- Sebia, H., Guyet, T., Pereira, M., Valdebenito, M., Berry, H. and Vidal, B., October (2024). Vascular Segmentation of Functional Ultrasound Images using Deep Learning, submitted, hal-04744271.
- Piette, C., Hubert, A., Perez, S., Berry, H., Touboul, J. and Venance, L., (2024). Striatal endocannabinoid-long-term potentiation mediates one- shot learning, submitted, bioRxiv.
- Sadoune, S., Richard, A., Talbot, F., Guyet, T., Boussel, L. and Berry, H. Automatic analysis of negation cues and scopes for medical texts in french using language models, submitted, hal-04564718.
- Quiblier, N., Rye, J.-M., Leclerc, P., Truong, H., Hannou, A., Heliot, L. and Berry, H., (2024). Enhancing Fluorescence Correlation Spectroscopy with Machine Learning for Advanced Analysis of Anomalous Diffusion, submitted, hal-04650578.
2024
2023
- Mouttou, A., Bremaud, E., Noero, J., Dibsy, R., Arone, C., Mak, J., Muriaux, D., Berry, H. and Favard, C., (2023). Quantification of membrane binding and diffusion using fluorescence correlation spectroscopy diffusion laws, Biophysical Journal, 122(11):2216-229. here also.
- Berry, H. (2023). Les utilisations de l'IA pour l'hopital et la sante publique : donnees necessaires, applications et obstacles potentiels. In Paul, C. and Le Metayer, D., eds., Maitriser leIA au service de leaction publique: Une responsabilite individuelle et collective, Collection : Au fil du debat, chapter 5, pages 83-94. Berger-Levrault. (in french)
2022
- Dembitskaya, Y., Perez, S., Piette, C., Berry, H., Magistretti, P. J. and Venance, L (2022). Lactate supply overtakes glucose when neural computational and cognitive loads scale up, Proceedings of the Academy of Sciences U.S.A., 119(47):e2212004119.
- Denizot, A., Arizono, M., Nägerl, U. V., Berry, H. and De Schutter, E. (2022). Astrocyte nanoscale morphology controls Ca2+ signals at tripartite synapses, Glia, 70:2378-2391. https://onlinelibrary.wiley.com/doi/abs/10.1002/glia.24258. preprint here.
- Blume Moyse, L. and Berry, H., (2022). Modelling the modulation of cortical up-down state switching by astrocytes, PLoS Computational Biology, 18(7):e1010296. Article + Supporting information available as a single file here.
- Berry, H. and Watier, L., March (2022). Pandemie de Covid-19. L’aide de l’IA et du numerique. In Nordlinger, B., Vilani, C. and de Fresnoye, O., eds., Medecine et intelligence artificielle. CNRS.
2021
- Denizot, A., Cali, C., Berry, H. and De Schutter, E., (2021) Stochastic Spatially-Extended Simulations Predict the Effect of ER Distribution on Astrocytic Microdomain Ca2+ Activity. In NANOCOM 2021: Eighth Annual ACM International Conference on Nanoscale Computing and Communication, pages 1-5. ACM, New York, NY, United States. https://hal.archives-ouvertes.fr/hal-03590777.
- Berry, H. and Genet, S. (2021) A model of On/Off transitions in neurons of the deep cerebellar nuclei: Deciphering the underlying ionic mechanisms. Journal of Mathematical Neuroscience, 11:1. https://hal.sorbonne-universite.fr/hal-03190183.
-
Badoual, A., Arizono, M., Denizot, A., Ducros, M., Berry, H., Valentin Nägerl, U. and Kervrann, C., (2021). Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images. In IEEE International Symposium on Biomedical Imaging. Nice, France. https://hal.inria.fr/hal-03106797.
2020
-
Kusters, R., Misevic, D., Berry, H., Cully, A., Le Cunff, Y., Dandoy, L., Diaz-Rodriguez, N., Ficher, M., Grizou, J., Othmani, A., Palpanas, T., Komorowski, M., Loiseau, P., Moulin Frier, C., Nanini, S., Quercia, D., Sebag, M., Soulie Fogelman, F., Taleb, S., Tupikina, L., Sahu, V., Vie, J.- J. and Wehbi, F. (2020) Interdisciplinary research in artificial intelligence: Challenges and opportunities. Frontiers in Big Data, 3:45. www.frontiersin.org/article/10.3389/fdata.2020.577974.
- Woringer M., Izeddin I., Favard C. and Berry H. (2020) Anomalous diffusion in living cells: bridging the gap between experiments and models through collaborative challenges, Frontiers in Physics, 8:134. doi: 10.3389/fphy.2020.00134
- Lenk K., Satuvuori E., Lallouette J., Ladron-de-Guevara A., Berry H. and Hyttinen J.A.K. (2020) A Computational Model of Interactions Between Neuronal and Astrocytic Networks: The Role of Astrocytes in the Stability of the Neuronal Firing Rate, Frontiers in Computational Neuroscience, 13:92. doi: 10.3389/fncom.2019.00092
- Denizot A., Berry H. and Venugopal, S. (2020) Intracellular Calcium Signals in Astrocytes, Computational Modeling of , In Jaeger D. and Jung R., eds., Encyclopedia of Computational Neuroscience, https://hal.inria.fr/hal-02419317v1, Springer, New York, NY
- Gangarossa, G., Perez, S., Dembitskaya, Y., Prokin, I., Berry, H. and Venance, L., (2020). BDNF controls bidirectional endocannabinoid-plasticity at corticostriatal synapses. Cerebral Cortex, 1(30):197-217. doi.org/10.1093/cercor/bhz081.
2019
- Caranta, C., Monod, H., Berry, H., Chelle, M., Génard, M., Jourdan, F., Lannou, C., Maguin, E., Medale, F., Oddou-Muratorio, S., Rogel Gaillard, C., Traas, J. (2019). Réflexion prospective interdisciplinaire. Approches prédictives pour la biologie et l'écologie. Rapport de synthèse (in French). 40 pp., DOI : 10.15454/1.5783037069682676e12, https://prodinra.inra.fr/record/491139
- Denizot, A., Arizono, M., Nagerl, V. U., Soula, H. and Berry, H.,
(2019). Simulation of calcium
signaling in fine astrocytic processes: effect of spatial properties
on spontaneous activity. PLoS Computational
Biology, 15(8):e1006795. doi.org/10.1371/journal.pcbi.1006795.
- Abou, B. and Berry, H., eds., (2019). Sexe et Genre: de la Biologie
a la Sociologie. Editions Materiologiques, Paris.
https://materiologiques.com/sciences-philosophie-2275-9948/282-sexe-et-genre-de-la-biologie-a-la-sociologie.html
- De Pitta, M. and Berry, H., eds., (2019). Computational Glioscience.
Springer Series in Computational Neuroscience. Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8
- De Pitta, M. and Berry, H., (2019). A neuron-glial perspective for
computational neuroscience. In De Pitta, M. and Berry, H., eds., Computational
Glioscience, pages 3-35. Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8.
