Publications

See also my Google Scholar page.

  1. M. Beyeler, A. Rokem, G. Boynton, I. Fine (2017). Learning to see again: Biological constraints on cortical plasticity and the implications for sight restoration technologies. Journal of Neural Engineering preprint.
  2. C.S. Lee, A.J. Tyring, N.P. Deruyter, Y. Wu, A. Rokem, A.Y. Lee (2017). Deep-learning based, automated segmentation of macular edema in optical coherence tomography. Biomedical Optics Express preprint.
  3. M. Beyeler, G. M. Boynton, I. Fine, A Rokem (2017). pulse2percept: A Python-based simulation framework for bionic vision. preprint. software
  4. P. Mehta, S. Dorkenwald, D. Zhao, T. Kaftan, A. Cheung, M. Balazinska, A. Rokem, A. Connolly, J. Vanderplas, Y. AlSayyad (2017). Comparative Evaluation of Big-Data Systems on Scientific Image Analytics Workloads. Proceedings of the VLDB Endowment, Volume 10. preprint
  5. C. Holdgraf, A. Culich, A Rokem, F. Deniz, M. Alegro, D. Ushizima (2017) Portable learning environments for hands-on computational instruction: Using container- and cloud-based technology to teach data science. Practice & Experience in Advanced Research Computing (PEARC) 2017. preprint
  6. R. Neto Henriques, A. Rokem, E. Garyfallidis, S. St-Jean, E.T. Peterson, M. Correia (2017). [Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging. ReScience pdf
  7. M. Lee, R. Dottle, C. Espino, I. Subkhan, A. Rokem, A. Mashhadi (2017). A Tool for Estimating and Visualizing Poverty Maps. Proceedings of the Netmob Conference pdf.
  8. U. Ferizi, B. Scherrer, T. Schneider, M. Alipoor, O. Eufracio, R.H.J. Fick, R. Deriche, M. Nilsson, A.K. Loya-Olivas, M. Rivera, D.H.J. Poot, A. Ramirez-Manzanares, J.L. Marroquin, A. Rokem, C. Pötter, R.F. Dougherty, K. Sakaie, C. Wheeler-Kingshott, S.K. Warfield, T. Witzel, L.L. Wald, J.G. Raya, D.C. Alexander (2017). Diffusion MRI microstructure models with in vivo human brain Connectom data: results from a multi-group comparison. NMR in Biomedicine pdf.
  9. A. Rokem, H. Takemura, A. Bock, K.S. Scherf, M. Behrmann, B.A. Wandell, I. Fine, H. Bridge, F. Pestilli (2017). The visual white matter: The application of diffusion MRI and fiber tractography to vision science. Journal of Vision 17:4. pdf.
  10. K. Desimone, A. Rokem, K. Schneider (2016). Popeye: a population receptive field esimation tool. Journal of Open Source Software: 10.21105/joss.00103. Paper. Software.
  11. A. Ahmadia, J. Allen, P. Banaszkiewicz, E. Becker, T. Bekolay, J. Blischak, A. Boughton, E. Bray, A. Cabunoc Mayes, S Crouch, N. Davis, M. Davis, J. Duckles, R. Emonet, F.-A. Fortin, I. Gonzalez, C.Hamm, M. Hansen, R. Harris, F. Henninger, K. Hinsen, A. Hodge, M. Jackson, W. T. King, J. Kitzes, C. Koch, T. Liversidge, F. Michonneau, B. Mills, L. Nederbragt, A. O’Leary, E. Patitsas, A. Pawlik, F. Perez, J. Pipitone, T. Poisot, A. Rokem, R. Silva, T. Teal, T. Tröndle, F. Tweedie, J.-J. Vie, J. Walker, A. Walsh, B. Weaver, E. White, C. Wilkerson, J. Williams, G. Wilson, A. van der Walt (2016). Software carpentry: Instructor training. Link.
  12. A. Mezer, A. Rokem, S. Berman, T. Hastie, and B. A. Wandell (2016). Evaluating quantitative proton-density-mapping methods. Human Brain Mapping. pdf
  13. K. Gorgolewski, R. Auer, , V. Calhoun, C. Craddock, S. Das, E. Duff, G. Flandin, S. Ghosh, T. Glatard, Y. Halchenko, D. Handwerker, M. Hanke, D. Keator, X. Li, S. Michael, C. Maumet, N.B. Nichols, T. Nichols J. Pellman, J.B. Poline, A. Rokem, G. Schaefer, V. Sochat, W. Triplett, J. Turner, G. Varoquaux, R. Poldrack (2016). The Brain Imaging Data Structure, a format for organizing and describing outputs of neuroimaging experiments Scientific Data pdf.
