2013 PUBLICATIONS
Lainscsek, C., Weyhenmeyer, J., Hernandez, M.E., Poizner, H., Sejnowski, T.J. Non-linear dynamical classification of short time series of the rössler system in high noise regimes. (2013) Frontiers in Neurology. 4:182. DOI: 10.3389/fneur.2013.00182
Lainscsek, C., Hernandez, M.E., Weyhenmeyer, J., Sejnowski, T.J., Poizner, H. Non-linear dynamical analysis of EEG time series distinguishes patients with Parkinson's disease from healthy individuals. (2013) Frontiers in Neurology. 4:200. DOI: 10.3389/fneur.2013.00200
Pfaff, S., Shaham, S. Development of neurons and glia. (2013) Current Opinion in Neurobiology. 23(6):901-2.
Grindberg, R.V., Yee-Greenbaum, J.L., McConnell, M.J., Novotny, M., O'Shaughnessy, A.L., Lambert, G.M., Araúzo-Bravo, M.J., Lee, J., Fishman, M., Robbins, G.E., Lin, X., Venepally, P., Badger, J.H., Galbraith, D.W., Gage, F.H., Lasken, R.S. RNA-sequencing from single nuclei. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(49):19802-7. DOI: 10.1073/pnas.1319700110
Quintero, O.A., Unrath, W.C., Stevens, S.M., Manor, U., Kachar, B., Yengo, C.M. Myosin 3A kinase activity is regulated by phosphorylation of the kinase domain activation loop. (2013) Journal of Biological Chemistry. 288(52):37126-37137. DOI: 10.1074/jbc.M113.511014
Borowska, J., Jones, C.T., Zhang, H., Blacklaws, J., Goulding, M., Zhang, Y. Functional subpopulations of V3 interneurons in the mature mouse spinal cord. (2013) Journal of Neuroscience. 33(47):18553-65. DOI: 10.1523/JNEUROSCI.2005-13.2013
Del Barrio, M.G., Bourane, S., Grossmann, K., Schüle, R., Britsch, S., O'Leary, D.D., Goulding, M. A transcription factor code defines nine sensory interneuron subtypes in the mechanosensory area of the spinal cord. (2013) PLOS One. 8(11):e77928. DOI: 10.1371/journal.pone.0077928
Reilly, M.T., Faulkner, G.J., Dubnau, J., Ponomarev, I., Gage, F.H. The role of transposable elements in health and diseases of the central nervous system. (2013) Journal of Neuroscience. 33(45):17577-86. DOI: 10.1523/JNEUROSCI.3369-13.2013
McConnell, M.J., Lindberg, M.R., Brennand, K.J., Piper, J.C., Voet, T., Cowing-Zitron, C., Shumilina, S., Lasken, R.S., Vermeesch, J.R., Hall, I.M., Gage, F.H. Mosaic copy number variation in human neurons. (2013) Science. 342(6158):632-7. DOI: 10.1126/science.1243472
Marchetto, M.C.N., Narvaiza, I., Denli, A.M., Benner, C., Lazzarini, T.A., Nathanson, J.L., Paquola, A.C.M., Desai, K.N., Herai, R.H., Weitzman, M.D., Yeo, G.W., Muotri, A.R., Gage, F.H. Differential L1 regulation in pluripotent stem cells of humans and apes. (2013) Nature. 503(7477):525-529. DOI: 10.1038/nature12686
Bekinschtein, P., Kent, B.A., Oomen, C.A., Clemenson, G.D., Gage, F.H., Saksida, L.M., Bussey, T.J. BDNF in the dentate gyrus is required for consolidation of "pattern-separated" memories. (2013) Cell Reports. 5(3):759-68. DOI: 10.1016/j.celrep.2013.09.027
Miller, J.A., Nathanson, J., Franjic, D., Shim, S., Dalley, R.A., Shapouri, S., Smith, K.A., Sunkin, S.M., Bernard, A., Bennett, J.L., Lee, C.K., Hawrylycz, M.J., Jones, A.R., Amaral, D.G., Šestan, N., Gage, F.H., Lein, E.S. Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. (2013) Development. 140(22):4633-44. DOI: 10.1242/dev.097212
