2019
- Qian, Y., Piatkevich K. D., Mc Larney, B., Abdelfattah, A. S., Mehta, S., Murdock, M. H., Gottschalk, S., Molina, R. S., Zhang, W., Chen, Y., Wu, J., Drobizhev, M., Hughes, T. E., Zhang, J., Schreiter, E. R., Shoham, S., Razansky, D., Boyden, E. S., & Campbell R. E., A genetically encoded near-infrared fluorescent calcium ion indicator, Nature Methods, (2019). doi: 10.1038/s41592-018-0294-6.
2018
- Shor E., Merdler U., Brosh I., Shoham S.† & Levenberg S.†, Induced neuro-vascular interactions robustly enhance functional attributes of engineered neural implants, Biomaterials, 180, 1-11 (2018). doi:10.1016/j.biomaterials.2018.07.001.
- Aharoni T. & Shoham S., Phase-controlled, speckle-free holographic projection with applications in precision optogenetics, Neurophotonics, 5(2), 025004 (2018). doi: 10.1117/1.NPh.5.2.025004.
- Plaksin M., Shapira E., Kimmel E. & Shoham S., Thermal transients excite neurons through universal intramembrane mechano-electrical effects, Phys. Rev. X., 8(1), 011043 (2018). doi: 10.1103/PhysRevX.8.011043.
2017
- Plaksin M., Kimmel E. & Shoham S.,Correspondence: Revisiting the theoretical cell membrane thermal capacitance response, Nature Communications, 8(1), 1431 (2017). doi: 10.1038/s41467-017-00435-5. Correspondence reply.
Original article: Shapiro M. G., Homma K., Villarreal S., Richter C.-P. & Bezanilla F., Infrared light excites cells by changing their electrical capacitance, Nature Communications, 3, 736 (2012). doi: 10.1038/ncomms1742.
- Weissler Y., Farah N. & Shoham S., Simulation of morphologically structured photo-thermal neural stimulation, Journal of Neural Engineering, 14(5), 055001 (2017). doi: 10.1088/1741-2552/aa7805.
- Boutte R. W., Merlin S., Yona G., Griffiths B., Angelucci A., Kahn I., Shoham S. & Blair S., Utah optrode array customization using stereotactic brain atlases and 3-D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates, Neurophotonics, 4(4), 041502 (2017). doi: 10.1117/1.NPh.4.4.041502.
- Deán-Ben X. L., Gottschalk S., Mc Larney B., Shoham S. & Razansky D., Advanced optoacoustic methods for multiscale imaging of in vivo dynamics, Chemical Society Review, 46(8), 2158-2198 (2017). doi: 10.1039/C6CS00765A.
- Deán-Ben X. L., Gottschalk S., Sela G., Shoham S. & Razansky D., Functional optoacoustic neuro-tomography of calcium fluxes in adult zebrafish brain in vivo, Optics Letters, 42(5), 959-962 (2017). doi: 10.1364/OL.42.000959.
- Marom A.*, Shor E.*, Levenberg S. & Shoham S., Spontaneous Activity Characteristics of 3D “Optonets”, Frontiers in Neuroscience, 10, 602 (2017). doi: 10.3389/fnins.2016.00602.
2016
- Deán-Ben X. L.*, Sela G.*, Lauri A.*, Kneipp M., Ntziachristos V., Westmeyer G.†, Shoham S.† & Razansky D.†, Functional optoacoustic neuro-tomography (FONT) for scalable whole-brain monitoring of calcium indicators, Light: Science & Applications, 5, e16201 (2016). doi: 10.1038/lsa.2016.201.
Media: Press release (Hebrew), medicalphysicsweb - Plaksin M., Kimmel E. & Cell-Type-Selective Effects of Intramembrane Cavitation as a Unifying Theoretical Framework for Ultrasonic Neuromodulation, eNeuro, 3(3), (2016). doi: ,
- Naor O.*, Krupa S.* & Shoham S., Ultrasonic neuromodulation, Journal of Neural Engineering, 13(3), 031003 (2016). doi: 10.1088/1741-2560/13/3/031003.
- Schejter Bar-Noam A., Farah N. & Shoham S., Correction-free remotely scanned two-photon in vivo mouse retinal imaging, Light: Science & Applications, 5, e16007 (2016). doi: 10.1038/Isa.2016.7.
