Research Papers

GA Silva (2024) Using quantum computing to infer dynamic behaviors of biological and artificial neural networks. arXiv https://arxiv.org/abs/2403.18963. PDF

JJ Li, S Pardo Guerra, K Basu and GA Silva (2023) A categorical framework for quantifying emergent effects in network toplogy. arXiv https://arxiv.org/abs/2311.17403. PDF

V Kurien George, A Gupta, and GA Silva (2023) Identifying steady state in the network dynamics of spiking neural networks. Heliyon https://doi.org/10.1016/j.heliyon.2023.e13913. PDF

T Chen, Y Park, A Saad-Eldin, Z Lubberts, A Athreya, BD Pedigo, JT Vogelstein, F Puppo, GA Silva, AR Muotri, W Yang, GM White, and CE Priebe (2023) Discovering a change point and piecewise linear structure in a time series of organoid networks via the iso-mirror Applied Network Science https://doi.org/10.1007/s41109-023-00564-5. PDF

S Pardo G and GA Silva (2021) Information entropy re-defined in a category theory context using preradicals. arXiv 2112.06064. PDF

VK George, V Morar, W Yang, J Larson, B Tower, S Mahajan, A Gupta, C White, and GA Silva (2021) Learning without gradient descent encoded by the dynamics of a neurobiological model. arXiv https://arxiv.org/abs/2103.08878. PDF

F Puppo, D Pre, A Bang, and GA Silva (2020) Super-selective reconstruction of causal and direct connectivity with application to in-vitro iPSC neuronal networks. Frontiers in Neuroscience doi.org/10.3389/fnins.2021.647877 [bioRxiv version:https://doi.org/10.1101/2020.05.08.085191.] PDF

F Puppo, S Sadegh, CA Trujillo, M Thunemann, E Campbell, M Vandenberghe, X Shan, I Akkouh, Evan Miller, BL  Bloodgood, GS Silva, AM Dale, GT Einevoll, S Djurovic, OA Andreassen, AR Muotri, and A Devor (2021) All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors. Frontiers in Cellular Neuroscience. 15:671549. doi: 10.3389/fncel.2021.671549 [bioRxiv:https://www.biorxiv.org/content/10.1101/2021.01.18.427081] PDF

P Wang, S Sapra, VK George, and GA Silva (2021) Generalizable machine learning in neuroscience using graph neural networks. Frontiers in Artificial Intelligence doi.org/10.3389/frai.2021.618372. PDF

VK George, F Puppo and GA Silva (2021) Computing temporal sequences associated with dynamic patterns on the C. elegans connectome. Frontiers in Systems Neuroscience doi.org/10.3389/fnsys.2021.564124. PDF [bioRxiv version https://doi.org/10.1101/2020.04.28.067124. PDF]

F Puppo, D Pre, A Bang, and GA Silva (2021) Super-selective reconstruction of causal and direct connectivity with application to in-vitro iPSC neuronal networks. Frontiers in Neuroscience doi.org/10.3389/fnins.2021.647877. PDF [bioRxiv verison https//doi.org/10.1101/2020.05.08.085191. PDF]

VK George, V Morar, W Yang, B Tower, B Larson, S Marhajan, A Gupta, C White and GA Silva (2021) Learning without gradient descent encoded by the dynamics of a neurobiological model. arXiv 2103.08878. PDF

F Puppo, S Sadegh, CA Trujillo, M Thunemann, EP Campbell, M Vandenberghe, X Shan, IA Akkouh, EW Miller, BL Bloodgood, GA Silva, AM Dale, GT Einevoll, S Djurovic, OA Adreassen, AR Muotri, and A Devor (2021) All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors. Frontiers in Cellular Neuroscience doi.org/10.3389/fncel.2021.671549. PDF

S Pardo G and GA Siva (2020) Information flows as a path least resistance: A category theory approach using preradicals. arXiv 2012.02886 PDF

N Bhattacharya and GA Silva (2020) Stability and complexity analysis of finite difference algorithms for the time fractional diffusion equation. arXiv 2007.08660. PDF

JM Roldan, S Pardo G, VK George, and GA Silva (2020) Construction of edge-ordered multidirected graphlets for comparing dynamics of spatial temporal neural networks. arXiv 2006.15971. PDF