  14. R.C. Craddock, D.S. Margulies, P. Bellec, B.N. Nichols, S. Alcauter, F.A. Barrios, Y. Burnod, C.J. Cannistraci, J. Cohen-Adad, B. De Leener, S. Dery, J. Downar, K. Dunlop, A.R. Franco, C. S. Froehlich, A.J. Gerber, S.S. Ghosh, T.J. Grabowski, S. Hill, A.S. Heinsfeld, R. M. Hutchison, P. Kundu, A.R. Laird, S.-L. Liew, D.J. Lurie, D.G. McLaren, F. Meneguzzi, M. Mennes, S. Mesmoudi, D. O’Connor, E.H. Pasaye, S. Peltier, J.-B. Poline, G. Prasad, R.F. Pereira, P.-O. Quirion, A. Rokem, Z.S. Saad, Y. Shi, S.C. Strother, R. Toro, L.Q. Uddin, J.D. Van Horn , J.W. Van Meter, R.C. Welsh, T. Xu 2016. Brainhack: a collaborative workshop for the open neuroscience community. Gigascience, 5:16. Paper
  15. Q. Tian, A. Rokem, R.D. Folkreth, A. Nummenmaa, F. Qiuyun, B.L. Edlow, J.A. McNab (2016). Postmortem diffusion spectrum imaging of whole, ex vivo human brains using 300 mT/m gradients: A study of effects of q-space sampling. Magnetic Resonance in Medicine pdf.
  16. S. Ajina, F. Pestilli, A. Rokem, C. Kennard, H. Bridge (2015). Human blindsight is mediated by an intact geniculo-extrastriate pathway. eLife 4:e08935, pdf.
  17. A. Rokem, C. Aragon, A. Arendt, B. Fiore-Gartland, B. Hazelton, J. Hellerstein, B. Herman, B. Howe, E. Lazowska, M. Parker, V. Staneva, S. Stone, A, Tanweer, J. Vanderplas (2015). Building an urban data science summer program at the University of Washington eScience Institute. The Bloomberg Data Science 4 Good Exchange pdf
  18. A. Rokem, J. Yeatman, F. Pestilli, K.N. Kay, A. Mezer, S. van der Walt, B.A. Wandell (2015). Evaluating the accuracy of diffusion MRI models in white matter. PLoS One, DOI: 10.1371/journal.pone.0123272. pdf.
  19. H. Takemura, A. Rokem, J. Winawer, J.D. Yeatman, B.A. Wandell, F. Pestilli (2015) A Major Human White Matter Pathway Between Dorsal and Ventral Visual Cortex. Cerebral Cortex, DOI: 10.1093/cercor/bhv064 pdf.
  20. B.A. Wandell, A. Rokem, L.M. Perry, G. Schaefer, R.F. Dougherty (2015). Data management to support reproducible research. arXiv 1502.06900. pdf
  21. C. Zheng, F. Pestilli, A. Rokem (2014). Quantifying error in estimates of human brain fiber directions using Earth Mover’s Distance. NIPS OTML workshop 2014. pdf.
  22. J. Yeatman, K.S. Weiner, F. Pestilli, A. Rokem, A. Mezer, B.A. Wandell (2014). The vertical occipital fasciculus: A century of controversy resolved by in vivo measurements. PNAS , 111:E5214–E5223. pdf.
  23. C. Zheng, F. Pestilli, A. Rokem (2014). Deconvolution of High Dimensional Mixtures via Boosting, with Application to Diffusion-Weighted MRI of Human Brain. Advances in Neural Information Processing 27 (NIPS 2014). pdf.
