Systems Neuroscience (online course)

Background Reading

pdf -- Gross, C.G. (1997) From Imhotep to Hubel and Wiesel. In K.S. Rockland, J.H. Kaas and A.Peters (eds.), Cerebral Cortex, Vol. 12, Springer, pp. 31-36, excerpt on Cell Doctrine.

pdf -- Zigmond, M.J., F.E. Bloom, S.C. Landis, J.L. Roberts, and L.R. Squire eds. (1999) Fundamental Neuroscience, Academic Press, Chaps. 5, 6, and part of 7, pp. 107-165.

pdf -- Douglas, R., H. Markram, and K. Martin (2004) Neocortex. In G.M. Shepherd (ed.), Synaptic Organization In the Brain, Oxford, pp. 499-558.

pdf -- Kasthuri, N., [19 others], and J.W. Lichtman (2015) Saturated reconstruction of a volume of neocortex. Cell 162:648-661.

pdf -- Dan, Y. and M.-M. Poo (2005) Spike timing-dependent plasticity: from synapse to perception. Physiological Reviews 86:1033-1048.

pdf -- Hopfield, J.J. (1984) Neurons with graded response have collective computational properties like those of two-state neurons. Proceedings of the National Academy of Science USA 81:3088-3092.

pdf -- Linsker, R. (1986) From basic network principles to neural architecture: Emergence of spatial-opponent cells. Proceedings of the National Academy of Science USA 83:7508- 7512.

pdf -- Sereno, M.I. (1991) The brain in two pages.

pdf -- Sadler, T.W. (2005) Embryology of neural tube development American Journal of Medical Genetics Part C 135C:2-8.

pdf -- Hoerder-Suabedissen, A. and Z. Molnar (2015) Development, evolution and pathology of neocortical subplate neurons. Nature Reviews Neuroscience 16:133-146.

pdf -- Tallinen, T., J.Y. Chung, F. Rousseau, N. Girard, J. Lefevre, and L. Mahadevan (2016) On the growth and form of cortical convolutions. Nature Physics 12:588-593.

pdf -- Grove, E.A. and T. Fukuchi-Shimogori (2003) Generating the cerebral cortical area map. Annual Review of Neuroscience 26:335-380.

pdf -- McLaughlin, T. and D.M. O'Leary (2005) Molecular gradients and development of retinotopic maps. Annual Review of Neuroscience 28:327-355.

pdf -- Williams, R.W., D. Hogan and P.E. Garraghty (1994) Target recognition and visual maps in the thalamus of achiasmatic dogs. Nature 367:637-639.

    Additional background, development

pdf -- O'Leary, D.D.M. (1989) Do cortical areas emerge from a protocortex? Trends in Neurosciences 12:400-406.

pdf -- Ghosh, A., A. Antonioni, S.K. McConnell, and C.J. Shatz (1990) Requirement for subplate neurons in the formation of thalamocortical connections. Nature 347:179-181.

pdf -- Hahm, J.-O, R.B. Langdon, and M. Sur (1991) Disruption of retinogeniculate afferent segregation by antagonists to NMDA receptors. Nature 351:568-570.

pdf -- Brown, A., P.A. Yates, P. Burrola, D. Ortuno, A. Vaidya, T.H. Jessell, S.L. Pfaff, D.D.M. O'Leary, and G. Lemke (2000) Topographic mapping from the retina to the midbrain is controlled by relative but not absolute levels of EphA receptor signaling. Cell 102:77-88.

pdf -- Hatten, M.E. (1999) Central nervous system neuronal migration. Annual Review of Neurosciences 22:511-539.

pdf -- Rhinn, M. and M. Brand (2001) The midbrain-hindbrain boundary organizer. Current Opinion in Neurobiology 11:34-42.

pdf -- Rhinn, M., A. Picker, and M. Brand (2006) Global and local mechanisms of forebrain and midbrain patterning. Current Opinion in Neurobiology 16:5-12.

