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Convergent evolution in silico reveals shape and dynamic principles of directed locomotion.
bioRxiv 2022
Biazzi RB, Fujita A, Takahashi DY (2022) 
Social-vocal brain networks in a non-human primate.
bioRxiv 2021.12.01.470701; doi:
Takahashi DY, El Hady A, Zhang YS, Liao DA, Montaldo G, Urban A, Ghazanfar AA

Peer-reviewed articles

* = equal contribution
# = co-corresponding authors

Vocal communication

Active neural coordination of motor behaviors with internal states.
Proceedings of National Academy of Science, 119 (39) e2201194119, 2022
Zhang Y.S., Takahashi D.Y., El Hady A., Liao D.A., Ghazanfar A.A.  
Prenatal development of neonatal vocalizations.
eLife, 11, e78485, 2022
Narayanan D.Z., # Takahashi D.Y., Kelly L.M., Hlavaty S.I., Huang J. and # Ghazanfar A.A.  
A mechanism for punctuating equilibria during mammalian vocal development.
PLoS computational biology, 18(6), e1010173, 2022
Varella T.T., Zhang Y.S., #Takahashi D.Y. and #Ghazanfar A.A. 
Domestication phenotype linked to vocal behavior in marmoset monkeys.
Current Biology, v. 30, 5026–5032, 2020
Ghazanfar A.A., Kelly L.M., Takahashi D.Y., Winters S., Terrett R., Higham J.P.
Vocal state change through laryngeal development.
Nature Communication, doi: 10.1038/s41467-019-12588-6, 2019
Zhang Y.S., Takahashi D.Y., Liao D.A., #Ghazanfar A.A. and #Elemans C.P.H.
Vocal and locomotor coordination develops in association with the autonomic nervous system.
eLife, 8: e41853. doi: 10.7554/eLife.41853, 2019
Gustison M.L., Borjon J.I., #Takahashi D.Y. and #Ghazanfar A.A.
Volition and learning in primate vocal behavior.
Animal Behaviour, v. 151,, 2019
Ghazanfar A.A., Liao D.A. and Takahashi D.Y.
Vocal learning via social reinforcement by infant marmoset monkeys.
Current Biology, v. 27, 1844-1852, doi: 10.1016/j.cub.2017.05.004, 2017
#Takahashi D.Y., Liao D.A., #Ghazanfar A.A.
Vocal development in a Waddington landscape.
eLife, 6:e20782. doi: 10.7554/eLife.20782, 2017
*Teramoto Y., *#Takahashi D.Y., #Holmes P., #Ghazanfar A.A.
Arousal dynamics drive vocal production in marmoset monkeys.
Journal of Neurophysiology, early access doi:10.1152/jn.00136.2016
Borjon J.I., #Takahashi D.Y., Cervantes D.C. and #Ghazanfar A.A.
Early development of turn-taking with parents shapes vocal acoustics in infant marmoset monkeys.
Philosophical Transaction of Royal Society B, v 371, doi: 10.1098/rstb.2015.0370, 2016
*Takahashi D.Y., *Fenley A.R. and Ghazanfar A.A.
The developmental dynamics of marmoset monkey vocal production.
Science, v. 349, 730-734, 2015
#Takahashi D.Y., Fenley A.R., Teramoto Y., Narayanan D.Z., Borjon J.I., Holmes P. and #Ghazanfar A.A.
 Supplementary material
Cooperative vocal control in marmoset monkeys via vocal feedback.
Journal of Neurophysiology, v. 114, 274-283, 2015
Choi J.Y., #Takahashi D.Y. and #Ghazanfar A.A.
The evolution of speech: vision, rhythm, cooperation.
Trends in Cognitive Sciences, v. 18, 543-553, 2014
Ghazanfar A.A. and Takahashi D.Y.
Facial expressions and the evolution of the speech rhythm.
Journal of Cognitive Neuroscience, v. 26, 1196-1207, 2014
Ghazafar A. and Takahashi D.Y.
Coupled oscillator dynamics of vocal turn-taking in monkeys.
Current Biology, v. 23, 2162-2168, 2013
#Takahashi D.Y., Narayanan D.Z., #Ghazanfar A.A.
Cineradiography of monkey lip-smacking reveals putative precursors of speech dynamics.
Current Biology, v. 22, p. 1176-1186, 2012
#Ghazanfar A.A., Takahashi D.Y., Mathur N., #Fitch W.T.

