I am interested in the computations that permit intelligent agents to perform inference, planning, and control.  This includes specifically how the brain builds representations, plans, and produces actions.  I am also interested in leveraging statistical tools to enable more rigorous experimental investigation and analysis of data related to how the brain implements these computations.  Towards this end, I enjoy working on normative solutions to neuroscience problems and collaborating on increasingly naturalistic neuroscience experiments that investigate ethologically relevant behaviors and capacities.

My research thus far has related to methods for analyzing neuroscience-related data, brain-computer interfacing, and other topics.  Feel free to check out my google scholar profile. 


Bayesian methods for event analysis of intracellular currents. *Josh Merel, *Ben Shababo, Alex Naka, Hillel Adesnik, Liam Paninski. (Journal of Neuroscience Methods, 2016) [*Equal authorship contribution][link][arxiv][github]

Population-level representation of a temporal sequence underlying skilled behavior. Michel A. Picardo, *Josh Merel, *Kalman A. Katlowitz, *Daniela Vallentin, Daniel E. Okobi, Sam E. Benezra, Rachel C. Clary, Eftychios A. Pnevmatikakis, Liam Paninski, Michael A. Long. (Neuron, 2016) [*Equal authorship contribution][link][code]

Neuroprosthetic decoder training as imitation learning. Josh Merel, David Carlson, Liam Paninski, John P. Cunningham. (PLoS Computational Biology, 2016) [link][github

Simultaneous denoising, deconvolution, and demixing of calcium imaging data. Eftychios A. Pnevmatikakis, Daniel Soudry, Yuanjun Gao, Tim Machado, Josh Merel, David Pfau, Thomas Reardon, Yu Mu, Clay Lacefield, Weijian Yang, Misha Ahrens, Randy Bruno, Tom Jessell, Rafael Yuste, Darcy S. Peterka, Liam Paninski. (Neuron, 2016) [link][code]

Encoder-Decoder optimization for brain-computer interfaces. Josh Merel, Donald M. Pianto, John P. Cunningham, Liam Paninski. (PLoS Computational Biology, 2015) [link][code]

The spatiotemporal receptive fields of barrel cortex neurons revealed by reverse correlation of synaptic input . Alejandro Ramirez, Eftychios A. Pnevmatikakis, Josh Merel, Kenneth D. Miller, Liam Paninski, Randy M. Bruno . (Nature Neuroscience 2014) [link] ...contributed statistical methods/analyses, including a multi-neuron regularization technique described in online methods section "Separability and shared structure".

A multi-agent control framework for co-adaptation in brain-computer interfaces. *Josh Merel, *Roy Fox, Tony Jebara, Liam Paninski. (NIPS 2013) [*Equal authorship contribution] [pdf] [code]

Bayesian spike inference from calcium imaging data. Eftychios A. Pnevmatikakis, Josh Merel, Ari Pakman, Liam Paninski. (Asilomar Conference on Signals, Computers and Systems 2013) [pdf] [code]

Decoding Arm and Hand Movements Across Layers of the Macaque Frontal Cortices. Yan T. Wong, Mariana Vigeral, David Putrino, David Pfau, Josh Merel, Liam Paninski, Bijan Pesaran. (in IEEE EMBS 2012) [pdf]