Feng Cui

Associate Professor

College of Science

Thomas H. Gosnell School of Life Sciences

2023 Submissions

Journal Paper

Olatunji, Isaac and Feng Cui. "Multimodal AI for prediction of distant metastasis in carcinoma patients." Frontiers in Bioinformatics 3. (2023): 1131021. Web. ˜

Subramanya, Sridevi K., et al. "Deep learning for histopathological segmentation of smooth muscle in the urinary bladder." BMC Medical Informatics and Decision Making 23. (2023): 122. Web. ˜

2022 Submissions

Journal Paper

Rynkiewicz, Patrick, et al. "Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains." Journal of Biomolecular Structure and Dynamics 40. 21 (2022): 10978-10996. Web. ˜

Kc, Kishan, et al. "Predicting Biomedical Interactions with Higher-Order Graph Convolutional Networks." IEEE/ACM Transaction on Computational Biology and Bioinformatics 19. 2 (2022): 676-687. Web. ˜

2021 Submissions

Journal Paper

Gupta, Aditya, Andrew J. Rosato, and Feng Cui. "Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools." Journal of Biomolecular Structure and Dynamics 39. 16 (2021): 6084–6098. Web. ˜

Freewoman, Julia M, Rajiv Snape, and Feng Cui. "Temporal gene regulation by p53 is associated with the rotational setting of its binding sites in nucleosomes." Cell Cycle 20. 8 (2021): 792-807. Web. ˜

Kc, Kishan, et al. "Machine learning predicts nucleosome binding modes of transcription factors." BMC Bioinformatics 22. (2021): 166. Web. ˜

Published Conference Proceedings

Kc, Kishan, et al. "Interpretable Structured Learning with Sparse Gated Sequence Encoder for Protein-Protein Interaction Prediction." Proceedings of the 2020 25th International Conference on Pattern Recognition (ICPR), 10-15 Jan. 2021, Milan, Italy. Ed. Rita Cucchiara, Alberto Del Bimbo, and Stan Sclaroff. Milan, Italy: n.p., 2021. Web. *

2020 Submissions

Journal Paper

Yin, Peng-Nien, et al. "Histopathological distinction of non-invasive and invasive bladder cancers using machine learning approaches." BMC Medical Informatics and Decision Making 20. 1 (2020): 162. Web. ˜

2019 Submissions

Journal Paper

Zhang, Jimmy F., et al. "BioVR: a platform for virtual reality assisted biological data integration and visualization." BMC Bioinformatics 20. (2019): 78. Web. *

KC, Kishan, et al. "GNE: a deep learning framework for gene network inference by aggregating biological information." BMC Systems Biology 13. (2019): 38. Web. *

Wright, Gregory M and Feng Cui. "The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes." Nucleic Acids Research 47. 15 (2019): 7942–7954. Print. *

2018 Submissions

Published Conference Proceedings

Li, Rui, et al. "Sparse Covariance Modeling in High Dimensions with Gaussian Processes." Proceedings of the Neural Information Processing Systems 2018. Ed. S. Bengio, et al. Montreal, Canada: n.p., 2018. Web. *

Bao, Feifei, et al. "P53 Binding Sites in Normal and Cancer Cells are Characterized by Distinct Chromatin Context." Proceedings of the AACR Annual Meeting 2018. Ed. Chi Van Dang. Chicago, IL: n.p., 2018. Print.

2017 Submissions

Journal Paper

F., Bao, et al. "P53 Binding Sites in Normal and Cancer Cells are Characterized by Distinct Chromatin Context." Cell Cycle 16. 21 (2017): 2073-2085. Print. *

2016 Submissions

Journal Paper

Cole, Hope A., et al. "Novel Nucleosomal Particles Containing Core Histones and Linker DNA but no Histone H1." Nucleic Acids Research 44. 2 (2016): 573-581. Print. *

Ocampo, Josefina, et al. "The Proto-chromatosome: A Fundamental Subunit of Chromatin?" Nucleus 7. 4 (2016): 382-387. Print. *

2015 Submissions

Journal Paper

LoVerso, Peter R and Feng Cui. "A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor." Bioinformatics and Biology Insights 9. (2015): 165-174. Print. *

LoVerso, Peter R, Christopher M Wachter, and Feng Cui. "Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells." Bioinformatics and Biology Insights 9. (2015): 153-164. Print. *

Norouzi, Davood, et al. "Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription." AIMS Biophysics 2. 4 (2015): 613-629. Print. *

2014 Submissions

Journal Paper

Cui, Feng and Victor B. Zhurkin. "Rotational Positioning of Nucleosomes Facilitates Selective Binding of p53 to Response Elements Associated with Cell Cycle Arrest." Nucleic Acids Research 42. 2 (2014): 836-847. Print. ˜

Cui, Feng, et al. "Prediction of Nucleosome Rotational Positioning in Yeast and Human Genomes Based on Sequence-dependent DNA Anisotropy." BMC Bioinformatics 15. (2014): 313. Print. ˜

Alharbi, Bader A., et al. "nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning." Genomics Proteomics and Bioinformatics 12. 5 (2014): 249-253. Print. ˜

2012 Submissions

Journal Paper

Cui, F, et al. "Transcriptional Activation of Yeast Genes Disrupts Intragenic Nucleosome Phasing." Nucleic Acids Research 40. 21 (2012): 10753-10764. Print. *

Macvanin, M, et al. "Noncoding RNAs Binding to the Nucleoid Protein HU in Escherichia Coli." Journal of Bacteriology 194. 22 (2012): 6046-6055. Print. *