elephant.bib

@article{Wen13_20110610,
  title={Multivariate Granger causality: an estimation framework based on factorization of the spectral density matrix},
  author={Wen, Xiaotong and Rangarajan, Govindan and Ding, Mingzhou},
  journal={Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  volume={371},
  number={1997},
  pages={20110610},
  year={2013},
  publisher={The Royal Society Publishing}
}

@article{Wilson72_420,
  title={The factorization of matricial spectral densities},
  author={Wilson, G Tunnicliffe},
  journal={SIAM Journal on Applied Mathematics},
  volume={23},
  number={4},
  pages={420--426},
  year={1972},
  publisher={SIAM}
}

@article{Dhamala08_354,
  title={Analyzing information flow in brain networks with nonparametric Granger causality},
  author={Dhamala, Mukeshwar and Rangarajan, Govindan and Ding, Mingzhou},
  journal={Neuroimage},
  volume={41},
  number={2},
  pages={354--362},
  year={2008},
  publisher={Elsevier}
}

@misc{Ding06_0608035,
  title={Granger Causality: Basic Theory and Application to Neuroscience},
  author={Mingzhou Ding and Yonghong Chen and Steven L. Bressler},
  year={2006},
  eprint={q-bio/0608035},
  archivePrefix={arXiv},
  primaryClass={q-bio.QM}
}

@article{Lachaux99_194,
  author = {Lachaux, Jean-Philippe and Rodriguez, Eugenio and Martinerie, Jacques and Varela, Francisco J.},
  title = {Measuring phase synchrony in brain signals},
  journal = {Human Brain Mapping},
  volume = {8},
  number = {4},
  pages = {194-208},
  doi = {https://doi.org/10.1002/(SICI)1097-0193(1999)8:4<194::AID-HBM4>3.0.CO;2-C},
  year = {1999}
}

@article{Vinck11_1548,
  title={An improved index of phase-synchronization for electrophysiological data in the presence of volume-conduction, noise and sample-size bias},
  author={Vinck, M. and Oostenveld, R. and {van Wingerden}, M. and Battaglia, F. and Pennartz, C.},
  journal={NeuroImage},
  volume={55},
  number = {4},
  pages={1548--1565},
  year={2011},
  issn = {1053-8119},
  doi = {https://doi.org/10.1016/j.neuroimage.2011.01.055}
}

@article{Granger69_424,
  title={Investigating causal relations by econometric models and cross-spectral methods},
  author={Granger, Clive WJ},
  journal={Econometrica: journal of the Econometric Society},
  volume={37},
  pages={424--438},
  year={1969},
  doi={10.2307/1912791}
}

@article{Gruen02_43,
  title={Unitary events in multiple single-neuron spiking activity: I. Detection and significance},
  author={Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
  year={2002},
  journal={Neural Comp.},
  volume={14},
  number={1},
  pages={43--80},
  doi={10.1162/089976602753284455}
}

@article{Gruen02_81,
  title={Unitary events in multiple single-neuron spiking activity: II. Nonstationary data},
  author={Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
  year={2002},
  journal={Neural Comp.},
  volume={14},
  number={1},
  pages={81--119},
  doi={10.1162/089976602753284464}
}

@article{Gruen03,
  title={Effects across trial non-stationarity on joint-spike events},
  author={Gr\"{u}n, S. and Riehle, A. and Diesmann, M.},
  year={2003},
  journal={Biol. Cyb.},
  volume={88},
  number={5},
  pages={335--51},
  doi={10.1007/s00422-002-0386-2}
}

@article{Gruen09_1126,
  title={Data-driven significance estimation of precise spike correlation},
  author={Gr\"{u}n, S.},
  year={2009},
  journal={J. Neurophysiol.},
  number={101},
  pages={1126--1140},
  doi={10.1152/jn.00093.2008}
}

@article{Gruen99_67,
  title={Detecting unitary events without discretization of time},
  author={Gr{\"u}n, S. and Diesmann, M. and Grammont, F. and Riehle, A. and Aertsen, A.},
  journal={J.  Neurosci. Meth.},
  year={1999},
  volume={94},
  number={1},
  pages={67--79},
  doi={10.1016/s0165-0270(99)00126-0}
}

