F.H., Van Den Bosch, L., Robberecht, W., Gitler, A.D. Modifiers of C9orf72 dipeptide repeat toxicity connect nucleocytoplasmic transport defects to FTD/ALS. (2015) Nature Neuroscience. 18(9):1226-9. DOI: 10.1038/nn.4085

Firth, A.L., Menon, T., Parker, G.S., Qualls, S.J., Lewis, B.M., Ke, E., Dargitz, C.T., Wright, R., Khanna, A., Gage, F.H., Verma, I.M. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. (2015) Cell Reports. 12(9):1385-90. DOI: 10.1016/j.celrep.2015.07.062

Wang, J., Telese, F., Tan, Y., Li, W., Jin, C., He, X., Basnet, H., Ma, Q., Merkurjev, D., Zhu, X., Liu, Z., Zhang, J., Ohgi, K., Taylor, H., White, R.R., Tazearslan, C., Suh, Y., Macfarlan, T.S., Pfaff, S.L., Rosenfeld, M.G. LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. (2015) Nature Neuroscience. 18(9):1256-64. DOI: 10.1038/nn.4069

Deng, W., Gage, F.H. The effect of immature adult-born dentate granule cells on hyponeophagial behavior is related to their roles in learning and memory. (2015) Frontiers in Systems Neuroscience. 9:34. DOI: 10.3389/fnsys.2015.00034

Coggan, J.S., Sejnowski, T.J., Prescott, S.A. Cooperativity between remote sites of ectopic spiking allows afterdischarge to be initiated and maintained at different locations. (2015) Journal of Computational Neuroscience. 39(1):17-28. DOI: 10.1007/s10827-015-0562-8

Huh, D., Sejnowski, T.J. Spectrum of power laws for curved hand movements. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(29):E3950-8. DOI: 10.1073/pnas.1510208112

Han, J., Sarkar, A., Gage, F.H. MIR137: big impacts from small changes. (2015) Nature Neuroscience. 18(7):931-3. DOI: 10.1038/nn.4045

Schultz, M.D., He, Y., Whitaker, J.W., Hariharan, M., Mukamel, E.A., Leung, D., Rajagopal, N., Nery, J.R., Urich, M.A., Chen, H., Lin, S., Lin, Y., Jung, I., Schmitt, A.D., Selvaraj, S., Ren, B., Sejnowski, T.J., Wang, W., Ecker, J.R. Human body epigenome maps reveal noncanonical DNA methylation variation. (2015) Natur. 523(7559):212-6. DOI: 10.1038/nature14465

Lainscsek, C., Weyhenmeyer, J., Sejnowski, T.J., Letellier, C. Discovering independent parameters in complex dynamical systems. (2015) Chaos Solitons Fractals. 76:182-189. DOI: 10.1016/j.chaos.2015.04.001

Lee, H., Kim, M., Kim, N., Macfarlan, T., Pfaff, S.L., Mastick, G.S., Song, M.R. Slit and Semaphorin signaling governed by Islet transcription factors positions motor neuron somata within the neural tube. (2015) Experimental Neurology. 269:17-27. DOI: 10.1016/j.expneurol.2015.03.024

Zhao, C., Jou, J., Wolff, L.J., Sun, H., Gage, F.H. Spine morphogenesis in newborn granule cells is differentially regulated in the outer and middle molecular layers. (2015) Journal of Vergleichende Neurologie. 523(10):1588. DOI: 10.1002/cne.23800

Krzisch, M., Temprana, S.G., Mongiat, L.A., Armida, J., Schmutz, V., Virtanen, M.A., Kocher-Braissant, J., Kraftsik, R., Vutskits, L., Conzelmann, K.K., Bergami, M., Gage, F.H., Schinder, A.F., Toni, N. Pre-existing astrocytes form functional perisynaptic processes on neurons generated in the adult hippocampus. (2015) Brain Structure & Function. 220(4):2027-42. DOI: 10.1007/s00429-014-0768-y

Mo, A., Mukamel, E.A., Davis, F.P., Luo, C., Henry, G.L., Picard, S., Urich, M.A., Nery, J.R., Sejnowski, T.J., Lister, R., Eddy, S.R., Ecker, J.R., Nathans, J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. (2015) Neuron. 86(6):1369-84. DOI: 10.1016/j.neuron.2015.05.018

