HST.723J | Spring 2005 | Graduate

Neural Coding and Perception of Sound


The assignments in this class consist of 4 written theme discussion reports, 3 written laboratory reports, approximately 3 oral paper presentations, and reading of 25-30 papers.

Guidelines for writing Theme Reports (PDF)

Guidelines for Oral Paper Presentations (PDF)

Much of the learning is done by theme discussions of scientific papers. A block of lectures provides the background for reading the papers in each theme. Students are expected to read all the theme papers, then each paper is presented orally to the class by one student, followed by a discussion. At the end of a theme discussion, students write a report summarizing what they learned from the papers.

Below is a bibliography of the scientific papers per theme.


  1. Masking and frequency selectivity
  2. Cellular mechanisms in the cochlear nucleus
  3. Binaural interactions
  4. Pitch and temporal coding
  5. Neural maps and plasticity
  6. Auditory scene analysis and object formation

Theme 1: Masking and Frequency Selectivity

Pointers to Theme 1 Papers (PDF)

Background (not discussed, for reference only)

Moore, B. C. J., ed. “Frequency analysis and masking.” In Handbook of Perception and Cognition: Hearing. 2nd ed. London, UK: Academic, 1995, pp. 161-205. ISBN: 9780125056267.

Oxenham, A. J., and S. P. Bacon. “Cochlear compression: Perceptual measures and implications for normal and impaired hearing.” Ear Hearing 24 (2004): 352-366.

Dallos, P. “Overview: Cochlear neurobiology.” In The Cochlea. Edited by P. Dallos, A. N. Popper, and R. R. Fay. New York, NY: Springer, 1996, pp. 1-43. ISBN: 9780387944494.

Psychophysics and Otoacoustic Emissions

Moore, B. C. J. “Psychophysical tuning curves measured in simultaneous and forward masking.” J Acoust Soc Am 63 (1978): 524-532.

Oxenham, A. J., and C. J. Plack. “A behavioral measure of basilar-membrane nonlinearity in listeners with normal and impaired hearing.” J Acoust Soc Am 101 (1997): 3666-3675.

Oxenham, A. J., and C. A. Shera. “Estimates of human cochlear tuning at low levels using forward and simultaneous masking.” J Assoc Res Otoloaryngol 4 (2003): 541-554.

Cochlear Physiology and Modeling

Delgutte, B. “Physiological mechanisms of masking.” In Basic Issues in Hearing. Edited by H. Duifhuis, J. W. Horst, and H. P. Wit. London, UK: Academic, 1988, pp. 204-214. ISBN: 9780122233463.

Ruggero, M. A., L. Robles, and N. C. Rich. “Two-tone suppression in the basilar membrane of the cochlea: Mechanical basis of auditory-nerve rate suppression.” J Neurophysiol 68 (1992): 1087-1099.

Cai, Y., and C. D. Geisler. “Suppression in auditory-nerve fibers of cats using low-side suppressors. III. Model results.” Hearing Res 96 (1996): 126-140.

Further Reading (not discussed)

Shera, C. A., J. J. Guinan Jr., and A. J. Oxenham. “Revised estimates of human cochlear tuning from otoacoustic and behavioral measurements.” Proc. Natl Acad Sci 99 (2002): 3318-3323. [A precursor to the Oxenham & Shera (2003) paper also including measurements of otoacoustic emissions.]

Delgutte, B. “Physiological mechanisms of psychophysical masking: Observations from auditory-nerve fibers.” J Acoust Soc Am 87 (1990): 791-809. [A more detailed version of the 1988 paper.]

Theme 2: Cellular Mechanisms in the Cochlear Nucleus

Pointers to Theme 2 Papers (PDF)


Rhode, W. S., and S. Greenberg. “Physiology of the cochlear nuclei.” In The Mammalian Auditory Pathway: Neurophysiology. Edited by A. N. Popper, and R. R. Fay. New York, NY: Springer, 1992, pp. 94-152. ISBN: 9780387978017.

Koch, C., and I. Seguev. “The role of single neurons in information processing.” Nature Neurosci 3 (2000): 1171-1177. [A concise overview of the computational capabilities of single neurons.]


May, B. J., and M. B. Sachs. “Dynamic range of neural rate responses in the ventral cochlear nucleus of awake cats.” J Neurophysiol 68 (1992): 1589-1602.

Kopp-Scheinpflug, C., S. Dehmel, G. J. Dörrscheidt, and R. Rübsamen. “Interaction of excitation and inhibition in anteroventral cochlear nucleus neurons that receive large endbulb synaptic endings.” J Neurosci 22 (2002): 11004-11018.