pdf -- Sereno, M.I. (1988) The visual system. In W. von Seelen, G. Shaw, and U.M. Leinhos (eds.), Organization of Neural Networks. Weinheim: VCH Verlagsgesellschaft, pp. 167-184.

pdf -- Callaway, E.M. (2005) Structure and function of parallel pathways in the primate early visual system Journal of Physiology 566:13-19.

pdf -- Yabuta, N.H., A. Sawatari, and E.M. Callaway (2001) Two functional channels from primary visual cortex to dorsal visual cortical areas. Science 292:297-300.

pdf -- Ohzawa, I. (1998) Mechanisms of stereoscopic vision: the disparity energy model. Current Opinion in Neurobiology 8:509-515.

pdf -- Sincich, L.C. and J.C. Horton (2005) The circuitry of V1 and V2 intergration of color, form, and motion. Annual Review of Neuroscience 28:303-326.

pdf -- Sereno, M.I. and J.M. Allman (1991) Cortical visual areas in mammals. In A.G. Leventhal (ed.), The Neural Basis of Visual Function. Macmillan, pp. 160-172.

pdf -- Sereno, M.I., C.T. McDonald, and J.M. Allman (1994) Analysis of retinotopic maps in extrastriate cortex. Cerebral Cortex 4:601-620.

pdf -- Felleman, D.J. and D.C. Van Essen (1991) Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex 1:1-47.

pdf -- Tanaka, K. (1998) Representation of visual motion in the extrastriate visual cortex. In T. Watanabe (ed.), High-level motion processing. MIT Press, pp. 295-313.

pdf -- Sereno, M.I. and M.E. Sereno (1991) Learning to see rotation and dilation with a Hebb rule. In R.P. Lippmann, J.E. Moody, and D.S. Touretzky (eds.), Advances in Neural Information Processing Systems 3. Morgan Kaufmann Publishers, pp. 320-326.

pdf -- Colby, C.L. and M.E. Goldberg (1999) Space and attention in parietal cortex. Annual Review of Neurosciences 22:319-349.

pdf -- Huang, R.-S. and M.I. Sereno (2013) Bottom-up retinotopic organization supports top-down mental imagery. The Open Neuroimaging Journal 7:58-67.

pdf -- Sereno, M.I., C.T. McDonald, and J.M. Allman (2015) Retinotopic organization of extrastriate cortex in the owl monkey - dorsal and lateral areas. Visual Neuroscience 32:e021, 39 pages.

pdf -- Haenny, P.E., J.H.R. Maunsell, and P.H. Schiller (1988) State dependent activity in monkey visual cortex. II. Retinal and extraretinal factors. Experimental Brain Research 69:245-259.

pdf -- Desimone, R. and J. Duncan (1995) Neural mechanisms of selective visual attention. Annual Review of Neuroscience 18:193-222.

pdf -- Sereno, A.B. and J.H.R. Maunsell (1998) Shape selectivity in primate lateral intraparietal cortex. Nature 395:500-503.

pdf -- Logothetis, N.K. and J. Pauls (1995) Psychophysical and physiological evidence for viewer-centered object representations in the primate. Cerebral Cortex 5:270-288.

pdf -- Rolls, E.T., N.C. Aggelopoulos, and F. Zheng (2003) The receptive fields of inferior temporal cortex neurons in natural scenes. Journal of Neuroscience 23:339-348.

pdf -- Wang, G., M. Tanifuji, and K. Tanaka (1998) Functional architecture in monkey inferotemporal cortex revealed by in vivo optical imaging. Neuroscience Research 32:33-46.

pdf -- Ponce, C.R., W. Xiao, P.F. Schade, T.S. Hartmann, G. Kreiman, and M.S. Livingstone (2019) Evolving super stimuli for real neurons using deep generate networks bioRxiv 10.1101:516484v1

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System -- Somatosensory System. Springer-Verlag, pp. 149-164.

