(Ahrens, 2013) Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Misha B Ahrens, Michael B Orger, Drew N Robson, Jennifer M Li & Philipp J Keller, Nature Methods 10, 413–420, 2013.

(Barnett, 2009) Granger causality and transfer entropy are equivalent for Gaussian variables. Barnett, L., Barrett, A.B., Seth, A.K., Phys. Rev. Lett. 103, 238701, 2009

(Bonifazi, 2009) GABAergic hub neurons orchestrate synchrony in developing hippocampal networks. Bonifazi, P., Goldin, M., Picardo, M.A., Jorquera, I., Cattani, A., Bianconi, G., Represa, A., Ben-Ari, Y., and Cossart, R. Science 326, 1419–1424, 2009.

(Battaglia, 2012) Dynamic Effective Connectivity of Inter-Areal Brain Circuits. Demian Battaglia, Annette Witt, Fred Wolf, Theo Geisel, PLoS Computational Biology 8(3), 2012.

(Braitenberg-Schüz, 1991) Anatomy of the cortex: Statistics and geometry. Braitenberg, V.; Schüz, A.,

New York, NY, US: Springer-Verlag Publishing, 1991.

(Cause-effect, 2008-2011) For a bibliography, see

(Chung, 2013) Structural and molecular interrogation of intact biological systems, Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron S. Andalman, Thomas J. Davidson, Julie J. Mirzabekov, Kelly A. Zalocusky, Joanna Mattis, Aleksandra K. Denisin, Sally Pak, Hannah Bernstein, Charu Ramakrishnan, Logan Grosenick, Viviana Gradinaru & Karl Deisseroth, Nature 497, 332–337, May 2013.

(Duan, 2013) Nanoelectronics-biology frontier: From nanoscopic probes for action potential recording in live cells to three-dimensional cyborg tissues. Duan X, Fu TM, Liu J, Lieber CM., Nano Today. 8(4):351-373, 2013.

(Eytam-Marom, 2006) Dynamics and effective topology underlying synchronization in networks of cortical neurons. Eytan, D., and Marom, S., J. Neuroscience 26, 8465–8476, 2006.

(Friston, 2003) Dynamic causal modelling. Friston, K.J., Harrison, L., and Penny, W., NeuroImage 19, 1273–1302, 2003.

(Grienberger, 2012) Imaging Calcium in Neurons. Grienberger C, Konnerth A (2012) Neuron 73: 862–885, 2012.

(Guyon, 2013) Results and Analysis of the “Cause-Effect Pairs” challenge. Techreport (in preparation).

(Heider, 2010) Two-Photon Imaging of Calcium in Virally Transfected Striate Cortical Neurons of Behaving Monkey. Heider B, Nathanson JL, Isacoff EY, Callaway EM, Siegel RM, PLoS ONE 5(11), 2010.

(Ivenshitz, 2010) Neuronal density determines network connectivity and spontaneous activity in cultured hippocampus. Ivenshitz, M. & Segal, M. Journal of Neurophysiology 104, 1052–1060 (2010).

(Kaufman, 2006) Alon Kaufman, Gideon Dror, Isaac Meilijson, Eytan Ruppin: Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity. PLoS Computational Biology 2(12) (2006).

(Livet, 2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman, Nature 450, 56-62, November 2007.

(Mainen, 1999) Two-photon imaging in living brain slices. Mainen ZF, Maletic-Savatic M, Shi SH, Hayashi Y, Malinow R, et al. Methods 18: 231–239, 1999.

(Maschio, 2012) Two-photon calcium imaging in the intact brain. Maschio MD, Beltramo R, De Stasi AM, Fellin T. Adv Exp Med Biol.;740:83-102, 2012.

(Mishchencko, 2001) Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data. Mishchencko, Y., Vogelstein, J.T., and Paninski, L. A Ann Appl Stat 5, 1229–1261, 2011.

(Milham, 2012) Open Neuroscience Solutions for the Connectome-wide Association Era, Michael Peter Milham, Neuron 73, January 26, 2012, Elsevier.

(Moneta-Spirtes, 2005) Graph-based search procedures for vector autoregressive models, Alessio Moneta and Peter Spirtes. LEM Working Paper 2005/14, Sant’Anna School of Advanced Studies, 2005.

(Nolte-Muller, 2010) Localizing and Estimating Causal Relations of Interacting Brain Rhythms. Guido Nolte, and Klaus-Robert Müller, Front Hum Neurosci. 2010; 4: 209, 2010.

