Team Publications

Romain Goutagny’s publication list

(click here for publications by Demian Battaglia)

Original research articles

• Borcuk C, Héraud C, Herbeaux K, Diringer M, Panzer É, Scuto J, Hashimoto S, Saido TC, Saito T, Goutagny R, Battaglia D, Mathis C (2022) Early memory deficits and extensive brain network disorganization in the AppNL-F/MAPT double knock-in mouse model of familial Alzheimer’s disease. Aging Brain 2:100042.
• Pousinha PA, Mouska X, Bianchi D, Temido-Ferreira M, Rajão-Saraiva J, Gomes R, Fernandez SP,  Salgueiro-Pereira AR, Gandin C,  Raymond EF, Barik J, Goutagny R, Bethus I, Lopes LV, Migliore M, Marie H. (2019). The Amyloid Precursor Protein C-Terminal Domain Alters CA1 Neuron Firing, Modifying Hippocampus Oscillations and Impairing Spatial Memory Encoding. Cell Rep, 29 (2), 317-331.e5.
• Salgueiro-Pereira AR, Duprat F, Pousinha PA, Loucif A, Douchamps V, Regondi C, Ayrault M, Eugie M, Stunault MI, Escayg A, Goutagny R, Gnatkovsky V, Frassoni C, Marie H, Bethus I, Mantegazza M. (2019). A two-hit story: Seizures and genetic mutation interaction sets phenotype severity in SCN1A epilepsies. Neurobiol Dis. 2019 May;125:31-44.
• Fasano C, Rocchetti J, Pietrajtis K, Zander JF, Manseau F, Sakae DY, Marcus-Sells M, Ramet L, Morel LJ, Carrel D, Dumas S, Bolte S, Bernard V, Vigneault E, Goutagny R, Ahnert-Hilger G, Giros B, Daumas S, Williams S, El Mestikawy S. (2017). Regulation of the Hippocampal Network by VGLUT3-Positive CCK- GABAergic Basket Cells. Front Cell Neurosci. 2017 May 16;11:140. 
• Hamm V, Héraud C, Bott JB, Herbeaux K, Strittmatter C, Mathis C, Goutagny R (2017). Differential contribution of APP metabolites to early cognitive deficits in TgCRND8 mouse model of Alzheimer’s disease. Sci Adv. 2017 Feb 24;3(2):e1601068.
• Bott JB, Héraud C, Cosquer B, Herbeaux K, Aubert J, Sartori M, Goutagny R*, Mathis C* (2016). APOE-Sensitive Cholinergic Sprouting Compensates for Hippocampal Dysfunctions Due to Reduced Entorhinal Input. J Neurosci. 36(40):10472-10486. *: Equal contributors
• Bott JB, Muller MA, Jackson J, Aubert J, Cassel JC, Mathis C, Goutagny R (2016). Spatial Reference Memory is Associated with Modulation of Theta-Gamma Coupling in the Dentate Gyrus. Cereb Cortex. 26(9):3744-53.
• Lithfous S, Tromp D, Dufour A, Pebayle T, Goutagny R, Després O (2015). Decreased theta power at encoding and cognitive mapping deficits in elderly individuals during a spatial memory task. Neurobiol Aging. 36(10):2821-9.
• Jackson J, Amilhon B, Goutagny R, Bott JB, Manseau F, Kortleven C, Bressler SL, Williams S (2014). Reversal of theta rhythm flow through intact hippocampal circuits. Nat Neurosci. 17(10):1362-70.
• Goutagny R, Gu N, Cavanagh C, Jackson J, Chabot JG, Quirion R, Krantic S, Williams S (2013). Alterations in hippocampal network oscillations and theta-gamma coupling arise before Aβ overproduction in a mouse model of Alzheimer’s disease. Eur J Neurosci. 37(12):1896-902. 
• Goutagny R, Loureiro M, Jackson J, Chaumont J, Williams S, Isope P, Kelche C, Cassel JC, Lecourtier L (2013). Interactions between the lateral habenula and the hippocampus: implication for spatial memory processes. Neuropsychopharmacology. 38(12):2418-26. 
• Gu N, Jackson J, Goutagny R, Lowe G, Manseau F, Williams S (2013). NMDA-dependent phase synchronization between septal and temporal CA3 hippocampal networks. J Neurosci. 33(19):8276-87. 
• Jego S, Salvert D, Renouard L, Mori M, Goutagny R, Luppi PH, Fort P (2012). Tuberal hypothalamic neurons secreting the satiety molecule Nesfatin-1 are critically involved in paradoxical (REM) sleep homeostasis. PLoS One. 7(12):e52525.