Gage, F.H., Temple, S. Neural stem cells: generating and regenerating the brain. (2013) Neuron. 80(3):588-601. DOI: 10.1016/j.neuron.2013.10.037
Deshmukh, V.A., Tardif, V., Lyssiotis, C.A., Green, C.C., Kerman, B., Kim, H.J., Padmanabhan, K., Swoboda, J.G., Ahmad, I., Kondo, T., Gage, F.H., Theofilopoulos, A.N., Lawson, B.R., Schultz, P.G., Lairson, L.L. A regenerative approach to the treatment of multiple sclerosis. (2013) Nature. 502(7471):327-332. DOI: 10.1038/nature12647
Devor, A., Bandettini, P.A., Boas, D.A., Bower, J.M., Buxton, R.B., Cohen, L.B., Dale, A.M., Einevoll, G.T., Fox, P.T., Franceschini, M.A., Friston, K.J., Fujimoto, J.G., Geyer, M.A., Greenberg, J.H., Halgren, E., Hämäläinen, M.S., Helmchen, F., Hyman, B.T., Jasanoff, A., Jernigan, T.L., Judd, L.L., Kim, S.G., Kleinfeld, D., Kopell, N.J., Kutas, M., Kwong, K.K., Larkum, M.E., Lo, E.H., Magistretti, P.J., Mandeville, J.B., Masliah, E., Mitra, P.P., Mobley, W.C., Moskowitz, M.A., Nimmerjahn, A., Reynolds, J.H., Rosen, B.R., Salzberg, B.M., Schaffer, C.B., Silva, G.A., So, P.T., Spitzer, N.C., Tootell, R.B., Van Essen, D.C., Vanduffel, W., Vinogradov, S.A., Wald, L.L., Wang, L.V., Weber, B., Yodh, A.G. The challenge of connecting the dots in the B.R.A.I.N. (2013) Neuron. 80(2):270-4. DOI: 10.1016/j.neuron.2013.09.008
Cortes, J.M., Desroches, M., Rodrigues, S., Veltz, R., Muñoz, M.A., Sejnowski, T.J. Short-term synaptic plasticity in the deterministic Tsodyks-Markram model leads to unpredictable network dynamics. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(41):16610-5. DOI: 10.1073/pnas.1316071110
Herzog, C.D., Brown, L., Kruegel, B.R., Wilson, A., Tansey, M.G., Gage, F.H., Johnson, E.M., Bartus, R.T. Enhanced neurotrophic distribution, cell signaling and neuroprotection following substantia nigral versus striatal delivery of AAV2-NRTN (CERE-120). (2013) Neurobiol. Dis. 58:38-48. DOI: 10.1016/j.nbd.2013.04.011
Aljadeff, J., Segev, R., Berry, M.J., Sharpee, T.O. Spike triggered covariance in strongly correlated gaussian stimuli. (2013) PLOS Computational Biology. 9(9):e1003206. DOI: 10.1371/journal.pcbi.1003206
Ruiz, O., Lustig, B.R., Nassi, J.J., Cetin, A., Reynolds, J.H., Albright, T.D., Callaway, E.M., Stoner, G.R., Roe, A.W. Optogenetics through windows on the brain in the nonhuman primate. (2013) Journal of Neurophysiology. 110(6):1455-67. DOI: 10.1152/jn.00153.2013
Hsu, C.C., White, N.M., Hayashi, M., Lin, E.C., Poon, T., Banerjee, I., Chen, J., Pfaff, S.L., Macagno, E.R., Dorrestein, P.C. Microscopy ambient ionization top-down mass spectrometry reveals developmental patterning. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(37):14855-60. DOI: 10.1073/pnas.1310618110
Timofeev, I., Sejnowski, T.J., Bazhenov, M., Chauvette, S., Grand, L.B. Age dependency of trauma-induced neocortical epileptogenesis. (2013) Frontiers in Cellular Neuroscience. 7:154. DOI: 10.3389/fncel.2013.00154