pdf -- Iwamura, Y. (1998) Hierarchical somatosensory processing. Current Opinion in Neurobiology 8:522-528.

pdf -- Kaas, J.H. (2000) The reorganization of sensory and motor maps after injury in adult mammals. In M.S. Gazzaniga, ed., The New Cognitive Neurosciences, MIT Press, pp. 223-236.

pdf -- Pons, T.P., P.E. Garraghty, A.K. Ommaya, J.H. Kaas, E. Taub, and M. Mishkin (1991) Massive cortical reorganization after sensory deafferentation in adult macaques. Science 252: 1857-1860.

pdf -- Buonomano, D.V. and M.M. Merzenich (1998) Cortical plasticity: from synapses to maps. Annual Review of Neuroscience 21:149-186.

pdf -- D.R. Sengelaub, N. Muja, A.C. Mills, W.A. Myers, J.D. Churchill, and P.E. Garraghty (1997) Denervation-induced sprouting of intact peripheral afferents into the cuneate nucleus of adult rats. Brain Research 769:256-262.

pdf -- Calford, M.B., and R. Tweedale (1990) Interhemispheric transfer of plasticity in the cerebral cortex. Science 249:805-807.

pdf -- Kim, S.S., M. Gomez-Ramirez, P.H. Thakur, and S.S. Hsiao (2015) Multimodal interactions between proprioceptive and cutaneous signals in primary somatosensory cortex. Neuron 86:555-566.

pdf -- Huang, R.-S. and M.I. Sereno (2006) Dodecapus: An MR-compatible system for somatosensory stimulation. Neuroimage 34:1060-1073.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System -- Auditory System. Springer-Verlag, pp. 165-179.

pdf -- Konishi, M., T.T. Takahashi, H. Wagner, W.E. Sullivan, and C.E. Carr (1988) Neurophysiological and anatomical substrates of sound localization in the the owl. In G.M. Edelman, W.E. Gall, and W.M Cowan (eds.), Auditory Function: Neurobiological Bases of Hearing. John Wiley and Sons, pp. 721-745.

pdf -- McAlpine, D., D. Jiang, A.R. Palmer (2001) A neural code for low-frequency sound localization in mammals. Nature Neuroscience 4:396-401.

pdf -- Brand, A., O. Behrend, T. Marquardt, D. McAlpine, and B. Grothe (2002) Precise inhibition is essential for microsecond interaural time difference coding. Nature 417:543-547.

pdf -- Carr, C.E. and C. Koppl (2004) Coding interaural time differences at low best frequencies in the barn owl. Journal of Physiology - Paris 98:99-112.

pdf -- Kulkarni, A. and H.S. Colburn (1998) Role of spectral detail in sound-source localization. Nature 396:747-749.

pdf -- Suga, N. (1988) Auditory neuroethology and speech processing: complex-sound processing by combination-sensitive neurons. In G.M. Edelman, W.E. Gall, and W.M Cowan (eds.), Auditory Function: Neurobiological Bases of Hearing. John Wiley and Sons, pp. 679-720.

pdf -- deCharms, R.C., D.T. Blake, and M.M. Merzenich (1998) Optimizing sound features for cortical neurons. Science 280:1439-1443.

pdf -- Rauschecker, J.P. (1998) Cortical processing of complex sounds. Current Opinion in Neurobiology 8:516-521.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 247-278.

pdf -- Sparks, D.L. and R. Hartwich-Young (1989) The deep layers of the superior colliculus. In R.H. Wurtz and M.E. Goldberg (eds.) The Neurobiology of Saccadic Eye Movements. Elsevier, pp. 213-255.

pdf -- Sommer, M.A. and R.H. Wurtz (2006) Influence of the thalamus on spatial visual processing in frontal cortex. Nature 444:374-377.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 185-196.