Preprint available at: hal-01995849v1
- De Pitta, M., Ben-Jacob, E. and Berry, H., (2019). G protein-coupled
receptor-mediated calcium signaling in astrocytes. In De Pitta, M. and
Berry, H., eds., Computational Glioscience, pages 115-150.
Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8.
Preprint available at: hal-01995850v1
- Lallouette, J., De Pitta, M. and Berry, H., (2019). Astrocyte
networks and intercellular calcium propagation. In De Pitta, M. and
Berry, H., eds., Computational Glioscience, pages 177-210.
Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8.
Preprint available at: hal-01995852v1
2018
- Xu, H., Perez, S., Cornil, A., Detraux, B., Prokin, I., Cui, Y.,
Degos, B., Berry, H., De Kerchove D'Exaerde, A. and Venance, L., (2018).
Dopamine- endocannabinoid
interactions mediate spike-timing dependent potentiation in the
striatum. Nature Communications 9:4118. doi:
10.1038/s41467-018-06409-5.
- Foncelle, A., Mendes, A., Jdrzejewska-Szmek, J., Valtcheva, S.,
Berry, H., Blackwell, K. T. and Venance, L., (2018). Modulation
of spike-timing dependent plasticity: towards the inclusion of a third
factor in computational models. Frontiers in Computational
Neuroscience, 12:49. doi:
10.3389/fncom.2018.00049
- Cui Y, Prokin I, Mendes A, Berry H, Venance L. (2018). Robustness
of STDP to spike timing jitter. Scientific Reports, 8:8139.
Supplementary Information available here.
- Yi C, Theillon J, Koulakoff A, Berry H, Giaume C. (2018). Monitoring
gap junctional communication in astrocytes from acute adult mouse
brain slices using the gap-frap technique. J. Neuroscience
Methods 303:103-113 hal-01734652.
- Cui Y, Yang Y, Ni Z, Dong Y, Cai G, Foncelle A, Ma S, Sang K, Tang S,
Li Y, Shen Y, Berry H, Wu S and Hu H (2018). Astroglial-
Kir4.1 in lateral habenula drives neuronal bursts in depression. Nature
554:323-327 (doi:10.1038/nature25752).
--> This article was commented in the ``News and
views'' section of the journal: Howe WM & Kenny PJ (2018). Burst
firing sets the stage for depression. Nature 554:304-305.
- Oschmann, F., Berry, H., Obermayer, K. and Lenk, K., (2018). From
in silico astrocyte cell models to neuron-astrocyte network models: A
review. Brain Research Bulletin, 136:76-84. hal-01461928.
2016
- Cui, Y., Prokin, I., Xu, H., Delord, B., Genet, S., Venance, L. and
Berry, H., (2016). Endocannabinoid
dynamics gate spike-timing dependent depression and potentiation.
eLife, 5:e13185. doi:
10.7554/eLife.13185.
- Berry, H. , Lepoutre, T. and Mateos Gonzalez, A. (2016). Quantitative
convergence towards a self similar profile in an age-structured
renewal equation for subdiffusion. Acta Applicandae
Mathematicae,145:15-45, doi:10.1007/s10440-016-0048-3. arXiv:1503.08552
2015
- Chaker, Z., Aïd, S., Berry, H. and Holzenberger, M. (2015). Suppression
of IGF-I signals in neural stem cells enhances neurogenesis and
olfactory function during aging . Aging Cell,
14(5):847-856, doi: 10.1111/acel.12365
- Cui Y., Paille V., Xu H., Genet S., Delord B., Fino E., Berry H. and
Venance L. (2015). Endocannabinoids
mediate bidirectional striatal spike-timing dependent plasticity.
J Physiology (London), 593(13), 2833-2849, doi:10.1113/JP270324
- Caré, B., LoVan, A., Berry, H. and Soula, H. (2015). Signalisation
sous contraintes spatiales. Consquences sur les conditions de stabilité
et de bifurcation. s. in Glade, N. and Stephanou, A. (Eds), Le
vivant critique et chaotique, chapter 6, pages 199-222. Editions
Matériologiques, Paris.
2014
- Wallach, G., Lallouette, J., Herzog, N., De Pittà, M., Ben
Jacob, E., Berry, H. and Hanein, Y. (2014). Glutamate
mediated astrocytic filtering of neuronal activity. PLoS
Computational Biology, 10(12), e1003964.
Supplementary Material availble here
- Lo Van A., Soula H. and Berry H. (2014). Space-induced
bifurcation in repression-based transcriptional circuits BMC
Systems Biology ,8:125.
- Berry, H. & Soula, H. A. (2014)
Spatial distributions at equilibrium under heterogeneous transient
subdiffusion Frontiers in Physiology, 5:437.
- Soula H., Caré B., Beslon G. and Berry H. (2014). Comments
to
the Editor. Reply to the Comment by V.P. Shkilev on ``Anomalous versus
slowed-down Brownian diffusion in the ligand-binding equilibrium''.
Biophysical Journal,106(11):2544-2546.
- Lallouette, J., De Pittà, M., Ben-Jacob, E. and Berry, H., (2014). Sparse
short-distance connections enhance calcium wave propagation in a 3D
model of astrocyte networks. Frontiers Computational
Neuroscience, 8:45.
- Berry H., and Chaté H. (2014). Anomalous
diffusion due to hindering by mobile obstacles undergoing Brownian
motion or Orstein-Ulhenbeck processes. Physical Review E,
89(2):022708.
2013
- Soula H., Caré B., Beslon G. and Berry H. (2013). Anomalous
versus slowed-down brownian diffusion in the ligand-binding
equilibrium. Biophysical Journal, 105:2064-2073.
- Naudé J., Cessac B., Berry H. & Delord B. (2013). Effects
of Cellular Homeostatic Intrinsic Plasticity on Dynamical and
Computational Properties of Biological Recurrent Neural Networks.
Journal of Neuroscience, 33(38):15032-15043
- Cui Y., Paille V., Delord B., Genet S., Fino E., Venance L. and
Berry, H. (2013). Endocannabinoids
mediate spike-timing dependent potentiation and depression: a
model-based experimental approach. 22nd Annual Computational
Neuroscience Meeting (CNS 2013), Paris, France (BMC
Neuroscience, 14(Suppl 1):O1).
- Coquel,A., Jacob,J., Primet,M., Demarez,A., Dimiccoli,M., Julou,T.,
Moisan,L., Lindner,A. and Berry, H. (2013). Localization
of protein aggregation in escherichia coli is governed by diffusion
and nucleoid macromolecular crowding effect. PLoS
Computational Biology. 9:e1003038.
- Lallouette, J. and Berry, H. (2013).
Topology drives calcium wave propagation in 3d astrocyte networks.
In Proceedings of the European Conference on Complex Systems 2012,
Gilbert, T., Kirkilionis, M. and Nicolis, G., eds. , Springer
Proceedings in Complexity, pages 453-463.