Tang, X., Zhou, L., Wagner, A.M., Marchetto, M.C., Muotri, A.R., Gage, F.H., Chen, G. Astroglial cells regulate the developmental timeline of human neurons differentiated from induced pluripotent stem cells. (2013) Stem Cell Research. 11(2):743-57. DOI: 10.1016/j.scr.2013.05.002
Toyama, B.H., Savas, J.N., Park, S.K., Harris, M.S., Ingolia, N.T., Yates, J.R., Hetzer, M.W. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. (2013) Cell. 154(5):971-982. DOI: 10.1016/j.cell.2013.07.037
Osakada, F., Callaway, E.M. Design and generation of recombinant rabies virus vectors. (2013) Nature Protocols. 8(8):1583-1601. DOI: 10.1038/nprot.2013.094
Lister, R.*, Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D., Yu, M., Tonti-Filippini, J., Heyn, H., Hu, S., Wu, J.C., Rao, A., Esteller, M., He, C., Haghighi, F.G., Sejnowski, T.J., Behrens, M.M.*, Ecker, J.R.* Global epigenomic reconfiguration during mammalian brain development. (2013) Science. 341(6146):1237905. DOI: 10.1126/science.1237905
Francius, C., Harris, A., Rucchin, V., Hendricks, T.J., Stam, F.J., Barber, M., Kurek, D., Grosveld, F.G., Pierani, A., Goulding, M., Clotman, F. Identification of multiple subsets of ventral interneurons and differential distribution along the rostrocaudal axis of the developing spinal cord. (2013) PLOS One. 8(8):e70325. DOI: 10.1371/journal.pone.0070325
Furness, D.N., Johnson, S.L., Manor, U., Rüttiger, L., Tocchetti, A., Offenhauser, N., Olt, J., Goodyear, R.J., Vijayakumar, S., Dai, Y., Hackney, C.M., Franz, C., Di Fiore, P.P., Masetto, S., Jones, S.M., Knipper, M., Holley, M.C., Richardson, G.P., Kachar, B., Marcotti, W. Progressive hearing loss and gradual deterioration of sensory hair bundles in the ears of mice lacking the actin-binding protein Eps8L2. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(34):13898-13903. DOI: 10.1073/pnas.1304644110
Ben Isaac, E., Manor, U., Kachar, B., Yochelis, A., Gov, N.S. Linking actin networks and cell membrane via a reaction-diffusion-elastic description of nonlinear filopodia initiation. (2013) Phys Rev E Stat Nonlin Soft Matter Phys. 88(2):022718. DOI: 10.1103/PhysRevE.88.022718
Sung, T.C., Chen, Z., Thuret, S., Vilar, M., Gage, F.H., Riek, R., Lee, K.F. P45 forms a complex with FADD and promotes neuronal cell survival following spinal cord injury. (2013) PLOS One. 8(7):e69286. DOI: 10.1371/journal.pone.0069286
Sharpee, T.O. Computational identification of receptive fields. (2013) Annual Review of Neuroscience. 36:103-20. DOI: 10.1146/annurev-neuro-062012-170253
Hatch, E.M., Fischer, A.H., Deerinck, T.J., Hetzer, M.W. Catastrophic nuclear envelope collapse in cancer cell micronuclei. (2013) Cell. 154(1):47-60. DOI: 10.1016/j.cell.2013.06.007
Nienborg, H., Hasenstaub, A., Nauhaus, I., Taniguchi, H., Huang, Z.J., Callaway, E.M. Contrast dependence and differential contributions from somatostatin- and parvalbumin-expressing neurons to spatial integration in mouse V1. (2013) Journal of Neuroscience. 33(27):11145-11154. DOI: 10.1523/JNEUROSCI.5320-12.2013