• Ducharme G, Lowe GC, Goutagny R, Williams S (2012). Early alterations in hippocampal circuitry and theta rhythm generation in a mouse model of prenatal infection: implications for schizophrenia. PLoS One.7(1):e29754.
• Lowe GC, Goutagny R, Ducharme G, Jackson J, Williams S (2012). Early network alterations in the subiculum of offspring following gestational maternal immune activation. Schizophr Res. 134(2-3):300-1. 
• Jackson J, Goutagny R, Williams S (2011). Fast and slow γ rhythms are intrinsically and independently generated in the subiculum. J Neurosci. 2011 Aug 24;31(34):12104-17. 
• Huh CY, Goutagny R, Williams S (2010). Glutamatergic neurons of the mouse medial septum and diagonal band of Broca synaptically drive hippocampal pyramidal cells: relevance for hippocampal theta rhythm. J Neurosci. 2010 Nov 24;30(47):15951-61.
• Léger L, Sapin E, Goutagny R, Peyron C, Salvert D, Fort P, Luppi PH (2010). Dopaminergic neurons expressing Fos during waking and paradoxical sleep in the rat. J Chem Neuroanat. 2010 Jul;39(4):262-71.
• Goutagny R*, Jackson J*, Williams S (2009). Self-generated theta oscillations in the hippocampus. Nat Neurosci. 2009 Dec;12(12):1491-3. *: Equal contributors
• Sapin E, Lapray D, Bérod A, Goutagny R, Léger L, Ravassard P, Clément O, Hanriot L, Fort P, Luppi PH (2009). Localization of the brainstem GABAergic neurons controlling paradoxical (REM) sleep. PLoS One. 2009;4(1):e4272.
• Léger L, Goutagny R, Sapin E, Salvert D, Fort P, Luppi PH (2009). Noradrenergic neurons expressing Fos during waking and paradoxical sleep deprivation in the rat. J Chem Neuroanat. 2009 May;37(3):149-57. 
• Manseau F, Goutagny R, Danik M, Williams S (2008). The hippocamposeptal pathway generates rhythmic firing of GABAergic neurons in the medial septum and diagonal bands: an investigation using a complete septohippocampal preparation in vitro. J Neurosci. 2008 Apr 9;28(15):4096-107.
• Adamantidis A, Salvert D, Goutagny R, Lakaye B, Gervasoni D, Grisar T, Luppi PH, Fort P (2008). Sleep architecture of the melanin-concentrating hormone receptor 1-knockout mice. Eur J Neurosci. 2008 Apr;27(7):1793-800.
• Goutagny R, Luppi PH, Salvert D, Lapray D, Gervasoni D, Fort P (2008). Role of the dorsal paragigantocellular reticular nucleus in paradoxical (rapid eye movement) sleep generation: a combined electrophysiological and anatomical study in the rat. Neuroscience. 2008 Mar 27;152(3):849-57.
• Goutagny R, Manseau F, Jackson J, Danik M, Williams S (2008). In vitro activation of the medial septum-diagonal band complex generates atropine-sensitive and atropine-resistant hippocampal theta rhythm: an investigation using a complete septohippocampal preparation. Hippocampus. 2008;18(6):531-5.
• Goutagny R, Comte JC, Salvert D, Gomeza J, Yamada M, Wess J, Luppi PH, Fort P (2005). Paradoxical sleep in mice lacking M3 and M2/M4 muscarinic receptors. Neuropsychobiology. 2005;52(3):140-6. 
• Goutagny R, Luppi PH, Salvert D, Gervasoni D, Fort P (2005). GABAergic control of hypothalamic melanin-concentrating hormone-containing neurons across the sleep-waking cycle. Neuroreport. 2005 Jul 13;16(10):1069-73. 
• Verret L*, Goutagny R*, Fort P, Cagnon L, Salvert D, Léger L, Boissard R, Salin P, Peyron C, Luppi PH (2003). A role of melanin-concentrating hormone producing neurons in the central regulation of paradoxical sleep. BMC Neurosci. 2003 Sep 9;4:19. *: Equal contributors