GA Silva (2019) The effect of signaling latencies and refractory node states on the dynamics of networks. Neural Computation. 31:2492-2522. PDF. [arXiv preprint version 1804.07609. PDF]

F Puppo, V George, and GA Silva (2018) An optimized structure-function design principle underlies efficient signaling dynamics in neurons. Nature Scientific Reports 8:10460. PDF

H Uhlirova, K Kılıç, P Tian, S Sakadˇzic, L Gagnon, M Thunemann, M Desjardins, PA. Saisan, K Nizar, MA Yasseen, DJ Hagler Jr, M Vandenberghe, S Djurovic, OA. Andreassen, GA Silva, E Masliah, D Kleinfeld, S Vinogradov, RB. Buxton, GT. Einevoll, DA Boas, AM Dale, and A Devor (2016) The roadmap for estimation of cell-type- specific neuronal activity from non- invasive measurements. Philosophical Transactions B. 371:20150356. PDF

S Ha, M Khraiche, A Akinin, Y Jin, WR Freeman, GA Silva, and G Cauwenberghs (2016) Towards high-resolution retinal prostheses with direct optical addressing and inductive telemetry. Journal of Neural Engineering 13:056008. PDF

H Uhlirova, K Kilic, P Tian, PA Saisan, Q Cheng, KL Weldy2 S Sakadzic, F Razoux, M Vandenberghe, K Nizar, VB Sridhar, TC Steed, M Abashin, Y Fainman, E Masliah, S Djurovic, OA Andreassen, GT Einevoll, GA Silva, DA Boas, RB Buxton, AM Dale1, S Devor (2016) Cell type specificity of neurovascular coupling in cerebral cortex. eLife 2016;10.7554/eLife.14315. PDF

S-Y Eun, K Nguyen-Ta, GA Silva, and S-J Kim (2016) Assembly and calcium binding properties of quantum dot-calmodulin calcium sensor. Journal Nanoscience and Nanotechnology. 16:2065-2068.

CL MacDonald, N Bhattacharya, BP Sprouse, and GA Silva (2015) Efficient computation of the Grunwald-Letnikov fractional diffusion derivative using adaptive time step memory. Journal of Computational Physics 297:231-236. [arXiv versions 1004.5128 and 1505.03967] PDF

J Blumling III and GA Silva (2015) Sulforhodamine B-loaded polyethyleneimine/silica hybrid nanoparticles. Journal of Nanoneuroscience. 6:73-77.

M Buibas and GA Silva (2015) Algebraic identification of the effective connectivity of constrained geometric network models of neural signaling. arXiv 1505.03964. PDF

B Maranhao, P Biswas, JL Duncan KE Branham, GA Silva MA Naeem, SN Khan, S Riazuddin, JF Hejtmancik, JR Heckenlively, SA Riazuddin, PL Lee, and R Ayyagari (2014) exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels. Genomics 103:169-176. PDF

CL MacDonald and GA Silva (2013) A positive feedback cell signaling nucleation model of astrocyte dynamics. Frontiers in Neuroengineering 6:4. doi: 10.3389/fneng.2013.00004. PDF

K Nizar, P Tian, Q Cheng, PA Saisan, H Uhlirova, L reznichenko, K Weldy, TY Steed, VB Sridhar, CL MacDonald, J Cui, S Sakadzic, DA Boas, TI Beka, GT Einevoll, J Chen, E Masliah, AM Dale, GA Silva, and A Devor (2013) In vivo stimulus-induced vasodilation precedes astrocytic calcium increase. Journal of Neuroscience 33:8411-8422. PDF

S-J Kim, J Blumling, MC Davidson, H Saad, S-Y Eun, and GA Silva (2012) Calcium and EDTA induced folding and unfolding of calmodulin on functionalized quantum dot surfaces. Journal of Nanoneuroscience 2:75-81. PDF

C Evans, M Fitzgerald, T Clemons, M House, B Padman, J Shaw, M Saunders, A Harvey, B Zdyrko, I Luzinov, GA Silva, S Dunlop, KS Iyer (2011) Multimodal analysis of PEI-mediated endocytosis of nanoparticles in neural cells. ACS Nano 5:8640-8648. PDF

M Buibas and GA Silva (2011) A framework for simulating and estimating the state and functional topology of complex dynamic geometric networks. Neural Computation 23:183-214. [arXiv 0908.3934].

