Publications - Zador Lab

Journal Papers

Bhattasali, N., Zador, A. M., & Engel, T. (2022). “Neural Circuit Architectural Priors for Embodied Control.” Advances in Neural Information Processing Systems 35: 12744-12759.
Barabási, D.,…, Zador. AM., et al. (2023) “Neuroscience needs Network Science.” arXiv:2305.06160.
Zador, AM., Escola, S., Richards, B. et al. (2023) “Catalyzing next-generation Artificial Intelligence through NeuroAI.” Nat Commun 14: 1597.
Chen, X., Fischer, S., Zhang, A., Gillis, J., Zador, AM. (2023) “Modular cell type organization of cortical areas revealed by in situ sequencing”. bioRxiv 2022.11.06.515380.
Funamizu, A., Marbach, F., Zador, AM. (2023) “Stable sound decoding despite modulated sound representation in the auditory cortex”. bioRxiv 2023.01.31.526457.
Yuan, L., Chen, X., Zhan, H., Gilbert, H., Zador, AM. (2023) “Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq”. bioRxiv 2023.02.18.528865.
Goodwin, D., Vaughan, A., Leible, D., Alon, S., Henry, G., Cheng, A., Chen, X., Zhang, R., Xue, A., Wassie, A., Sinha, A., Bando, Y., Kajita, A., Marblestone, A., Zador, AM, Boyden, E., Church, G., Kohman, R. (2023) “Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics”. bioRxiv 2022.07.31.502046.
Zador, AM., Escola, S., et al. (2022) “Toward Next-Generation Artificial Intelligence: Catalyzing the NeuroAI Revolution”. arXiv:2210.08340.
Zhang, A., Zador, AM. (2022) “Diversity and task-dependence of task representations in V1 during freely-moving decisions”. bioRxiv 2022.07.06.498845.
Koulakov, A., Shuvaev, S., Lachi, D., Zador, A. (2022) “Encoding innate ability through a genomic bottleneck”. bioRxiv 2021.03.16.435261.
Chen Y, Chen X, Baserdem B, Zhan H, Li Y, Davis MB, Kebschull JM, Zador, AM, Koulakov, AA, Albeanu, DF. (2022) “High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex”. Cell, 185: 4117-4134.
Aguillon-Rodriguez, V, Angelaki, D, Bayer, H, Bonacchi, N, Cazettes, F, Chapuis, G, … & Zador, AM. (2021). “Standardized and reproducible decision-making in mice”. eLife, 10. e63711.
Muñoz-Castaneda, R., Zador AM, et al. (2021). “Cellular Anatomy of the Mouse Primary Motor Cortex”. Nature, 598: 159-166.
Alexei Koulakov, Sergey Shuvaev, Anthony Zador (2021) “Encoding innate ability through a genomic bottleneck”. bioRxiv, doi: https://doi.org/10.1101/2021.03.16.435261
Sun Y., Chen X., Fischer S., Lu S., Gillis J., Zador A.M. (2021) “Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared accross the cortex”. Nat Neurosci. doi.org/10.1101/2020.08.25.266460.
Chen S, Loper J, Chen X, Vaughan A, Zador AM, Paninski L. “BARcode DEmixing through Non-negative Spatial Regression (BarDensr)”. PLoS Comput Biol. 2021 Mar 8;17(3):e1008256. doi: 10.1371/journal.pcbi.1008256. Epub ahead of print. PMID: 33684106.
Lu S, Ortiz C, Fürth D, Fischer S, Meletis K, Zador AM, Gillis J. (2021) “Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain”. PLoS biology, 19(7) e3001341.
Ghosh, S. , Zador A.M. (2020) Corticostriatal Plasticity Established by Initial Learning Persists After Behavioral Reversal. eNeuro. 2021 Feb 4:ENEURO.0209-20.2021. doi: 10.1523/ENEURO.0209-20.2021. Epub ahead of print. PMID: 33547044.