Neural Modeling

Kalluri, S., and B. Delgutte. “Mathematical model of cochlear nucleus onset neurons: I. Point neuron with many, weak synaptic inputs.” J Comput Neurosci 14 (2003): 71-90.

Theme 3: Binaural Interactions

Pointers to Theme 3 Papers (PDF)


Grantham, D. W. “Spatial hearing and related phenomena.” In Handbook of Perception and Cognition: Hearing. Edited by B. C. J. Moore. London, UK: Academic, 1995, pp. 297-345. ISBN: 9780125056267.

Trussell, L. O. “Physiological mechanisms for coding timing in auditory neurons.” Ann Rev Physiol 61 (1999): 477-496.

Grothe, B. “New roles for synaptic inhibition in sound localization.” Nature Rev Neurosci 4 (2003): 540-50.


MacPherson, E. A., and J. C. Middlebrooks. “Listener weighting of cues for lateral angle: The duplex theory of sound localization revisited.” J Acoust Soc Am 111 (2002): 2219-2236.

Tollin, D. J., and T. C. T. Yin. “Psychophysical investigation of an auditory spatial illusion in cats: The precedence effect.” J Neurophysiol 90 (2003): 2149–2162.

Freyman, R. L., U. Balakrishnan, and K. S. Helfer. “Spatial release from informational masking in speech recognition.” J Acoust Soc Am 109 (2001): 2112-2122.

Neurophysiology and Neural Modeling

Reyes, A. D., E. W. Rubel, and W. J. Spain. “In vitro analysis of optimal stimuli for phase locking and time-delayed modulation of firing in avian nucleus laminaris neurons.” J Neurosci 16 (1996): 993-1007.

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

Zhou, Y., L. E. Carney, and H. S. Colburn. “A model for ITD sensitivity in the MSO: Interaction of excitatory and inhibitory synaptic inputs, channel dynamics, and cellular morphology.” J Neurosci. (In press)

Further Reading

Carr, C. E., and M. Konishi. “A circuit for detection of interaural time differences in the brainstem of the barn owl.” J Neurosci 10 (1990): 3227-3246. [Provides useful background on the avian homolog of the MSO for the Reyes et al. (1996) paper.]

McAlpine D., D. Jiang, and A. R. Palmer. “A neural code for low-frequency sound localization in mammals.” Nature Neurosci 4 (2001): 396-401. [Additional data challenging the Jeffress model of ITD coding. Closely related to the Brand et al. (2002) paper.]

Freyman, R. L., K. S. Helfer, D. D. McCall, and R. K. Clifton. “The role of perceived spatial separation on the unmasking of speech.” J Acoust Soc Am 106 (1999): 3578-3588. [Original report of spatial release from information masking.]

Theme 4: Pitch and Temporal Coding

Pointers to Theme 4 Papers (PDF)


Houtsma, A. J. “Pitch perception.” In Handbook of Perception and Cognition: Hearing. Edited by B. C. J. Moore. London, UK: Academic, 1995, pp. 267-295. ISBN: 9780125056267.

Lewine, J. D., and W. W. Orrison Jr. “Magentoencephalography and magnetic source imaging.” In Functional Brain Imaging. Edited by W. W. Orrison, J. D. Lewine, J. A. Sanders, and M. F. Hartshorne. St. Louis, MO: Mosby, 1995, pp. 369-417. ISBN: 9780815165095. [Tutorial on the magnetoencephalographic technique used by Krumbholz et al. (2003).]

Functional Neuroimaging

Krumbholz, K., R. D. Patterson, A. Seither-Preisler, C. Lammertmann, and B. Lütkenhöner. “Neuromagnetic evidence for a pitch processing center in Heschl’s gyrus.” Cerebral Cortex 13 (2003): 765–772.

Penagos H., J. R. Melcher, and A. J. Oxenham. “A neural representation of pitch salience in nonprimary human auditory cortex revealed with functional magnetic resonance imaging.” J Neurosci 24 (2004): 6810-6815.


Dai, H. “On the relative importance of individual harmonics in pitch judgments.” J Acoust Soc Am 107 (2000): 953-959.

Darwin, C. J., R. W. Hukin, and B. Y. Al Khatib. “Grouping in pitch perception: Evidence for sequential constraints.” J Acoust Soc Am 98 (1995): 880-885.

Neurophysiology and Neural Modeling

Shamma, S., and D. Klein. “The case of the missing pitch templates: How harmonic templates emerge in the early auditory system.” J Acoust Soc Am 107 (2000): 2631-2644.