M Buibas, D Yu, K Nizar, and GA Silva (2010) Mapping the Spatiotemporal Dynamics of Calcium Signaling in Cellular Neural Networks Using Optical Flow. Annals of Biomedical Engineering 38:2520-2531. [arXiv 0912.0265].

SK Chow, D Yu, CL MacDonald, M Buibas, and GA Silva (2010) Amyloid-β-peptide directly induces spontaneous calcium oscillations, intercellular calcium waves, and gliosis in rat cortical astrocytes. ASN Neuro 2(1):art:e00026.doi:10.1042/AN20090035. PDF

D Yu, M Buibas, Z Singer, I Lee, and GA Silva (2009) Characterization of calcium mediated intracellular and intercellular signaling in the rMC-1 glial cell line. Cellular and Molecular Bioengineering 2:144-155 .PDF

S Pathak, R Tolentino, K Nguyen, L DAmico, E Barron, L Cheng, WR Freeman, and GA Silva (2009) Quantum dot labeling and imaging of GFAP intermediate filaments and gliosis in the rat neural retina and dissociated astrocytes. Journal of Nanoscience and Nanotechnology 9:5047-5054. PDF

F Mojana, L Cheng, D-WG Bartsch, GA Silva, I Kozak, N Nigam, and WR Freeman (2008) The role of abnormal vitreomacular adhesion in age-related macular degeneration: Spectral OCT and surgical results. American Journal of Ophthalmology 146:218-227. PDF

C MacDonald, D Yu, M Buibas, and GA Silva (2008) Diffusion modeling of ATP signaling suggests a partially regenerative mechanism underlies astrocyte intercellular calcium waves. Frontiers in Neuroengineering 1:1-13.

I Falkenstein, L Cheng, F Wong-Staal, A Tammewar, E Barron, GA Silva, Q-X Li, D Yu, G Liu, N Ke, J MacDonald, and WR Freeman (2008) Toxicity and intraocular properties of a novel long acting anti-proliferative and anti-angiogenic compound IMS2186. Current Eye Research 33:599-609.

M Hashemi, M Buibas, and GA Silva (2008) Automated detection of intercellular signaling in astrocyte networks using the converging squares algorithm. Journal of Neuroscience Methods 170:294-299. PDF

S Pathak, MC Davidson, and GA Silva (2007) Characterization of the functional binding properties of antibody conjugated quantum dots. NanoLetters 7:1839-1845. PDF

I Kozak, OR Kayikcioglul, Cheng, I Falkenstein, GA Silva, D Yu, and WR Freeman (2006) The effect of recombinant human hyaluronidase on dexamethasone penetration into the posterior segment of the eye after sub-Tenon’s injection. Journal of Ocular Pharmacology and Therapeutics 22:362-369.

M Ho, D Yu, MC Davidson, and GA Silva (2006) Comparison of standard surface chemistries for culturing mesenchymal stem cells prior to neural differentiation. Biomaterials 27:4333-4339. PDF

S Pathak, E Cao, MC Davidson, S Jin, and GA Silva (2006) Quantum dot applications in neuroscience: New tools for probing neurons and glia. Journal of Neuroscience 26:1893-1895. PDF

GA Silva, C Czeisler, KL Niece, E Beniash, D Harrington, JA Kessler, and SI Stupp (2004) Selective differentiation of neural progenitor cells by high-density epitope nanofibers. Science 303:1352-1355. PDF

GA Silva and DR Pepperberg (2004) Step response of mouse rod photoreceptors modeled in terms of elemental photic signals. IEEE Transactions on Biomedical Engineering 51:3-12. PDF

GA Silva, JR Hetling, and DR Pepperberg (2001) Dynamic and steady-state light adaptation of mouse rod photoreceptors in vivo. Journal of Physiology 534:203-216. PDF

GA Silva, E Theriault, LR Mills, PS Pennefather, and CJ Feeney (1999) Group I and II metabotropic glutamate receptor expression in cultured rat spinal cord astrocytes. Neuroscience Letters 263:117- 120. PDF

GA Silva, CJ Feeney, LR Mills, and E Theriault (1998) A novel and rapid method for culturing pure rat spinal cord astrocytes on untreated glass. Journal of Neuroscience Methods 80: 75-79. PDF