Skip to content

Commit

Permalink
GITBOOK-297: add new publication
Browse files Browse the repository at this point in the history
  • Loading branch information
@fedorov @gitbook-bot
fedorov authored and gitbook-bot committed May 17, 2023
1 parent 143f5c9 commit a121ed8
Showing 1 changed file with 8 additions and 7 deletions.
15 changes: 8 additions & 7 deletions idc-key-pointers.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

1. Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S., Aerts, H. J. W. L., Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D., Clifford, W., Herrmann, M. D., Höfener, H., Octaviano, I., Osborne, C., Paquette, S., Petts, J., Punzo, D., Reyes, M., Schacherer, D. P., Tian, M., White, G., Ziegler, E., Shmulevich, I., Pihl, T., Wagner, U., Farahani, K. & Kikinis, R. NCI Imaging Data Commons. _Cancer Res._ 81, 4188–4193 (2021). [http://dx.doi.org/10.1158/0008-5472.CAN-21-0950](http://dx.doi.org/10.1158/0008-5472.CAN-21-0950)
2. Gorman, C., Punzo, D., Octaviano, I., Pieper, S., Longabaugh, W. J. R., Clunie, D. A., Kikinis, R., Fedorov, A. Y. & Herrmann, M. D. Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology. _Nat. Commun._ 14, 1–15 (2023). [http://dx.doi.org/10.1038/s41467-023-37224-2](http://dx.doi.org/10.1038/s41467-023-37224-2)
3. Schacherer, D. P., Herrmann, M. D., Clunie, D. A., Höfener, H., Clifford, W., Longabaugh, W. J. R., Pieper, S., Kikinis, R., Fedorov, A. & Homeyer, A. The NCI Imaging Data Commons as a platform for reproducible research in computational pathology. _arXiv \[cs.CV]_ (2023). at \<http://arxiv.org/abs/2303.09354> [http://arxiv.org/abs/2303.09354](http://arxiv.org/abs/2303.09354)
3. Schacherer, D. P., Herrmann, M. D., Clunie, D. A., Höfener, H., Clifford, W., Longabaugh, W. J. R., Pieper, S., Kikinis, R., Fedorov, A. & Homeyer, A. The NCI Imaging Data Commons as a platform for reproducible research in computational pathology. _arXiv \[cs.CV]_ (2023). at <[http://arxiv.org/abs/2303.09354](http://arxiv.org/abs/2303.09354)>&#x20;
4. Bridge, C. P., Gorman, C., Pieper, S., Doyle, S. W., Lennerz, J. K., Kalpathy-Cramer, J., Clunie, D. A., Fedorov, A. Y. & Herrmann, M. D. Highdicom: a Python Library for Standardized Encoding of Image Annotations and Machine Learning Model Outputs in Pathology and Radiology. _J. Digit. Imaging_ 35, 1719–1737 (2022). [http://dx.doi.org/10.1007/s10278-022-00683-y](http://dx.doi.org/10.1007/s10278-022-00683-y)

## Publications referencing IDC (a subset)
Expand All @@ -21,11 +21,12 @@
See the full list, as curated by Google Scholar, [here](https://scholar.google.com/scholar?oi=bibs\&hl=en\&cites=8052604365477078213).
{% endhint %}

