working papers

  • JT Vogelstein, et al. Graph Classification using Signal Subgraphs: Applications in Statistical Connectomics. Submitted. arxiv, code, repo.
  • W Gray, et al. MR Connectome Automated Pipeline. Accepted pending minor revisions to IEEE EMBS. code.
  • JT Vogelstein, et al. Shuffled Graph Classification: Theory and Applications in Statistical Connectomics. To be submitted to IEEE PAMI any day now.
  • JT Vogelstein, et al. Fast Inexact Graph Matching with Applications in Connectomics To be submitted to IEEE PAMI any day now.
  • Roberts NJ*, Vogelstein JT*, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The Predictive Capacity of Personal Genome Sequencing. To be submitted to Science Translational Medicine any day now.

journal publications

  1. CE Priebe, JT Vogelstein, D Bock. Optimizing the quantity/quality trade-off in connectome inference. Accepted to Communications in Statistics---Theory and Methods. arvix.
  2. JT Vogelstein, et al. Are mental properties supervenient on brain properties? . Nature Scientific Reports, (1):100, 2011 .
  3. SB Hofer, et al. Differential tuning and population dynamics of excitatory and inhibitory neurons reflect differences in local intracortical connectivity. abstract, pdf (including supp). Nature Neuroscience, 2011.
  4. Vogelstein JT, Packer AM, Machado TA, Sippy T, Babadi B, Yuste R, Paninski L. Fast non-negative deconvolution for spike train inference from population calcium imaging. J Neurophys, 104:3691-3704, 2010.
  5. Mishchenko Y, Vogelstein JT, Paninski L. A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data. Annals of Applied Statistics, in press.
  6. Paninski L, Ahmadian Y, Ferreira D, Koyama S, Rahnama Rad K, Vidne M, Vogelstein JT, Wu W. A new look at state-space models for neural data. Journal of Computational Neuroscience, 2009.
  7. Vogelstein JT, Watson BO, Packer AM, Jedynak B, Yuste R, Paninski L. Spike inference from calcium imaging using sequential Monte Carlo methods. Biophysical Journal, 2009.
  8. Vogelstein RJ, Mallik K, Vogelstein JT, Cauwenberghs G. Reconfigurable Silicon Array of Integrate-and-Fire Neurons with Conductance-Based Synapses. IEEE Transactions on Neural Networks, 18(1):253-65, 2007.
  9. Vogelstein JT, Angelaki D, Snyder L. Accuracy of saccades to remembered targets depends on body orientation in space. J Neurophys, 90(1):521-4, 2003.
  10. Vogelstein JT, Vogelstein JV, Vogelstein B. Testing the effects of genetic variations using MINIME technology. Science, 286:2300-2301, 1999. (Essay)
  11. Greenspan DL, Connolly DC, Wu R, Lei RY, Vogelstein JT, Kim YT, Mok JE, Munoz N, Bosch FX, Shah K, Cho KR. Loss of FHIT expression in cervical carcinoma cell lines and primary tumors. Cancer Research, 57(21):4692-8, 1999.

other publications

  1. R Yuste, J MacLean, JT Vogelstein, L Paninski. Imaging Action Potentials with Calcium Indicators. Cold Spring Harb Protoc; 2011; doi:10.1101/pdb.prot5650. abstract, pdf.