Media: Press release (Hebrew, English), The Jerusalem Post, Labrigger
2015
- Farah N., Levinsky A., Brosh I., Kahn I. & Shoham S., Holographic fiber bundle system for patterned optogenetic activation of large-scale neuronal networks, Neurophotonics, 2(4), 045002 (2015). doi: 10.1117/1.NPh.2.4.045002.
- Paluch S., Mayblum T., Dana H., Brosh I., Geffen I. & Shoham S., All-optical bidirectional neural interfacing using hybrid multiphoton holographic optogenetic stimulation, Neurophotonics, 2(3), 031208 (2015). doi: 10.1117/1.NPh.2.3.031208.
- Marom A.*, Mahto S.K.*, Shor E., Sznitman J. & Shoham S., Microfluidic Chip for Site-specific Neuropharmacological Treatment & Activity Probing of 3D Neuronal ‘Optonet’ Cultures, Advanced Healthcare Materials, 4(10), 1477 (2015). doi: 10.1002/adhm.201570060.
- Kneipp M., Turner J., Estrada H., Shoham S. & Razansky D., Effects of the murine skull in optoacoustic brain microscopy, Journal of Biophotonics, 9(1-2), 117-123 (2015). doi: 10.1002/jbio.201400152.
2014
- Dana H., Marom A., Paluch S., Dvorkin R., Brosh I. & Shoham S., Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks, Nature Communications, 5, 3997 (2014). doi: 10.1038/ncomms4997.
(Free access link on Europe PubMed) - Plaksin M., Shoham S. & Kimmel E., Intramembrane Cavitation as a Predictive Bio-Piezoelectric Mechanism for Ultrasonic Brain Stimulation, Physical Review X, 4(1), 011004 (2014). doi: 10.1103/PhysRevX.4.011004.
- Tankus A., Fried I. & Shoham S., Cognitive-motor brain–machine interfaces, Journal of Physiology-Paris, 108(1), 38-44 (2014). doi: 10.1016/j.jphysparis.2013.05.005.
2013
- Farah N., Zoubi A., Matar S., Golan L., Marom A., Butson C.R., Brosh I. & Shoham S., Holographically patterned activation using photo-absorber induced neural–thermal stimulation, Journal of Neural Engineering, 10(5), 056004 (2013). doi: 10.1088/1741-2560/10/5/056004.
- Reutsky-Gefen I., Golan L., Farah N., Schejter A., Tsur L., Brosh I. & Shoham S., Holographic optogenetic stimulation of patterned neuronal activity for vision restoration, Nature Communications, 4, 1509 (2013). doi: 10.1038/ncomms2500.
Media: Press release (Hebrew,English), Maariv (Hebrew), Radio Interview (Hebrew), OpenOptogenetics - Dana H., Kruger N., Ellman A. & Shoham S., Line temporal focusing characteristics in transparent and scattering media, Optics Express, 21(5), 5677-5687 (2013). doi: 10.1364/OE.21.005677.
2012
- Tankus A., Fried I. & Shoham S., Sparse decoding of multiple spike trains for brain-machine interfaces, Journal of Neural Engineering, 9(5), 054001 (2012). doi: 10.1088/1741-2560/9/5/054001.
- Tankus A., Fried I. & Shoham S., Structured neuronal encoding and decoding of human speech features, Nature Communications, 3, 1015 (2012). doi: 10.1038/ncomms1995.
Media: Press Release, Daily Mail, Jerusalem Post, Haaretz (Hebrew, English), Radio Interview (Hebrew) - Ma R., Söntges S., Shoham S., Ntziachristos V. & Razansky D., Fast scanning coaxial optoacoustic microscopy, Biomedical Optics Express, 3(7), 1724-1731 (2012). doi: 10.1364/BOE.3.001724.
- Schejter A., Tsur L., Farah N., Reutsky-Gefen I., Falick Y., & Shoham S., Cellular Resolution Panretinal Imaging of Optogenetic Probes Using a Simple Funduscope, Translational Vision Science and Technology, 1(2), 4 (2012). doi: 10.1167/tvst.1.2.4.
- Dana H. & Shoham S., Remotely scanned multiphoton temporal focusing by axial grism scanning, Optics Letters, 37(14), 2913-2915 (2012). doi: 10.1364/OL.37.002913.
