diff --git a/.gitignore b/.gitignore index 4665142..2430561 100644 --- a/.gitignore +++ b/.gitignore @@ -23,3 +23,6 @@ Thumbs.db *~ .env .env.*.local + +uv.lock +.local/* diff --git a/content/about/publications.md b/content/about/publications.md index cd78a52..b03028a 100644 --- a/content/about/publications.md +++ b/content/about/publications.md @@ -4,226 +4,226 @@ linkTitle: "Publications" type: docs weight: 60 --- -1. Rorden, C., Béranger, B., Cheng, H., Clemence, M., Debacker, C., Fernandez, B., Halchenko, Y., Harms, M., Holla, B., Innis, I., Kuijer, J., Levitas, D., Litinas, K., Luci, J., Newman-Norlund, R., Peltier, S., Rehwald, W., Reid, R., Rogers, B., Schwarz, C., Shin, J., Ganesan, V., Ganji, S., Morgan, P. (2025). *DICOM datasets for reproducible neuroimaging research across manufacturers and software versions*. *Scientific Data*, 12(1). [https://doi.org/10.1038/s41597-025-05503-w](https://doi.org/10.1038/s41597-025-05503-w) +1. Rorden, C., Béranger, B., Cheng, H., Clemence, M., Debacker, C., Fernandez, B., Halchenko, Y. O., Harms, M. P., Holla, B., Innis, I., Kuijer, J. P. A., Levitas, D., Litinas, K., Luci, J., Newman-Norlund, R., Peltier, S., Rehwald, W., Reid, R. I., Rogers, B., … Morgan, P. S.. (2025). DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data, 12(1). https://doi.org/10.1038/s41597-025-05503-w -2. Chhetri, Tek Raj, Chen, Yibei, Trivedi, Puja, Jarecka, Dorota, Haobsh, Saif, Ray, Patrick, Ng, Lydia, Ghosh, Satrajit S. (2025). *STRUCTSENSE: A Task-Agnostic Agentic Framework for Structured Information Extraction with Human-In-The-Loop Evaluation and Benchmarking*. *arXiv*. [https://doi.org/10.48550/arXiv.2507.03674](https://doi.org/10.48550/arXiv.2507.03674) +2. Chhetri, T. R., Chen, Y., Trivedi, P., Jarecka, D., Haobsh, S., Ray, P., Ng, L., & Ghosh, S. S.. (2025). STRUCTSENSE: A Task-Agnostic Agentic Framework for Structured Information Extraction with Human-In-The-Loop Evaluation and Benchmarking. arXiv. https://doi.org/10.48550/ARXIV.2507.03674 -3. Taylor, Paul A., Aggarwal, Himanshu, Bandettini, Peter, Barilari, Marco, Bright, Molly, Caballero-Gaudes, Cesar, Calhoun, Vince, Chakravarty, Mallar, Devenyi, Gabriel, Evans, Jennifer, Garza-Villarreal, Eduardo, Rasgado-Toledo, Jalil, Gau, Remi, Glen, Daniel, Goebel, Rainer, Gonzalez-Castillo, Javier, Gulban, Omer Faruk, Halchenko, Yaroslav, Handwerker, Daniel, Hanayik, Taylor, Lauren, Peter, Leopold, David, Lerch, Jason, Mathys, Christian, McCarthy, Paul, McLeod, Anke, Mejia, Amanda, Moia, Stefano, Nichols, Thomas, Pernet, Cyril, Pessoa, Luiz, Pfleiderer, Bettina, Rajendra, Justin, Reyes, Laura, Reynolds, Richard, Roopchansingh, Vinai, Rorden, Chris, Russ, Brian, Sundermann, Benedikt, Thirion, Bertrand, Torrisi, Salvatore, Chen, Gang (2025). *Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation*. *arXiv*. [https://doi.org/10.48550/arXiv.2504.07824](https://doi.org/10.48550/arXiv.2504.07824) +3. Taylor, P. A., Aggarwal, H., Bandettini, P., Barilari, M., Bright, M., Caballero-Gaudes, C., Calhoun, V., Chakravarty, M., Devenyi, G., Evans, J., Garza-Villarreal, E., Rasgado-Toledo, J., Gau, R., Glen, D., Goebel, R., Gonzalez-Castillo, J., Gulban, O. F., Halchenko, Y., Handwerker, D., … Chen, G.. (2025). Go Figure: Transparency in neuroscience images preserves context and clarifies interpretation. arXiv. https://doi.org/10.48550/ARXIV.2504.07824 -4. Chen, Y., Jarecka, D., Abraham, S., Gau, R., Ng, E., Low, D., Bevers, I., Johnson, A., Keshavan, A., Klein, A., Clucas, J., Rosli, Z., Hodge, S., Linkersdörfer, J., Bartsch, H., Das, S., Fair, D., Kennedy, D., Ghosh, S. (2025). *Standardizing Survey Data Collection to Enhance Reproducibility: Development and Comparative Evaluation of the ReproSchema Ecosystem*. *Journal of Medical Internet Research*, 27(), e63343. [https://doi.org/10.2196/63343](https://doi.org/10.2196/63343) +4. Chen, Y., Jarecka, D., Abraham, S. A., Gau, R., Ng, E., Low, D. M., Bevers, I., Johnson, A., Keshavan, A., Klein, A., Clucas, J., Rosli, Z., Hodge, S. M., Linkersdörfer, J., Bartsch, H., Das, S., Fair, D., Kennedy, D., & Ghosh, S. S.. (2025). Standardizing Survey Data Collection to Enhance Reproducibility: Development and Comparative Evaluation of the ReproSchema Ecosystem. Journal of Medical Internet Research, 27, 63343. https://doi.org/10.2196/63343 -5. Pedroza‐Sotelo, K., Schwarb, H., Auerbach, R., Ghosh, S., Henin, A., Hofmann, S., Pizzagalli, D., Yendiki, A., Whitfield‐Gabrieli, S., Gabrieli, J., Hubbard, N. (2025). *Evidence of Disrupted Hippocampal Gray‐ and White‐Matter Development in Adolescent Anxiety Disorders, Independent From Early‐Life Stress*. *Hippocampus*, 35(5). [https://doi.org/10.1002/hipo.70028](https://doi.org/10.1002/hipo.70028) +5. Pedroza‐Sotelo, K., Schwarb, H., Auerbach, R. P., Ghosh, S. S., Henin, A., Hofmann, S. G., Pizzagalli, D. A., Yendiki, A., Whitfield‐Gabrieli, S., Gabrieli, J. D. E., & Hubbard, N. A.. (2025). Evidence of Disrupted Hippocampal Gray‐ and White‐Matter Development in Adolescent Anxiety Disorders, Independent From Early‐Life Stress. Hippocampus, 35(5). https://doi.org/10.1002/hipo.70028 -6. Szczepanik, M., Wagner, A., Heunis, S., Waite, L., Eickhoff, S., Hanke, M. (2024). *Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort*. *Neuroinformatics*, 22(4), 635-645. [https://doi.org/10.1007/s12021-024-09665-7](https://doi.org/10.1007/s12021-024-09665-7) +6. Szczepanik, M., Wagner, A. S., Heunis, S., Waite, L. K., Eickhoff, S. B., & Hanke, M.. (2024). Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics, 22(4), 635–645. https://doi.org/10.1007/s12021-024-09665-7 -7. Renton, A., Dao, T., Johnstone, T., Civier, O., Sullivan, R., White, D., Lyons, P., Slade, B., Abbott, D., Amos, T., Bollmann, S., Botting, A., Campbell, M., Chang, J., Close, T., Dörig, M., Eckstein, K., Egan, G., Evas, S., Flandin, G., Garner, K., Garrido, M., Ghosh, S., Grignard, M., Halchenko, Y., Hannan, A., Heinsfeld, A., Huber, L., Hughes, M., Kaczmarzyk, J., Kasper, L., Kuhlmann, L., Lou, K., Mantilla-Ramos, Y., Mattingley, J., Meier, M., Morris, J., Narayanan, A., Pestilli, F., Puce, A., Ribeiro, F., Rogasch, N., Rorden, C., Schira, M., Shaw, T., Sowman, P., Spitz, G., Stewart, A., Ye, X., Zhu, J., Narayanan, A., Bollmann, S. (2024). *Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging*. *Nature Methods*, 21(5), 804-808. [https://doi.org/10.1038/s41592-023-02145-x](https://doi.org/10.1038/s41592-023-02145-x) +7. Renton, A. I., Dao, T. T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., Lyons, P., Slade, B. M., Abbott, D. F., Amos, T. J., Bollmann, S., Botting, A., Campbell, M. E. J., Chang, J., Close, T. G., Dörig, M., Eckstein, K., Egan, G. F., Evas, S., … Bollmann, S.. (2024). Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21(5), 804–808. https://doi.org/10.1038/s41592-023-02145-x -8. Hubbard, N., Bauer, C., Siless, V., Auerbach, R., Elam, J., Frosch, I., Henin, A., Hofmann, S., Hodge, M., Jones, R., Lenzini, P., Lo, N., Park, A., Pizzagalli, D., Vaz-DeSouza, F., Gabrieli, J., Whitfield-Gabrieli, S., Yendiki, A., Ghosh, S. (2024). *The Human Connectome Project of adolescent anxiety and depression dataset*. *Scientific Data*, 11(1). [https://doi.org/10.1038/s41597-024-03629-x](https://doi.org/10.1038/s41597-024-03629-x) +8. Hubbard, N. A., Bauer, C. C. C., Siless, V., Auerbach, R. P., Elam, J. S., Frosch, I. R., Henin, A., Hofmann, S. G., Hodge, M. R., Jones, R., Lenzini, P., Lo, N., Park, A. T., Pizzagalli, D. A., Vaz-DeSouza, F., Gabrieli, J. D. E., Whitfield-Gabrieli, S., Yendiki, A., & Ghosh, S. S.. (2024). The Human Connectome Project of adolescent anxiety and depression dataset. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-03629-x -9. Torabi, M., Mitsis, G., Poline, J. (2024). *On the variability of dynamic functional connectivity assessment methods*. *GigaScience*, 13(). [https://doi.org/10.1093/gigascience/giae009](https://doi.org/10.1093/gigascience/giae009) +9. Torabi, M., Mitsis, G. D., & Poline, J.-B.. (2024). On the variability of dynamic functional connectivity assessment methods. GigaScience, 13. https://doi.org/10.1093/gigascience/giae009 -10. Burdinski, D., Kodibagkar, A., Potter, K., Schuster, R., Evins, A., Ghosh, S., Gilman, J. (2024). *Impact of year-long cannabis use for medical symptoms on brain activation during cognitive processes*. *Journal unknown*. [https://doi.org/10.1101/2024.04.29.24306516](https://doi.org/10.1101/2024.04.29.24306516) +10. Burdinski, D., Kodibagkar, A., Potter, K., Schuster, R., Evins, A. E., Ghosh, S., & Gilman, J.. (2024). Impact of year-long cannabis use for medical symptoms on brain activation during cognitive processes. https://doi.org/10.1101/2024.04.29.24306516 -11. Poldrack, R., Markiewicz, C., Appelhoff, S., Ashar, Y., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Benar, C., Bertazzoli, G., Bhogawar, S., Blair, R., Bortoletto, M., Boudreau, M., Brooks, T., Calhoun, V., Castelli, F., Clement, P., Cohen, A., Cohen-Adad, J., D’Ambrosio, S., de Hollander, G., de la Iglesia-Vayá, M., de la Vega, A., Delorme, A., Devinsky, O., Draschkow, D., Duff, E., DuPre, E., Earl, E., Esteban, O., Feingold, F., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gau, R., Gholam, J., Ghosh, S., Giacomel, A., Gillman, A., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y., Handwerker, D., Hardcastle, N., Herholz, P., Hermes, D., Honey, C., Innis, R., Ioanas, H., Jahn, A., Karakuzu, A., Keator, D., Kiar, G., Kincses, B., Laird, A., Lau, J., Lazari, A., Legarreta, J., Li, A., Li, X., Love, B., Lu, H., Marcantoni, E., Maumet, C., Mazzamuto, G., Meisler, S., Mikkelsen, M., Mutsaerts, H., Nichols, T., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T., Oostenveld, R., Ort, E., Park, P., Pawlik, M., Pernet, C., Pestilli, F., Petr, J., Phillips, C., Poline, J., Pollonini, L., Raamana, P., Ritter, P., Rizzo, G., Robbins, K., Rockhill, A., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J., Salo, T., Schirner, M., Smith, R., Spisak, T., Sprenger, J., Swann, N., Szinte, M., Takerkart, S., Thirion, B., Thomas, A., Torabian, S., Varoquaux, G., Voytek, B., Welzel, J., Wilson, M., Yarkoni, T., Gorgolewski, K. (2024). *The past, present, and future of the brain imaging data structure (BIDS)*. *Imaging Neuroscience*, 2(), 1-19. [https://doi.org/10.1162/imag_a_00103](https://doi.org/10.1162/imag_a_00103) +11. Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Benar, C. G., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., … Gorgolewski, K. J.. (2024). The past, present, and future of the brain imaging data structure (BIDS). Imaging Neuroscience, 2. https://doi.org/10.1162/imag_a_00103 -12. Kliemann, D., Galdi, P., Van De Water, A., Egger, B., Jarecka, D., Adolphs, R., Ghosh, S. (2024). *Resting-State Functional Connectivity of the Amygdala in Autism: A Preregistered Large-Scale Study*. *American Journal of Psychiatry*, 181(12), 1076-1085. [https://doi.org/10.1176/appi.ajp.20230249](https://doi.org/10.1176/appi.ajp.20230249) +12. Kliemann, D., Galdi, P., Van De Water, A. L., Egger, B., Jarecka, D., Adolphs, R., & Ghosh, S. S.. (2024). Resting-State Functional Connectivity of the Amygdala in Autism: A Preregistered Large-Scale Study. American Journal of Psychiatry, 181(12), 1076–1085. https://doi.org/10.1176/appi.ajp.20230249 -13. Lin, D., Backus, D., Chakraborty, S., Liew, S., Valero-Cuevas, F., Patten, C., Cotton, R. (2024). *Transforming modeling in neurorehabilitation: clinical insights for personalized rehabilitation*. *Journal of NeuroEngineering and Rehabilitation*, 21(1). [https://doi.org/10.1186/s12984-024-01309-w](https://doi.org/10.1186/s12984-024-01309-w) +13. Lin, D. J., Backus, D., Chakraborty, S., Liew, S.-L., Valero-Cuevas, F. J., Patten, C., & Cotton, R. J.. (2024). Transforming modeling in neurorehabilitation: clinical insights for personalized rehabilitation. Journal of NeuroEngineering and Rehabilitation, 21(1). https://doi.org/10.1186/s12984-024-01309-w -14. Low, D., Rao, V., Randolph, G., Song, P., Ghosh, S. (2024). *Identifying bias in models that detect vocal fold paralysis from audio recordings using explainable machine learning and clinician ratings*. *PLOS Digital Health*, 3(5), e0000516. [https://doi.org/10.1371/journal.pdig.0000516](https://doi.org/10.1371/journal.pdig.0000516) +14. Low, D. M., Rao, V., Randolph, G., Song, P. C., & Ghosh, S. S.. (2024). Identifying bias in models that detect vocal fold paralysis from audio recordings using explainable machine learning and clinician ratings. PLOS Digital Health, 3(5), 0000516. https://doi.org/10.1371/journal.pdig.0000516 -15. Sokołowski, A., Bhagwat, N., Chatelain, Y., Dugré, M., Hanganu, A., Monchi, O., McPherson, B., Wang, M., Poline, J., Sharp, M., Glatard, T. (2024). *Longitudinal brain structure changes in Parkinson’s disease: A replication study*. *PLOS ONE*, 19(1), e0295069. [https://doi.org/10.1371/journal.pone.0295069](https://doi.org/10.1371/journal.pone.0295069) +15. Sokołowski, A., Bhagwat, N., Chatelain, Y., Dugré, M., Hanganu, A., Monchi, O., McPherson, B., Wang, M., Poline, J.-B., Sharp, M., & Glatard, T.. (2024). Longitudinal brain structure changes in Parkinson’s disease: A replication study. PLOS ONE, 19(1), 0295069. https://doi.org/10.1371/journal.pone.0295069 -16. Halchenko, Y., Goncalves, M., Ghosh, S., Velasco, P., Visconti di Oleggio Castello, M., Salo, T., Wodder, J., Hanke, M., Sadil, P., Gorgolewski, K., Ioanas, H., Rorden, C., Hendrickson, T., Dayan, M., Houlihan, S., Kent, J., Strauss, T., Lee, J., To, I., Markiewicz, C., Lukas, D., Butler, E., Thompson, T., Termenon, M., Smith, D., Macdonald, A., Kennedy, D. (2024). *HeuDiConv — flexible DICOM conversion into structured -directory layouts*. *Journal of Open Source Software*, 9(99), 5839. [https://doi.org/10.21105/joss.05839](https://doi.org/10.21105/joss.05839) +16. Halchenko, Y. O., Goncalves, M., Ghosh, S., Velasco, P., Visconti di Oleggio Castello, M., Salo, T., Wodder, J. T., Hanke, M., Sadil, P., Gorgolewski, K. J., Ioanas, H.