Wall, N.R., De La Parra, M., Callaway, E.M., Kreitzer, A.C. Differential innervation of direct- and indirect-pathway striatal projection neurons. (2013) Neuron. 79(2):347-360. DOI: 10.1016/j.neuron.2013.05.014
Sharpee, T.O., Kouh, M., Reynolds, J.H. Trade-off between curvature tuning and position invariance in visual area V4. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(28):11618-23. DOI: 10.1073/pnas.1217479110
Kaardal, J., Fitzgerald, J.D., Berry, M.J., Sharpee, T.O. Identifying functional bases for multidimensional neural computations. (2013) Neural Computation. 25(7):1870-90. DOI: 10.1162/NECO_a_00465
Golomb, B.A., Brenner, S., Chalfie, M., Glashow, S.L., Glauber, R.J., Hubel, D.H., Maskin, E.S., Greengard, P., Gross, D.J., Roberts, R., Tonegawa, S., Wilczek, F.A., Brown, E.M., Sejnowski, T.J. Chocolate habits of Nobel prizewinners. (2013) Nature. 499(7459):409. DOI: 10.1038/499409a
Lainscsek, C., Sejnowski, T.J. Electrocardiogram classification using delay differential equations. (2013) Chaos. 23(2):023132. DOI: 10.1063/1.4811544
Nandy, A.S., Sharpee, T.O., Reynolds, J.H., Mitchell, J.F. The fine structure of shape tuning in area V4. (2013) Neuron. 78(6):1102-15. DOI: 10.1016/j.neuron.2013.04.016
Yu, D.X., Marchetto, M.C., Gage, F.H. Therapeutic translation of iPSCs for treating neurological disease. (2013) Cell Stem Cell. 12(6):678-88. DOI: 10.1016/j.stem.2013.05.018
Vilchez, D., Boyer, L., Lutz, M., Merkwirth, C., Morantte, I., Tse, C., Spencer, B., Page, L., Masliah, E., Berggren, W.T., Gage, F.H., Dillin, A. FOXO4 is necessary for neural differentiation of human embryonic stem cells. (2013) Aging Cell. 12(3):518-22. DOI: 10.1111/acel.12067
Ji, B., Wang, X., Pinto-Duarte, A., Kim, M., Caldwell, S., Young, J.W., Behrens, M.M., Sejnowski, T.J., Geyer, M.A., Zhou, X. Prolonged Ketamine Effects in Sp4 Hypomorphic Mice: Mimicking Phenotypes of Schizophrenia. (2013) PLOS One. 8(6):e66327. DOI: 10.1371/journal.pone.0066327
Chukoskie, L., Snider, J., Mozer, M.C., Krauzlis, R.J., Sejnowski, T.J. Learning where to look for a hidden target. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110 Suppl :10438-10445. DOI: 10.1073/pnas.1301216110
Egawa, N., Kitaoka, S., Tsukita, K., Naitoh, M., Takahashi, K., Yamamoto, T., Adachi, F., Kondo, T., Okita, K., Asaka, I., Aoi, T., Watanabe, A., Yamada, Y., Morizane, A., Takahashi, J., Ayaki, T., Ito, H., Yoshikawa, K., Yamawaki, S., Suzuki, S., Watanabe, D., Hioki, H., Kaneko, T., Makioka, K., Okamoto, K., Takuma, H., Tamaoka, A., Hasegawa, K., Nonaka, T., Hasegawa, M., Kawata, A., Yoshida, M., Nakahata, T., Takahashi, R., Marchetto, M.C., Gage, F.H., Yamanaka, S., Inoue, H. Response to comment on "Drug screening for ALS using patient-specific induced pluripotent stem cells". (2013) Science Translational Medicine. 5(188):188lr2. DOI: 10.1126/scitranslmed.3005697
Li, Y., Stam, F.J., Aimone, J.B., Goulding, M., Callaway, E.M., Gage, F.H. Molecular layer perforant path-associated cells contribute to feed-forward inhibition in the adult dentate gyrus. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(22):9106-11. DOI: 10.1073/pnas.1306912110
