Selected Publications

Multiregion neuronal activity: the forest and the trees

Machado, T.A.^*, Kauvar, I.V.^*, Deisseroth, K.

Nature Reviews Neuroscience 23: 683-704 (2022)

Invited review. Cover article.

Link to PDF, Link to Nat Rev Neuro, ^* denotes co-first authorship.

Cortical Observation by Synchronous Multifocal Optical Sampling Reveals Widespread Population Encoding of Actions

Kauvar, I.V.^*, Machado, T.A.^*, Yuen, E., Kochalka, J., Choi, M., Allen, W., Wetzstein, G., Deisseroth, K.

Neuron 107: 1-17 (2020)

Link to PDF, Link to Neuron, ^* denotes co-first authorship.

Cortical layer-specific critical dynamics triggering perception

Marshel, J.H.^*, Kim, Y.S.^*, Machado, T.A.^*, Quirin S.^*, Benson, B., Kadmon, J., Raja, C., Chibukhchyan, A., Ramakrishnan, C., Inoue, M., Shane, J., McKnight, D., Yoshizawa, S., Kato, H., Ganguli, S., Deisseroth, K.

Science 365 (6453), eaaw5202 (2019)

Article in New York Times.

Link to PDF, Link to Science, ^* denotes co-first authorship.

Primacy of flexor locomotor pattern revealed by ancestral reversion of motor neuron identity

Machado, T.A., Pnevmatikakis, E., Paninski, L., Jessell, T.M., Miri, A.

Cell 162: 338-350 (2015)

Cover article.

Link to PDF, Link to Cell.

CloudReg: Automatic Terabyte-Scale Cross-Modal Brain Volume Registration

Chandrashekhar, V., Crowley, D., Crow, A.K., Wright, M.A., Hsueh, B.Y., Gore, F., Machado, T.A., Branch, A., Rosenblum, J.S., Deisseroth, K., Vogelstein J.T.

Nature Methods 18, 845–846 (2021).

Community-based benchmarking improves spike inference from two-photon calcium imaging data

Berens, P. et al.

PLOS Computational Biology 14 (5), e10006157 (2018).

Simultaneous denoising, deconvolution, and demixing of calcium imaging data

Pnevmatikakis, E.A., Soudry, D., Gao, Y., Machado, T.A., Merel, J., Pfau, D., Reardon, T., Mu, Y., Lacefield, C., Yang, W., Ahrens, M., Bruno, R., Jessell T.M., Peterka D.S., Yuste, R., Paninski, L.

Neuron 89 (2): 285–299 (2016).

Robust and scalable bayesian analysis of spatial neural data

Rad, K. R., Machado, T.A., Jessell, T., Paninski, L.

Annals of Applied Statistics 11 (2): 598-637 (2017).

Spinal Inhibitory Interneuron Diversity Delineates Variant Motor Microcircuits

Bikoff, J.B., Gabitto, M.I., Rivard, A.F., Drobac, E., Machado, T.A., Miri, A., Brenner-Morton, S., Famojure, E., Diaz, C., Alvarez, F.J, Mentis, G.Z., Jessell, T.

Cell 165 (1): 207-219 (2016).

Clustered factor analysis of multineuronal spike data

Buesing, L., Machado, T.A., Cunningham, J.P., Paninski, L.

Advances in Neural Information Processing Systems: 3500-3508 (2014).

Efficient coding of spatial information in the primate retina

Doi, E., Gauthier, J.L., Field, G.D., Shlens, J., Sher, A., Greschner, M., Machado, T.A., Jepson, L.H., Mathieson, K., Gunning, D.E., Litke, A.M., Paninski, L., Chichilnisky, E.J., Simoncelli, E.P.

Journal of Neuroscience 32 (46): 16256-16264 (2012)

Fast non-negative deconvolution for spike train inference from population calcium imaging

Vogelstein, J.T., Packer, A.M., Machado, T.A., Sippy, T., Babadi, B., Yuste, R., Paninski, L.

Journal of Neurophysiology 104 (6): 3691-3704 (2010)

Functional connectivity in the retina at the resolution of photoreceptors

Field, G.D., Gauthier, J.L., Sher, A., Greschner, M., Machado, T.A., Jepson, L.H., Shlens, J., Gunning, D.E., Mathieson, K., Dabrowski, W., Paninski, L., Litke, A.M., Chichilnisky, E.J..

Nature 467 (7316): 673- 677 (2010)