Chethan is a Postdoctoral Research Associate In the Neural Prosthetics Laboratory at Stanford, working with Profs. Jaimie Henderson and Krishna Shenoy. His current research interests include the development of reliable, high-performance decoding algorithms for neural prosthetics, and understanding the role of neural dynamics in motor cortex. His primary research focus is the clinical translation of Brain-Machine Interface algorithms with research participants with tetraplegia, as part of the BrainGate2 clinical trials.

Chethan received his bachelors degrees from North Carolina State University in Computer Engineering and Physics in 2002, and his Ph.D. in Electrical Engineering from Cornell University in 2010, working with Prof. Sheila Nirenberg. His thesis work focused on the visual system, investigating the ability of the retina to adjust itself to different environments, and the affects of these adjustments on information transmission between the retina and the brain. Afterwards, as a Postdoctoral Researcher with Prof. Nirenberg, he developed devices for precise optical stimulation of neural circuitry, both for basic science and clinical applications.

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Honors & Awards

  • Dean's Fellowship, Stanford University (2012)
  • Postdoctoral Fellowship, Craig H. Neilsen Foundation for Spinal Cord Injury Research (2013-2015)

Professional Education

  • Doctor of Philosophy, Cornell University (2011)
  • Bachelor of Science, North Carolina State Univ At Raleigh (2002)
  • Bachelor of Arts, North Carolina State Univ At Raleigh (2002)

Stanford Advisors

Current Research and Scholarly Interests

Brain-Machine Interfaces to restore function for people with paralysis

All Publications

  • Virtual typing by people with tetraplegia using a self-calibrating intracortical brain-computer interface. Science translational medicine Jarosiewicz, B., Sarma, A. A., Bacher, D., Masse, N. Y., Simeral, J. D., Sorice, B., Oakley, E. M., Blabe, C., Pandarinath, C., Gilja, V., Cash, S. S., Eskandar, E. N., Friehs, G., Henderson, J. M., Shenoy, K. V., Donoghue, J. P., Hochberg, L. R. 2015; 7 (313): 313ra179-?


    Brain-computer interfaces (BCIs) promise to restore independence for people with severe motor disabilities by translating decoded neural activity directly into the control of a computer. However, recorded neural signals are not stationary (that is, can change over time), degrading the quality of decoding. Requiring users to pause what they are doing whenever signals change to perform decoder recalibration routines is time-consuming and impractical for everyday use of BCIs. We demonstrate that signal nonstationarity in an intracortical BCI can be mitigated automatically in software, enabling long periods (hours to days) of self-paced point-and-click typing by people with tetraplegia, without degradation in neural control. Three key innovations were included in our approach: tracking the statistics of the neural activity during self-timed pauses in neural control, velocity bias correction during neural control, and periodically recalibrating the decoder using data acquired during typing by mapping neural activity to movement intentions that are inferred retrospectively based on the user's self-selected targets. These methods, which can be extended to a variety of neurally controlled applications, advance the potential for intracortical BCIs to help restore independent communication and assistive device control for people with paralysis.

    View details for DOI 10.1126/scitranslmed.aac7328

    View details for PubMedID 26560357

  • Clinical translation of a high-performance neural prosthesis. Nature medicine Gilja, V., Pandarinath, C., Blabe, C. H., Nuyujukian, P., Simeral, J. D., Sarma, A. A., Sorice, B. L., Perge, J. A., Jarosiewicz, B., Hochberg, L. R., Shenoy, K. V., Henderson, J. M. 2015; 21 (10): 1142-1145


    Neural prostheses have the potential to improve the quality of life of individuals with paralysis by directly mapping neural activity to limb- and computer-control signals. We translated a neural prosthetic system previously developed in animal model studies for use by two individuals with amyotrophic lateral sclerosis who had intracortical microelectrode arrays placed in motor cortex. Measured more than 1 year after implant, the neural cursor-control system showed the highest published performance achieved by a person to date, more than double that of previous pilot clinical trial participants.

    View details for DOI 10.1038/nm.3953

    View details for PubMedID 26413781

  • Neural population dynamics in human motor cortex during movements in people with ALS. eLife Pandarinath, C., Gilja, V., Blabe, C. H., Nuyujukian, P., Sarma, A. A., Sorice, B. L., Eskandar, E. N., Hochberg, L. R., Henderson, J. M., Shenoy, K. V. 2015; 4


    The prevailing view of motor cortex holds that motor cortical neural activity represents muscle or movement parameters. However, recent studies in non-human primates have shown that neural activity does not simply represent muscle or movement parameters; instead, its temporal structure is well-described by a dynamical system where activity during movement evolves lawfully from an initial pre-movement state. In this study, we analyze neuronal ensemble activity in motor cortex in two clinical trial participants diagnosed with Amyotrophic Lateral Sclerosis (ALS). We find that activity in human motor cortex has similar dynamical structure to that of non-human primates, indicating that human motor cortex contains a similar underlying dynamical system for movement generation.