pdf -- Wurtz, R.H. and D.P. Munoz (1995) Role of monkeys superior colliculus in control of saccades and fixation. In M.S. Gazzaniga (ed.), The Cognitive Neurosciences, MIT Press, pp. 533-548.

pdf -- Rodgers, C., D.P. Munoz, S.H. Scott, and M. Pare (2006) Discharge properties of monkey tectoreticular neurons. Journal of Neurophysiology 95:3502-3511.

pdf -- Sereno, M.I. and R.-S. Huang (2006) A human parietal face area contains aligned head-centered visual and tactile maps. Nature Neuroscience 9:1337-1343.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 221-236.

pdf -- Sereno, M.I., J. Diedrichsen, M. Tachrount, G. Testa-Silva, H. d'Arceuil, and C. De Zeeuw (2020) The human cerebellum has almost 80% of the surface area of the neocortex. Proceedings of the National Academy of Sciences USA 117:19538-19543.

pdf -- Thompson, R.F. and D.J. Krupa (1994) Organization of memory traces in the mammalian brain. Annual Review of Neuroscience 17:519-549.

pdf -- Hoover, J.E. and P.L. Strick (1993) Multiple output channels in the basal ganglia. Science 259:819-821.

pdf -- Hoover, J.E. and P.L. Strick (1999) The organization of cerebellar and basal ganglia outputs to primary motor cortex as revealed by retrograde transneuronal transport of Herpes Simplex Virus Type 1. Journal of Neuroscience 19:1446-1463.

pdf -- Clower, D.M., R.P. Dum, P.L. Strick (2005) Basal ganglia and cerebellar inputs to 'AIP'. Cerebral Cortex 15:913-920.

pdf -- Kaji, R., R. Urushihara, N. Murase, H. Shimazu, S. Goto (2005) Abnormal sensory gating in basal ganglia disorders. Journal of Neurology 252 [Suppl 4]:IV/13-IV/16.

pdf -- Carpenter, A.F., A.P. Georgopoulos and G. Pellizzer (1999) Motor cortical encoding of serial order in a context-recall task. Science 283:1752-1757.

pdf -- Rizzolatti, G., L. Fogassi, and V. Gallese (2000) Cortical mechanisms subserving object grasping and action recognition: A new view on the cortical motor functions. In M.S. Gazzaniga, ed., The New Cognitive Neurosciences, MIT Press, pp. 539-552.

pdf -- Graziano, M. (2006) The organization of behavioral repertoire in motor cortex. Annual Review of Neuroscience 29:105-134.

pdf -- Muller, R.U., J.B. Ranck, and J.S. Taube (1996) Head direction cells: properties and functional significance. Current Opinion in Neurobiology 6:196-206.

pdf -- Zhang, K. (1996) Representation of spatial orientation by the intrinsic dynamics of the head-direction cell ensemble: a theory. Journal of Neuroscience 16:2112-2126.

pdf -- Fyhn, M., S. Molden, M.P. Witter, E.I. Moser, and M.B. Moser (2004) Spatial representation in the entorhinal cortex. Science 305:1258-1264.

pdf -- Hafting, T.., Fyhn, S. Molden, M.-B. Moser, E.I. Moser (2005) Microstructure of a spatial map in the entorhinal cortex. Nature 436:801-806.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 293-309, 323-344.

pdf -- Muller, R.U., J.L. Kubie, and J.B. Ranck (1987) Spatial firing patterns of hippocampal complex-spike cells in a fixed environment. Journal of Neuroscience 7:1935-1950.

pdf -- Muller, R.U. and J.L. Kubie (1987) The effects of changes in the environment on the spatial firing of hippocampal complex-spike cells. Journal of Neuroscience 7:1951- 1968.

pdf -- Taube, J.S., R.U. Muller, and J.B. Ranck (1990) Head-direction cells recorded from the postsubiculum in freely moving rats. I. description and quantitative analysis. Journal of Neuroscience 10:420-435.