- Berry, H. (2013). Modélisation de la diffusion-réaction dans les
milieux intracellulaires encombrés. in Glade, N. and Stephanou,
A. (Eds), Le vivant discret et continu, chapter 9, pages
241-266. Editions Matériologiques, Paris.
- Berry, H. and Beslon, G. (2013). De la modélisation comme poésie. La
modélisation de systèmes biologiques complexes vue par deux
modélisateurs. in Varenne, F. and Silberstein, M. (Eds), Modéliser
& simuler. Epistémologies et pratiques de la modélisation et de la
simulation, volume 1, chapter 11. Editions Matériologiques, Paris.
2012
- De Pittà, M., Volman, V., Berry, H., Parpura V, Volterra, A. and
Ben-Jacob, E. (2012).
Computational quest for understanding the role of astrocyte signaling
in synaptic transmission and plasticity. Frontiers in
Computational Neuroscience, 6:98.
- Vlassopoulos, N., Fatès, N., Berry, H. and Girau, B., (2012).
Large-scale Simulations on FPGAs: Finding the Asymptotic Critical
Threshold of the Greenberg-Hastings Cellular Automata. Journal of
Cellular Automata, 7(1):5-29.
- Naudé, J., Paz, J., Berry, H. and Delord, B., (2012)
A theory of rate coding control by intrinsic plasticity effects. PLoS
Computational Biology, 8:e1002349.
- De Pittà, M., Volman, V., Berry, H., Liaudet, N., Volterra, A. and
Ben-Jacob, E., (2012). A compartmental approach to modeling of calcium
events in astrocyte processes. (Abstract). In Society for
Neuroscience Annual Meeting , New Orleans, LA. Program No.
541.07. 2012 Neuroscience Meeting Planner. Online.
2011
- De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E. (2011)
A tale of two stories: astrocyte regulation of synaptic depression and
facilitation. PLoS Computational Biology, 7: e1002293.
Supplementary Materials availble here
This article has been selected for the Faculty
of 1000 Cell Biology. Read the review here.
- Hashmi, A., Berry, H., Temam, O. and Lipasti, M., June (2011). Automatic
abstraction and fault tolerance in cortical microachitectures. In
38th ACM/IEEE International Symposium on Computer Architecture, ISCA
2011. San Jose, CA, USA.
- Venance, L., Cui, Y., Paille, V., Delord, B., Genet, S. and Berry,
H., (2011). Sub-second induction unveils a switch from nmda- to
endocannabinoid ltp. (Abstract). In Society for Neuroscience Annual
Meeting , Washington, DC. Program No. 348.04. 2011 Neuroscience
Meeting Planner. Online.
- De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E., (2011).
Astrocyte regulation of long-term synaptic plasticity. (Abstract). In Society
for Neuroscience Annual Meeting , Washington, DC. Program No.
663.20. 2011 Neuroscience Meeting Planner. Online.
- Berry, A., De Pittà, M., Volman, V. and Ben-Jacob, E., (2011).
Astrocyte regulation of presynaptic plasticity. (Abstract). In
Society for Neuroscience Annual Meeting , Washington, DC. Program
No. 663.10. 2011 Neuroscience Meeting Planner. Online.
- Berry, H. and Fates, N. (2011)
Robustness of the critical behavior in the stochastic
Greenberg-Hastings cellular automaton model. Int. J.
Unconventional Computing, 7:65-85.
2010
- Goldberg, M., De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2010) Nonlinear
gap-junctions enable long-distance propagation of pulsating calcium
waves in astrocyte networks. PLoS Computational Biology,
6: e1000909.
Supplementary Materials availble here
- Genet, S., Sabarly, L., Guigon, E., Berry, H. and Delord, B. (2010)
Dendritic signals command firing dynamics in a mathematical model of
cerebellar Purkinje cells. Biophysical Journal, 99:
427-436.
Supplementary Materials availble here
- Goldberg, M., De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2010). On the determinants of calcium wave propagation distance in
astrocyte networks: nonlinear gap junctions and oscillatory modes.
(Abstract). In 40th annual meeting of the Society for Neuroscience.
Society for Neuroscience, San Diego, CA. Program No. 552.22. 2010
Neuroscience Meeting Planner. Online.
- Auras, D., Girbal, S., Berry, H., Temam, O. and Yehia, S., Oct.
(2010). Memory Interface for Multi-Purpose Multi-Stream Accelerators. In
International Conference on Compilers, Architectures and Synthesis
for Embedded Systems, CASES 2010, Scottsdale, AZ, USA.
- Auras, D., Girbal, S., Berry, H., Temam, O. and Yehia, S., June
(2010). CMA: Chip
multi-accelerator. In 8th IEEE Symposium on Application
Specific Processors, SASP 2010. Anaheim, CA, USA.
- Vlassopoulos, N., Fates, N., Berry, H. and Girau, B., June (2010). An
FPGA design for the stochastic greenberg-hastings cellular automata.
In W. Smari editor, The 2010 International Conference on High
Performance Computing and Simulation, HPCS 2010 Caen, France,
pages 565-574, IEEE.
- Girbal, S., Yehia, S., Berry, H., and Temam, O. January (2010). Stream
and Memory Hierarchy Design for Multi-Purpose Accelerators. In 1st
Workshop on SoC Architecture, Accelerators and Workloads (SAW-1).
Bangalore, India
- Fates, N.A. and Berry, H. (2010) Critical
phenomena in a discrete stochastic reaction-diffusion medium. In
Peper, F., ed., Fourth International Workshop on Natural Computing,
IWNC 2009, Himeji, Japan, Sep. 23-25, 2009. Proceedings in
Information and Communications Technology, 2:141-148.
2009
- Hashmi, A., Berry, H., Temam, O. and Lipasti, M., December (2009). Leveraging
progress in neurobiology for computing systems. In 1st
Workshop on New Directions in Computer Architecture (NDCA-1).
New-York, New-York, USA.
- Berry, H. et Cessac, B. (2009) Du
chaos dans les neurones Pour La Science, November 2009,
385:108-115 (in French). Also available as an )i(nterstices
web article.
- De Pittà, M., Goldberg, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2009) Glutamate regulation of
calcium and IP3 oscillating and pulsating dynamics in astrocytes.
Journal of Biological Physics, 35: 383-411.
This article has been selected for the Faculty
of 1000 Biology. Read the review here.
- F. Jiang, H. Berry and M. Schoenauer. (2009) The
impact of network topology on self-organizing maps. In Proc
First ACM/SIGEVO Summit on Genetic and Evolutionary Computation,
GEC-2009, Shanghai, China, June 12 -14, 2009, pp 247-254.
- Yehia, S., Girbal, S., Berry, H. and Temam, O. (2009) Reconciling
Specialization
and Flexibility Through Compound Circuits. In 15th
International Symposium on High-Performance Computer Architecture,
HPCA, Raleigh, North Carolina, US, Feb. 14-18, 2009.