Stiefel, K.M., Englitz, B., Sejnowski, T.J. Origin of intrinsic irregular firing in cortical interneurons. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(19):7886-7891. DOI: 10.1073/pnas.1305219110
Gifford, W.D., Pfaff, S.L., Macfarlan, T.S. Transposable elements as genetic regulatory substrates in early development. (2013) Trends in Cell Biology. 23(5):218-26. DOI: 10.1016/j.tcb.2013.01.001
Yin, L., Geng, Y., Osakada, F., Sharma, R., Cetin, A.H., Callaway, E.M., Williams, D.R., Merigan, W.H. Imaging light responses of retinal ganglion cells in the living mouse eye. (2013) Journal of Neurophysiology. 109(9):2415-2421. DOI: 10.1152/jn.01043.2012
Gire, D.H., Restrepo, D., Sejnowski, T.J., Greer, C., De Carlos, J.A., Lopez-Mascaraque, L. Temporal processing in the olfactory system: can we see a smell? (2013) Neuron. 78(3):416-432. DOI: 10.1016/j.neuron.2013.04.033
Rangel, L.M., Quinn, L.K., Chiba, A.A., Gage, F.H., Aimone, J.B. A hypothesis for temporal coding of young and mature granule cells. (2013) Frontiers in Neuroscience. 7:75. DOI: 10.3389/fnins.2013.00075
Saremi, S., Sejnowski, T.J., Sharpee, T.O. Double-gabor filters are independent components of small translation-invariant image patches. (2013) Neural Computation. 25(4):922-39. DOI: 10.1162/NECO_a_00418
Wang, X., Pinto-Duarte, A., Sejnowski, T.J., Behrens, M.M. How Nox2-containing NADPH oxidase affects cortical circuits in the NMDA receptor antagonist model of schizophrenia. (2013) Antioxidants & Redox Signaling. 18(12):1444-62. DOI: 10.1089/ars.2012.4907
Jeanne, J.M., Sharpee, T.O., Gentner, T.Q. Associative learning enhances population coding by inverting interneuronal correlation patterns. (2013) Neuron. 78(2):352-63. DOI: 10.1016/j.neuron.2013.02.023
Regner, B.M., Vučinić, D., Domnisoru, C., Bartol, T.M., Hetzer, M.W., Tartakovsky, D.M., Sejnowski, T.J. Anomalous diffusion of single particles in cytoplasm. (2013) Biophysical Journal. 104(8):1652-60. DOI: 10.1016/j.bpj.2013.01.049
Wang, X., Zhao, Y., Zhang, X., Badie, H., Zhou, Y., Mu, Y., Loo, L.S., Cai, L., Thompson, R.C., Yang, B., Chen, Y., Johnson, P.F., Wu, C., Bu, G., Mobley, W.C., Zhang, D., Gage, F.H., Ranscht, B., Zhang, Y.W., Lipton, S.A., Hong, W., Xu, H. Loss of sorting nexin 27 contributes to excitatory synaptic dysfunction by modulating glutamate receptor recycling in Down's syndrome. (2013) Nature Medicine. 19(4):473-80. DOI: 10.1038/nm.3117
Deng, W., Mayford, M., Gage, F.H. Selection of distinct populations of dentate granule cells in response to inputs as a mechanism for pattern separation in mice. (2013) Elife. 2:e00312. DOI: 10.7554/eLife.00312
Hinckley, C.A., Pfaff, S.L. Imaging spinal neuron ensembles active during locomotion with genetically encoded calcium indicators. (2013) Ann. N. Y. Acad. Sci. 1279:71-9. DOI: 10.1111/nyas.12092
Franks, T.M., Hetzer, M.W. The role of Nup98 in transcription regulation in healthy and diseased cells. (2013) Trends in Cell Biology. 23(3):112-7. DOI: 10.1016/j.tcb.2012.10.013