conferences

  1. Vogelstein JT, Fishkind DE, Sussman DL, Priebe CE. Large Graph Classification: Theory and Statistical Connectomics Applications. IMA conference on Large Graphs, 2011.
  2. Vogelstein JT, Sussman DL, Tang M, Fishkind DE, Priebe CE. Dot Product Embedding in Large (Errorfully Observed) Graphs with Applications in Statistical Connectomics. IMA conference on Large Graphs, 2011.
  3. Vogelstein JT, Perlman E, Bock D, Lee W-C, Chang M, Kasthuri B, Kazhdan M, Reid C, Lichtman J, Burns R, Vogelstein RJ. Open Connectome Project: collectively reverse engineering the brain one synapse at a time. Neuroinformatics, 2011.
  4. Vogelstein JT, Gray W, Vogelstein RJ, Bogovic J, Resnick S, Prince J, Priebe CE. Connectome Classification: Statistical Graph Theoretic Methods for Analysis of MR-Connectome Data. Organization for Human Brain Mapping, 2011.
  5. Vogelstein JT, Gray W, Martin JG, Coppersmith GC, Dredze M, Bogovic J, Prince JL, Resnick SM, Priebe CE, Vogelstein RJ. Connectome Classification using statistical graph theory and machine learning. Society for Neuroscience, 2011.
  6. Gray WR, Bogovic JA, Vogelstein JT, Ye C, Landman BA, Prince JL, Vogelstein RJ. Magnetic resonance connectome automated pipeline and repeatability analysis. Society for Neuroscience, 2011.
  7. Vogelstein JT, Priebe CE, Burns R, Vogelstein RH, Lichtman J. Measuring and Reconstructing the Brain at the Synaptic Scale: Towards a Bioļ¬delic Human Brain in silico. DARPA Neural Engineering, Science and Technology Forum, 2010. (abstract.)
  8. Gray WR, Vogelstein JT, Bogovic J, Carass A, Prince JL, Landman B, Pham D, Ferrucci L, Resnick SM, Priebe CE, Vogelstein RJ. Graph-Theoretical Methods for Statistical Inference on MR Connectome Data. DARPA Neural Engineering, Science and Technology Forum, 2010. (abstract.)
  9. Vogelstein JT, Bogovic J, Carass A, Gray WR, Prince JL, Landman B, Pham D, Ferrucci L, Resnick SM, Priebe CE, Vogelstein RJ. Graph-Theoretical Methods for Statistical Inference on MR Connectome Data. Organization for Human Brain Mapping, 2010. (abstract.)
  10. Vogelstein JT, Vogelstein RJ, Priebe CE. A Neurocognitive Graph-Theoretical Approach to Understanding the Relationship Between Minds and Brains.CSHL conference on Neural Circuits, 2010.
  11. Vogelstein JT, Mishchenko Y, Packer AM, Machado TA, Yuste R, Paninski L. Towards Confirming Neural Circuit Inference from Population Calcium Imaging. COSYNE, 2010.
  12. Vogelstein JT, Mishchenko Y, Packer AM, Machado TA, Yuste R, Paninski L. Towards Confirming Neural Circuit Inference from Population Calcium Imaging. NIPS Workshop on Connectivity Inference in Neuroimaging, 2009.
  13. Vogelstein JT,Packer AM, Mishchenko Y, Yuste R, Paninski L. Towards Inferring Neural Circuits from Calcium Population Imaging. COSYNE, 2010.
  14. Vogelstein JT, Mishchenko Y, Packer AM, Machado TA, Yuste R, Paninski L. Towards Confirming Neural Circuit Inference from Population Calcium Imaging. Society forNeuroscience, 2009.
  15. Vogelstein JT,Packer AM, Mishchenko Y, Yuste R, Paninski L. Towards Inferring Neural Circuits from Calcium Population Imaging. COSYNE, 2009.
  16. Vogelstein JT, Babadi B, Watson BO, Yuste R, Paninski L. From Calcium Sensitive Fluorescence Movies to Spike Trains. Society forNeuroscience, 2008.
  17. Vogelstein JT, Paninski L. Spike Inference from Calcium Imaging using Sequential Monte Carlo Methods. Statistical and Applied Mathematical Sciences Institute (SAMSI) Program on Sequential Monte Carlo Methods, 2008.
  18. Vogelstein JT, Babadi B, Paninski L. Model-Based Optimal Inference of Spike Times and Calcium Dynamics given Noisy and Intermittent Calcium-Fluorescence Imaging. COSYNE, 2008. (spotlight.)
  19. Vogelstein JT, Babadi B, Watson BO, Yuste R, Paninski L. Inferring Spike Trains Given Calcium-Sensitive Fluorescence Observations. Statistical Analysis of Neural Data, 2008.
  20. Vogelstein JT, Paninski L. Inferring Spike Trains, Learning Tuning Curves, and Estimating Connectivity from Calcium Imaging. Integrative Approaches to Brain Complexity, 2008.
  21. Vogelstein JT, Jedynak B, Zhang K, Paninski L. Inferring Spike Trains, Neural Filters, and Network Circuits from in vivo Calcium Imaging. Society for Neuroscience, 2007. (abstract.)
  22. Vogelstein JT, Zhang K, Jedynak B, Paninski L. Maximum Likelihood Inference of Neuronal Dynamics under Noisy and Intermittent Observations using Sequential Monte Carlo EM Algorithms. COSYNE, 2007.
  23. Vogelstein JT, Zhang K, Paninski L. Society for Neuroscience, 2007. (abstract.)
  24. Vogelstein JT, Zhang K. A novel theory for simultaneous representation of multiple dynamic states in hippocampus. Society for Neuroscience, 2004. (abstract.)
  25. Vogelstein JT, Zhang K. A novel theory for simultaneous representation of multiple dynamic states in hippocampus. Society for Neuroscience, 2004. (abstract.)
  26. Vogelstein JT, Snyder LH, Warchol M, Angelaki DE. Up-down asymmetry in memory guided saccadic eye movements are independent of head orientation in space. Society for Neuroscience, 2002. (abstract.)