- Szameit A.*, Shechtman Y.*, Osherovich E.*, Bullkich E., Sidorenko P., Dana H., Steiner S., Kley E. B., Gazit S., Cohen-Hyams T., Shoham S., Zibulevsky M., Yavneh I., Eldar Y. C., Cohen O. & Segev M., Sparsity-based single-shot sub-wavelength coherent diffractive imaging, Nature Materials, 11(5), 455-459 (2012). doi: 10.1038/nmat3289.
- Naor O.*, Hertzberg Y.*, Zemel E., Kimmel E. & Shoham S.,Towards multifocal ultrasonic neural stimulation II: design considerations for an acoustic, Journal of Neural Engineering, 9(2), 026006 (2012). doi: 10.1088/1741-2560/9/2/026006.
2011
- Matar S., Golan L. & Shoham S., Reduction of two-photon holographic speckle using shift-averaging, Optics Express, 19(27), 25891-25899 (2011). doi: 10.1364/OE.19.025891.
- Dana H. & Shoham S., Numerical evaluation of temporal focusing characterisics in transparent and scattering media, Optics Express, 19(6), 4937-4948 (2011). doi: 10.1364/OE.19.004937.
- Krasovitski B., Frenkel V., Shoham S. & Kimmel E., Intramembrane Cavitation as a Unifying Mechanism for Ultrasound-Induced Bioeffects, PNAS, 108(8), 3258-3263 (2011). doi: 10.1073/pnas.1015771108.
2010
- Krumin M., Reutsky I. & Shoham S., Correlation-based analysis and generation of multiple spike trains using Hawkes models with an exogenous input, Frontiers in Computational Neuroscience, 4, 147 (2010). doi: 10.3389/fncom.2010.00147.
- Shoham S., Optogenetics meets optical wavefront shaping (News & Views), Nature Methods, 7(10), 798-799 (2010). doi: 10.1038/nmeth1010-798.
- Hertzberg Y.*, Naor O.*, Volovick A. & Shoham S., Towards multifocal ultrasonic neural stimulation: pattern generation algorithms, Journal of Neural Engineering, 7(5), 056002 (2010). doi: 10.1088/1741-2560/7/5/056002.
- Shoham S. & Deisseroth K., Special issue on optical neural engineering: advances in optical stimulation technology (Editorial), Journal of Neural Engineering, 7(4), 040201 (2010). doi: 10.1088/1741-2560/7/4/040201.
- Krumin M. & Shoham S., Multivariate auto-regressive modeling and Granger causality analysis of multiple spike trains, Computational Intelligence and Neuroscience, 2010, (2010). doi: 10.1155/2010/752428.
2009
- Golan L., Reutsky I., Farah N. & Shoham S., Design and characteristics of holographic neural photo-stimulation systems, Journal of Neural Engineering, 6(6), 066004 (2009). doi: 10.1088/1741-2560/6/6/066004.
- Krumin M., Shimron A. & Shoham S., Correlation-distortion based identification of Linear-Nonlinear-Poisson models, Journal of Computational Neuroscience [special issue on analysis of neural data], 29(1-2), 301-308 (2009). doi: 10.1007/s10827-009-0184-0.
- Yaeli S.*, Binyamin E.* & Shoham S., Form-function relations in cone-tipped stimulating microelectrodes, Frontiers in Neuroengineering [special issue on microelectrode technology for electrostimulation], 2(13), (2009). doi: 10.3389/neuro.16.013.2009.
- Sarig-Nadir O.*, Livnat N.*, Zajdman R., Shoham S. & Seliktar D., Laser Photoablation of Guidance Microchannels into Hydrogels Directs Cell Growth in Three Dimensions, Biophysical Journal, 96(11), 4743-4752 (2009). doi: 10.1016/j.bpj.2009.03.019.
| 1 | 2 | 3 | - Golan L. & Shoham S., Speckle elimination using shift-averaging in high-rate holographic projection, Optics Express, 17(3), 1330-1339 (2009). doi: 10.1364/OE.17.001330.
- Krumin M. & Shoham S., Generation of Spike Trains with Controlled Auto- and Cross-Correlation Functions, Neural Computation, 21(6), 1642-1664 (2009). doi: 10.1162/neco.2009.08-08-847.
