Publications

See also my Google Scholar page. preprint.

  1. J. Bain, J. Yeatman, R. Schurr, A. Rokem, and Mezer, A. (2019). Laterality of the arcuate fasciculus depends on choice of tractography. Human Brain Mapping
  2. C.S. Lee, A.J. Tyring, Y. Wu, S. Xiao, A. Rokem, N.P. Deruyter, Q. Zhang, A. Tufail, R.K. Wang, A.Y. Lee (2019). Generating retinal flow maps from structural optical coherence tomography with artificial intelligence. Scientific Reports paper.
  3. A. Keshavan, J. Yeatman, A. Rokem (2019). Combining citizen science and deep learning to amplify expertise in neuroimaging. paper interactive version. Frontiers in Neuroinformatics
  4. Huber, E., Neto Henriques, R., Owen, J. O., Rokem, A., and Yeatman, J. (2019). Applying microstructural models to understand the role of white matter in cognitive development. Developmental Cognitive Neuroscience
  5. Tian, Q., Yang, G., Leuze, C., Rokem, A., Edlow, B., and McNab, J. A. (2019). Model-free Fourier reconstruction of the ensemble average propagator from multi-shell diffusion MRI data. NeuroImage
  6. Huppenkothen, D., Arendt, A., Hogg, D. W., Ram, K., VanderPlas, J. T., and Rokem, A (2018). Hack weeks as a model for data science education and collaboration. Proceedings of the National Academy of Sciences, 115(36):8872–8877. paper.
  7. A. Richie-Halford, A. Rokem (2018). Cloudknot: A Python Library to Run your Existing Code on AWS Batch. Proceedings of the 17th Python in Science Conference (SciPy 2018) F. Akici, D. Lippa, D. Niederhut, M. Pacer (Eds.). paper software
  8. A. Rokem (2018). A short course about fitting models with the scipy.optimize module. Journal of Open Source Education 1(2): 16. pdf.
  9. E. Huber, P.M. Donnelly, A. Rokem, J.D. Yeatman (2018). Rapid and widespread white matter plasticity during an intensive reading intervention. Nature Communications 9: 2260. pdf
  10. J.D. Yeatman, A. Richie-Halford, J.K. Smith, A. Keshavan, A. Rokem (2018). AFQ-Browser: Supporting reproducible human neuroscience research through browser-based visualization tools. Nature Communications 9: 940 pdf, software.
  11. A.M. Smith, K.E. Niemeyer, D.S. Katz, L.A. Barba, G. Githinji, M. Gymrek, K.D. Huff, C.R. Madan, A.C. Mayes, K.M. Moerman, P. Prins, K. Ram, A. Rokem, T.K. Teal, R.V. Guimera, J.T. Vanderplas (2018). Journal of Open Source Software (JOSS): design and first-year review. PeerJ Computer Science 4:e147 pdf.
  12. S. Xiao, F. Bucher, Y. Wu, A. Rokem, C.S. Lee, K.V. Marra, R. Fallon,6 S. Diaz-Aguilar, E. Aguilar, M. Friedlander, and A.Y. Lee (2017). Fully automated, deep learning segmentation of oxygen-induced retinopathy images. JCI Insight 2: e97585. pdf
  13. K. Polimis, A. Rokem, B. Hazelton (2017). Confidence Intervals for Random Forests in Python. Journal of Open Source Software, 2: 124. pdf software
  14. 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.
  15. 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, software.
  16. M. Beyeler, G. M. Boynton, I. Fine, A Rokem (2017). pulse2percept: A Python-based simulation framework for bionic vision. Proceedings of the 16th Python in Science Conference (SciPy 2018) K. Huff, D. Lippa, D. Niederhut, M. Pacer(Eds.) pdf, software.
  17. 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
  18. 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
  19. 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
  20. 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.
  21. 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, software.
  22. 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.
  23. 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.
  24. 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.
  25. A. Mezer, A. Rokem, S. Berman, T. Hastie, and B. A. Wandell (2016). Evaluating quantitative proton-density-mapping methods. Human Brain Mapping. pdf
  26. 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.
  27. 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
  28. 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.
  29. 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.
  30. 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
  31. 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.
  32. 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.
  33. B.A. Wandell, A. Rokem, L.M. Perry, G. Schaefer, R.F. Dougherty (2015). Data management to support reproducible research. arXiv 1502.06900. pdf
  34. 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.
  35. 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.
  36. 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.
  37. F. Pestilli, J. Yeatman, A. Rokem, K. Kay, B.A. Wandell (2014). Evaluation and statistical inference for human connectomes. Nature Methods pdf , supplement
  38. 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
  39. 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
  40. 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)
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. A. Rokem and M. Ahissar (2009) Interactions of cognitive and auditory abilities in congenitally blind individuals. Neuropsychologia 47:843-8. pdf
  55. 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
  56. 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