@article{Riehle97_1950,
  title={Spike synchronization and rate modulation differentially involved in motor cortical function},
  author={Riehle, A. and Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
  year={1997},
  journal={Science},
  volume={278},
  number={5345},
  pages={1950--1953},
  doi={10.1126/science.278.5345.1950}
}

@article{Seth07_1667,
  author={Seth, A. },
  title={Granger causality},
  year={2007},
  journal={Scholarpedia},
  volume={2},
  number={7},
  pages={1667},
  doi={10.4249/scholarpedia.1667},
  note={revision \#127333}
}

@article{Stella19_104022,
  title={3d-{SPADE}: {S}ignificance evaluation of spatio-temporal patterns of various temporal extents},
  author={Stella, A. and Quaglio, P. and Torre, E. and Gr{\"u}n, S.},
  year={2019},
  journal={Biosystems},
  volume={185},
  pages={104022},
  doi={10.1016/j.biosystems.2019.104022}
}

@article{Torre16_e1004939,
  title={ASSET: analysis of sequences of synchronous events in massively parallel spike trains},
  author={Torre, E. and Canova, C. and Denker, M. and Gerstein, G. and Helias, M. and Gr{\"u}n, S.},
  year={2016},
  journal={PLoS Comp. Biol.},
  volume={12},
  number={7},
  pages={e1004939},
  doi={10.1371/journal.pcbi.1004939}
}

@article{Ciba18_136,
  title={Spike-contrast: A novel time scale independent and multivariate measure of spike train synchrony},
  author={Ciba, M. and Isomura, T. and Jimbo, Y. and Bahmer, A. and Thielemann, C.},
  year={2018},
  journal={J. Neurosci. Meth.},
  volume={293},
  pages={136--143},
  doi={10.1016/j.jneumeth.2017.09.008}
}

@article{Rostami17_3,
  title={[{Re}] {S}pike synchronization and rate modulation differentially involved in motor cortical function},
  author={Rostami, V. and Ito, J. and Denker, M. and Gr{\"u}n, S.},
  year={2017},
  journal={ReScience},
  volume={3},
  number={1},
  pages={3},
  doi={10.5281/zenodo.583814}
}

@article{Gerstein2004_203,
  title={Searching for significance in spatio-temporal firing patterns},
  author={Gerstein, George L},
  journal={Acta Neurobiologiae Experimentalis},
  volume={64},
  number={2},
  pages={203--208},
  year={2004},
  publisher={Warsaw; Nencki Institute of Experimental Biology; 1999}
}

@article{Louis2010_127,
  title={Surrogate spike train generation through dithering in operational time},
  author={Louis, Sebastien GR and Diesmann, Markus and others},
  journal={Frontiers in computational neuroscience},
  volume={4},
  pages={127},
  year={2010},
  publisher={Frontiers}
}

@incollection{Louis2010_359,
  title={Generation and selection of surrogate methods for correlation analysis},
  author={Louis, Sebastien and Borgelt, Christian and Gr{\"u}n, Sonja},
  booktitle={Analysis of Parallel Spike Trains},
  volume={7},
  pages={359--382},
  year={2010},
  publisher={Springer},
  doi={10.1007/978-1-4419-5675-0_17}
}

@incollection{Eggermont2010_77,
  title={Pair-correlation in the time and frequency domain},
  author={Eggermont, Jos J},
  booktitle={Analysis of parallel spike trains},
  volume={7},
  pages={77--102},
  year={2010},
  publisher={Springer},
  doi={10.1007/978-1-4419-5675-0_5}
}

@article{Hatsopoulos2007_5105,
  title={Encoding of movement fragments in the motor cortex},
  author={Hatsopoulos, Nicholas G and Xu, Qingqing and Amit, Yali},
  journal={Journal of Neuroscience},
  volume={27},
  number={19},
  pages={5105--5114},
  year={2007},
  publisher={Soc Neuroscience}
}

@article{Rossum2001_751,
  title={A novel spike distance},
  author={Rossum, MCW van},
  journal={Neural computation},
  volume={13},
  number={4},
  pages={751--763},
  year={2001},
  publisher={MIT Press}
}