Other peer-reviewed publications (reviews, method articles, proceedings)

• Aguilera M, Douchamps V, Battaglia D, Goutagny R. (2022). How Many Gammas? Redefining Hippocampal Theta-Gamma Dynamic During Spatial Learning. Front Behav Neurosci. 16:811278.
• Hamm V, Héraud C, Cassel JC, Mathis C, Goutagny R (2015). Precocious Alterations of Brain Oscillatory Activity in Alzheimer’s Disease: A Window of Opportunity for Early Diagnosis and Treatment. Front Cell Neurosci.9:491.
• Goutagny R, Krantic S (2013). Hippocampal oscillatory activity in Alzheimer’s disease: toward the identification of early biomarkers? Aging Dis. 4(3):134-40.
• Luppi PH, Gervasoni D, Verret L, Goutagny R, Peyron C, Salvert D, Leger L, Fort P (2006). Paradoxical (REM) sleep genesis: the switch from an aminergic-cholinergic to a GABAergic-glutamatergic hypothesis. J Physiol Paris. 2006 Nov-Dec;100(5-6):271-83.
• Goutagny R, Verret L, Fort P, Salvert D, Léger L, Luppi PH, Peyron C (2004). Posterior hypothalamus and regulation of vigilance states. Arch Ital Biol. 2004 Jul;142(4):487-500.
• Luppi PH, Gervasoni D, Boissard R, Verret L, Goutagny R, Peyron C, Salvert D, Leger L, Barbagli B, Fort P (2004). Brainstem structures responsible for paradoxical sleep onset and maintenance. Arch Ital Biol. 2004 Jul;142(4):397-411.

Invited book chapters

• Amilhon B, Ducharme G, Jackson J, Goutagny R, Willimas S. Theta Rhythm in Hippocampus and Cognition. In Neuronal Oscillations of Wakefulness and Sleep: Windows on Spontaneous Activity of the Brain. 1st ed. 2020. edited by Dang-Vu T and Courtemanche R for Springer Books. ISBN: 978-1-0716-0653;
• Goutagny R, Jackson J, Manseau F and Williams S (2011). An intact septo-hippocampal preparation for investigating the mechanisms of hippocampal oscillation. In Electrophysiological Recording Techniques edited by Vertes RP and Stackman RW for Humana Press.
• Luppi PH, Gervasoni D, Verret L, Goutagny R, Peyron C, Salvert D, Leger L and Fort P (2007). Gamma-aminobutyric acid and the regulation of paradoxical, or rapid eye movement sleep. In Neurochemistry of Sleep and Wakefulness edited by Monti J, Pandi-Perumal SR. and Sinton CM for Cambridge University Press.
• Luppi PH, Boissard R, Gervasoni D, Verret L, Goutagny R, Peyron C, Salvert D, Leger L, Barbagli B and Fort P (2004). The Network Responsible for Paradoxical Sleep Onset and Maintenance: A New Theory Based on the Head-restrained Rat Model. In: Sleep: Circuits and Function edited by Luppi PH for CRC Press.

Demian Battaglia’s publication list

(click here for publications by Romain Goutagny)

Original research articles

• Pedreschi, N., Battaglia, D., Barrat, A. (2022) The temporal rich club phenomenon. Nature Physics, doi:10.1038/s41567-022-01634-8.

• Spaeth, L., Bahuguna, J., Gagneux, T., Dorgans, K., Sugihara, I., Poulain, B., Battaglia, D.*, Isope, P.* (2022). Cerebellar connectivity maps embody individual adaptive behavior. Nature Communications 13, 580 _{[*shared last authorship]}.