Rowe, H.M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T.S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S.L., Trono, D. TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. (2013) Genome Research. 23(3):452-61. DOI: 10.1101/gr.147678.112
Alivisatos, A.P., Andrews, A.M., Boyden, E.S., Chun, M., Church, G.M., Deisseroth, K., Donoghue, J.P., Fraser, S.E., Lippincott-Schwartz, J., Looger, L.L., Masmanidis, S., McEuen, P.L., Nurmikko, A.V., Park, H., Peterka, D.S., Reid, C., Roukes, M.L., Scherer, A., Schnitzer, M., Sejnowski, T.J., Shepard, K.L., Tsao, D., Turrigiano, G., Weiss, P.S., Xu, C., Yuste, R., Zhuang, X. Nanotools for neuroscience and brain activity mapping. (2013) ACS Nano. 7(3):1850-66. DOI: 10.1021/nn4012847
Alivisatos, A.P., Chun, M., Church, G.M., Deisseroth, K., Donoghue, J.P., Greenspan, R.J., McEuen, P.L., Roukes, M.L., Sejnowski, T.J., Weiss, P.S., Yuste, R. Neuroscience. The brain activity map. (2013) Science. 339(6125):1284-5. DOI: 10.1126/science.1236939
Liang, Y., Franks, T.M., Marchetto, M.C., Gage, F.H., Hetzer, M.W. Dynamic association of NUP98 with the human genome. (2013) PLOS Genetics. 9(2):e1003308. DOI: 10.1371/journal.pgen.1003308
Saremi, S., Sejnowski, T.J. Hierarchical model of natural images and the origin of scale invariance. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(8):3071-3076. DOI: 10.1073/pnas.1222618110
Tanaka, H., Sejnowski, T.J. Computing reaching dynamics in motor cortex with Cartesian spatial coordinates. (2013) Journal of Neurophysiology. 109(4):1182-1201. DOI: 10.1152/jn.00279.2012
Kinney, J.P., Spacek, J., Bartol, T.M., Bajaj, C.L., Harris, K.M., Sejnowski, T.J. Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil. (2013) Journal of Comparative Neurology. 521(2):448-464. DOI: 10.1002/cne.23181
Srinivasan, L., Asaad, W.F., Ginat, D.T., Gale, J.T., Dougherty, D.D., Williams, Z.M., Sejnowski, T.J., Eskandar, E.N. Action initiation in the human dorsal anterior cingulate cortex. (2013) PLOS One. 8(2):e55247. DOI: 10.1371/journal.pone.0055247
Shimozaki, K., Clemenson, G.D., Gage, F.H. Paired related homeobox protein 1 is a regulator of stemness in adult neural stem/progenitor cells. (2013) Journal of Neuroscience. 33(9):4066-75. DOI: 10.1523/JNEUROSCI.4586-12.2013
Volman, V., Bazhenov, M., Sejnowski, T.J. Divide and conquer: functional segregation of synaptic inputs by astrocytic microdomains could alleviate paroxysmal activity following brain trauma. (2013) PLOS Computational Biology. 9(1):e1002856. DOI: 10.1371/journal.pcbi.1002856
Toyama, B.H., Hetzer, M.W. Protein homeostasis: live long, won't prosper. (2013) Nature Reviews Molecular Cell Biology. 14(1):55-61. DOI: 10.1038/nrm3496
Kurian, L., Sancho-Martinez, I., Nivet, E., Aguirre, A., Moon, K., Pendaries, C., Volle-Challier, C., Bono, F., Herbert, J.M., Pulecio, J., Xia, Y., Li, M., Montserrat, N., Ruiz, S., Dubova, I., Rodriguez, C., Denli, A.M., Boscolo, F.S., Thiagarajan, R.D., Gage, F.H., Loring, J.F., Laurent, L.C., Izpisua Belmonte, J.C. Conversion of human fibroblasts to angioblast-like progenitor cells. (2013) Nature Methods. 10(1):77-83. DOI: 10.1038/nmeth.2255