Kressel AM, Tsaava T, Levine YA, Chang EH, Addorisio ME, Chang Q, Burbach BJ, Carnevale D, Lembo G, Zador AM, Andersson U, Pavlov VA, Chavan SS, Tracey KJ. Identification of a brainstem locus that inhibits tumor necrosis factor. Proc Natl Acad Sci U S A. 2020 Nov 24;117(47):29803-29810. doi: 10.1073/pnas.2008213117. Epub 2020 Nov 9. PMID: 33168718; PMCID: PMC7703602.
Huang L., Kebschull J.M., Furth D., Musall S., Kaufman M.T., Churchland A.K., Zador A.M. (2020) “BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals”. Cell. 2020 Jul 9;182(1):177-188.e27. doi: 10.1016/j.cell.2020.05.029.
Kim Dore, Yvonne Pao, Jose Soria Lopez, Sage Aronson, Huiqing Zhan, Sanchari Ghosh, Sabina Merrill, Anthony M. Zador, Roberto Malinow, and Justus M. Kebschull. (2020) “SYNPLA, a method to identify synapses displaying plasticity after learning“ PNAS 117 (6) 3214-3219.
Chen X., Sun Y., Zhan H., Kebschull J.M., Fischer S., Matho K., Huang Z.J. Gillis J., Zador A.M.(2019) “High-throughput mapping of long-range neuronal projection using in situ sequencing”. Cell, 179: 772-786 doi: 10.1016/j.cell.2019.09.023
Zador A.M. (2019) “A Critique of Pure Learning: What Artificial Neural Networks can Learn form Animal Brains”. Nature Communications, 10:3770.
Shuvaev S.A., Baserdem, B., Zador A.M., Koulakov, A.A. (2019) “Network cloning using DNA barcodes”. PNAS 116 (19) 9610-9615.
Kebschull J.M., Zador A.M. (2018) “Cellular barcoding: lineage tracing, screening and beyond”. Nature Methords 15, 871-879.
Han Y., Kebschull J.M., Campbell R.A.A., Cowan D., Imhof F., Zador A.M. and Mrsic-Flogel T.D. (2018) “The logic of single-cell projections from visual cortex”. Nature, 556: 51-56.
Chen, X., Sun, Y., Church, G.M., Lee, J.H. and Zador A.M. (2018) “Efficient in situ barcode sequencing using padlock probe-based BaristaSeq”. Nucleic Acids Research, 46(4): e22. doi: 10.1093/nar/gkx1206
Peikon ID, Kebschull JM, Vagin VV, Ravens DI, Sun YC, Brouzes E, Corrêa IR Jr, Bressan D, Zador AM. Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res. 2017 Jul 7;45(12):e115. doi: 10.1093/nar/gkx292. PMID: 28449067; PMCID: PMC5499584.
Kebschull J.M., Garcia da Silva P. Reid, A.P., Peikon, I.D., Albeanu, D.F. and Zador, A.M. (2016) “High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA”. Neuron, 91(5): 975-987.
Kebschull J.M., Garcia da Silva P. and Zador A.M. (2015) “A New Defective Helper RNA to Produce Recombinant Sindbis Virus that Infects Neurons but does not Propagate”. Frontiers in Neuroanatomy, 10: 56.
Xiong, Q., Znamenskiy, P., & Zador, A.M. (2015) “Selective corticostriatal plasticity during acquisition of an auditory discrimination task”. Nature, 521: 348-51.
Kebschull JM and Zador AM (2015) “Sources of PCR-induced distortions in high-throughput sequencing data sets”. Nucleic Acids Research, 43(21): e143.
Jaramillo & Zador, A.M. (2014) “Mice and rats achieve similar levels of performance in an adaptive decision-making task”. Frontiers in Systems Neuroscience, 8: 173.
Peikon, I., Gizatullina, D. and Zador, A. (2014) “In vivo generation of DNA sequence diversity for cellular barcoding”. Nucleic Acids Research, 42(16): e127
Jaramillo, S., Borges, K., and Zador, A.M. (2014) “Auditory Thalamus and Auditory Cortex Are Equally Modulated by Context during Flexible Categorization of Sounds”. J. Neursoci., 34(15): 5291-5301.