(Orlandi, 2013) Orlandi, J.G., Stetter, O., Soriano, J., Geisel, T., and Battaglia, D. (2013). Transfer Entropy reconstruction and labeling of neuronal connections from simulated calcium imaging. ArXiv 1309.4287.

(Patti-Isacoff, 2013) Measuring membrane voltage with fluorescent proteins. Patti J, Isacoff EY., Cold Spring Harb Protoc. 2013, (7):606-13, Jul 2013.

(Pearl, 2000) Causality: Models, Reasoning, and Inference. Judea Pearl, Cambridge University Press, 2000.

(Popescu-Guyon, 2013) Causality in Time Series: Challenges in Machine Learning, volume 5, Florin Popescu and Isabelle Guyon, Editors, Microtome, 2013.

(Ryali, 2012) Estimation of functional connectivity in fMRI data using stability selection-based sparse partial correlation with elastic net penalty. Srikanth Ryali, Tianwen Chen, Kaustubh Supekar, and Vinod Menon, Neuroimage. 2012 February 15; 59(4): 3852–3861, 2012.

(Reiner-Isacoff, 2013) The Brain Prize 2013: the optogenetics revolution, Andreas Reiner, Ehud Y. Isacoff, Trends in Neuroscience, Volume 36, Issue 10, Pages 557–560, October 2013.

(Ruiz, 2013) Optogenetics through windows on the brain in the nonhuman primate. Ruiz O, Lustig BR, Nassi JJ, Cetin A, Reynolds JH, Albright TD, Callaway EM, Stoner GR, Roe AW. J Neurophysiol. 2013 Sep;110(6):1455-67, 2013.

(Schreiber, 2000) Measuring Information Transfer, Thomas Schreiber, Physical Review Letters, Vol.85,

pp 461-464, 2000.

(Seung, 2012) Connectome: How the Brain's Wiring Makes Us Who We Are. Sebastian Seung. Houffton Mifflin Harcourt Publishing, 2012.

(Soriano, 2008) Development of input connections in neural cultures. Soriano, J., Rodríguez Martínez, M., Tlusty, T. & Moses, E. Proc. Natl. Acad. Sci. U.S.A. 105, 13758–13763 (2008).

(Steinmetz, 2013) Testing for effects of different stimuli on neuronal firing relative to background activity. Peter N Steinmetz and Chris Thorp, Journal of Neural Engineering Volume 10 Number 5, 2013.

(Stetter, 2012) Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals, Olav Stetter, Demian Battaglia, Jordi Soriano, Theo Geisel, PLOS Computational Biology, August 2012, Volume 8, Issue 8.

(Stosiek, 2003) In vivo two-photon calcium imaging of neuronal networks, Christoph Stosiek, Olga Garaschuk, Knut Holthoff, and Arthur Konnerth, PNAS, vol. 100 no. 12, pp 7319–7324, 2003.

(Suzuki, 2013) Carbon nanotube multi-electrode array chips for noninvasive real-time measurement of dopamine, action potentials, and postsynaptic potentials, Ikuro Suzuki, Mao Fukuda, Keiichi Shirakawa, Hideyasu Jiko, Masao Gotoh,. Biosensors and Bioelectronics, Volume 49, 15, Pages 270–275, 2013.

(Truccolo, 2005) A point process framework for relating neural spiking activity to spiking history, neural ensemble, and extrinsic covariate effects. Truccolo, W., Eden, U., Fellows, M.R., Donoghue, J.P., and Brown, E.N. J. Neurophysiol 93, 1074–1089, 2005.

(Vogelstein, 2009) Spike inference from calcium imaging using sequential Monte Carlo methods. Vogelstein, J.T., Watson, B.O., Packer, A.M., Yuste, R., Jedynak, B., and Paninski, L. Biophys J. 97, 636–655, 2009.

(Wibral, 2011) Transfer entropy in magnetoencephalographic data: Quantifying information flow in cortical and cerebellar networks. Wibral M, Rahm B, Rieder M, Lindner M, Vicente R, et al. Prog Biophys Mol Biol 105: 80–97, 2011.

(White, 1986) The structure of the nervous system of the nematode Caenorhabditis elegans. White JG, S outhgate E, Thomson JN, Brenner S, Philos Trans R Soc Lond B Biol Sci. 1986 Nov 12;314(1165):1-340.