2008
- Berry,H. (2008) Nonequilibrium
phase
transition in scattered cell communities coupled by
auto/paracrine-like signalling in Pollack, G. and Chin,
W.-C. (Eds), Phase transitions in Cell Biology, Springer,
pp.23-41. preprint HAL
- F. Jiang, H. Berry, and M. Schoenauer (2008) Supervised
and Evolutionary Learning of Echo State Networks. Proc 10th
international Conference on Parallel Problem Solving From Nature: PPSN
X, Dortmund, Germany, September 13 - 17, 2008, G. Rudolph et al.,
Eds, Lecture Notes In Computer Science, 5199:215-224.
- F. Jiang, H. Berry and M. Schoenauer. (2008) Unsupervised Learning of
Echo State Networks: Balancing the Double Pole. Genetic and
Evolutionary Computation Conference, GECCO-2008, July, Atlanta,
GA, USA.
- J. Naudé, S. Genet, H. Berry, J. Paz, and B. Delord. (2008) A
formalization of the computational impact of intrinsic plasticity. In NeuroComp'08:
19-26, Marseille, France, 08-11 October 2008
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2008)
A mathematical analysis of the effects of Hebbian learning rules on
the dynamics and structure of discrete-time random recurrent neural
networks. Neural Computation, 20:2937-2966.
2007
- Berry, H. and Temam, O. (2007) Modeling
self-developing biological neural networks. Neurocomputing,70:
2723-2734.
- Delord, B., Berry, H., Guigon, E. and Genet, S. (2007)
A new principle for information storage in an enzymatic pathway model.
PLoS Computational Biology, 3: e124.
- F. Jiang, H. Berry and M. Schoenauer. (2007)
Optimizing the topology of complex neural networks. European
Conference on Complex Systems (ECCS'07), October, Dresden,
Germany.
- Siri, B., Quoy, M., Cessac, B., Delord, B. and Berry, H. (2007)
Effects of Hebbian learning on the dynamics and structure of random
networks with inhibitory and excitatory neurons. Journal of
Physiology (Paris),101:136-148.
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2007) )
Local learning rules and bifurcations in the global dynamics of random
recurrent neural networks . European Conference on Complex
Systems (ECCS'07), October, Dresden, Germany.
2006
- Berry, H. and Quoy, M. (2006) Structure
and dynamics of random recurrent neural networks. Adaptive
Behavior, 14:129-137.
- Berry, H., Gracia-Pérez, D. and Temam, O. (2006) Chaos
in computer performance. CHAOS , 16:013110. arXiv:nlin.AO/0506030.
- Genet, S., Delord, B., Sabarly, L., Guigon, E., and Berry, H. (2006)
On the propagation of Ca-dependent plateau and valley potentials in
cerebellar Purkinje cells and how they drive the cell output. In NeuroComp'06:167-170,
Pont-à-Mousson, France, 23-24 October 2006.
- Gracia Pérez, D., Berry, H. and Temam, O. (2006)
The practicality dimension of sampling. IEEE micro ,26:14-28.
- Pellenc, D., Berry, H. and Gallet, O. (2006) Adsorption-induced
fibronectin aggregation and fibrillogenesis. Journal Colloid
Interface Science , 298:132-144.
- Siri, B., Berry, H., Cessac, B., Delord, B., Quoy, M., and Temam, O.
(2006) Learning-induced topological effects on dynamics in neural
networks. In NeuroComp'06:206--209, Pont-à-Mousson, France,
23-24 October 2006.
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2006) Topological
and dynamical structures induced by Hebbian learning in random neural
networks. In International Conference on Complex Systems, ICCS
2006, Boston, MA, USA, June 2006.
2005
- Berry, H. and Temam, O. (2005) Characterizing
self-developing biological neural networks: A first step towards their
application to computing systems. Lecture Notes in Computer
Science, 3512:306-317. arXiv:q-bio.NC/0505021.
- Berry, H. and Quoy, M. (2005) Structure and dynamics of random
recurrent neural networks. In Active agents and their environments
as dynamical systems, workshop held during the VIIIth European
Conference on Artificial Life (ECAL). University of Kent,
Canterbury, Kent (UK),05-08 September 2005.
- Caron-Lormier, G. and Berry, H. (2005) Amplification
and oscillations in the fak/src kinase system during integrin
signaling. Journal of Theoretical Biology, 232:235-248
- Gracia Pérez, D., Berry, H. and Temam, O. (2005) EDCA:
A new clustering approach for sampling. In MoBS: Workshop on
Modeling, Benchmarking, and Simulation, workshop held during the
the 32nd Annual International Symposium on Computer Architecture (ISCA),
Madison, Wisconsin, USA, June 04, 2005
- Gracia Pérez, D., Berry, H. and Temam, O. (2005) Budgeted region
sampling (BeERS): Wisely allocating simulated instructions for a better
accuracy/ speed/ applicability tradeoff. In 5th IEEE International
Symposium on Signal Processing and Information Technology. Athens,
Greece, December 2005.
- Pellenc, D., Gallet, O. and Berry, H. (2005) Adsorption-induced
conformational changes in protein diffusion-aggregation surface
assemblies. Physical Review E, 72:051904.
2003
2002
- Berry, H. (2002) Monte-carlo
simulations of enzyme kinetics in two dimensions: fractal kinetics and
spatial segregation. Biophysical Journal, 83:1891-1901.
- Di Martino, P., Gagniere, H., Berry, H. and Bret, L., (2002) Antibitotic
resistance
and virulence properties of pseudomonas aeruginosa strains from
ventilated patients with pneumonia in intensive care units:
comparison with imipenem resistant extra-respiratory tract isolates from
uninfected patients. Microbes Infections, 4:613-620.
- Larreta Garde, V. and Berry, H. (2002) Modeling
extracellular matrix degradation balance with proteinase /
transglutaminase cycle. Journal of Theoretical Biology,
217:105-124.
2000
- Berry, H., Pelta, J., Lairez, D. and Larreta-Garde, V. (2000) Gel-sol
transition can describe the proteolysis of extracellular matrix gels.
Biochimica Biophysica Acta, 1524:110-117.
- Pelta, J., Berry, H., Fadda, G., Pauthe, E., and Lairez, D. (2000) Statistical
conformation of human plasma fibronectin. Biochemistry,
39:5146-5554.
1999
1998
1997
1996
- Blum Moyse, L., and Berry, H. (2024). A Coupled Neural Field Model for the Standard Consolidation Theory, Journal of Theoretical Biology, 588:111818, hal-04527872.
- Mouttou, A., Bremaud, E., Noero, J., Dibsy, R., Arone, C., Mak, J., Muriaux, D., Berry, H. and Favard, C., (2023). Quantification of membrane binding and diffusion using fluorescence correlation spectroscopy diffusion laws, Biophysical Journal, 122(11):2216-229. here also.