Znamenskiy, P. and Zador, A. (2013) “Corticostriatal neurones in auditory cortex drive decisions during auditory descrimination” Nature, 497:482-486
Hromadka, T., DeWeese, M. and Zador, A. (2013) “Up states are rare in awake auditory cortex”. J. Neuropysiol, 109:1989-1995.
Zador, A., Dubnau, J.,Oyibo, H., Zhan, H., Gang, C. and Peikon, I. (2012) “Sequencing the connectome”. Plos Biology, 10:e1001411
Yang, Y. and Zador A.M. (2012) “Differences in Sensitivity to Neural Timing amount Cortical Areas”. J. Neurosci 32: 15142-15147.
Xiong, Q., Oviedo, H.V., Trotman, L.C. and Zador A.M. (2012) “PTEN regulation of local and long-range connections in mouse auditory cortex”. J. Neurosci 32: 1643-52.
Jaramillo, S. and Zador A.M. (2011) “The auditory cortex mediates the perceptual effects of acoustic temporal expectation “. Nature Neuroscience, 14:246-51.
Oviedo, H., Bureau, I., Svoboda, K. and Zador A.M. (2010) “The functional asymmetry of auditory cortex is reflected in the organization of local circuits”. Nature Neuroscience, 13:1413-1420.
Asari, H. and Zador A.M. (2009) “Long-lasting context dependendence constrains neural encoding models in rodent auditory cortex”. J Neurophysiol 102(5): 2638-56.
Lima, S., Znamenskiy, P., Hromadka, T. and Zador A.M. (2009) “PINP: A new method of tagging neuronal populations for identification during in vivo electrophysiological recording”. PLoS ONE, 4(7): e6099
Otazu, G., Tai, L-H., Yang, Y. and Zador A.M. (2009) “Engaging in an auditory task suppresses responses in auditory cortex”. Nature Neuroscience, 2(5):646-54
Koulakov, A., Hromadka, T. and Zador A.M. (2009) “Correlated connectivity and the distribution of firing rates in the neocortex”. J. Neuroscience 29: 3685-94
Yang, Y., DeWeese, M.R., Otazu, G. and Zador A.M. (2008) “Millisecond-scale differences in neural activity in auditory cortex can drive decisions”. Nature Neuroscience, 11: 1262-3.
Hromadka, T., DeWeese, M. and Zador, A.M. (2008) “Sparse Representation of Sounds in the Unanesthetized Auditory Cortex”. PLoS Biol, 6: e16
Hromadka, T. and Zador, A.M. (2007) “Toward the mechanisms of auditory attention”. Hearing Research, 229: 180-5
DeWeese, M. and Zador, A. (2006) “Non-Gaussian membrane potential dynamics imply sparse, synchronous activity in auditory cortex”. J. Neurosci, 26:12206-12218
Asari, A., Pearlmutter B. and Zador, A. (2006) “Sparse representations for the cocktail party problem”. J. Neurosci, 26: 7477-7490.
DeWeese, M., Hromadka, T. and Zador A. (2005) “Reliability and representational bandwidth in the auditory cortex”. Neuron, 48: 479-488.
Wehr, M and Zador, A. (2005) “Synaptic mechanisms of forward suppression in rat auditory cortex”. Neuron, 47:437-445. (See Faculty of 1000 Commentary) … (See N&V)
Rumpel, S., LeDoux, J., Zador, A., and Malinow, R.. (2005) “Postsynaptic receptor trafficking underlying amygdala associative learning”. Science, 308:83-88 (See Faculty of 1000 Commentary) … (See N&V)
DeWeese, M., and Zador, A. (2004) “Shared and Private Variability in the Auditory Cortex”. J. Neurophys, 92: 1840-55 (See Faculty of 1000 Commentary)
Machens, C., Wehr, M. and Zador, A. (2004) “Linearity of cortical receptive fields measured with natural sounds”. J. Neurosci, 24:1089-1100. (See Faculty of 1000 Commentary)
Wehr, M. and Zador, A. (2003) “Balanced inhibition underlies tuning and sharpens spike timing in auditory cortex “. Nature, 426:442-446. (See Faculty of 1000 Commentary)
DeWeese, M., Wehr, M. and Zador, A. (2003) “Binary spiking in auditory cortex “. J. Neurosci, 23: 7940-7949. (See Faculty of 1000 Commentary)
Natschlager, T., Maass, W. and Zador, A. (2001) “Efficient Temporal Processing with Dynamic Synapses”. Network, 12: 75-87.
