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Publications

2i2c
Project Jupyter

This page lists some major publications I have been involved with. It is generated automatically via the ORCID API. Here’s a blog post describing the approach I use for this.

YearPublications
2023Zheng et al. (2023)
2022DuPre et al. (2022)
2021Rokem et al. (2021), Gentemann et al. (2021)
2019Appelhoff et al. (2019), Holdgraf et al. (2018), Wasser et al. (2019), Yarkoni et al. (2019)
2018Geiger et al. (2018), Geiger et al. (2018), Jupyter et al. (2018)
2017Holdgraf et al. (2017), Holdgraf et al. (2017)
2016Holdgraf et al. (2016)
2014Martin et al. (2014)
2012Sfondouris et al. (2012)
References
  1. Zheng, W., Perez, F., Holdgraf, C., Snow, T., Grigsby, S., Sapienza, F., Sundell, E., Siegfried, M., Taylor, J., & Community, E. B. (2023). Jupyter Book-based Supplemental Material: a FAIR Practice to Connect Research Articles with Scientific Data. 10.22541/essoar.170365259.97416177/v1
  2. DuPre, E., Holdgraf, C., Karakuzu, A., Tetrel, L., Bellec, P., Stikov, N., & Poline, J.-B. (2022). Beyond advertising: New infrastructures for publishing integrated research objects. PLOS Computational Biology, 18(1), e1009651. 10.1371/journal.pcbi.1009651
  3. Rokem, A., Dichter, B., Holdgraf, C., & Ghosh, S. S. (2021). Pan-neuro: interactive computing at scale with BRAIN datasets. 10.31219/osf.io/mwh2b
  4. Gentemann, C. L., Holdgraf, C., Abernathey, R., Crichton, D., Colliander, J., Kearns, E. J., Panda, Y., & Signell, R. P. (2021). Science Storms the Cloud. AGU Advances, 2(2). 10.1029/2020av000354
  5. Appelhoff, S., Sanderson, M., Brooks, T., van Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A., & Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software, 4(44), 1896. 10.21105/joss.01896
  6. Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D’Ambrosio, S., David, O., Devinsky, O., Dichter, B., flinker, adeen, Foster, B., Gorgolewski, K. J., Groen, I. I. A., Groppe, D., Gunduz, A., Hamilton, L. S., Honey, C. J., Jas, M., Knight, R., Lachaux, J.-P., … Hermes, D. (2018). BIDS-iEEG: an extension to the brain imaging data structure (BIDS) specification for human intracranial electrophysiology. 10.31234/osf.io/r7vc2
  7. Wasser, L., Joseph, M., McGlinchy, J., Palomino, J., Korinek, N., Holdgraf, C., & Head, T. (2019). EarthPy: A Python package that makes it easier to explore and plot raster and vector data using open source Python tools. Journal of Open Source Software, 4(43), 1886. 10.21105/joss.01886
  8. Yarkoni, T., Markiewicz, C., de la Vega, A., Gorgolewski, K., Salo, T., Halchenko, Y., McNamara, Q., DeStasio, K., Poline, J.-B., Petrov, D., Hayot-Sasson, V., Nielson, D., Carlin, J., Kiar, G., Whitaker, K., DuPre, E., Wagner, A., Tirrell, L., Jas, M., … Blair, R. (2019). PyBIDS: Python tools for BIDS datasets. Journal of Open Source Software, 4(40), 1294. 10.21105/joss.01294
  9. Geiger, R. S., Varoquaux, N., Cabasse, C., & Holdgraf, C. (2018). The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries: A Collaborative Ethnography of Documentation Work. 10.31235/osf.io/2fdhr
  10. Jupyter, P., Bussonnier, M., Forde, J., Freeman, J., Granger, B., Head, T., Holdgraf, C., Kelley, K., Nalvarte, G., Osheroff, A., Pacer, M., Panda, Y., Perez, F., Ragan-Kelley, B., & Willing, C. (2018). Binder 2.0 - Reproducible, interactive, sharable environments for science at scale. Proceedings of the 17th Python in Science Conference, 113–120. 10.25080/majora-4af1f417-011
  11. Holdgraf, C., Culich, A., Rokem, A., Deniz, F., Alegro, M., & Ushizima, D. (2017). Portable Learning Environments for Hands-On Computational Instruction: Using Container- and Cloud-Based Technology to Teach Data Science. Practice and Experience in Advanced Research Computing 2017: Sustainability, Success and Impact, 1–9. 10.1145/3093338.3093370
  12. Holdgraf, C. R., de Heer, W., Pasley, B., Rieger, J., Crone, N., Lin, J. J., Knight, R. T., & Theunissen, F. E. (2016). Rapid tuning shifts in human auditory cortex enhance speech intelligibility. Nature Communications, 7(1). 10.1038/ncomms13654
  13. Martin, S., Brunner, P., Holdgraf, C., Heinze, H.-J., Crone, N. E., Rieger, J., Schalk, G., Knight, R. T., & Pasley, B. N. (2014). Decoding spectrotemporal features of overt and covert speech from the human cortex. Frontiers in Neuroengineering, 7. 10.3389/fneng.2014.00014
  14. Sfondouris, J. L., Quebedeaux, T. M., Holdgraf, C., & Musto, A. E. (2012). Combined process automation for large-scale EEG analysis. Computers in Biology and Medicine, 42(1), 129–134. 10.1016/j.compbiomed.2011.10.017
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