1. Jiang, P., Sinha, S., Aldape, K., Hannenhalli, S., Sahinalp, C. & Ruppin, E. Big data in basic and translational cancer research. _Nat. Rev. Cancer_ 22, 625–639 (2022). [http://dx.doi.org/10.1038/s41568-022-00502-0](http://dx.doi.org/10.1038/s41568-022-00502-0)
2. Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J., Arias-Camison, R., Arena, S., Taylor, A. J., Nikolov, M., Tyler, M., Lin, J.-R., Burlingame, E. A., Human Tumor Atlas Network, Chang, Y. H., Farhi, S. L., Thorsson, V., Venkatamohan, N., Drewes, J. L., Pe’er, D., Gutman, D. A., Herrmann, M. D., Gehlenborg, N., Bankhead, P., Roland, J. T., Herndon, J. M., Snyder, M. P., Angelo, M., Nolan, G., Swedlow, J. R., Schultz, N., Merrick, D. T., Mazzili, S. A., Cerami, E., Rodig, S. J., Santagata, S. & Sorger, P. K. MITI minimum information guidelines for highly multiplexed tissue images. _Nat. Methods_ 19, 262–267 (2022). [http://dx.doi.org/10.1038/s41592-022-01415-4](http://dx.doi.org/10.1038/s41592-022-01415-4)
3. Wahid, K. A., Glerean, E., Sahlsten, J., Jaskari, J., Kaski, K., Naser, M. A., He, R., Mohamed, A. S. R. & Fuller, C. D. Artificial intelligence for radiation oncology applications using public datasets. _Semin. Radiat. Oncol._ 32, 400–414 (2022). [http://dx.doi.org/10.1016/j.semradonc.2022.06.009](http://dx.doi.org/10.1016/j.semradonc.2022.06.009)
4. Hartley, M., Kleywegt, G. J., Patwardhan, A., Sarkans, U., Swedlow, J. R. & Brazma, A. The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. _J. Mol. Biol._ 167505 (2022). doi:10.1016/j.jmb.2022.167505 [http://dx.doi.org/10.1016/j.jmb.2022.167505](http://dx.doi.org/10.1016/j.jmb.2022.167505)
5. Diaz-Pinto, A., Alle, S., Nath, V., Tang, Y., Ihsani, A., Asad, M., Pérez-García, F., Mehta, P., Li, W., Flores, M., Roth, H. R., Vercauteren, T., Xu, D., Dogra, P., Ourselin, S., Feng, A. & Cardoso, M. J. MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images. _arXiv \[cs.HC]_ (2022). at \<http://arxiv.org/abs/2203.12362> [http://arxiv.org/abs/2203.12362](http://arxiv.org/abs/2203.12362)
6.
1. Kulkarni, P., Kanhere, A., Yi, P. H. & Parekh, V. S. Text2Cohort: Democratizing the NCI Imaging Data Commons with natural language cohort discovery. _arXiv \[cs.LG]_ (2023). at <[http://arxiv.org/abs/2305.07637](http://arxiv.org/abs/2305.07637)> &#x20;
2. Jiang, P., Sinha, S., Aldape, K., Hannenhalli, S., Sahinalp, C. & Ruppin, E. Big data in basic and translational cancer research. _Nat. Rev. Cancer_ 22, 625–639 (2022). [http://dx.doi.org/10.1038/s41568-022-00502-0](http://dx.doi.org/10.1038/s41568-022-00502-0)
3. Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J., Arias-Camison, R., Arena, S., Taylor, A. J., Nikolov, M., Tyler, M., Lin, J.-R., Burlingame, E. A., Human Tumor Atlas Network, Chang, Y. H., Farhi, S. L., Thorsson, V., Venkatamohan, N., Drewes, J. L., Pe’er, D., Gutman, D. A., Herrmann, M. D., Gehlenborg, N., Bankhead, P., Roland, J. T., Herndon, J. M., Snyder, M. P., Angelo, M., Nolan, G., Swedlow, J. R., Schultz, N., Merrick, D. T., Mazzili, S. A., Cerami, E., Rodig, S. J., Santagata, S. & Sorger, P. K. MITI minimum information guidelines for highly multiplexed tissue images. _Nat. Methods_ 19, 262–267 (2022). [http://dx.doi.org/10.1038/s41592-022-01415-4](http://dx.doi.org/10.1038/s41592-022-01415-4)
4. Wahid, K. A., Glerean, E., Sahlsten, J., Jaskari, J., Kaski, K., Naser, M. A., He, R., Mohamed, A. S. R. & Fuller, C. D. Artificial intelligence for radiation oncology applications using public datasets. _Semin. Radiat. Oncol._ 32, 400–414 (2022). [http://dx.doi.org/10.1016/j.semradonc.2022.06.009](http://dx.doi.org/10.1016/j.semradonc.2022.06.009)
5. Hartley, M., Kleywegt, G. J., Patwardhan, A., Sarkans, U., Swedlow, J. R. & Brazma, A. The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. _J. Mol. Biol._ 167505 (2022). doi:10.1016/j.jmb.2022.167505 [http://dx.doi.org/10.1016/j.jmb.2022.167505](http://dx.doi.org/10.1016/j.jmb.2022.167505)
6. Diaz-Pinto, A., Alle, S., Nath, V., Tang, Y., Ihsani, A., Asad, M., Pérez-García, F., Mehta, P., Li, W., Flores, M., Roth, H. R., Vercauteren, T., Xu, D., Dogra, P., Ourselin, S., Feng, A. & Cardoso, M. J. MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images. _arXiv \[cs.HC]_ (2022). at <[http://arxiv.org/abs/2203.12362](http://arxiv.org/abs/2203.12362)>&#x20;
7.

\

0 comments on commit a121ed8

Please sign in to comment.