  24. F. Pestilli, J. Yeatman, A. Rokem, K. Kay, B.A. Wandell (2014). Evaluation and statistical inference for human connectomes. Nature Methods pdf , supplement
  25. E. Garyfallidis, M. Brett, B. Amirbekian, A. Rokem, S. van der Walt, M. Descoteaux, I. Nimmo-Smith and Dipy Contributors (2014). Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics 8:8. link
  26. K.N. Kay, A. Rokem, J. Winawer, R.F. Dougherty B.A Wandell (2013). GLMdenoise: a fast, automated technique for denoising task-based fMRI data. Frontiers in Brain Imaging Methods 7:247. link
  27. E.A. McDevitt*, A. Rokem*, M.A. Silver, and S.C. Mednick (2014). Sex differences in sleep-dependent perceptual learning. Vision Research 99:172-179. pdf (* equal contributors)
  28. J.H. Yoon, S.L. Sheremata, A. Rokem, and M.A. Silver (2013). Windows to the soul: vision science as a tool for studying biological mechanisms of information processing deficits in schizophrenia. Frontiers in Psychopathology. 4:681 pdf
  29. K.N. Kay, J. Winawer, A. Rokem, A. Mezer and B.A. Wandell (2013) A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex. PLoS Computational Biology 9: e1003079. pdf
  30. A. Rokem and M.A. Silver (2013). The benefits of cholinergic enhancement during perceptual learning are long-lasting. Frontiers in Computational Neuroscience: 7:66 link
  31. A.A. Kosovicheva, S.L. Sheremata, A. Rokem, A.N. Landau, and M.A. Silver(2012). Cholinergic enhancement reduces orientation-specific surround suppression but not visual crowding. Frontiers in Behavioral Neuroscience 6: 61. pdf
  32. A. Rokem, A. Landau, W. Prinzmetal, D. Wallace, M.A. Silver and M. D’Esposito (2012). Modulation of inhibition of return by the dopamine D2 receptor agonist bromocriptine depends on individual DAT1 genotype. Cerebral Cortex 22: 1133-8. pdf
  33. A. Rokem, J.H. Yoon, R.E. Ooms, R.J. Maddock, M. J. Minzenberg and M.A. Silver (2011). Broader visual orientation tuning in patients with schizophrenia. Frontiers in Human Neuroscience 5: 127 pdf
  34. A. Rokem and M.A. Silver (2010) Cholinergic enhancement augments magnitude and specificity of visual perceptual learning in healthy humans. Current Biology 20: 1723-1728 pdf; supplementary materials
  35. A. Rokem, A. N. Landau, D. Garg, W. Prinzmetal and M.A. Silver (2010). Effects of cholinergic enhancement on voluntary and involuntary visual spatia attention in healthy humans. Neuropsychopharmacology 35: 2538-44. pdf
  36. J.H. Yoon, R.J. Maddock, A. Rokem, M.A. Silver, M.J. Minzenberg, J.D. Ragland and C.S. Carter (2010). Gamma-aminobutyric acid concentration is reduced in visual cortex in schizophrenia and correlates with orientation-specific surround suppression. Journal of Neuroscience 30:3777-3781. pdf
  37. A. Rokem, M. Trumpis and F. Perez (2009). Nitime: time-series analysis for neuroimaging data. In Proceedings of the 8th Python in Science Conference (SciPy 2009) G. Varoquaux, S. van der Walt, J. Millman (Eds.) pdf
  38. J. Yoon, A. Rokem, M.A. Silver, M.J. Minzenberg and C.S. Carter (2009). Diminished Orientation-Specific Contextual Modulation of Visual Processing in Schizophrenia. Schizophrenia Bulletin 35: 1078-84 pdf
  39. A. Rokem and M.A. Silver (2009) A model of encoding and decoding in V1 and MT accounts accounts for motion perception anisotropies in the human visual system. Brain Research 1299: 3-16. pdf
  40. H. Eyherabide, A. Rokem, A.V.M. Herz, I. Samengo (2009) Bursts generate a non-reducible spike-pattern code. Frontiers in Neuroscience 3: 8-14. pdf
  41. A. Rokem and M. Ahissar (2009) Interactions of cognitive and auditory abilities in congenitally blind individuals. Neuropsychologia 47:843-8. pdf
  42. H.G. Eyherabide, A. Rokem, A.V.M. Herz and I. Samengo (2008). Burst Firing as a Neural Code in an Insect Auditory System. Frontiers in Computational Neuroscience 2:3. pdf
  43. A. Rokem, S. Watzl, T. Gollisch, M. Stemmler, A.V.M. Herz and I. Samengo (2006). Spike-Timing Precision Underlies the Coding Efficiency of Auditory Receptor Neurons. The Journal of Neurophysiology 95: 2541-2552. pdf