pdf -- Zugaro, M.B., A Berthoz, and S.I. Wiener (2001) Background, but not foreground, spatial cues are taken as references for head direction responses by rat anterodorsal thalamus neurons. Journal of Neuroscience 21:RC154.

pdf -- Yoganarasimha, D. and J.J. Knierim (2004) Coupling between place cells and head direction cells during relative translations and rotation of distal landmarks. Experimental Brain Research 160:344-359.

pdf -- Sargolini, F., M. Fyhn, T. Hafting, B.L. McNaughton, M.P. Witter, M.B. Moser, and E.I. Moser (2006) Conjunctive representation of position, direction, and velocity in entorhinal cortex. Science 312:758-762.

pdf -- Brivanlou, I.H., J.L.M. Dantzker, C.F. Stevens, and E.M. Callaway (2004) Topographic specificity of functional connections from hippocampal CA3 to CA1. Proceedings of the National Academcy of Science USA 101:2560-2565.

pdf -- Sereno, M.I. (1998) Brain mapping in animals and humans. Current Opinion in Neurobiology 8:188-194.

pdf -- Sereno, M.I. and R.B.H. Tootell (2005) From monkeys to humans: what do we now know about brain homologies? Current Opinion in Neurobiology 15:135-144.

pdf -- Orban, G.A., D. Van Essen, W. Vanduffel (2004) Comparative mapping of higher visual areas in monkeys and humans. Trends in Cognitive Science 8:315-324.

pdf -- Savage-Rumbaugh, S.S., K. McDonald, R.A. Sevcik, W.D. Hopkins, and E. Rubert (1986) Spontaneous symbol acquisition and communicative use by pygmy chimpanzees (Pan paniscus) Journal of Experimental Psychology: General 115:211- 235.

pdf -- Sereno, M.I. (1991) Language and the primate brain. In Proceedings, Thirteenth Annual Conference of the Cognitive Science Society, Lawrence Erlbaum Assoc., pp. 79-84.

pdf -- Doupe, A.J. and P.K. Kuhl (1999) Birdsong and human speech. Annual Review of Neuroscience 22:567-631.

pdf -- [chronological collection of articles and letters from 2004-2006 on the debate about the status of the skeleton, tools, and brain of the Flores Island hominin, Homo floresiensis, from Science and PNAS]

pdf -- Sereno, M.I. (2005) Language origins without the semantic urge. Cogsci Online Journal 3:1-12.

pdf -- Sereno, M.I. (2014) Origin of symbol-using systems: speech, but not sign, without the semantic urge. Philosophical Transactions of the Royal Society B 369(1651):20130303.

pdf -- Huettel, S.A, A.W.Song, and G. McCarthy (2004) Functional Magnetic Resonance Imaging, Chap. 4, pp. 75-97.

pdf -- precis of Sereno hand-written Neuroimaging notes (full notes here)

pdf -- Sereno, M.I., A.M. Dale, J.B. Reppas, K.K. Kwong, J.W. Belliveau, T.J. Brady, B.R. Rosen, and R.B.H. Tootell (1995) Borders of multiple visual areas in human revealed by functional magnetic resonance imaging. Science 268:889-893.

pdf -- Tootell, R.B., N.K. Hadjikhani, W. Vanduffel, A.K. Liu, J.D. Mendola, M.I. Sereno, A.M. Dale (1998) Functional analysis of primary visual cortex (V1) in humans. Proceedings of the National Academy of Sciences USA 95:811-817.

pdf -- Tootell, R.B.H., J.D. Mendola, N.K. Hadjikhani, P.J. Ledden, A.K. Liu, J.B. Reppas, M.I. Sereno, and A.M. Dale (1997) Functional analysis of V3A and related areas in human visual cortex. Journal of Neuroscience 17:1060-7078.

pdf -- Hadjikhani, N., A.K. Liu, A.M. Dale, P. Cavanagh et al. (1998) Retinotopy and color sensitivity in human visual cortical area V8. Nature Neuroscience 1:235-241.