-I., Rorden, C., Hendrickson, T. J., Dayan, M., Houlihan, S. D., Kent, J., Strauss, T., Lee, J., To, I., … Kennedy, D. N.. (2024). HeuDiConv — flexible DICOM conversion into structured +directory layouts. Journal of Open Source Software, 9(99), 5839. https://doi.org/10.21105/joss.05839 -17. Ioanas, H., Macdonald, A., Halchenko, Y. (2024). *Neuroimaging article reexecution and reproduction assessment system*. *Frontiers in Neuroinformatics*, 18(). [https://doi.org/10.3389/fninf.2024.1376022](https://doi.org/10.3389/fninf.2024.1376022) +17. Ioanas, H.-I., Macdonald, A., & Halchenko, Y. O.. (2024). Neuroimaging article reexecution and reproduction assessment system. Frontiers in Neuroinformatics, 18. https://doi.org/10.3389/fninf.2024.1376022 -18. Plis, S., Masoud, M., Hu, F., Hanayik, T., Ghosh, S., Drake, C., Newman-Norlund, R., Rorden, C. (2024). *Brainchop: Providing an Edge Ecosystem for Deployment of Neuroimaging Artificial Intelligence Models*. *Aperture Neuro*, 4(). [https://doi.org/10.52294/001c.123059](https://doi.org/10.52294/001c.123059) +18. Plis, S. M., Masoud, M., Hu, F., Hanayik, T., Ghosh, S. S., Drake, C., Newman-Norlund, R., & Rorden, C.. (2024). Brainchop: Providing an Edge Ecosystem for Deployment of Neuroimaging Artificial Intelligence Models. Aperture Neuro, 4. https://doi.org/10.52294/001c.123059 -19. Larivière, S., Bayrak, Ş., Vos de Wael, R., Benkarim, O., Herholz, P., Rodriguez-Cruces, R., Paquola, C., Hong, S., Misic, B., Evans, A., Valk, S., Bernhardt, B. (2023). *BrainStat: A toolbox for brain-wide statistics and multimodal feature associations*. *NeuroImage*, 266(), 119807. [https://doi.org/10.1016/j.neuroimage.2022.119807](https://doi.org/10.1016/j.neuroimage.2022.119807) +19. Larivière, S., Bayrak, Ş., Vos de Wael, R., Benkarim, O., Herholz, P., Rodriguez-Cruces, R., Paquola, C., Hong, S.-J., Misic, B., Evans, A. C., Valk, S. L., & Bernhardt, B. C.. (2023). BrainStat: A toolbox for brain-wide statistics and multimodal feature associations. NeuroImage, 266, 119807. https://doi.org/10.1016/j.neuroimage.2022.119807 -20. Kiar, G., Clucas, J., Feczko, E., Goncalves, M., Jarecka, D., Markiewicz, C., Halchenko, Y., Hermosillo, R., Li, X., Miranda-Dominguez, O., Ghosh, S., Poldrack, R., Satterthwaite, T., Milham, M., Fair, D. (2023). *Align with the NMIND consortium for better neuroimaging*. *Nature Human Behaviour*, 7(7), 1027-1028. [https://doi.org/10.1038/s41562-023-01647-0](https://doi.org/10.1038/s41562-023-01647-0) +20. Kiar, G., Clucas, J., Feczko, E., Goncalves, M., Jarecka, D., Markiewicz, C. J., Halchenko, Y. O., Hermosillo, R., Li, X., Miranda-Dominguez, O., Ghosh, S., Poldrack, R. A., Satterthwaite, T. D., Milham, M. P., & Fair, D.. (2023). Align with the NMIND consortium for better neuroimaging. Nature Human Behaviour, 7(7), 1027–1028. https://doi.org/10.1038/s41562-023-01647-0 -21. Poline, J., Das, S., Glatard, T., Madjar, C., Dickie, E., Lecours, X., Beaudry, T., Beck, N., Behan, B., Brown, S., Bujold, D., Beauvais, M., Caron, B., Czech, C., Dharsee, M., Dugré, M., Evans, K., Gee, T., Ippoliti, G., Kiar, G., Knoppers, B., Kuehn, T., Le, D., Lo, D., Mazaheri, M., MacFarlane, D., Muja, N., O’Brien, E., O’Callaghan, L., Paiva, S., Park, P., Quesnel, D., Rabelais, H., Rioux, P., Legault, M., Tremblay-Mercier, J., Rotenberg, D., Stone, J., Strauss, T., Zaytseva, K., Zhou, J., Duchesne, S., Khan, A., Hill, S., Evans, A. (2023). *Data and Tools Integration in the Canadian Open Neuroscience Platform*. *Scientific Data*, 10(1). [https://doi.org/10.1038/s41597-023-01946-1](https://doi.org/10.1038/s41597-023-01946-1) +21. Poline, J.