Callaway, E.M., Luo, L. Monosynaptic Circuit Tracing with Glycoprotein-Deleted Rabies Viruses. (2015) Journal of Neuroscience. 35(24):8979-8985. DOI: 10.1523/JNEUROSCI.0409-15.2015

Juavinett, A.L., Callaway, E.M. Pattern and Component Motion Responses in Mouse Visual Cortical Areas. (2015) Current Biology. 25(13):1759-1764. DOI: 10.1016/j.cub.2015.05.028

Kerman, B.E., Kim, H.J., Padmanabhan, K., Mei, A., Georges, S., Joens, M.S., Fitzpatrick, J.A., Jappelli, R., Chandross, K.J., August, P., Gage, F.H. In vitro myelin formation using embryonic stem cells. (2015) Entwicklung. 142(12):2213-25. DOI: 10.1242/dev.116517

Nimmerjahn, A., Bergles, D.E. Large-scale recording of astrocyte activity. (2015) Aktuelle Meinungen in der Neurobiologie. 32:95-106. DOI: 10.1016/j.conb.2015.01.015

Johnson, T., Bartol, T., Sejnowski, T., Mjolsness, E. Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics. (2015) Phys Biol. 12(4):045005. DOI: 10.1088/1478-3975/12/4/045005

Mukherjee, S., Hsieh, W.L., Smith, N., Goulding, M., Heikenfeld, J. Electrokinetic pixels with biprimary inks for color displays and color-temperature-tunable smart windows. (2015) Appl Opt. 54(17):5603-5609.

Sejnowski, T.J. Vernon Mountcastle: Father of neuroscience. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(21):6523-4. DOI: 10.1073/pnas.1506644112

Izpisua Belmonte, J.C., Callaway, E.M., Caddick, S.J., Churchland, P., Feng, G., Homanics, G.E., Lee, K.F., Leopold, D.A., Miller, C.T., Mitchell, J.F., Mitalipov, S., Moutri, A.R., Movshon, J.A., Okano, H., Reynolds, J.H., Ringach, D., Sejnowski, T.J., Silva, A.C., Strick, P.L., Wu, J., Zhang, F. Gehirne, Gene und Primaten. (2015) Neuron. 86(3):617-31. DOI: 10.1016/j.neuron.2015.03.021

Bardy, C., van den Hurk, M., Eames, T., Marchand, C., Hernandez, R.V., Kellogg, M., Gorris, M., Galet, B., Palomares, V., Brown, J., Bang, A.G., Mertens, J., Böhnke, L., Boyer, L., Simon, S., Gage, F.H. Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(20):E2725-34. DOI: 10.1073/pnas.1504393112

Jorgenson, L.A., Newsome, W.T., Anderson, D.J., Bargmann, C.I., Brown, E.N., Deisseroth, K., Donoghue, J.P., Hudson, K.L., Ling, G.S., MacLeish, P.R., Marder, E., Normann, R.A., Sanes, J.R., Schnitzer, M.J., Sejnowski, T.J., Tank, D.W., Tsien, R.Y., Ugurbil, K., Wingfield, J.C. The BRAIN Initiative: developing technology to catalyse neuroscience discovery. (2015) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370(1668). DOI: 10.1098/rstb.2014.0164

Calhoun, A.J., Tong, A., Pokala, N., Fitzpatrick, J.A., Sharpee, T.O., Chalasani, S.H. Neural Mechanisms for Evaluating Environmental Variability in Caenorhabditis elegans. (2015) Neuron. 86(2):428-41. DOI: 10.1016/j.neuron.2015.03.026

Pei, L., Mu, Y., Leblanc, M., Alaynick, W., Barish, G.D., Pankratz, M., Tseng, T.W., Kaufman, S., Liddle, C., Yu, R.T., Downes, M., Pfaff, S.L., Auwerx, J., Gage, F.H., Evans, R.M. Dependence of hippocampal function on ERRγ-regulated mitochondrial metabolism. (2015) Zellstoffwechsel. 21(4):628-36. DOI: 10.1016/j.cmet.2015.03.004

Adamowicz, D.H., Mertens, J., Gage, F.H. Alzheimer's disease: distinct stages in neurogenic decline? (2015) Biological Psychiatry. 77(8):680-2. DOI: 10.1016/j.biopsych.2015.02.021