Emergence of locomotion

Predicting soft robot's locomotion fitness
Proceedings of Genetic and Evolutionary Computation Conference Companion, 81-82, 2021
Biaggi R.B., Fujita, A., Takahashi D.Y.

Statistical methods for connectivity analysis

Inference of the topology of geomagnetic field multipole interactions.
The European Physical Journal Special Topics, in press, 2021
Raphaldini B., Teruya A.S.W., Raupp C.F.M., Dias P.L.S., Takahashi D.Y.
Information flow between MJO-related waves: a network approach on the wave space.
The European Physical Journal Special Topics, in press, 2021
Raphaldini B., Teruya A.S.W., Raupp C.F.M., Dias P.L.S., Takahashi D.Y.
Stratospheric ozone and quasi-biennial oscillation (QBO) interaction with the tropical troposphere on intraseasonal and interannual timescales: a normal-mode perspective.
Earth System Dynamics, v. 12, 83-101, 2020
Raphaldini B., Teruya A.S.W., Dias P.L.S., Massaroppe L., Takahashi D.Y.
A semi-parametric statistical test to compare complex networks.
Journal of Complex Networks, v. 8, cnz028, 2020
Fujita A., Lira E.S., Santos S.S., Bando S.Y., Soares G.E., Takahashi D.Y.
Correlation between graphs with an application to brain network analysis.
Computational Statistics & Data Analysis, v. 109, 76-92, 2017
Fujita A., Takahashi D.Y., Balardin J.B., Vidal M.C., Sato J.R.
A statistical method to distinguish functional brain networks.
Frontiers in Neuroscience, v. 11, doi:10.3389/fnins.2017.00066, 2017
Fujita A., Vidal M.C., Takahashi D.Y.
ANOCVA in R: A Software to Compare Clusters between Groups and Its Application to the Study of Autism Spectrum Disorder.
Frontiers in Neuroscience, v. 11, doi:10.3389/fnins.2017.00016, 2017
Vidal M.C., Sato J.R., Balardin J.B., Takahashi D.Y., Fujita A.
Statistical Methods in Graphs: Parameter Estimation, Model Selection, and Hypothesis Test.
Mathematical Foundations and Applications of Graph Entropy, v. 98, 183-202, 2016
Santos S.S., Takahashi D.Y., Sato J.R., Ferreira C.E., Fujita A.
Directed Transfer function: Unified asymptotic theory and some of its implications.
IEEE Transactions of Biomedical Engineering, 10.1109/TBME.2016.2550199, 2016
Baccalá L.A., Takahashi D.Y. and Sameshima, K.
Sharp oracle inequalities and slope heuristic for specification probabilities estimation in discrete random fields.
Bernoulli, v. 22, 325-344, 2016
*Lerasle M. and *Takahashi D.Y.
 MATLAB routines
On statistical performance of Granger-causal connectivity estimators
Brain informatics, 10.1007/s40708-015-0015-1, 1-15, 2015
Sameshima K., Takahashi D.Y., and Baccalá L.A.
Identifying interacting pairs of sites in Ising models on a countable set
Brazilian Journal of Probability and Statistics, v. 29, 443-459, 2015
*Galves A., *Orlandi E., and *Takahashi D.Y.
A non-parametric statistical test to compare clusters with applications in functional magnetic resonance imaging data.
Statistics in Medicine, v. 33, 4949-4962, 2014
Fujita A., Takahashi D.Y., Patriota A.G., Sato J.R.
Canonical information flow decomposition among neural structure subsets.
Frontiers in Neuroinformatics, doi: 10.3389/fninf.2014.00049, 2014
Takahashi D.Y., Baccalá L.A., Sameshima K.
A non-parametric method to estimate the number of clusters.
Computational Statistics and Data Analysis, v. 73, 27-39, 2014
Fujita A., Takahashi D.Y., Patriota A.
On the statistical performance of connectivity estimators in the frequency domain.
Lecture Notes in Computer Science, v. 8609, 412-423, 2014
Sameshima K., Takahashi D.Y., and Baccalá L.A.
A comparative study of statistical methods used to identify dependencies between gene expression signals
Briefing in Bioinformatics, doi: 10.1093/bib/bbt051, 2013
Santos S.S., Takahashi D.Y., Nakata A., Fujita A.
Unified asymptotic theory for all partial directed coherence forms
Philosophical Transactions of the Royal Society A, v. 371, 20120158, 2013
Baccalá L.A., de Brito C.S., Takahashi D.Y., Sameshima K.
Measuring network's entropy in ADHD: A new approach to investigate neuropsychiatric disorders
Neuroimage, v77, p. 44-51, 2013
Sato J.R.,Takahashi D.Y., Hoexeter M.Q., Massirer K.M., Fujita A.
Discriminating different classes of biological networks by analyzing the graphs spectra distribution.
PLoS ONE, 7(12): e49949. doi:10.1371/journal.pone.0049949, 2012
Takahashi D.Y., Sato J.R., Ferreira C.E., Fujita A.
An oracle approach for interaction neighborhood estimation in random fields.
Electronic Journal of Statistics, v 5, p. 534-571, 2011
*Lerasle M. and *Takahashi D.Y.
MATLAB routines used to run the experiments
Information theoretic interpretation of frequency domain connectivity measures.
Biological Cybernetics, v.103, p. 463-469, 2010.
Takahashi D.Y., Baccalá L.A. and Sameshima K.
Hyperdopaminergia and NMDA Receptor Hypofunction Disrupt Neural Phase Signaling.
The Journal of Neuroscience, v. 29, p. 8215-8224, 2009.
Dzirasa K., Ramsey A. J., Takahashi D.Y., Stapleton J., Potes J.M., Williams J.K., Gainetdinov R.R., Sameshima K., Caron M.G., Nicolelis M.A.L.
Frequency domain connectivity identification: An application of partial directed coherence in fMRI.
Human Brain Mapping, v. 30, p. 452-461, 2009.
Sato J.R., Takahashi D.Y., Arcuri S.M., Sameshima K., Morettin P.A., Baccalá L.A.
Partial directed coherence asymptotics for VAR processes of infinite order.
International Journal of Bioelectromagnetism, v. 10, p. 31-36, 2008.
Takahashi D.Y., Baccalá L.A., Sameshima K.
Connectivity Inference via Partial Directed Coherence. 
Journal of Applied Statistics, v. 34, p. 1259-1273, 2007.
Takahashi D.Y., Baccalá L.A., Sameshima K.
A method to produce evolving functional connectivity maps during the course of an fMRI experiment using wavelet based time-varying Granger causality. 
NeuroImage, v. 31, p. 187-196, 2006.
Sato J.R., Felix M. de M., Takahashi D.Y., Amaro Junior E., Brammer M.J., Morettin P.A.
Intervention Models in Functional Connectivity Identification Applied to fMRI.
International Journal of Biomedical Imaging, v. 2006, p. 1-7, 2006.
Sato J.R., Takahashi D.Y., Cardoso E.F., Martin M.G.M., Amaro Junior E., Morettin P.A.