- Matar S., Golan L., Farah N., Reutsky I. & Shoham S., Holographic photo-stimulation for dynamic control of neuronal population activity, Proceedings of IEEE 4th International Conference on Neural Engineering, 84-87 (2009).
2007
- Bobrowski O., Meir R., Shoham S. & Eldar Y.C., A neural network implementing optimal state estimation based on dynamic spike train decoding, NIPS (2007).
- Farah N., Reutsky I. & Shoham S.,Patterned Optical Activation of Retinal Ganglion Cells, Proceedings of the 29th Annual International Conference of the IEEE EMBS, 6368-6370 (2007). doi: 10.1109/IEMBS.2007.4353812.
- Osan R., Zhu L., Shoham S. & Tsien J.Z., Subspace Projection Approaches to Classification and Visualization of Neural Network-Level Encoding Patterns, PLoS ONE, 2(5), e404 (2007). doi: 10.1371/journal.pone.0000404.
2006
- Shoham S., O`Connor D. & Segev R., How silent is the brain: is there a ‘‘dark matter’’ problem in neuroscience?, Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology ,192(8), 777-784 (2006). doi:10.1007/s00359-006-0117-6.
- Guillory K.S., Shoham S. & Normann R.A., Discrete stimulus estimation from neural responses in the turtle retina, Vision Research, 46(12), 1876-1885 (2006). doi:10.1016/j.visres.2005.12.001.
2005
- Shoham S.*, O’Connor D.H.*, Sarkisov D.V. & Wang S.S.H., Rapid neurotransmitter uncaging in spatially defined patterns, Nature Methods, 2(11), 837-843 (2005). doi: 10.1038/NMETH793.
| 1 | 2 | - Shoham S., Paninski L., Fellows M.R., Hatsopoulos N.G., Donoghue J.P. & Normann R.A., Statistical Encoding Model for a Primary Motor Cortical Brain-Machine Interface, IEEE Transactions on Biomedical Engineering, 52(7), 1312-1322 (2005). doi:10.1109/TBME.2005.847542.
- Lin L.*, Osan R.*, Shoham S., Zuo W., Jin W. & Tsien J.Z., Identification of network-level coding units for real-time representation of episodic experiences in the hippocampus, PNAS, 102(17), 6125-6130 (2005). doi: 10.1073/pnas.0408233102.
2004
- Stein R.B., Weber D.J., Aoyagi Y., Prochazka A., Wagenaar J.B.M., Shoham S. & Normann R.A., Coding of position by simultaneously recorded sensory neurones in the cat dorsal root ganglion, Journal of Physiology, 560(3), 883-896 (2004). doi: 10.1113/jphysiol.2004.068668.
- Paninski L., Shoham S., Fellows M.R., Hatsopoulos N.G. & Donoghue J.P., Superlinear Population Encoding of Dynamic Hand Trajectory in Primary Motor Cortex, Journal of Neuroscience, 24(39), 8551-8561 (2004). doi: 10.1523/JNEUROSCI.0919-04.2004.
- Shoham S. & Nagarajan S.S., The Theory of CNS Recording, in: Neurprosthetics: Theory and Applications, Horch KW & Dhillon GS editors, World scientific, New Jersey (2004).
- Stein R.B., Aoyagi Y., Weber D.J., Shoham S. & Normann R.A., Encoding mechanisms for sensory neurons studied with a multielectrode array in the cat Dorsal Root Ganglion, Canadian Journal of Physiology and Pharmacology, 82(9), 757-768 (2004). doi: 10.1139/y04-075.
- Reed C.L., Shoham S. & Halgren E., Neural substrates of tactile object recognition: an fMRI Study, Human Brain Mapping, 21(4), 236-246 (2004). doi: 10.1002/hbm.10162.
2003
- Shoham S., Fellows M.R. & Normann R.A., Robust, automatic spike sorting using mixtures of multivariate t-distributions, Journal of Neuroscience Methods, 127(2), 111-122 (2003). doi: 10.1016/S0165-0270(03)00120-1.
2002
- Shoham S., Robust clustering bydeterministic agglomeration EM of mixtures of multivariate t-distributions, Pattern Recognition, 35(5), 1127-1142 (2002).
2001
- Shoham S., Halgren E., Maynard E.M., & Normann R.A., Motor-cortical activity in tetraplegics, Nature, 413, 793 (2001). doi: 10.1038/35101651.