-B., Das, S., Glatard, T., Madjar, C., Dickie, E. W., Lecours, X., Beaudry, T., Beck, N., Behan, B., Brown, S. T., Bujold, D., Beauvais, M., Caron, B., Czech, C., Dharsee, M., Dugré, M., Evans, K., Gee, T., Ippoliti, G., … Evans, A. C.. (2023). Data and Tools Integration in the Canadian Open Neuroscience Platform. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-01946-1 -22. Wang, Q., Aljassar, M., Bhagwat, N., Zeighami, Y., Evans, A., Dagher, A., Pike, G., Sadikot, A., Poline, J. (2023). *Reproducibility of cerebellar involvement as quantified by consensus structural MRI biomarkers in advanced essential tremor*. *Scientific Reports*, 13(1). [https://doi.org/10.1038/s41598-022-25306-y](https://doi.org/10.1038/s41598-022-25306-y) +22. Wang, Q., Aljassar, M., Bhagwat, N., Zeighami, Y., Evans, A. C., Dagher, A., Pike, G. B., Sadikot, A. F., & Poline, J.-B.. (2023). Reproducibility of cerebellar involvement as quantified by consensus structural MRI biomarkers in advanced essential tremor. 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A., Eklund, A., Esteban, O., Flandin, G., Ghosh, S. S., Guntupalli, J. S., Jenkinson, M., Keshavan, A., Kiar, G., Liem, F., … Poldrack, R. A.. (2017). BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLOS Computational Biology, 13(3), 1005209. https://doi.org/10.1371/journal.pcbi.1005209 -105. Klein, A., Ghosh, S., Bao, F., Giard, J., Häme, Y., Stavsky, E., Lee, N., Rossa, B., Reuter, M., Chaibub Neto, E., Keshavan, A. (2017). *Mindboggling morphometry of human brains*. *PLOS Computational Biology*, 13(2), e1005350. [https://doi.org/10.1371/journal.pcbi.1005350](https://doi.org/10.1371/journal.pcbi.1005350) +105. Klein, A., Ghosh, S. S., Bao, F. S., Giard, J., Häme, Y., Stavsky, E., Lee, N., Rossa, B., Reuter, M., Chaibub Neto, E., & Keshavan, A.. (2017). Mindboggling morphometry of human brains. PLOS Computational Biology, 13(2), 1005350. https://doi.org/10.1371/journal.pcbi.1005350 -106. Bandrowski, A., Martone, M. (2016). *RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods*. *Neuron*, 90(3), 434-436. [https://doi.org/10.1016/j.neuron.2016.04.030](https://doi.org/10.1016/j.neuron.2016.04.030) +106. Bandrowski, A. E., & Martone, M. E.. (2016). RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods. Neuron, 90(3), 434–436. https://doi.org/10.1016/j.neuron.2016.04.030 -107. Maumet, C., Auer, T., Bowring, A., Chen, G., Das, S., Flandin, G., Ghosh, S., Glatard, T., Gorgolewski, K., Helmer, K., Jenkinson, M., Keator, D., Nichols, B., Poline, J., Reynolds, R., Sochat, V., Turner, J., Nichols, T. (2016). *Sharing brain mapping statistical results with the neuroimaging data model*. *Scientific Data*, 3(1). [https://doi.org/10.1038/sdata.2016.102](https://doi.org/10.1038/sdata.2016.102) +107. 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Frontiers in Neuroinformatics, 10. https://doi.org/10.3389/fninf.2016.00034 diff --git a/data/publications.yaml b/data/publications.yaml new file mode 100644 index 0000000..8e4baba --- /dev/null +++ b/data/publications.yaml @@ -0,0 +1,112 @@ +publication-dois: +- 10.1038/s41597-025-05503-w +- 10.48550/arXiv.2507.03674 +- 10.48550/arXiv.2504.07824 +- 10.2196/63343 +- 10.1002/hipo.70028 +- 10.1007/s12021-024-09665-7 +- 10.1038/s41592-023-02145-x +- 10.1038/s41597-024-03629-x +- 10.1093/gigascience/giae009 +- 10.1101/2024.04.29.24306516 +- 10.1162/imag_a_00103 +- 10.1176/appi.ajp.20230249 +- 10.1186/s12984-024-01309-w +- 10.1371/journal.pdig.0000516 +- 10.1371/journal.pone.0295069 +- 10.21105/joss.05839 +- 10.3389/fninf.2024.1376022 +- 10.52294/001c.123059 +- 10.1016/j.neuroimage.2022.119807 +- 10.1038/s41562-023-01647-0 +- 10.1038/s41597-023-01946-1 +- 10.1038/s41598-022-25306-y +- 10.1101/2023.08.01.551505 +- 10.1101/2023.08.16.552472 +- 10.1159/000530358 +- 10.21203/rs.3.rs-2649734/v1 +- 10.3389/fnhum.2023.1237651 +- 10.3389/fnimg.2022.1098604 +- 10.3389/fnimg.2023.1099301 +- 10.3389/fninf.2023.1174156 +- 10.3389/fnins.2023.1233416 +- 10.1148/radiol.230096 +- 10.1007/s10548-022-00935-8 +- 10.1007/s12021-021-09557-0 +- 10.1016/j.neuroimage.2022.119612 +- 10.1016/j.neuroimage.2022.119623 +- 10.1016/j.neuron.2021.11.017 +- 10.1038/s41398-022-02211-6 +- 10.1038/s41592-022-01681-2 +- 10.1038/s41597-022-01682-y +- 10.1038/s41598-022-19356-5 +- 10.1093/gigascience/giac013 +- 10.1148/radiol.210385 +- 10.12688/f1000research.108008.2 +- 10.1371/journal.pcbi.1009651 +- 10.3389/fnhum.2022.749767 +- 10.7554/eLife.79277 +- 10.1002/hbm.25351 +- 10.1007/s12021-020-09509-0 +- 10.1007/s12021-021-09517-8 +- 10.1007/s12021-021-09522-x +- 10.1007/s12021-021-09533-8 +- 10.1016/j.mex.2021.101595 +- 10.1016/j.neuroimage.2021.118683 +- 10.1016/j.neuron.2021.04.001 +- 10.1016/j.nicl.2021.102790 +- 10.1038/s41597-021-01033-3 +- 10.1038/s41598-021-87069-2 +- 10.1038/s41598-021-94733-0 +- 10.1093/gigascience/giaa155 +- 10.1093/gigascience/giab055 +- 10.12688/f1000research.25306.2 +- 10.1515/nf-2020-0037 +- 10.21105/joss.03262 +- 10.2196/22369 +- 10.7554/eLife.71774 +- 10.7554/eLife.72129 +- 10.1002/lio2.354 +- 10.1016/j.neuroimage.2019.116330 +- 10.1016/j.nicl.2020.102240 +- 10.1016/j.nicl.2020.102242 +- 10.1016/j.nicl.2020.102266 +- 10.1038/s41586-020-2314-9 +- 10.1038/s41596-020-0327-3 +- 10.1038/s41597-020-0486-7 +- 10.1101/2020.11.23.20235945 +- 10.1146/annurev-neuro-100119-110036 +- 10.12688/f1000research.24544.1 +- 10.1016/j.neulet.2019.01.037 +- 10.1016/j.neuroimage.2019.116091 +- 10.1038/s41597-019-0031-8 +- 10.12688/mniopenres.12772.2 +- 10.1371/journal.pone.0210028 +- 10.21105/joss.01294 +- 10.3233/JPD-191775 +- 10.3389/fninf.2019.00001 +- 10.3389/fninf.2019.00003 +- 10.7554/eLife.48932 +- 10.1007/s12021-018-9379-8 +- 10.1038/sdata.2018.29 +- 10.1093/database/bay130 +- 10.1093/gigascience/giy077 +- 10.1109/TMI.2018.2831261 +- 10.3389/fnins.2018.00727 +- 10.7554/eLife.36652 +- 10.1007/s12021-017-9331-3 +- 10.1007/s12021-017-9335-z +- 10.1038/nn.4500 +- 10.1038/nn.4550 +- 10.1038/nrn.2016.167 +- 10.1038/sdata.2017.59 +- 10.1093/cercor/bhx030 +- 10.12688/f1000research.10783.2 +- 10.1371/journal.pcbi.1005209 +- 10.1371/journal.pcbi.1005350 +- 10.1016/j.neuron.2016.04.030 +- 10.1038/sdata.2016.102 +- 10.1038/sdata.2016.44 +- 10.1073/pnas.1608282113 +- 10.1093/gerona/glw236 +- 10.3389/fninf.2016.00034 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..ec0adab --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,10 @@ +[project] +name = "repronim-publications" +version = "0.1.0" +description = "Scripts for generating ReproNim publications from DOIs" +requires-python = ">=3.10" +dependencies = [ + "citeproc-py[full]>=0.9.0", + "pyyaml>=6.0", + "duecredit>=0.9.0", +] diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 0000000..e70b7cc --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,12 @@ +# Publication Generation + +Regenerate publications from DOIs in `data/publications.yaml`: + +Run from the root of this repo: + +```bash +datalad run -m "Generate publications from DOIs" \ + --input data/publications.yaml \ + --output content/about/publications.md \ + "uv run python scripts/generate_publications.py" +``` diff --git a/scripts/generate_publications.py b/scripts/generate_publications.py new file mode 100755 index 0000000..d49c515 --- /dev/null +++ b/scripts/generate_publications.