• Durieux, L., Herbeaux, K., Borcuk, C., […] Battaglia, D., Majchrzak, M., Lecourtier, L. (2022). Functional brain-wide network mapping during acute stress exposure in rats: Interaction between the lateral habenula and cortical, amygdalar, hypothalamic and monoaminergic regions. Eur J Neurosci 56(8):5154-5176. doi: 10.1111/ejn.15803. Epub 2022 Sep 22. PMID: 35993349.

• Borcuk, C., Héraud, C., Herbeaux, K., […] Goutagny, R., Battaglia, D., Mathis, C. (2022). Early memory deficits and extensive brain network disorganization in the AppNL-F/MAPT double knock-in mouse model of familial Alzheimer’s disease. Aging Brain 2: 100042. doi:10.1016/j.nbas.2022.100042

• Schiepek, G., Viol, K., […] Battaglia, D.*, Jirsa, V.* (2021). Pathologically reduced neural flexibility recovers during psychotherapy of OCD patients. Neuroimage Clin 32, 102844. _{[* Shared last authorship]}.

• Arbabyazd, D.M., Shen, K., Wang, Z., Hofman-Apitius, M., Mcintosh, A.R., Battaglia, D.*, Jirsa, V.*, (2021). Completion and augmentation of connectomic datasets in dementia and Alzheimer’s Disease using Virtual Patient Cohorts. eNeuro, 0475, 1-33 _{[* Shared last authorship]}.

• Battaglia, D., Boudou, T., Hansen, E.C.A., Lombardo, D., Chettouf, S., Daffertshofer, A., Mcintosh, A.R., Zimmermann, J., Ritter, P., Jirsa, V. (2020). Dynamic Functional Connectivity between order and randomness and its evolution across the human adult lifespan. Neuroimage 222, 117156.

• Lombardo, D., Cassé-Perrot, C., Ranjeva, J.-P., Le Troter, A., Guye, M., Wirsich, J., Payoux, P., Bartrés-Faz, D., Bordet, R., Richardson, J.C., Félician, O., Jirsa, V., Blin, O., Didic, M.* Battaglia, D.* (2020). Modular slowing of resting-state dynamic Functional Connectivity as a marker of cognitive dysfunction induced by sleep deprivation. NeuroImage 222, 117155. _{[* Shared last authorship]}.

• L. Papadopoulos, C.W. Lynn, D. Battaglia*, D.S. Bassett* (2020). Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state. PLoS Comput Biol 16, e1008144. _{[* Shared last authorship].}

• S. Castro, W. El-Deredy, D. Battaglia*, P. Orio* (2020). Cortical ignition dynamics is tightly linked to the core organisation of the human connectome. PLoS Comput Bio 16, e1007686 _{[* Shared last authorship].}

• N. Pedreschi, C. Bernard, W. Clawson, P. Quilichini, A. Barrat*, D. Battaglia* (2020). Dynamic core periphery structure of information sharing networks in entorhinal cortex and hippocampus. Network Neurosci 4, 946–975. _{[* Shared last authorship]}.

• N. Deschle, A. Daffertshofer, D. Battaglia & E. A. Martens (2019) Directed flow of information in chimera states. Frontiers in Applied Mathematics and Statistics 5, 28.

• W. Clawson, A.F. Vicente, M. Ferraris, C. Bernard, D. Battaglia* & P. Quilichini* (2019) Computing hubs in the hippocampus and cortex. Science Advances5, eaa4843. _{[* Shared last authorship]}.

• A. Palmigiano, T. Geisel, F. Wolf & D. Battaglia (2017) Flexible information routing by transient synchrony, Nature Neuroscience 20, 1014–1022.

• M. Helmer, M. Schottdorf, A. Neef, D. & D. Battaglia. Gender bias in scholarly peer review. eLife 6, e21718 (2017).

• M. Helmer, V. Kozyrev, V. Stephan, S. Treue, T. Geisel & D. Battaglia. Model-Free Estimation of Tuning Curves and Their Attentional Modulation, Based on Sparse and Noisy Data. PLoS ONE 11, e0146500 (2016).

• C. Kirst, M. Timme & D. Battaglia. Dynamic information routing in complex networks. Nat Comms 7, 11061 (2016).

