diff --git a/README.md b/README.md index 94c38b8..0f51ec5 100644 --- a/README.md +++ b/README.md @@ -21,9 +21,9 @@ If you use BioNeuralNet in your research, we kindly ask that you cite our paper: -> Ramos, V., Hussein, S., et al. (2025). -> [**BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool**](https://arxiv.org/abs/2507.20440). -> *arXiv preprint arXiv:2507.20440* | [**DOI: 10.48550/arXiv.2507.20440**](https://doi.org/10.48550/arXiv.2507.20440). +> Ramos, V., et al. (2026). +> [**BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool**](https://academic.oup.com/bioinformatics/article/42/6/btag365/8705525). +> *Bioinformatics*, Volume 42, Issue 6, btag365 | [**DOI: 10.1093/bioinformatics/btag365**](https://doi.org/10.1093/bioinformatics/btag365). For your convenience, you can use the following BibTeX entry: @@ -32,14 +32,17 @@ For your convenience, you can use the following BibTeX entry: BibTeX Citation ```bibtex -@misc{ramos2025bioneuralnetgraphneuralnetwork, - title={BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool}, - author={Vicente Ramos and Sundous Hussein and Mohamed Abdel-Hafiz and Arunangshu Sarkar and Weixuan Liu and Katerina J. Kechris and Russell P. Bowler and Leslie Lange and Farnoush Banaei-Kashani}, - year={2025}, - eprint={2507.20440}, - archivePrefix={arXiv}, - primaryClass={cs.LG}, - url={https://arxiv.org/abs/2507.20440}, +@article{ramos2026bioneuralnet, + title={BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool}, + author={Ramos, Vicente and Hussein, Sundous and Abdel-Hafiz, Mohamed and Sarkar, Arunangshu and Liu, Weixuan and Kechris, Katerina J. and Bowler, Russell P. and Lange, Leslie and Banaei-Kashani, Farnoush}, + journal={Bioinformatics}, + volume={42}, + number={6}, + pages={btag365}, + year={2026}, + month={June}, + doi={10.1093/bioinformatics/btag365}, + url={https://doi.org/10.1093/bioinformatics/btag365} } ``` @@ -63,7 +66,6 @@ For complete documentation, tutorials, and examples, please visit our Read the D - [8. License](#9-License) - [9. Contact](#10-Contact) - [10. References](#11-References) -- [11. Citation](#11-Citation) ## 1. Installation @@ -355,35 +357,8 @@ See the [LICENSE](LICENSE) file for details. ## 10. References -[1] Abdel-Hafiz, M., Najafi, M., et al. "Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification." *Frontiers in Big Data*, 5 (2022). [DOI: 10.3389/fdata.2022.894632](https://doi.org/10.3389/fdata.2022.894632) +[1] Abdel-Hafiz, M., et al. (2022). "Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification." *Frontiers in Big Data*, 5. [DOI: 10.3389/fdata.2022.894632](https://doi.org/10.3389/fdata.2022.894632) -[2] Hussein, S., Ramos, V., et al. "Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach." In *2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*, Lisbon, Portugal, 2024, pp. 4371-4378. [DOI: 10.1109/BIBM62325.2024.10822233](https://doi.org/10.1109/BIBM62325.2024.10822233) +[2] Hussein, S., et al. (2024). "Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach." In *2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*, Lisbon, Portugal, pp. 4371-4378. [DOI: 10.1109/BIBM62325.2024.10822233](https://doi.org/10.1109/BIBM62325.2024.10822233) -[3] Liu, W., Vu, T., Konigsberg, I. R., Pratte, K. A., Zhuang, Y., & Kechris, K. J. (2023). "Network-Based Integration of Multi-Omics Data for Biomarker Discovery and Phenotype Prediction." *Bioinformatics*, 39(5), btat204. [DOI: 10.1093/bioinformatics/btat204](https://doi.org/10.1093/bioinformatics/btat204) - - -## 11. Citation - -If you use BioNeuralNet in your research, we kindly ask that you cite our paper: - -> Vicente Ramos, et al. (2025). -> [**BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool**](https://arxiv.org/abs/2507.20440). -> *arXiv preprint arXiv:2507.20440*. - -For your convenience, you can use the following BibTeX entry: - -
- BibTeX Citation - -```bibtex -@misc{ramos2025bioneuralnetgraphneuralnetwork, - title={BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool}, - author={Vicente Ramos and Sundous Hussein and Mohamed Abdel-Hafiz and Arunangshu Sarkar and Weixuan Liu and Katerina J. Kechris and Russell P. Bowler and Leslie Lange and Farnoush Banaei-Kashani}, - year={2025}, - eprint={2507.20440}, - archivePrefix={arXiv}, - primaryClass={cs.LG}, - url={https://arxiv.org/abs/2507.20440}, -} -``` -
+[3] Liu, W., et al. (2024). "Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization." *BMC Bioinformatics*, 25(1), 276. [DOI: 10.1186/s12859-024-05900-9](https://doi.org/10.1186/s12859-024-05900-9) diff --git a/docs/source/index.rst b/docs/source/index.rst index d8111e1..929211a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -210,9 +210,9 @@ Citation If you use BioNeuralNet in your research, we kindly ask that you cite our paper: - Ramos, V., Hussein, S., et al. (2025). - `BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool `_. - *arXiv preprint arXiv:2507.20440* | `DOI: 10.48550/arXiv.2507.20440 `_. + Ramos, V., et al. (2026). + `BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool `_. + *Bioinformatics*, Volume 42, Issue 6, btag365 | `DOI: 10.1093/bioinformatics/btag365 `_. .. toctree:: :maxdepth: 2 @@ -240,5 +240,5 @@ Indices and References * :ref:`modindex` * :ref:`search` -.. [1] Liu, W., Vu, T., Konigsberg, I. R., Pratte, K. A., Zhuang, Y., & Kechris, K. J. (2023). "Network-Based Integration of Multi-Omics Data for Biomarker Discovery and Phenotype Prediction." *Bioinformatics*, 39(5), btat204. DOI: `10.1093/bioinformatics/btat204 `_. -.. [2] Hussein, S., Ramos, V., et al. "Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach." In *2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*, Lisbon, Portugal, 2024, pp. 4371-4378. DOI: `10.1109/BIBM62325.2024.10822233 `_. \ No newline at end of file +.. [1] Liu, W., et al. (2024). "Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization." *BMC Bioinformatics*, 25(1), 276. DOI: `10.1186/s12859-024-05900-9 `_. +.. [2] Hussein, S., et al. (2024). "Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach." In *2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*, Lisbon, Portugal, pp. 4371-4378. DOI: `10.1109/BIBM62325.2024.10822233 `_.