Curriculum Vitae
Joe W. Graham, Ph.D.


Contact Information

Email:          joe.w.graham@gmail.com

Web:            research.joegraham.name

LinkedIn:      ch.linkedin.com/in/joewgraham


Work Experience
Dura-Bernal Lab

    02/2020 -- Present:    Research Scientist
  • Developing, documenting, promoting, and training new users in NetPyNE, a Python package for the development, simulation, parallelization, analysis, and optimization of biological neuronal networks using the NEURON simulator.
  • Utilizing NetPyNE to create and assist in the development of models of a variety of neural circuits and scales.
SUNY Downstate Medical Center
Department of Physiology and Pharmacology 

    11/2016 -- 11/2019:    Contract Neuroscientist
  • Utilized a variety of software tools (NEURON, Python, NetPyNE) to develop simulations and analysis in support of Embedded Ensemble Encoding (EEE) Theory.
  • Developed and refined morphologically-simplified models of cortical neurons.
  • Created network models of cortical form and function.
  • Contributed to the open-source simulation framework NetPyNE.

    08/2010 -- 11/2013:    Postdoctoral Scholar 

  • Revamped, refined and improved the neuronal morphology data processing software toolchain.  
  • Led the development of a Python-based neuronal morphology analysis toolkit (Pneumatk).
  • Produced machine learning software for the objective classification of neuronal morphologies.
  • Synthesized virtual neocortical neuronal morphologies.
  • Coordinated the Morphology Working Group.


    12/2008 -- 06/2009:    Adjunct Researcher 
    06/2008 -- 12/2008:    Postdoctoral Scholar 

  • Completed a program for the analysis of neuronal morphology, the fitting of basic morphological parameters, and the generation of realistic virtual morphologies.  
  • Quantified a set of basic morphological parameters in experimentally reconstructed motoneurons which was sufficient to generate virtual motoneurons with dendritic morphometric properties statistically indistinguishable from the reconstructions.

Arizona State University
Center for Rehabilitation Neuroscience and Rehabilitation Engineering

    11/2003 -- 06/2008:    Graduate Research Associate 

  • Assembled and developed a complete intracellular electrophysiology and vital signs monitoring system for an in vivo rodent model, including the design of custom equipment.
  • Developed morphologically-simplified computational models of motoneuron electrophysiology in short-term and long-term spinal cord injury.
  • Created algorithms for the analysis and generation of neuronal morphology.

Arizona State University
Ira A. Fulton School of Engineering

    09/2004 -- 12/2004:    Guest Lecturer -- BME413 Biomedical Instrumentation Course

  • Delivered a series of lectures on the theory and clinical application of basic biomedical instrumentation to an upper-level undergraduate class.
  • Developed presentation materials, homework assignments, and quiz and test questions.
    
    10/1999 -- 10/2001:    Tutor and Study-Group Facilitator -- Engineering Tutoring Center

  • Tutored undergraduate engineering students in science, engineering, math, physics, and statistics courses.
  • Organized and facilitated student study group sessions.


Education

Arizona State University

Ira A. Fulton School of Engineering

Harrington Department of Bioengineering


    5/2008: Doctor of Philosophy        

    National Science Foundation IGERT Graduate Research Fellow    

    Specialization: neural and musculoskeletal form and function

    Sub-specialization: German language

    Grade Point Average: 4.0 


    5/2001: Bachelor of Science in Engineering

    National Merit Scholar, ASU Parents Association Scholar

    Specialization: neuroscience and biomechanics

    Minor: Spanish language

    Grade Point Average: 3.86 (summa cum laude)



Specialized Training
National Science Foundation
Integrative Graduate Education and Research Training (IGERT) Fellowship
Program: Neural and Musculoskeletal Adaptations in Form and Function

    10/2001 -- 05/2008: NSF-IGERT Research Fellow

  • Took specialized, interdisciplinary IGERT courses with labs in anatomy & biomechanics, computation & visualization, and experimental neurophysiology.
  • Interacted and collaborated with students and faculty from bioengineering, biology, anthropology, kinesiology, math & statistics, computer science, and neuroscience.
  • Presented research results in poster and lecture format annually during the public IGERT Research Day conference.
  • Fellowship included three years of full funding and subsequent research and travel support.

The Ohio State University
Spinal Cord Injury Techniques Course

    07/2004 -- 08/2004

  • Learned surgical, animal care, and outcome measurement techniques for rodent models of spinal cord injury.
  • Interacted with spinal cord injury experts from diverse backgrounds including basic science, applied engineering, and clinical.

The Neurosciences Institute
Neuroscience Workshop on Internal Models of Motor Control

    07/2002 -- 08/2002

  • Attended a series of interactive lectures and workshops concerning current theories of internal models for motor control.
  • Critically analyzed published experimental data and their implications for internal models.


