Journal Papers

• Liu, T., Benjamin, A. S., Zador, A. M. (2025). “Token-Level Uncertainty-Aware Objective for Language Model Post-Training”. arXiv preprint, arXiv: 2503.16511.
• Kerstjens, S., Engert, F., Zador, A. M., Douglas, R. J. (2024). “Eigengene reveals invariant global spatial patterns across mouse and fish brain development.” bioRxiv, 2024-09.
• Lachi, D., Huang, A., Mavor-Parker, A. N., Ghosh, A., Zador, A., Richards, B. (2024). “Stochastic Wiring of Cell Types Enhances Fitness by Generating Phenotypic Variability.” bioRxiv, 2024-08.
• Isko, E. C., Harpole, C. E., Zheng, X. M., Zhan, H., Davis, M. B., Zador, A. M., Banerjee, A. (2024). “Selective expansion of motor cortical projections in the evolution of vocal novelty.” bioRxiv, 2024.09.13.612752.
• Yuan, L., Chen, X., Zhan, H., Henry, G.L., Zador, A.M. (2024). “Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.” Nat Commun. 15(1):8371.  doi:10.1038/s41467-024-52756-x
• Shuvaev, S., Lachi, D., Koulakov, A., Zador, A., (2024). “Encoding innate ability through a genomic bottleneck”. PNAS 121 (38) e2409160121.
• Chen, X., Fischer, S., Rue, M. C. P., Zhang, A., Mukherjee, D., Kanold, P. O., Gillis, J., & Zador, A. M. (2024). “Whole-cortex in situ sequencing reveals input-dependent area identity.” Nature, 1-10.
• Reid, A. P., Hromadka, T., & Zador, A. M. (2024). “Early dynamics of excitation and inhibition maintain late frequency tuning in auditory cortex.” bioRxiv, 2024-01.
• Zhang, A., & Zador, A. M. (2023). “Neurons in the primary visual cortex of freely moving rats encode both sensory and non-sensory task variables.” PLoS biology, 21(12), e3002384.
• Findling, C.,…, Zador, A.M., et al. (2023). “Brain-wide representations of prior information in mouse decision-making.” BioRxiv, 2023-07.
• Barabási, D.,…, Zador. AM., et al. (2023) “Neuroscience Needs Network Science.” J Neurosci. 2023;43(34):5989-5995. doi:10.1523/JNEUROSCI.1014-23.2023
• Zador, AM., Escola, S., Richards, B. et al. (2023) “Catalyzing next-generation Artificial Intelligence through NeuroAI.” Nat Commun 14: 1597.
• Funamizu, A., Marbach, F., Zador, AM. (2023) “Stable sound decoding despite modulated sound representation in the auditory cortex”. Current Biology 33, 4470–4483.
• 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.
• Bhattasali, N., Zador, A. M., & Engel, T. (2022). “Neural Circuit Architectural Priors for Embodied Control.” Advances in Neural Information Processing Systems 35: 12744-12759.
• 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.
• Sun Y. C., Chen X., Fischer S., Lu S., Zhan H., Gillis J., & Zador A. M. (2021). “Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections.” Nature neuroscience, 24(6), 873–885. https://doi.org/10.1038/s41593-021-00842-4
• 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.
• Chen, S., Loper, J., Chen, X., Vaughan, A., Zador, A. M., & Paninski, L. (2021). “BARcode DEmixing through Non-negative Spatial Regression (BarDensr)”. PLoS Comput Biol, 17(3):e1008256. doi: 10.1371/journal.pcbi.1008256. 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 and what artificial neural networks can learn from 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.