@article{Wieland2015_040901,
  title={Slow fluctuations in recurrent networks of spiking neurons},
  author={Wieland, Stefan and Bernardi, Davide and Schwalger, Tilo and Lindner, Benjamin},
  journal={Physical Review E},
  volume={92},
  number={4},
  pages={040901},
  year={2015},
  publisher={APS}
}

@article{Cutts2014_14288,
  title={Detecting pairwise correlations in spike trains: an objective comparison of methods and application to the study of retinal waves},
  author={Cutts, Catherine S and Eglen, Stephen J},
  journal={Journal of Neuroscience},
  volume={34},
  number={43},
  pages={14288--14303},
  year={2014},
  publisher={Soc Neuroscience},
  doi={10.1523/JNEUROSCI.2767-14.2014}
}

@article{Holt1996_1806,
  title={Comparison of discharge variability in vitro and in vivo in cat visual cortex neurons},
  author={Holt, Gary R and Softky, William R and Koch, Christof and Douglas, Rodney J},
  journal={Journal of neurophysiology},
  volume={75},
  number={5},
  pages={1806--1814},
  year={1996},
  publisher={American Physiological Society Bethesda, MD}
}

@article{Shinomoto2003_2823,
  title={Differences in spiking patterns among cortical neurons},
  author={Shinomoto, Shigeru and Shima, Keisetsu and Tanji, Jun},
  journal={Neural computation},
  volume={15},
  number={12},
  pages={2823--2842},
  year={2003},
  publisher={MIT Press}
}

@article{Shinomoto2009_e1000433,
  title={Relating neuronal firing patterns to functional differentiation of cerebral cortex},
  author={Shinomoto, Shigeru and Kim, Hideaki and Shimokawa, Takeaki and Matsuno, Nanae and Funahashi, Shintaro and Shima, Keisetsu and Fujita, Ichiro and Tamura, Hiroshi and Doi, Taijiro and Kawano, Kenji and others},
  journal={PLoS Comput Biol},
  volume={5},
  number={7},
  pages={e1000433},
  year={2009},
  publisher={Public Library of Science}
}

@article{Shimazaki2010_171,
  title={Kernel bandwidth optimization in spike rate estimation},
  author={Shimazaki, Hideaki and Shinomoto, Shigeru},
  journal={Journal of computational neuroscience},
  volume={29},
  number={1-2},
  pages={171--182},
  year={2010},
  publisher={Springer}
}

@inproceedings{Gruen2007_96,
  title={Impact of higher-order correlations on coincidence distributions of massively parallel data},
  author={Gr{\"u}n, Sonja and Abeles, Moshe and Diesmann, Markus},
  booktitle={International School on Neural Networks, Initiated by IIASS and EMFCSC},
  volume={5286},
  pages={96--114},
  year={2007},
  organization={Springer}
}

@article{Torre2013_132,
  title={Statistical evaluation of synchronous spike patterns extracted by frequent item set mining},
  author={Torre, Emiliano and Picado-Mui{\~n}o, David and Denker, Michael and Borgelt, Christian and Gr{\"u}n, Sonja},
  journal={Frontiers in computational neuroscience},
  volume={7},
  pages={132},
  year={2013},
  publisher={Frontiers}
}

@article{Quaglio2017_41,
  title={Detection and evaluation of spatio-temporal spike patterns in massively parallel spike train data with spade},
  author={Quaglio, Pietro and Yegenoglu, Alper and Torre, Emiliano and Endres, Dominik M and Gr{\"u}n, Sonja},
  journal={Frontiers in computational neuroscience},
  volume={11},
  pages={41},
  year={2017},
  publisher={Frontiers}
}

@article{Stella2019_104022,
  title={3d-SPADE: Significance evaluation of spatio-temporal patterns of various temporal extents},
  author={Stella, Alessandra and Quaglio, Pietro and Torre, Emiliano and Gr{\"u}n, Sonja},
  journal={Biosystems},
  volume={185},
  pages={104022},
  year={2019},
  publisher={Elsevier}
}

