To cite the functional chi-squared test in publications, use
Zhang Y, Song M (2013). “Deciphering interactions in causal networks without parametric assumptions.” arXiv Molecular Networks, arXiv:1311.2707. https://arxiv.org/abs/1311.2707.
To cite the exact functional test using dynamic and quadratic programming in publications, use
Nguyen HH, Zhong H, Song M (2020). “Optimality, accuracy, and efficiency of an exact functional test.” In Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, IJCAI-20, 2683–2689. doi:10.24963/ijcai.2020/372.
To cite the exact functional test using quadratic programming in publications, use
Zhong H, Song M (2019). “A fast exact functional test for directional association and cancer biology applications.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(3), 818–826. doi:10.1109/TCBB.2018.2809743.
To cite the simulate_tables() function in publications, use
Sharma R, Kumar S, Zhong H, Song M (2017). “Simulating noisy, nonparametric, and multivariate discrete patterns.” The R Journal, 9(2), 366–377. doi:10.32614/RJ-2017-053.
To cite the function index in publications, use
Zhong H, Song M (2019b). “Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs.” BMC Med Genomics, 12(7), 129. doi:10.1186/s12920-019-0565-9.
and
Kumar S, Zhong H, Sharma R, Li Y, Song M (2018). “Scrutinizing functional interaction networks from RNA-binding proteins to their targets in cancer.” In IEEE International Conference on Bioinformatics and Biomedicine, 185–190. doi:10.1109/BIBM.2018.8621502.
To cite the adapted functional chi-squared test in publications, use
Kumar S, Song M (2022). “Overcoming biases in causal inference of molecular interactions.” Bioinformatics, 38(10), 2818–2825. doi:10.1093/bioinformatics/btac206.
Corresponding BibTeX entries:
@Article{zhang2013deciphering, title = {Deciphering interactions in causal networks without parametric assumptions}, journal = {arXiv Molecular Networks}, year = {2013}, pages = {arXiv:1311.2707}, author = {Yang Zhang and Mingzhou Song}, url = {https://arxiv.org/abs/1311.2707}, }
@InProceedings{Nguyen2020EFT, author = {Hien H. Nguyen and Hua Zhong and Mingzhou Song}, booktitle = {Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, {IJCAI-20}}, title = {Optimality, accuracy, and efficiency of an exact functional test}, year = {2020}, pages = {2683--2689}, doi = {10.24963/ijcai.2020/372}, }
@Article{zhong2019eft, title = {A fast exact functional test for directional association and cancer biology applications}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, year = {2019}, volume = {16}, number = {3}, pages = {818--826}, author = {Hua Zhong and Mingzhou Song}, doi = {10.1109/TCBB.2018.2809743}, }
@Article{sharma2017simulating, title = {Simulating noisy, nonparametric, and multivariate discrete patterns}, journal = {The R Journal}, year = {2017}, volume = {9}, number = {2}, pages = {366--377}, author = {Ruby Sharma and Sajal Kumar and Hua Zhong and Mingzhou Song}, doi = {10.32614/RJ-2017-053}, }
@Article{Zhong2019FANTOM5, author = {Hua Zhong and Mingzhou Song}, doi = {10.1186/s12920-019-0565-9}, journal = {BMC Med Genomics}, number = {7}, pages = {129}, title = {Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs}, volume = {12}, year = {2019b}, }
@InProceedings{KumarZSLS18, address = {Madrid, Spain}, author = {Sajal Kumar and Hua Zhong and Ruby Sharma and Yiyi Li and Mingzhou Song}, booktitle = {IEEE International Conference on Bioinformatics and Biomedicine}, doi = {10.1109/BIBM.2018.8621502}, pages = {185--190}, title = {Scrutinizing functional interaction networks from {RNA}-binding proteins to their targets in cancer}, year = {2018}, }
@Article{Kumar2022AFT, title = {Overcoming biases in causal inference of molecular interactions}, journal = {Bioinformatics}, year = {2022}, volume = {38}, number = {10}, pages = {2818--2825}, author = {Sajal Kumar and Mingzhou Song}, doi = {10.1093/bioinformatics/btac206}, }