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abdelhafizm merged 1 commit into from
Jul 6, 2026
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Updated citation after paper acceptance #109

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59 changes: 17 additions & 42 deletions README.md
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Expand Up @@ -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:
Expand All @@ -32,14 +32,17 @@ For your convenience, you can use the following BibTeX entry:
<summary>BibTeX Citation</summary>

```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}
}
```
</details>
Expand All @@ -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

Expand Down Expand Up @@ -355,35 +357,8 @@ See the [LICENSE](LICENSE) file for details.

## 10. References

<a id="1">[1]</a> 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)
<a id="1">[1]</a> 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)

<a id="2">[2]</a> 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)
<a id="2">[2]</a> 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)

<a id="3">[3]</a> 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:

<details>
<summary>BibTeX Citation</summary>

```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},
}
```
</details>
<a id="3">[3]</a> 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)
10 changes: 5 additions & 5 deletions docs/source/index.rst
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Expand Up @@ -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 <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>`_.

.. toctree::
:maxdepth: 2
Expand Down Expand Up @@ -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 <https://doi.org/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 <https://doi.org/10.1109/BIBM62325.2024.10822233>`_.
.. [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 <https://doi.org/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 <https://doi.org/10.1109/BIBM62325.2024.10822233>`_.
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