Reinagel, P. and Zador, A. (1999) “Natural Scenes at the Center of Gaze”. Network, 10: 341-50.
Maass, W. and Zador, A. (1999) “Dynamic stochastic synapses as computational units”. Neural Computation, 11:903-917.
Stevens, C.F. and Zador, A. (1998) “Input synchrony and the irregular firing of cortical neurons”. Nature Neuroscience, 3:210-217
Buracas, G., Zador, A., DeWeese, M. & Albright, T. (1998) “Efficient discrimination of temporal patterns by motion-sensitive neurons in primate visual cortex”. Neuron, 20:959-969.
Zador, A. (1998) “The Impact of synaptic unreliability on the information transmitted by spiking neurons“. J. Neurophysiol., 79:1219-1229 (click here for PDF) .
DeWeese, M. and Zador, A. (1998) “Asymmetric dynamics in optimal variance adaptation”. Neural Computation, 10:1179-1202 .
Zador, A. and Pearlmutter, B. (1996) “VC dimension of an integrate and fire neuron model”. Neural Computation, 8:611-624.
Mainen, Z., Carnevale, N.T., Zador, A., Claiborne, B.J., and Brown, T.H. (1996) “Electrotonic architecture of hippocampal CA1 pyramidal neurons based on three-dimensional reconstructions”. J. Neurophysiol. 76(3):1904-1923
Bulsara, A. and Zador, A. (1996) “Threshold detection of wideband signals: A noise-induced maximum in the mutual information”. Phys Rev. E, 54:2185-88.
Zador, A., Hagai, A-S., and Segev, I. (1995) “The Morphoelectrotonic Transform: A Graphical Approach to Dendritic Function”. J. Neurosci., 15:1669-1682
Zador, A., Koch, C. (1994) “Linearized Models of Calcium Dynamics: Formal Equivalence to the Cable Equation”. J. Neurosci., 14:4705-4715
Koch, C., Zador, A. (1993) “The function of dendritic spines: Devices subserving biochemical rather than electrical compartmentalization”. J. Neurosci., 13: 413-422.
Zador, A., Claiborne, B.J. and Brown, T.H. (1991). “Nonlinear Pattern Separation in Single Hippocampal Neurons with Active Dendritic Membrane.” NIPS, 4. 56-60.
Zador, A., Koch, C., and Brown, T.H. (1990). “Biophysical model of a hebbian synapse”. Proceedings of the National Academy of Science USA, 87:6718-22.

Proceedings, reviews, theses, etc

Zador, AM. Charles F. Stevens (1934–2022). Nat Neurosci (2022).
Koch C, Svoboda K, Bernard A, Basso MA, Churchland AK, Fairhall AL, Groblewski PA, Lecoq JA, Mainen ZF, Mathis MW, Olsen SR, Phillips JW, Pouget A, Saxena S, Siegle JH, Zador AM. (2022) “Next-generation brain observatories”. Neuron,:3661-3666.
Richards, B, Tsao, D, Zador, AM. (2022) “The application of artificial intelligence to biology and neuroscience”. Cell,:2640-2643.
Zador, AM. (2019) “A critique of pure learning and what artificial neural networks can learn from animal brains”. Nat Commun. Aug 21;10(1):3770.
Kebschull JM, Zador, AM. (2018) “Cellular barcoding: lineage tracing, screening and beyond”. Nat Methods. Nov;15(11):871-879.
Lee, AM, Tai, LH, Zador, AM, Wilbrecht L. (2015) “Between the primate and ‘reptilian’ brain: Rodent models demonstrate the role of corticostriatal circuits in decision making.” Neuroscience.
Livneh, U, Zador, AM. (2014) “Sensory systems: Sound processing takes motor control”. Nature 513: 180-181.