Winter, I. M., L. Wiegrebe, and R. D. Patterson. “The temporal representation of the delay of iterated ripple noise in the ventral cochlear nucleus of the guinea pig.” J Physiol 537 (2001): 553-566.

Further reading

Licklider, J. C. R. “A duplex theory of pitch perception.” Experientia 7 (1951): 128-134. [Original formulation of the interspike-interval/autocorrelation model of pitch.]

Plomp, R. “Pitch of complex tones.” J Acoust Soc Am 41 (1967): 1526-1533. [Original evidence for the dominance region in pitch.]

Wiegrebe, L., and R. Meddis. “The representation of periodic sounds in simulated sustained chopper units of the ventral cochlear nucleus.” J Acoust Soc Am 115 (2004): 1207-1218. [A temporal model of pitch extraction based on the results of Winter et al. (2001).]

Theme 5: Neural Maps and Plasticity

Pointers to Theme 5 Papers (PDF)


Semple, M. N., and B. H. Scott. “Cortical mechanisms in hearing.” Current Opin Neurobiol 13 (2003):167-173.

Huettel, Scott A., Allen W. Song, and Gregory McCarthy. “An introduction to fMRI.” Chapter 1 in Functional Magnetic Resonance Imaging. Sunderland, MA: Sinauer Associates, 2004, pp. 1-26. ISBN: 9780878932887.

Cacace, A. T., T. Tasciyan, and J. P. Cousins. “Principles of functional magnetic resonance imaging: Application to auditory neuroscience.” J Am Acad Audiol 11 (2000): 239-272.

Syka, J. “Plastic changes in the central auditory system after hearing loss, restoration of function, and during learning.” Physiol Rev 82 (2002): 601–636.

Functional Neuroimaging and Psychophysics

Belin, P., R. J. Zatorre, P. Lafaille, P. Ahad, and B. Pike. “Voice-selective areas in human auditory cortex.” Nature 403 (2000): 309-12.

Warren, J. D., and T. D. Griffths. “Distinct mechanisms for processing spatial sequences and pitch sequences in the human auditory brain.” J Neurosci 23 (2003): 5799–5804.

Hofman, van Riswick, and van Opstal. “Relearning sound localization with new ears.” Nature Neurosci 1 (1998): 417-421.


Kamke, M. R., M. Brown, and D.R.F. Irvine. “Plasticity in the tonotopic organization of the medial geniculate body in adult cats following restricted unilateral cochlear lesions.” J Comp Neurol 459 (2003): 355-367.

Bao, S., E. F. Chang, J. Woods, and M. M. Merzenich. “Temporal plasticity in the primary auditory cortex induced by operant perceptual learning.” Nature Neurosci 7 (2004): 974-981.

Fritz, J., S. Shamma, M. Elhilali, and D. Klein. “Rapid task-related plasticity of spectrotemporal receptive fields in primary auditory cortex.” Nature Neurosci 6 (2003): 1216-1223.

Further Reading

Robertson, D., and D. R. F. Irvine. “Plasticity of frequency organization in auditory cortex of guinea pigs with partial unilateral deafness.” J Comp Neurol 282 (1989): 456-471. [A precursor to the assigned Kamke et al. thalamus study describing plasticity in the auditory cortex.]

Bakin, J. S., and N. Weinberger. “Classical conditioning induces CS-specific receptive field plasticity in the auditory cortex of the guinea pig.” Brain Res 536 (1990): 271-286. [A classic study of rapid cortical plasticity associated with learning.]

Theme 6: Auditory Scene Analysis and Object Formation

Pointers to Theme 6 Papers (PDF)


Darwin, C. J. “Auditory grouping.” Trends Cogn Sci 1 (1997): 327-333.

Carlyon, R. P. “How the brain separates sounds.” Trends Cogn Sci 8 (2004): 465-471.


Darwin, C. J., and R. W. Hukin. “Effectiveness of spatial cues, prosody and talker characteristics in selective attention.” J Acoust Soc Am 107 (2000): 970-977.

Carlyon, R. P., R. Cusack, J. M. Foxton, and I. H. Robertson. “Effect of attention and unilateral neglect on auditory stream segregation.” J Exp Psychol Hum Percept Perform 27 (2001): 115-117.

Functional Neuroimaging

Gutschalk, A., C. Micheyl, J. R. Melcher, A. Rupp, M. Scherg, and A. J. Oxenham. “Neuromagnetic correlates of streaming in human auditory cortex.” J Neurosci. (In press)