- Dembitskaya, Y., Perez, S., Piette, C., Berry, H., Magistretti, P. J. and Venance, L (2022). Lactate supply overtakes glucose when neural computational and cognitive loads scale up, Proceedings of the Academy of Sciences U.S.A., 119(47):e2212004119.
- Denizot, A., Arizono, M., Nägerl, U. V., Berry, H. and De Schutter, E., Astrocyte nanoscale morphology controls Ca2+ signals at tripartite synapses, Glia, 70:2378-2391. preprint here.
- Blume Moyse, L. and Berry, H., (2022). Modelling the modulation of cortical up-down state switching by astrocytes, PLoS Computational Biology, 18(7):e1010296. Article + Supporting information available as a single file here.
- Berry, H. and Genet, S. (2021) A model of On/Off transitions in neurons of the deep cerebellar nuclei: Deciphering the underlying ionic mechanisms. Journal of Mathematical Neuroscience,, 11:1. https://hal.sorbonne-universite.fr/hal-03190183.
-
Kusters, R., Misevic, D., Berry, H., Cully, A., Le Cunff, Y., Dandoy, L., Diaz-Rodriguez, N., Ficher, M., Grizou, J., Othmani, A., Palpanas, T., Komorowski, M., Loiseau, P., Moulin Frier, C., Nanini, S., Quercia, D., Sebag, M., Soulie Fogelman, F., Taleb, S., Tupikina, L., Sahu, V., Vie, J.- J. and Wehbi, F. (2020) Interdisciplinary research in artificial intelligence: Challenges and opportunities. Frontiers in Big Data, 3:45. www.frontiersin.org/article/10.3389/fdata.2020.577974.
- Woringer M., Izeddin I., Favard C. and Berry H. (2020) Anomalous diffusion in living cells: bridging the gap between experiments and models through collaborative challenges, Frontiers in Physics, 8:134. doi: 10.3389/fphy.2020.00134
- Lenk K., Satuvuori E., Lallouette J., Ladron-de-Guevara A., Berry H. and Hyttinen J.A.K. (2020) A Computational Model of Interactions Between Neuronal and Astrocytic Networks: The Role of Astrocytes in the Stability of the Neuronal Firing Rate, Frontiers Computational Neuroscience, 13:92. doi: 10.3389/fncom.2019.00092.
- Denizot A., Berry H. and Venugopal, S. (2020) Intracellular Ca2+ Dynamics in Astrocytes: Modeling the Underlying Spatiotemporal Diversity
, Encyclopedia of Computational Neuroscience, https://hal.inria.fr/hal-02419317v1, in press
- Gangarossa, G., Perez, S., Dembitskaya, Y., Prokin, I., Berry, H. and Venance, L., (2020). BDNF controls bidirectional endocannabinoid-plasticity at corticostriatal synapses. Cerebral Cortex, 1(30):197-217. doi.org/10.1093/cercor/bhz081.
- Denizot, A., Arizono, M., Nagerl, V. U., Soula, H. and Berry, H.,
(2019). Simulation
of calcium signaling in fine astrocytic processes: effect of spatial
properties on spontaneous activity. PLoS
Computational Biology 15(8):e1006795. doi.org/10.1371/journal.pcbi.1006795.
- Xu, H., Perez, S., Cornil, A., Detraux, B., Prokin, I., Cui, Y.,
Degos, B., Berry, H., De Kerchove D'Exaerde, A. and Venance, L., (2018).
Dopamine-
endocannabinoid interactions mediate spike-timing dependent
potentiation in the striatum. Nature Communications 9:4118.
doi:
10.1038/s41467-018-06409-5.
- Foncelle, A., Mendes, A., Jdrzejewska-Szmek, J., Valtcheva, S.,
Berry, H., Blackwell, K. T. and Venance, L., (2018). Modulation
of spike-timing dependent plasticity: towards the inclusion of a third
factor in computational models. Frontiers in Computational
Neuroscience, 12:49. doi:
10.3389/fncom.2018.00049
- Cui Y, Prokin I, Mendes A, Berry H, Venance L. (2018). Robustness
of STDP to spike timing jitter. Scientific Reports, 8:8139.
Supplementary Information available here.
- Yi C, Theillon J, Koulakoff A, Berry H, Giaume C. (2018). Monitoring
gap junctional communication in astrocytes from acute adult mouse
brain slices using the gap-frap technique. J. Neuroscience
Methods. 303:103-113 hal-01734652.
- Cui Y, Yang Y, Ni Z, Dong Y, Cai G, Foncelle A, Ma S, Sang K, Tang S,
Li Y, Shen Y, Berry H, Wu S and Hu H (2018). Astroglial-
Kir4.1 in lateral habenula drives neuronal bursts in depression. Nature
554:323-327 (doi:10.1038/nature25752).
--> This article was commented in the ``News and
views'' section of the journal: Howe WM & Kenny PJ (2018). Burst
firing sets the stage for depression. Nature 554:304-305.
- Oschmann, F., Berry, H., Obermayera, K. and Lenk, K., (2018). From
in silico astrocyte cell models to neuron-astrocyte network models: A
review. Brain Research Bulletin, 136:76-84. hal-01461928.
- Cui, Y., Prokin, I., Xu, H., Delord, B., Genet, S., Venance, L. and
Berry, H., (2016). Endocannabinoid
dynamics gate spike-timing dependent depression and potentiation.
eLife, 5:e13185. doi:
10.7554/eLife.13185.
- Berry, H. , Lepoutre, T. and Mateos Gonzalez, A. (2016). Quantitative
convergence towards a self similar profile in an age-structured
renewal equation for subdiffusion. Acta Applicandae
Mathematicae,145:15-45, doi:10.1007/s10440-016-0048-3. arXiv:1503.08552
- Chaker, Z., Aïd, S., Berry, H. and Holzenberger, M. (2015). Suppression
of IGF-I signals in neural stem cells enhances neurogenesis and
olfactory function during aging . Aging Cell,
14(5):847-856, doi: 10.1111/acel.12365
- Cui Y., Paille V., Xu H., Genet S., Delord B., Fino E., Berry H. and
Venance L. (2015). Endocannabinoids
mediate bidirectional striatal spike-timing dependent plasticity.
J Physiology (London), 593(13), 2833-2849, doi:10.1113/JP270324
- Wallach, G., Lallouette, J., Herzog, N., De Pittà, M., Ben Jacob, E.,
Berry, H. and Hanein, Y. (2014). Glutamate
mediated astrocytic filtering of neuronal activity. PLoS
Computational Biology, 10(12), e1003964.
Supplementary Material availble here.
- Lo Van A., Soula H. and Berry H. (2014). Space-induced
bifurcation in repression-based transcriptional circuits BMC
Systems Biology , 8:125.
- Berry, H. & Soula, H. A. (2014)
Spatial distributions at equilibrium under heterogeneous transient
subdiffusion Frontiers in Physiology, 5:437.