Volunteer Service

    06/2005 -- 06/2007: Chapter President


  • Spearheaded the Tsurakú Project to improve the water and sanitary conditions in a village in Ecuador by focusing on culturally, environmentally and economically sustainable engineering solutions. 
  • Oversaw a $10,000 grant from the Ira A. Fulton School of Engineering for the Visualizing the Campus Metabolism project.  Aimed to reduce energy use in campus buildings via visual lobby displays of real-time and historical-usage data about electrical and water consumption and garbage/recycling generation, collected with specialized sensors.
  • Produced and delivered presentations during public general meetings, project planning meetings, and fundraising events.
  • Contributed to increasing engineering student global involvement by serving on the advisory board of the engineering college's Global Futures Initiative.


    10/2003 -- 06/2005: Member


  • Contributed to the Juarez Project to develop an off-grid school in Mexico.
  • Participated in and contributed to project planning meetings, fundraising efforts, and public meetings.
  • Mentored undergraduate bioengineering students' senior design projects of adaptive devices for handicapped people in Malawi.


Publications

Markram H, et al. Reconstruction and simulation of neocortical microcircuitry. Cell 2015, 163(2), 456–492.


Ramaswamy S, et al. The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex.

Frontiers in Neural Circuits 2015.


Graham JW. Algorithmic Reconstruction of Motoneuron Morphology. Encyclopedia of Computational Neuroscience 2013. SpringerReference. Editors: Jaeger D. and Jung R. 


Graham JW. Modeling motoneurons and the effects of spinal cord injury. Ph.D. Dissertation, Arizona State University 2008.


Graham J, Booth V and Jung R. Modeling motoneurons after spinal cord injury: Persistent inward currents and plateau potentials. Neurocomputing 2004, 65-66: 719-726.


Presentations

07/2020: Data-driven multiscale modeling with NetPyNE: new features and example models. Poster presented at Computational Neuroscience 2020, Online Conference


07/2019: Experiments and modeling of NMDA plateau potentials in cortical pyramidal neurons. Poster presented at Computational Neuroscience 2019, Barcelona, Spain


07/2019: The shape of thought: data-driven synthesis of neuronal morphology and the search for fundamental parameters of form. Poster presented at Computational Neuroscience 2019, Barcelona, Spain


11/2018: Embedded ensemble encoding: a hypothesis for reconciling cortical coding strategies. Poster presented at Neuroscience 2018, San Diego, CA.


11/2017: On the origin of nervous systems: The Versatile Gut Hypothesis. Poster presented at Neuroscience 2017, Washington D.C.


03/2017: Embedded Ensemble Encoding: A theory of brain cortex function. Poster presented at Interagency Modeling and Analysis Group: Multiscale Modeling Meeting 2017, Bethesda, MD.


11/2012: A Unifying Model of the Neocortical Column 4: Morphological Cell Types.  Poster presented at Neuroscience 2012, New Orleans, LA.


11/2011: Data-driven computational synthesis of neuronal morphologies.  Poster presented at Neuroscience 2011, Washington, DC.


11/2008: Morphologically realistic computational models of rat hindlimb motoneurons and the effects of spinal cord injury. Poster presented at Neuroscience 2008, Washington, DC.


11/2007: Morphologically realistic computational models of rat hindlimb motoneurons after spinal cord injury. Poster presented at Neuroscience 2007, San Diego, CA.

 

07/2007: Modeling morphological changes in spinal motoneurons after spinal cord injury to explore changes in electrical behavior. Poster presented at Computational Neuroscience 2007, Toronto, CN.


10/2006: Location and 3D reconstruction of motoneurons innervating gastrocnemius medialis and tibialis anterior in the rat.  Poster presented at Neuroscience 2006, Atlanta, GA.


02/2005: Combining experimental and computational neuroscience to explore spinal reflexes following spinal cord injury. Lecture and poster presented at IGERT Research Day at Arizona State University.


07/2004: Modeling motoneurons after spinal cord injury: Persistent inward currents and plateau potentials. Poster presented at Computational Neuroscience 2004 meeting, Baltimore, MD.


02/2003: Modeling motoneurons after spinal cord injury: Persistent inward currents and plateau potentials. Lecture and poster presented at IGERT Research Day at Arizona State University.


05/2001: Three-dimensional non-invasive wound measurement device. Poster presented at Senior Design Project Competition, Harrington Department of Bioengineering at Arizona State University (Third Place Winner).

 

Memberships

07/2006 –- Present        Society for Neuroscience

10/2004 –- 06/2008       Alpha Eta Mu Beta Bioengineering Honors Society

11/1998 –- 05/2001       Tau Beta Pi Engineering Honors Society