    View details for DOI 10.7554/eLife.07436

    View details for PubMedID 26099302

  • Recruitment of PfSET2 by RNA Polymerase II to Variant Antigen Encoding Loci Contributes to Antigenic Variation in P. falciparum PLOS PATHOGENS Ukaegbu, U. E., Kishore, S. P., Kwiatkowski, D. L., Pandarinath, C., Dahan-Pasternak, N., Dzikowski, R., Deitsch, K. W. 2014; 10 (1)


    Histone modifications are important regulators of gene expression in all eukaryotes. In Plasmodium falciparum, these epigenetic marks regulate expression of genes involved in several aspects of host-parasite interactions, including antigenic variation. While the identities and genomic positions of many histone modifications have now been cataloged, how they are targeted to defined genomic regions remains poorly understood. For example, how variant antigen encoding loci (var) are targeted for deposition of unique histone marks is a mystery that continues to perplex the field. Here we describe the recruitment of an ortholog of the histone modifier SET2 to var genes through direct interactions with the C-terminal domain (CTD) of RNA polymerase II. In higher eukaryotes, SET2 is a histone methyltransferase recruited by RNA pol II during mRNA transcription; however, the ortholog in P. falciparum (PfSET2) has an atypical architecture and its role in regulating transcription is unknown. Here we show that PfSET2 binds to the unphosphorylated form of the CTD, a property inconsistent with its recruitment during mRNA synthesis. Further, we show that H3K36me3, the epigenetic mark deposited by PfSET2, is enriched at both active and silent var gene loci, providing additional evidence that its recruitment is not associated with mRNA production. Over-expression of a dominant negative form of PfSET2 designed to disrupt binding to RNA pol II induced rapid var gene expression switching, confirming both the importance of PfSET2 in var gene regulation and a role for RNA pol II in its recruitment. RNA pol II is known to transcribe non-coding RNAs from both active and silent var genes, providing a possible mechanism by which it could recruit PfSET2 to var loci. This work unifies previous reports of histone modifications, the production of ncRNAs, and the promoter activity of var introns into a mechanism that contributes to antigenic variation by malaria parasites.

    View details for DOI 10.1371/journal.ppat.1003854

    View details for Web of Science ID 000332640900003

    View details for PubMedID 24391504

  • A system for optically controlling neural circuits with very high spatial and temporal resolution IEEE 13th International Conference on Bioinformatics and Bioengineering (BIBE) Pandarinath, C., Carlson, E. T., Nirenberg, S. 2013: 1-4
  • Retinal prosthetic strategy with the capacity to restore normal vision PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nirenberg, S., Pandarinath, C. 2012; 109 (37): 15012-15017


    Retinal prosthetics offer hope for patients with retinal degenerative diseases. There are 20-25 million people worldwide who are blind or facing blindness due to these diseases, and they have few treatment options. Drug therapies are able to help a small fraction of the population, but for the vast majority, their best hope is through prosthetic devices [reviewed in Chader et al. (2009) Prog Brain Res 175:317-332]. Current prosthetics, however, are still very limited in the vision that they provide: for example, they allow for perception of spots of light and high-contrast edges, but not natural images. Efforts to improve prosthetic capabilities have focused largely on increasing the resolution of the device's stimulators (either electrodes or optogenetic transducers). Here, we show that a second factor is also critical: driving the stimulators with the retina's neural code. Using the mouse as a model system, we generated a prosthetic system that incorporates the code. This dramatically increased the system's capabilities--well beyond what can be achieved just by increasing resolution. Furthermore, the results show, using 9,800 optogenetically stimulated ganglion cell responses, that the combined effect of using the code and high-resolution stimulation is able to bring prosthetic capabilities into the realm of normal image representation.