- Soula H., Caré B., Beslon G. and Berry H. (2014). Comments
to
the Editor. Reply to the Comment by V.P. Shkilev on ``Anomalous versus
slowed-down Brownian diffusion in the ligand-binding equilibrium''.
Biophysical Journal,106(11):2544-2546.
- Lallouette, J., De Pittà, M., Ben-Jacob, E. and Berry, H., (2014). Sparse
short-distance
connections enhance calcium wave propagation in a 3D model of
astrocyte networks. Frontiers Computational Neuroscience,
8:45.
- Berry H., and Chaté H. (2014). Anomalous
diffusion due to hindering by mobile obstacles undergoing Brownian
motion or Orstein-Ulhenbeck processes. Physical Review E,
89(2):022708.
- Soula H., Caré B., Beslon G. and Berry H. (2013). Anomalous
versus slowed-down brownian diffusion in the ligand-binding
equilibrium. Biophysical Journal, 105:2064-2073.
- Naudé J., Cessac B., Berry H. & Delord B. (2013). Effects
of Cellular Homeostatic Intrinsic Plasticity on Dynamical and
Computational Properties of Biological Recurrent Neural Networks.
Journal of Neuroscience, 33(38):15032-15043.
- Coquel,A., Jacob,J., Primet,M., Demarez,A., Dimiccoli,M.,
Julou,T., Moisan,L., Lindner,A. and Berry, H. (2013). Localization
of
protein
aggregation in escherichia coli is governed by diffusion and nucleoid
macromolecular crowding effect. PLoS Computational Biology,
9:e1003038.
- De Pittà, M., Volman, V., Berry, H., Parpura V, Volterra, A. and
Ben-Jacob, E. (2012).
Computational quest for understanding the role of astrocyte signaling
in synaptic transmission and plasticity. Frontiers in
Computational Neuroscience, 6:98.
- Vlassopoulos,N., Fatès, N., Berry, H. and Girau, B., (2012).
Large-scale Simulations on FPGAs: Finding the Asymptotic Critical
Threshold of the Greenberg-Hastings Cellular Automata. Journal of
Cellular Automata, 7(1):5-29.
- Naudé, J., Paz, J., Berry, H. and Delord, B., (2012)
A theory of rate coding control by intrinsic plasticity effects. PLoS
Computational Biology, 8:e1002349.
- Berry, H. and Chaté, H. (2011) Anomalous subdiffusion due to
obstacles : A critical survey.submitted, arXiv:1103.2206
- De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E. (2011)
A tale of two stories: astrocyte regulation of synaptic depression and
facilitation. PLoS Computational Biology, 7: e1002293.
Supplementary Materials availble here
This article has been selected for the Faculty
of 1000 Cell Biology. Read the review here.
- Berry, H. and Fates, N. (2011)
Robustness of the critical behavior in the stochastic
Greenberg-Hastings cellular automaton model. Int. J.
Unconventional Computing, 7:65-85.
- Goldberg, M., De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2010)
Nonlinear gap-junctions enable long-distance propagation of pulsating
calcium waves in astrocyte networks. PLoS Computational
Biology, 6: e1000909.
Supplementary Materials availble here
- Genet, S., Sabarly, L., Guigon, E., Berry, H. and Delord, B. (2010)
Dendritic signals command firing dynamics in a mathematical model of
cerebellar Purkinje cells. Biophysical Journal, 99:
427-436.
Supplementary Materials availble here
- De Pittà, M., Goldberg, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2009) Glutamate regulation of
calcium and IP3 oscillating and pulsating dynamics in astrocytes.
Journal of Biological Physics, 35: 383-411.
This article has been selected for the Faculty
of 1000 Biology. Read the review here.
- Lavelle, C., Berry, H., Beslon, G., Ginelli, F., Giavitto, J.L.,
Kapoula, Z., Le Bivic, A., Peyrieras, N., Radulescu, O., Six, A.,
Thomas-Vaslin, V. and Bourgine, P. (2008)
From molecules to organisms: towards multiscale integrated model of
biological systems. Theoretical Biology Insights,1: 13-22.
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2008)
A mathematical analysis of the effects of Hebbian learning rules on
the dynamics and structure of discrete-time random recurrent neural
networks. Neural Computation, 20:2937-2966.
- Siri, B., Quoy, M., Cessac, B., Delord, B. and Berry, H. (2007)
Effects of Hebbian learning on the dynamics and structure of random
networks with inhibitory and excitatory neurons. Journal of
Physiology (Paris),101:136-148.
- Berry, H. and Temam, O. (2007) Modeling
self-developing biological neural networks. Neurocomputing,70:
2723-2734.
- Delord, B., Berry, H., Guigon, E. and Genet, S. (2007)
A new principle for information storage in an enzymatic pathway model.
PLoS Computational Biology, 3: e124.
- Gracia Pérez, D., Berry, H. and Temam, O. (2006)
The practicality dimension of sampling. IEEE micro ,26:14-28.
- Berry, H. and Quoy, M. (2006) Structure
and dynamics of random recurrent neural networks. Adaptive
Behavior, 14:129-137.
- Pellenc, D., Berry, H. and Gallet, O. (2006) Adsorption-induced
fibronectin aggregation and fibrillogenesis. Journal Colloid
Interface Science , 298:132-144.
- Berry, H., Gracia-Pérez, D. and Temam, O. (2006) Chaos
in computer performance. CHAOS , 16:013110. arXiv:nlin.AO/0506030.
- Pellenc, D., Gallet, O. and Berry, H. (2005) Adsorption-induced
conformational changes in protein diffusion-aggregation surface
assemblies. Physical Review E, 72:051904.
- Caron-Lormier, G. and Berry, H. (2005) Amplification
and oscillations in the fak/src kinase system during integrin
signaling. Journal of Theoretical Biology, 232:235-248
- Berry, H. (2003) Chaos in a
bienzymatic cyclic model with two autocatalytic loops. Chaos,
Solitons & Fractals, 18:1001-1014.
- Berry, H. (2003) Nonequilibrium
phase transition in a self-activated biological network. Physical
Review
E, 67:031907.
- Berry, H. (2002) Monte-carlo
simulations of enzyme kinetics in two dimensions: fractal kinetics and
spatial segregation. Biophysical Journal, 83:1891-1901.
- Larreta Garde, V. and Berry, H. (2002) Modeling
extracellular matrix degradation balance with proteinase /
transglutaminase cycle. Journal of Theoretical Biology,
217:105-124.
- Di Martino, P., Gagniere, H., Berry, H. and Bret, L., (2002) Antibitotic
resistance and virulence properties of pseudomonas aeruginosa strains
from ventilated patients with pneumonia in intensive care units:
comparison with imipenem resistant extra-respiratory tract isolates from
uninfected patients. Microbes Infections, 4:613-620.
- Berry, H., Pelta, J., Lairez, D. and Larreta-Garde, V. (2000) Gel-sol
transition can describe the proteolysis of extracellular matrix gels.