• P. Wadewitz, K. Hammerschmidt, D. Battaglia, A. Witt, F. Wolf & J. Fischer. Characterizing Vocal Repertoires-Hard vs. Soft Classification Approaches. PLoS ONE 10, e0125785 (2015).

• E.C.A. Hansen*, D. Battaglia*, A. Spiegler, G. Deco & V.K. Jirsa. Functional connectivity dynamics: modeling the switching behavior of the resting state. NeuroImage 105, 525–535 (2015). _{[ *Shared first authorship].}

• J. Orlandi, O. Stetter, J. Soriano, T. Geisel and D. Battaglia, Transfer entropy reconstruction and labeling of neuronal connections from simulated calcium imaging, PLoS ONE 9:e98842 (2014).

• A. Witt, A. Palmigiano, A. Neef, A. El Hady, F. Wolf and D. Battaglia, Controlling the oscillation phase through precisely timed closed-loop optogenetic stimulation: a computational study, Frontiers in Neural Circuits 7:49 (2013).

• D. Battaglia, A. Karagiannis, T. Gallopin, H.W. Gutch and B. Cauli, Beyond the frontiers of neuronal types, Frontiers in Neural Circuits 7:13 (2013).

• O. Stetter, D. Battaglia, J. Soriano and T. Geisel, Model-free reconstruction of excitatory neuronal connectivity from calcium imaging signals, PLoS Computational Biology 8(8):e1002653 (2012).

• D. Battaglia, A. Witt, F. Wolf and T. Geisel, Dynamic effective connectivity of inter-areal brain circuits, PLoS Computational Biology 8(3):e1002438 (2012).

• D. Battaglia and D. Hansel, Synchronous chaos and broad band gamma rhythm in a minimal multi-layer model of striate cortex, PLoS Computational Biology 7(10):e1002176 (2011).

• A. Karagiannis*, T. Gallopin*, C. Dávid*, D. Battaglia*, H. Geoffroy, J. Rossier, E. Hillman, J. Staiger and B. Cauli, Classification of NPY-expressing cortical interneurons, Journal of Neuroscience 29(11):3642 (2009). _{[ *Shared first authorship].}

• D. Battaglia, N. Brunel and D. Hansel, Temporal decorrelation of collective oscillations in neural networks with local inhibition and long-range excitation, Physical Review Letters 99(23), 238106 (2007).

• D. Battaglia, A. Braunstein, J. Chavas and R. Zecchina, Source coding by efficient selection of ground state clusters, Physical Review E 72, 015103 (2005).

• D. Battaglia, G. Santoro and E. Tosatti, Optimization by quantum annealing: lessons from hard satisfiability problems, Physical Review E 71, 066707 (2005).

• D. Battaglia, M. Kolár and R. Zecchina, Minimizing energy below the glass thresholds, Physical Review E 70, 036107 (2004).

• D. Battaglia and M. Rasetti, Quantum-like diffusion over discrete sets, Physics Letters A 313, 8–15 (2003).

Other peer-reviewed publications (reviews, method articles, proceedings)

• M. Aguilera, V. Douchamps, D. Battaglia, R. Goutagny (2022). How Many Gammas? Redefining Hippocampal Theta-Gamma Dynamic During Spatial Learning. Frontiers in Behavioral Neuroscience 16, doi: 10.3389/fnbeh.2022.811278.

• V. Voutsa, D. Battaglia, L. J. Bracken, A. Brovelli, J. Costescu, M. D. Muñoz, B. D. Fath, A. Funk, M. Guirro, T. Hein, C. Kerschner, C. Kimmich, V. Lima, A. Messé, A. J. Parsons, J. Perez, R. Pöppl, C. Prell, S. Recinos, Y. Shi, S. Tiwari, L. Turnbull, J. Wainwright, H. Waxenecker, M.-T. Hütt (2021). Two classes of functional connectivity in dynamical processes in networks. J R Soc Interface 18(183), 20210486.