Stochastic processes

Gaussian concentration bounds for stochastic chains of unbounded memory.
Annals of Applied Probability,in press, 2022
*Chazottes J.R., *Gallo S., *Takahashi D.Y.
Self-switching Markov chains: emerging dominance phenomena.
Stochastic processes and their applications, 143, p. 254-284, 2021
*Gallo C., *Iacobelli G., *Ost G. and *Takahashi D.Y.
Mixing rates for potentials of non-summable variations.
Ergodic Theory and Dynamical System, FIrstView, doi: 10.1017/etds.2021.65, p. 1-18, 2021
*Gallesco C. and *Takahashi D.Y.
Dynamic uniqueness for stochastic chains with unbounded memory.
Stochastic Processes and their Applications, v. 128, p. 689-706, 2018
*Gallesco C., *Gallo S., *Takahashi D.Y.
Attractive regular stochastic chains: perfect simulation and phase transition.
Ergodic Theory and Dynamical System, v. 34, 1567-1586, 2014
*Gallo S. and *Takahashi D.Y.
Explicit estimates in the Bramson-Kalikow model
Nonlinearity, v. 27, 2281-2296, 2014
*Gallesco C., *Gallo S., *Takahashi D.Y.
Markov approximations of chains of infinite order in the $\bar{d}$-metric
Markov Processes and Related Fields, v. 19, 51-82, 2013
*Gallo S., *Lerasle M., *Takahashi D.Y.