Biochimica Biophysica Acta, 1524:110-117.
- Pelta, J., Berry, H., Fadda, G., Pauthe, E., and Lairez, D. (2000) Statistical
conformation of human plasma fibronectin. Biochemistry,
39:5146-5554.
- Berry, H. and Larreta Garde, V. (1999)
Oscillatory behavior of a simple kinetic model for proteolysis during
cell invasion. Biophysical Journal,77:655-665.
- Berry, H., Débat, H. and Larreta Garde, V. (1999)
Oxygen concentration determines regiospecificity in soybean
lipoxygenase-1 reaction via a branched kinetic scheme. Journal
of Biological Chemistry, 273:2769-2776.
- Berry, H., Pauthe, E., Gallet, O. and Larreta Garde, V. (1998) Proteolysis
of aggregated fibronectin: a model for in vivo matrix degradation.
Annals of the New York Academy of Sciences, 864:198-202.
- Berry, H., Débat, H. and Larreta Garde, V. (1997). Excess
substrate
inhibition of soybean lipoxygenase-1 is mainly oxygen-dependent. FEBS
Letters, 408:324-326.
- Berry, H., Lambert, C. and Larreta Garde, V. (1996) Influence
of
environment
modifications on enzyme catalysis: Comparison of macromolecular and
molecular effects of cosolvents on lipoxygenase reactions. Annals
of the New York Academy of Sciences, 799:290-297.
- Berry, H. (2023). Les utilisations de l'IA pour l'hopital et la sante publique : donnees necessaires, applications et obstacles potentiels. In Paul, C. and Le Metayer, D., eds., Maitriser leIA au service de leaction publique: Une responsabilite individuelle et collective, Collection : Au fil du debat, chapter 5, pages 83–94. Berger-Levrault. (in french)
- Denizot A., Berry H. and Venugopal, S. (2020) Intracellular Calcium Signals in Astrocytes, Computational Modeling of , In Jaeger D. and Jung R., eds., Encyclopedia of Computational Neuroscience, https://hal.inria.fr/hal-02419317v1, Springer, New York, NY
- Berry, H. and Watier, L., March (2022). Pandemie de Covid-19. L'aide de l'IA et du numerique. In Nordlinger, B., Vilani, C. and de Fresnoye, O., eds., Medecine et intelligence artificielle. CNRS.
- De Pitta, M. and Berry, H., (2019). A neuron-glial perspective for
computational neuroscience. In De Pitta, M. and Berry, H., eds., Computational
Glioscience, pages 3-35. Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8
Preprint available at: hal-01995849v1
- De Pitta, M., Ben-Jacob, E. and Berry, H., (2019). G protein-coupled
receptor-mediated calcium signaling in astrocytes. In De Pitta, M. and
Berry, H., eds., Computational Glioscience, pages 115-150.
Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8.
Preprint available at: hal-01995850v1
- Lallouette, J., De Pitta, M. and Berry, H., (2019). Astrocyte
networks and intercellular calcium propagation. In De Pitta, M. and
Berry, H., eds., Computational Glioscience, pages 177-210.
Springer.
https://link.springer.com/book/10.1007%2F978-3-030-00817-8.
Preprint available at: hal-01995852v1
- Caré, B., LoVan, A., Berry, H. and Soula, H. (2015). Signalisation
sous contraintes spatiales. Consquences sur les conditions de stabilité
et de bifurcation. s. in Glade, N. and Stephanou, A. (Eds), Le
vivant critique et chaotique, chapter 6, pages 199-222. Editions
Matériologiques, Paris.
- Berry, H. (2013). Modélisation de la diffusion-réaction dans les
milieux intracellulaires encombrés. in Glade, N. and Stephanou,
A. (Eds), Le vivant discret et continu, chapter 9, pages
241-266. Editions Matériologiques, Paris.
- Berry, H. and Beslon, G. (2013). De la modélisation comme poésie. La
modélisation de systèmes biologiques complexes vue par deux
modélisateurs. in Varenne, F. and Silberstein, M. (Eds), Modéliser
& simuler. Epistémologies et pratiques de la modélisation et de la
simulation, volume 1, chapter 11, pages 327-390. Editions
Matériologiques, Paris.
- Berry, H. (2008) Nonequilibrium
phase
transition in scattered cell communities coupled by
auto/paracrine-like signalling in Pollack, G. and Chin,
W.-C. (Eds), Phase transitions in Cell Biology, Springer,
pp.23-41. preprint HAL
- Denizot, A., Cali, C., Berry, H. and De Schutter, E., (2021) Stochastic Spatially-Extended Simulations Predict the Effect of ER Distribution on Astrocytic Microdomain Ca2+ Activity. In NANOCOM 2021: Eighth Annual ACM International Conference on Nanoscale Computing and Communication, pages 1-5. ACM, New York, NY, United States. https://hal.archives-ouvertes.fr/hal-03590777.
-
Badoual, A., Arizono, M., Denizot, A., Ducros, M., Berry, H., Valentin Nägerl, U. and Kervrann, C., (2021). Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images. In IEEE International Symposium on Biomedical Imaging. Nice, France. https://hal.inria.fr/hal-03106797.
- Cui Y., Paille V., Delord B., Genet S., Fino E., Venance L. and
Berry, H. (2013). Endocannabinoids
mediate spike-timing dependent potentiation and depression: a
model-based experimental approach. 22nd Annual Computational
Neuroscience Meeting (CNS 2013), Paris, France (BMC
Neuroscience, 14(Suppl 1):O1).
- Lallouette, J. and Berry, H. (2013).
Topology drives calcium wave propagation in 3d astrocyte networks.
In Proceedings of the European Conference on Complex Systems 2012,
Gilbert, T., Kirkilionis, M. and Nicolis, G., eds. , Springer
Proceedings in Complexity, pages 453-463.
- De Pittà, M., Volman, V., Berry, H., Liaudet, N., Volterra, A. and
Ben-Jacob, E., (2012). A compartmental approach to modeling of calcium
events in astrocyte processes. (Abstract). In Society for
Neuroscience Annual Meeting , New Orleans, LA. Program No.
541.07. 2012 Neuroscience Meeting Planner. Online.
- Hashmi, A., Berry, H., Temam,
O. and Lipasti, M., June (2011). Automatic
abstraction
and fault tolerance in cortical microachitectures. In 38th
ACM/IEEE International Symposium on Computer Architecture, ISCA 2011.
San Jose, CA, USA.
- Venance, L., Cui, Y., Paille, V., Delord, B., Genet, S. and Berry,
H., (2011). Sub-second induction unveils a switch from nmda- to
endocannabinoid ltp. (Abstract). In Society for Neuroscience Annual
Meeting , Washington, DC. Program No. 348.04. 2011 Neuroscience
Meeting Planner. Online.
- Berry, A., De Pittà, M., Volman, V. and Ben-Jacob, E., (2011).