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python3 +""" +Generate publications.md from list of DOIs using duecredit/citeproc-py. + +This script reads DOIs from data/publications.yaml and generates +formatted citations in APA style, writing to content/about/publications.md +""" + +import sys +import yaml +from pathlib import Path +from duecredit.io import format_bibtex, import_doi, BibTeX + + +def fetch_citation(doi): + """ + Fetch and format a single citation from a DOI. + + Args: + doi: DOI string (e.g., "10.1038/s41597-025-05503-w") + + Returns: + Formatted citation string in APA style, or None if fetch failed + """ + try: + # Add https://doi.org/ prefix if not present + doi_url = doi if doi.startswith('http') else f'https://doi.org/{doi}' + + # Fetch citation data and format as APA + bibtex_data = BibTeX(import_doi(doi_url)) + citation = format_bibtex(bibtex_data, style='apa') + + return citation + except Exception as e: + print(f"Warning: Failed to fetch DOI {doi}: {e}", file=sys.stderr) + return None + + +def generate_publications_markdown(dois, output_path): + """ + Generate the publications markdown file from a list of DOIs. + + Args: + dois: List of DOI strings + output_path: Path to write the generated markdown file + """ + # Frontmatter for the markdown file + frontmatter = """--- +Title: ReproNim Publications +linkTitle: "Publications" +type: docs +weight: 60 +--- +""" + + citations = [] + failed_dois = [] + + print(f"Fetching {len(dois)} publications...") + + for i, doi in enumerate(dois, 1): + print(f" [{i}/{len(dois)}] Fetching {doi}...", end=' ') + citation = fetch_citation(doi) + + if citation: + citations.append(citation) + print("✓") + else: + failed_dois.append(doi) + print("✗") + + # Write the markdown file + with open(output_path, 'w') as f: + f.write(frontmatter) + + for i, citation in enumerate(citations, 1): + f.write(f"{i}. {citation}\n\n") + + print(f"\nGenerated {len(citations)} citations to {output_path}") + + if failed_dois: + print(f"\nWarning: {len(failed_dois)} DOIs failed to fetch:") + for doi in failed_dois: + print(f" - {doi}") + + +def main(): + # Paths + repo_root = Path(__file__).parent.parent + doi_yaml = repo_root / 'data' / 'publications.yaml' + output_md = repo_root / 'content' / 'about' / 'publications.md' + + # Load DOIs from YAML + print(f"Loading DOIs from: {doi_yaml}") + with open(doi_yaml, 'r') as f: + data = yaml.safe_load(f) + dois = data.get('publication-dois', []) + + if not dois: + print("Error: No DOIs found in publications.yaml", file=sys.stderr) + sys.exit(1) + + # Optional: limit number of DOIs for testing (use first argument) + if len(sys.argv) > 1: + limit = int(sys.argv[1]) + print(f"Testing mode: processing first {limit} DOIs only") + dois = dois[:limit] + + # Generate publications + generate_publications_markdown(dois, output_md) + + print("\nDone! To add new publications:") + print(f" 1. Add DOI to {doi_yaml}") + print(f" 2. Run: uv run python scripts/generate_publications.py") + + +if __name__ == '__main__': + main()