pdf -- Sereno, M.I., S. Pitzalis, and A. Martinez (2001) Mapping of contralateral space in retinotopic coordinates by a parietal cortical area in humans. Science 294:1350-1353.

pdf -- Potter, M.C., J.F. Kroll, B. Yachzel, E. Carpenter, and J. Sherman (1986) Pictures in sentences: understanding without words. Journal of Experimental Psychology: General 115:281-294.

pdf -- Jackendoff, R. The connection between language and vision, Chapter 10 in Consciousness and the Computational Mind. MIT Press, pp. 193-212.

pdf -- Talavage, T.M., M.I. Sereno, J.R. Melcher, P.J. Ledden, B.R. Rosen and A.M. Dale (2004) Tonotopic organization in human auditory cortex revealed by progressions of frequency sensitivity. Journal of Neurophysiology 91:1282-1296.

pdf -- Burnstine, T.H., R.P. Lesser, J. Hart Jr., S. Uematsu, S.J. Zinreich, G.L. Krauss, R.S. Fisher, E.P.G. VIning, and B. Gordon (1990) Characterization of the basal temporal language arae in patients with temporal lobe epilepsy. Neurology 40:966-970.

pdf -- Puce, A., T. Allison, M. Asgari, J.C. Gore and G. McCarthy (1996) Differential sensitivity of human visual cortex to faces, letterstrings, and textures: a functional magnetic resonance imaging study. Journal of Neuroscience 16:5205-5215.

pdf -- Zatorre, R.J., E. Meyer, A. Gjedde, and A.C. Evans (1996) PET studies of phonetic processing of speech: review, replication, and reanalysis. Cerebral Cortex 6:21-30.

pdf -- Binder J.R., J.A. Frost, T.A. Hammeke, P.S. Bellgowan, J.A Springer, J.N. Jaufman, and E.T. Possing (2000) Human temporal lobe activation by speech and nonspeech sounds. Cerebral Cortex 10:512-528.

pds -- A. L. Roskies, J.A. Fiez, D.A. Balota, M.E. Raichle, and S.E. Petersen (2001) Task-Dependent Modulation of Regions in the Left Inferior Frontal Cortex during Semantic Processing. Journal of Cognitive Neuroscience 13:829-843.

pdf -- Bookheimer, S. (2002) Functional MRI of language: new approaches to understanding the cortical organization of semantic processing. Annual Reviews of Neuroscience 25:151-188.

pdf -- Binder, J.R., D.A. Medler, R. Desai, L.L. Conant, and E. Liebenthal (2005) Some neurophysiological constraints on models of word naming. NeuroImage 27:677-693

pdf -- Huang, R.-S. and M.I. Sereno (2018) Chapter 7. Multisensory and Sensorimotor Maps. In: The Parietal Lobe. Neurological and Neuropsychological Deficits (Handbook of Clinical Neurology), G. Vallar, H.B. Coslett (eds.), volume 151 (3rd series), Elsevier, pp. 141-161.

pdf -- Sood, M. and M.I. Sereno (2016) Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps. Human Brain Mapping 37:2784-2810.

pdf -- Sood, M. and M.I. Sereno (2018) Estimating the cortex-wide overlap between wordless narrative scene comprehension, reading comprehension, and topological visual, auditory, and somatomotor maps. bioRxiv 264002.

pdf, atlas/movies -- Sereno, M.I., M.R. Sood, and R.-S. Huang (2022) Topological maps and brain computations from low to high. Frontiers in System Neuroscience 16:787737.

pdf, movies -- Lei, V.L.C., T.I. Leong, C.T. Leong, L. Liu, C.U. Choi, M.I. Sereno, D. Li, and R.-S. Huang (2023) Phase-encoded fMRI tracks down brainstorms of natural language processing with sub-second precision. bioRxiv:2023.05.29.542546.

mp4 -- Sereno seminar lecture: "On Brainmaps"

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