reviewing

  • Reviewer, Annals of Applied Statistics, 2010 to Present.
  • Reviewer, Journal of Neurophysiology, 2009 to Present.

other talks

  • OOPSI: A Family of Optimal OPtical Spike Inference Algorithms for Inferring Neural Connectivity from Population Calcium Imaging. Dissertation Defense, 2009. (link to video and slides.)
  • From Calcium Imaging to Spikes, using State-Space Methods. Redwood Center for Theoretical Neuroscience, 2008. (link to video.)
  • a whole bunch, email me for slides.

unpublished work

  1. Vogelstein JT, Connor CE, et al. A Six Degree-Of-Freedom Two-Photon Microscope for Functional Imaging in Awake Behaving Primates, 2004 to Present.
  2. Vogelstein JT, Young ED. A Spiking Model of Ventral Cochlear Nucleus in Response to Complex Stimuli, 2004.
  3. Vogelstein JT, Moran D. A Hardware Emulator of Awake Behaving Macaque Primary Motor Cortex, 2003.

education

  • Ph.D. Neuroscience, Johns Hopkins School of Medicine, 2003-2009. (dissertation.)
  • M.S. Applied Mathematics & Statistics, Johns Hopkins University, 2009.
  • B.S. Biomedical Engineering, Washington University in St. Louis, 1998-2002.

academic experience

  • 2010 to Present: Postdoctoral Fellow under Professor Carey E Priebe, Department of Applied Mathematics and Statistics, Johns Hopkins University.
  • Summer of 2001: Research Assistant under Professor Randy O'Reilly, Department of Psychology, University of Colorado.
  • Summer of 1999: Research Assistant under Dr. Jeffrey Williams, Department of Neurosurgery, Johns Hopkins Hospital.
  • Summer of 1998: Research Assistant under Professor Kathy Cho, Department of Pathology, Johns Hopkins School of Medicine.

professional experience

  • 2004 to Present: Partner, Global Domain Partners, LLC.
  • Summer of 2000: Clinical Engineer, Johns Hopkins Hospital.

misc

  • Successfully completed Molecular Biology Summer Workshop. Smith College, Mass, USA, 2008.
  • Successfully completed Advanced Techniques in Molecular Neuroscience. Cold Spring Harbor, New York, USA, 2008.
  • Successfully audited Imaging Structure and Function of the Nervous System. Cold Spring Harbor, New York, USA, 2005.
  • Successfully completed Advanced Course in Computational Neuroscience. Obidos, Portugal, 2004.
  • Dean's List, Washington University, 2002.
  • Proficient Languages: English, Hebrew, Love, Matlab, LaTeX, HTML, CSS.

open lab

email: joshuav at jhu dot edu
office: 105C whitehead hall
phone: 443.858.9911
social networking:
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skype: joshyv
twitter: jovo
address:
3400 N Charles St
100 whitehead hall
baltimore, MD 21231, usa