    View details for DOI 10.1073/pnas.1207035109

    View details for Web of Science ID 000309208000063

    View details for PubMedID 22891310

  • Symmetry Breakdown in the ON and OFF Pathways of the Retina at Night: Functional Implications JOURNAL OF NEUROSCIENCE Pandarinath, C., Victor, J. D., Nirenberg, S. 2010; 30 (30): 10006-10014


    Several recent studies have shown that the ON and OFF channels of the visual system are not simple mirror images of each other, that their response characteristics are asymmetric (Chichilnisky and Kalmar, 2002; Sagdullaev and McCall, 2005). How the asymmetries bear on visual processing is not well understood. Here, we show that ON and OFF ganglion cells show a strong asymmetry in their temporal adaptation to photopic (day) and scotopic (night) conditions and that the asymmetry confers a functional advantage. Under photopic conditions, the ON and OFF ganglion cells show similar temporal characteristics. Under scotopic conditions, the two cell classes diverge-ON cells shift their tuning to low temporal frequencies, whereas OFF cells continue to respond to high. This difference in processing corresponds to an asymmetry in the natural world, one produced by the Poisson nature of photon capture and persists over a broad range of light levels. This work characterizes a previously unknown divergence in the ON and OFF pathways and its utility to visual processing. Furthermore, the results have implications for downstream circuitry and thus offer new constraints for models of downstream processing, since ganglion cells serve as building blocks for circuits in higher brain areas. For example, if simple cells in visual cortex rely on complementary interactions between the two pathways, such as push-pull interactions (Alonso et al., 2001; Hirsch, 2003), their receptive fields may be radically different under scotopic conditions, when the ON and OFF pathways are out of sync.

    View details for DOI 10.1523/JNEUROSCI.5616-09.2010

    View details for Web of Science ID 000280503500008

    View details for PubMedID 20668185

  • A novel mechanism for switching a neural system from one state to another FRONTIERS IN COMPUTATIONAL NEUROSCIENCE Pandarinath, C., Bomash, I., Victor, J. D., Prusky, G. T., Tschetter, W. W., Nirenberg, S. 2010; 4


    An animal's ability to rapidly adjust to new conditions is essential to its survival. The nervous system, then, must be built with the flexibility to adjust, or shift, its processing capabilities on the fly. To understand how this flexibility comes about, we tracked a well-known behavioral shift, a visual integration shift, down to its underlying circuitry, and found that it is produced by a novel mechanism - a change in gap junction coupling that can turn a cell class on and off. The results showed that the turning on and off of a cell class shifted the circuit's behavior from one state to another, and, likewise, the animal's behavior. The widespread presence of similar gap junction-coupled networks in the brain suggests that this mechanism may underlie other behavioral shifts as well.

    View details for DOI 10.3389/fncom.2010.00002

    View details for Web of Science ID 000283731200001

    View details for PubMedID 20407612

  • Ganglion Cell Adaptability: Does the Coupling of Horizontal Cells Play a Role? PLOS ONE Dedek, K., Pandarinath, C., Alam, N. M., Wellershaus, K., Schubert, T., Willecke, K., Prusky, G. T., Weiler, R., Nirenberg, S. 2008; 3 (3)


    The visual system can adjust itself to different visual environments. One of the most well known examples of this is the shift in spatial tuning that occurs in retinal ganglion cells with the change from night to day vision. This shift is thought to be produced by a change in the ganglion cell receptive field surround, mediated by a decrease in the coupling of horizontal cells.To test this hypothesis, we used a transgenic mouse line, a connexin57-deficient line, in which horizontal cell coupling was abolished. Measurements, both at the ganglion cell level and the level of behavioral performance, showed no differences between wild-type retinas and retinas with decoupled horizontal cells from connexin57-deficient mice.This analysis showed that the coupling and uncoupling of horizontal cells does not play a dominant role in spatial tuning and its adjustability to night and day light conditions. Instead, our data suggest that another mechanism, likely arising in the inner retina, must be responsible.

    View details for DOI 10.1371/journal.pone.0001714

    View details for Web of Science ID 000260586600010

    View details for PubMedID 18320035

  • Structural, microstructural, and electrical properties of gold films and Schottky contacts on remote plasma-cleaned, n-type ZnO{0001} surfaces JOURNAL OF APPLIED PHYSICS Coppa, B. J., Fulton, C. C., Kiesel, S. M., Davis, R. F., Pandarinath, C., Burnette, J. E., Nemanich, R. J., SMITH, D. J. 2005; 97 (10)

    View details for DOI 10.1063/1.1898436

    View details for Web of Science ID 000230168100040

  • Preparation and characterization of atomically clean, stoichlometric surfaces of AIN(0001) JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A Mecouch, W. J., Wagner, B. P., Reitmeier, Z. J., Davis, R. F., Pandarinath, C., Rodriguez, B. J., Nemanich, R. J. 2005; 23 (1): 72-77

    View details for DOI 10.1116/1.1830497

    View details for Web of Science ID 000226558900011