Alzheimer’s disease

Alzheimer's disease diagnosis disclosure in Brazil: a survey of specialized physicians' current practice and attitudes. 
 International Psychogeriatrics, v. 20, p. 471-481, 2008.
Raicher I., Shimizu M., Takahashi D.Y., Nitrini R., Caramelli P.
Disclosure of the diagnosis of Alzheimer's disease: caregivers' opinions in a Brazilian sample. 
Arquivos de Neuro-Psiquiatria, v. 66, p. 625-630, 2008.
Shimizu M., Raicher I., Takahashi D.Y., Caramelli P., Nitrini R.
qEEG spectral peak in Alzheimer's disease: a possible tool for treatment follow-up.
Dementia & neuropsychologia, v. 2, p. 9-12, 2008.
Raicher I., Takahashi D.Y., Kanda P.A.M., Nitrini R., Anghinah R.
Brief cognitive evaluation of patients attended in a general neurological outpatient clinic.
Arquivos de Neuro-Psiquiatria, v. 65, p. 299-303, 2007.
Vittielo A.P., Ciriaco J.G., Takahashi D.Y., Nitrini R, Caramelli P.
Mortality from dementia in a community-dwelling Brazilian population . 
International Journal of Geriatric Psychiatry, v. 20, n. 3, p. 247-253, 2005.
Nitrini R., Caramelli P., Herrera E., de Castro I., Bahia V.S., Anghinah R., Caixeta L., Radanovic M., Charchat-Fichman H., Porto C.S., Carthery M.T., Hartmann A.P.B.J., Huang N., Smid J., Lima P., Takahashi D.Y., Takada L.T.
Incidence of dementia in a community-dwelling Brazilian population.
Alzheimer Disease and Associated Disorders, v. 18, n. 4, p. 241-246, 2005.
Nitrini R., Caramelli P., Herrera E., Bahia V.S., Caixeta L., Radanovic M., Anghinah R., Charchat-Fichman H., Porto C.S., Carthery M.T., Hartmann A.P.B.J., Huang N., Smid J., Lima P., Takada, L.T., Takahashi, D.Y.
EEG alpha band coherence analysis in healthy adults: preliminary results.
Arquivos de Neuro-Psiquiatria, Brasil, v. 63, n. 1, p. 83-86, 2005.
Anghinah R., Caramelli P., Takahashi D.Y., Nitrini R., Sameshima K.
Hyperphosphorylated tau protein in the cerebrospinal fluid of patients with Alzheimer's disease and other dementias: preliminary findings. 
Arquivos de Neuro-Psiquiatria, v. 62, n. 3b, p. 751-755, 2004.
Hartmann A.P.B.J., de Almeida S.M., Livramento J.A., Nitrini R., Takahashi D.Y., Caramelli P.


Medical diagnosis

Comparison of of virtual cystoscopy and transabdominal ultrasonography with conventional cystoscopy for bladder tumor detection. 
Journal of Endourology, v. 22, p. 1725-1729, 2008.
Lopes R.I., Nogueira L., Albertotti C.J., Takahashi D.Y., Lopes R.N.
Comparison between Acoustic Rhinometry, Nasal Inspiratory Peak Flow, and Table of Scores in Patients with Rhitinis.
Arquivos de Otorrinolaringorologia, v. 9, n. 3, p. 203-211, 2005.
da Costa G.G.O., Ctenas B.B., Takahashi D.Y., Mion O., Mello Junior J.F., Butugan O.
Avaliando a complexidade da dinâmica cardiovascular por entropia amostral.
Revista Brasileira de Hipertenção, v. 12, n. 1, p. 27-32, 2005.
Sameshima K., Takahashi D.Y., Baccalá L.A.



Medidas de fluxo de informação com aplicação em neurociência.
(Measures of information flow with application in neuroscience)

My thesis was written in Portuguese. I tried to unify and understand the relationship between different measures of dependence used in neuroscience, physics, econometrics and information theory.