Amador-Arjona, A., Cimadamore, F., Huang, C.T., Wright, R., Lewis, S., Gage, F.H., Terskikh, A.V. SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(15):E1936-45. DOI: 10.1073/pnas.1421480112

Schafer, S.T., Han, J., Pena, M., von Bohlen Und Halbach, O., Peters, J., Gage, F.H. The Wnt adaptor protein ATP6AP2 regulates multiple stages of adult hippocampal neurogenesis. (2015) Journal of Neuroscience. 35(12):4983-98. DOI: 10.1523/JNEUROSCI.4130-14.2015

Li, P.H., Gauthier, J.L., Schiff, M., Sher, A., Ahn, D., Field, G.D., Greschner, M., Callaway, E.M., Litke, A.M., Chichilnisky, E.J. Anatomical identification of extracellularly recorded cells in large-scale multielectrode recordings. (2015) Journal of Neuroscience. 35(11):4663-4675. DOI: 10.1523/JNEUROSCI.3675-14.2015

Lainscsek, C., Sejnowski, T.J. Delay differential analysis of time series. (2015) Neural Computation. 27(3):594-614. DOI: 10.1162/NECO_a_00706

Clemenson, G.D., Lee, S.W., Deng, W., Barrera, V.R., Iwamoto, K.S., Fanselow, M.S., Gage, F.H. Enrichment rescues contextual discrimination deficit associated with immediate shock. (2015) Hippocampus. 25(3):385-92. DOI: 10.1002/hipo.22380

Lainscsek, C., Hernandez, M.E., Poizner, H., Sejnowski, T.J. Delay differential analysis of electroencephalographic data. (2015) Neural Computation. 27(3):615-27. DOI: 10.1162/NECO_a_00656

Brennand, K., Savas, J.N., Kim, Y., Tran, N., Simone, A., Hashimoto-Torii, K., Beaumont, K.G., Kim, H.J., Topol, A., Ladran, I., Abdelrahim, M., Matikainen-Ankney, B., Chao, S.H., Mrksich, M., Rakic, P., Fang, G., Zhang, B., Yates, J.R., Gage, F.H. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. (2015) Molekulare Psychiatrie. 20(3):361-8. DOI: 10.1038/mp.2014.22

Aljadeff, J., Stern, M., Sharpee, T. Transition to chaos in random networks with cell-type-specific connectivity. (2015) Phys. Rev. Lett. 114(8):088101. DOI: 10.1103/PhysRevLett.114.088101

Moldakarimov, S., Bazhenov, M., Sejnowski, T.J. Feedback stabilizes propagation of synchronous spiking in cortical neural networks. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(8):2545-50. DOI: 10.1073/pnas.1500643112

Kastner, D.B., Baccus, S.A., Sharpee, T.O. Critical and maximally informative encoding between neural populations in the retina. (2015) Verhandlungen der Nationalen Akademie der Wissenschaften der Vereinigten Staaten von Amerika. 112(8):2533-8. DOI: 10.1073/pnas.1418092112

Tanaka, H., Sejnowski, T.J. Motor adaptation and generalization of reaching movements using motor primitives based on spatial coordinates. (2015) Journal für Neurophysiologie. 113(4):1217-33. DOI: 10.1152/jn.00002.2014

Frost, W.N., Brandon, C.J., Bruno, A.M., Humphries, M.D., Moore-Kochlacs, C., Sejnowski, T.J., Wang, J., Hill, E.S. Monitoring Spiking Activity of Many Individual Neurons in Invertebrate Ganglia. (2015) Fortschritte der experimentellen Medizin und Biologie. 859:127-45. DOI: 10.1007/978-3-319-17641-3_5

Sejnowski, T.J. Consciousness. (2015) Daedalus. 144(1):123-132. DOI: 10.1162/DAED_a_00321

Bourane, S., Grossmann, K.S., Britz, O., Dalet, A., Del Barrio, M.G., Stam, F.J., Garcia-Campmany, L., Koch, S., Goulding, M. Identification of a spinal circuit for light touch and fine motor control. (2015) Zelle. 160(3):503-15. DOI: 10.1016/j.cell.2015.01.011