• L.M. Arbabyazd, D. Lombardo, O. Blin, M. Didic, D. Battaglia*, V. Jirsa* (2020). Dynamic Functional Connectivity as a complex random walk: Definitions and the dFCwalk toolbox. MethodsX 7, 101168. _{[* Shared last authorship].}

• J. Orlandi, B. Ray, D. Battaglia, I. Guyon, V. Lemaire, M. Saeed, A. Statnikov, O. Stetter & J. Soriano. First Connectomics Challenge: From Imaging to Connectivity. The Journal of Machine Learning Research: W &CP 46, 1–22 (2015). Reissued in Battaglia D. et al. (eds), Neural Connectomics Challenge. Springer (2017).
  

• I. Guyon, D. Battaglia, A. Guyon, V. Lemaire, J. Orlandi, B. Ray, M. Saeed, J. Soriano, A. Statnikov, O Stetter, Design of the first neuronal connectomics challenge: From imaging to connectivity, proceedings of the IEEE IJCNN conference (IEEE WCCI-IJCNN 2014, Beijing), pp. 2600–2607 (2014).
  

• O. Stetter, J. Soriano, T. Geisel & D. Battaglia. From structure to function, via dynamics, proceedings of the 12th Granada Seminar on Computational and Statistical Physics (La Herradura, Spain) – “Physics, Computation and the Mind”, edited by P.L. Garrido, J. Marro, J. Torres et al. Book Series: AIP Conference Proceedings, vol. 1510, pp. 64-73 (2013).
  

• D. Battaglia, Neuron-less neural-like networks with exponential association capacity at tabula rasa, proceedings of the workshop “Third International Work-Conference on the Interplay Between Natural and Artificial Computation” (IWINAC 2009, Santiago de Compostela), edited by J. Mira and J.R. Álvarez, Lecture Notes in Computer Science, Volume 5601/2009, pp. 184-194, Springer (2009).
  

• D. Battaglia and L. Stella, Optimisation through Quantum Annealing: Theory and some application, Contemporary Physics, Vol. 47, No. 4. (8220), 195-208 (2006).

• D. Battaglia, M. Kolár and R. Zecchina, From Statistical Physics Methods to Algorithms, International Journal of Modern Physics B, Vol. 20 (19), 2814-2823 (2006).

• J. Chavas, D. Battaglia, A. Cicutin et R. Zecchina, Construction and VHDL implementation of a fully local network with good reconstruction properties of the inputs, proceedings of the workshop “First International Work-Conference on the Interplay Between Natural and Artificial Computation” (IWINAC 2005, Las Palmas), edited by J. Mira and J.R. Álvarez, Lecture Notes in Computer Science, vol. 3562, pp. 385-394, Springer (2005).

• D. Battaglia, A. Braunstein, J. Chavas et R. Zecchina, Exact probing of glassy states by Survey Propagation, proceedings of the workshop “Statistical physics of disordered systems and its applications” (SPDSA, Hayama 2004), edited by K. Hukushima, K. Tanaka and H. Nishimori, Prog. Theor. Phys. Suppl. 157, 330-337 (2005).

Invited book chapters

• Battaglia D* and Brovelli A*,. Functional connectivity and neuronal dynamics: insights from computational methods, chapter in the book “The Cognitive Neurosciences” (6^th edition), edited by D. Poeppel, G.R. Mangun, M.S. Gazzaniga, MIT Press, chapter 62, p. 739 (2020) [* equal contributions].

• D. Battaglia, Information follows dynamics, chapter in the book “Directed Information Measures in Neuroscience”, edited by R. Vicente, M. Wibral and J. Lizier, pp. 111-136, Springer-Verlag (2014).

• D. Battaglia, G. Santoro, L. Stella, E. Tosatti and O. Zagordi, Deterministic and stochastic quantum annealing approaches, chapter in the book “Quantum Annealing and related optimization methods”, edited by B. Chakrabarti and A. Das, pp. 171-206, Springer-Verlag (2005).

Research monographs and books

• D. Battaglia, I. Guyon, V. Lemaire, J. Orlandi, B. Ray & J. Soriano (eds.), Neural Connectomics Challenge. The Springer series in Challenges in Machine learning. Springer (2017).  ISBN 978-3-319-53070-3.