Marblestone, A, Daugharthy, E, Kalhor, R, Peikon, I, Kebschull, J, Shipman, S, Mishchenko, Y, Lee, Jehyuk., Zador, AM. et. al. (2014) “Rosetta Brains: A strategy for molecularly-annotated connectomics”. arXiv 1404.5103.
Marblestone, A, Daugharthy, E, Kalhor, R, Peikon, I, Kebschull, J, Shipman, S, Mishchenko, Y, Darlrymple, D, Zador, AM. et. al. (2013) “Conneconomics: The economics of large-scale neural connectomics”. bioRxiv 001214.
Hromadka, T, and Zador, AM. (2009) “Representations in auditory cortex”. Curr Opin Neurobiol 19(4): 430-3.
Hromadka, T and Zador, AM. (2007) “Toward the mechanisms of auditory attention.” Hearing Research 229: 180-5.
DeWeese, M, and Zador, AM. (2006) “Neurobiology: efficiency measures” Nature 439: 920-921.
DeWeese, M, and Zador, AM. (2005) “Neural gallops across auditory streams” Neuron 48: 5-7.
DeWeese, M, Hromadka, T and Zador, AM. (2005) “Reliability and representational bandwidth in the auditory cortex”. Neuron 48: 479-488.
Machens, C. and Zador, AM. (2003) “Auditory modeling gets an edge” J. Neurophys, 90:3581-3582.
Zador, AM. (2003) “Self-consistent models of cortical dynamics” In: Modulation of Neuronal Responses: Implications for Active Vision. G.T. Buracas, Editor. IOS Press. pp. 309-317.
Zador, AM. (2001). “Synaptic connectivity and computation.” Nature Neuroscience, 4(12): 1157-8.
Zador, AM. (2000) “The basic unit of computation” Nature Neuroscience 3:1167.
deCharms, R. C. and Zador, AM. (2000) “Neural Representation and the Cortical Code” Ann. Rev. of Neurosci., 23: 613-47.
Zador, AM. (1999) “Synaptic Plasticity”. In Christof Koch, editor, Biophysics of Computing: Information Processing in Single Neurons. MIT Press.
Zador, AM and Pearlmutter, B. (1999) “Sparse matrix methods for modeling single neurons”. In Christof Koch, editor, Biophysics of Computing: Information Processing in Single Neurons. MIT Press.
Zador, AM. (1999) “Thalamocortical Synapses: Sparse but Stentorian.” Neuron, 23: 198-200.
Zador, AM. (1997) “Action Potentials Reconsidered”. Science, 277:772.
Zador, AM and Dobrunz, L. (1997) “Dynamic Synapses in the Cortex” Neuron, 19:1-4.
Smetters, D. and Zador, AM. (1996) “Synaptic transmission: noisy synapses and noisy neurons” Current Biology, 6: 1217-1218.
Stevens, C and Zador, AM. (1995) “Neural coding: The enigma of the brain” Current Biology, 5(12):1370-1.
Claiborne, B, Zador, AM, Mainen, Z, and Brown, T. (1992) “Computational models of hippocampal neurons”. In T. McKenna, J. Davis, and S.F. Zornetzer (Eds.), Academic Press, SD, CA, Single neuron computation. 62-80.
Brown, T, Zador, AM, Mainen, Z, and Claiborne, B. (1992) “Hebbian computations in hippocampal dendrites and spines”. In T. McKenna, J. Davis, and S.F. Zornetzer (Eds.), Single neuron computation. Academic Press, SD,CA 81-116.
Koch, C, Zador, AM and Brown, T. (1992) “Dendritic spines: convergence of theory and experiment” Science, 256:973-4.
Brown, T, Zador, AM, Mainen, Z, and Claiborne, B. (1991) “Hebbian modifications in hippocampal neurons,” In J. Davis and M. Baudry (Eds.), Long term potentiation: A debate of current issues. Cambridge, MA: MIT Press. (357-389).
Brown, T and Zador, A. (1990). “The hippocampus,” In G. Shepherd (Ed.), The synaptic organization of the brain (3rd ed., pp. 346-388). New York: Oxford University Press.