Astrocyte regulation of presynaptic plasticity. (Abstract). In
Society for Neuroscience Annual Meeting , Washington, DC. Program
No. 663.10. 2011 Neuroscience Meeting Planner. Online.
- Delord, B., Naude, J., Paz, J. and Berry, H., February (2011).
Modeling the effects of intrinsic plasticity on rate coding. In Computational
and Systems Neuroscience (COSYNE) 2011. Abstract.
- Goldberg, M., De Pittà, M., Volman, V., Berry, H. and Ben-Jacob, E.
(2010) On the determinants of calcium wave propagation distance in
astrocyte networks: nonlinear gap junctions and oscillatory modes.
(Abstract). In 40th annual meeting of the Society for Neuroscience.
Society for Neuroscience, San Diego, CA. Abstract No. 552.22. 2010
Neuroscience Meeting Planner. Online.
- Auras, D., Girbal, S., Berry, H., Temam, O. and Yehia, S., Oct.
(2010). Memory Interface for Multi-Purpose Multi-Stream Accelerators. In
International Conference on Compilers, Architectures and Synthesis
for Embedded Systems, CASES 2010, Scottsdale, AZ, USA.
- Auras, D., Girbal, S., Berry, H., Temam, O. and Yehia, S., June
(2010). CMA: Chip
multi-accelerator. In 8th IEEE Symposium on Application
Specific Processors, SASP 2010. Anaheim, CA, USA.
- Vlassopoulos, N., Fates, N., Berry, H. and Girau, B., June (2010). An
FPGA design for the stochastic greenberg-hastings cellular automata.
In W. Smari editor, The 2010 International Conference on High
Performance Computing and Simulation, HPCS 2010 Caen, France,
pages 565-574, IEEE.
- Girbal, S., Yehia, S., Berry, H., and Temam, O. January (2010). Stream
and Memory Hierarchy Design for Multi-Purpose Accelerators. In 1st
Workshop on SoC Architecture, Accelerators and Workloads (SAW-1).
Bangalore, India.
- Fates, N.A. and Berry, H. (2010) Critical
phenomena in a discrete stochastic reaction-diffusion medium. In
Peper, F., ed., Fourth International Workshop on Natural Computing,
IWNC 2009, Himeji, Japan, Sep. 23-25, 2009. Proceedings in
Information and Communications Technology, 2:141-148.
- Hashmi, A., Berry, H., Temam, O. and Lipasti, M., December (2009). Leveraging
progress in neurobiology for computing systems. In 1st
Workshop on New Directions in Computer Architecture (NDCA-1).
New-York, New-York, USA.
- F. Jiang, H. Berry and M. Schoenauer. (2009) The
impact of network topology on self-organizing maps. In Proc
First ACM/SIGEVO Summit on Genetic and Evolutionary Computation,
GEC-2009, Shanghai, China, June 12 -14, 2009, pp 247-254.
- Yehia, S., Girbal, S., Berry, H. and Temam, O. (2009) Reconciling
Specialization
and Flexibility Through Compound Circuits. In 15th
International Symposium on High-Performance Computer Architecture,
HPCA, Raleigh, North Carolina, US, Feb. 14-18, 2009.
- J. Naudé, S. Genet, H. Berry, J. Paz, and B. Delord. (2008) A
formalization of the computational impact of intrinsic plasticity. In NeuroComp'08:
19-26, Marseille, France, 08-11 October 2008.
- F. Jiang, H. Berry, and M. Schoenauer (2008) Supervised
and Evolutionary Learning of Echo State Networks. Proc 10th
international Conference on Parallel Problem Solving From Nature: PPSN
X, Dortmund, Germany, September 13 - 17, 2008, G. Rudolph et al.,
Eds, Lecture Notes In Computer Science, 5199:215-224.
- F. Jiang, H. Berry and M. Schoenauer. (2008) Unsupervised Learning of
Echo State Networks: Balancing the Double Pole. Genetic and
Evolutionary Computation Conference, GECCO-2008, July, Atlanta,
GA, USA.
- F. Jiang, H. Berry and M. Schoenauer. (2007)
Optimizing the topology of complex neural networks. European
Conference on Complex Systems (ECCS'07), October, Dresden,
Germany.
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2007) )
Local learning rules and bifurcations in the global dynamics of random
recurrent neural networks . European Conference on Complex
Systems (ECCS'07), October, Dresden, Germany.
- Genet, S., Delord, B., Sabarly, L., Guigon, E., and Berry, H. (2006)
On the propagation of Ca-dependent plateau and valley potentials in
cerebellar Purkinje cells and how they drive the cell output. In NeuroComp'06:167-170,
Pont-à-Mousson, France, 23-24 October 2006.
- Siri, B., Berry, H., Cessac, B., Delord, B., Quoy, M., and Temam, O.
(2006) Learning-induced topological effects on dynamics in neural
networks. In NeuroComp'06:206--209, Pont-à-Mousson, France,
23-24 October 2006.
- Siri, B., Berry, H., Cessac, B., Delord, B. and Quoy, M. (2006) Topological
and dynamical structures induced by Hebbian learning in random neural
networks. In International Conference on Complex Systems, ICCS
2006, Boston, MA, USA, June 2006.
- Berry, H. and Temam, O. (2005) Characterizing
self-developing biological neural networks: A first step towards their
application to computing systems. Lecture Notes in Computer
Science, 3512:306-317. arXiv:q-bio.NC/0505021.
- Gracia Pérez, D., Berry, H. and Temam, O. (2005) Budgeted region
sampling (BeERS): Wisely allocating simulated instructions for a better
accuracy/ speed/ applicability tradeoff. In 5th IEEE International
Symposium on Signal Processing and Information Technology. Athens,
Greece, December 2005.
- Berry, H. and Quoy, M. (2005) Structure and dynamics of random
recurrent neural networks. In Active agents and their environments
as dynamical systems, workshop held during the VIIIth European
Conference on Artificial Life (ECAL). University of Kent,
Canterbury, Kent (UK),05-08 September 2005.
- Gracia Pérez, D., Berry, H. and Temam, O. (2005) EDCA:
A new clustering approach for sampling. In MoBS: Workshop on
Modeling, Benchmarking, and Simulation, workshop held during the
the 32nd Annual International Symposium on Computer Architecture (ISCA),
Madison, Wisconsin, USA, June 04, 2005
- Caranta, C., Monod, H., Berry, H., Chelle, M., Génard, M., Jourdan, F., Lannou, C., Maguin, E., Medale, F., Oddou-Muratorio, S., Rogel Gaillard, C., Traas, J. (2019). Réflexion prospective interdisciplinaire. Approches prédictives pour la biologie et l'écologie. Rapport de synthèse (in French). 40 pp., DOI : 10.15454/1.5783037069682676e12, https://prodinra.inra.fr/record/491139
- Yehia, S., Temam, O. and Berry, H. (2010) Procede pour la conception
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