@article{Nawrot2008_374,
  title={Measurement of variability dynamics in cortical spike trains},
  author={Nawrot, Martin P and Boucsein, Clemens and Molina, Victor Rodriguez and Riehle, Alexa and Aertsen, Ad and Rotter, Stefan},
  journal={Journal of neuroscience methods},
  volume={169},
  number={2},
  pages={374--390},
  year={2008},
  publisher={Elsevier}
}

@article{Kuhn2003_67,
  title={Higher-order statistics of input ensembles and the response of simple model neurons},
  author={Kuhn, Alexandre and Aertsen, Ad and Rotter, Stefan},
  journal={Neural computation},
  volume={15},
  number={1},
  pages={67--101},
  year={2003},
  publisher={MIT Press}
}

@article{Staude2010_327,
  title={CuBIC: cumulant based inference of higher-order correlations in massively parallel spike trains},
  author={Staude, Benjamin and Rotter, Stefan and Gr{\"u}n, Sonja},
  journal={Journal of computational neuroscience},
  volume={29},
  number={1-2},
  pages={327--350},
  year={2010},
  publisher={Springer}
}

@article{Le2001_83,
  title={Comparison of Hilbert transform and wavelet methods for the analysis of neuronal synchrony},
  author={Le Van Quyen, Michel and Foucher, Jack and Lachaux, Jean-Philippe and Rodriguez, Eugenio and Lutz, Antoine and Martinerie, Jacques and Varela, Francisco J},
  journal={Journal of neuroscience methods},
  volume={111},
  number={2},
  pages={83--98},
  year={2001},
  publisher={Elsevier}
}

@article{Farge1992_395,
  title={Wavelet transforms and their applications to turbulence},
  author={Farge, Marie},
  journal={Annual review of fluid mechanics},
  volume={24},
  number={1},
  pages={395--458},
  year={1992},
  publisher={Annual reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}

@article{Stoica2005,
  title={Spectral analysis of signals},
  author={Stoica, Petre and Moses, Randolph L and others},
  journal={Prentice Hall},
  year={2005},
  publisher={Pearson Prentice Hall Upper Saddle River, NJ}
}

@article{Messer2014_2027,
  title={A multiple filter test for the detection of rate changes in renewal processes with varying variance},
  author={Messer, Michael and Kirchner, Marietta and Schiemann, Julia and Roeper, Jochen and Neininger, Ralph and Schneider, Gaby and others},
  journal={The Annals of Applied Statistics},
  volume={8},
  number={4},
  pages={2027--2067},
  year={2014},
  publisher={Institute of Mathematical Statistics},
  doi={10.1214/14-AOAS782}
}

@article{Russo2017_e19428,
  title={Cell assemblies at multiple time scales with arbitrary lag constellations},
  author={Russo, Eleonora and Durstewitz, Daniel},
  journal={Elife},
  volume={6},
  pages={e19428},
  year={2017},
  publisher={eLife Sciences Publications Limited}
}

@article{Yu2008_1881,
  title={Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity},
  author={Yu, Byron M and Cunningham, John P and Santhanam, Gopal and Ryu, Stephen and Shenoy, Krishna V and Sahani, Maneesh},
  journal={Advances in neural information processing systems},
  volume={21},
  pages={1881--1888},
  year={2008}
}

@article{Deger12_443,
	author = {Deger, Moritz and Helias, Moritz and Boucsein, Clemens and Rotter, Stefan},
	journal = {Journal of Computational Neuroscience},
	number = 3,
	pages = {443--463},
	title = {Statistical properties of superimposed stationary spike trains},
	volume = 32,
	year = 2012}


@article{de_blasi19_169,
	title = {Total spiking probability edges: {A} cross-correlation based method for effective connectivity estimation of cortical spiking neurons},
	volume = {312},
	shorttitle = {Total spiking probability edges},
	doi = {10.1016/j.jneumeth.2018.11.013},
	language = {en},
	journal = {Journal of Neuroscience Methods},
	author = {{De Blasi}, Stefano and Ciba, Manuel and Bahmer, Andreas and Thielemann, Christiane},
	month = jan,
	year = {2019},
	pages = {169--181},
}