Feng Cui Headshot

Feng Cui

Associate Professor

Thomas H. Gosnell School of Life Sciences
College of Science
Graduate Director of Bioinformatics
fxcsbi@rit.edu
585-475-4115
Office Location
GOS-1336

Feng Cui

Associate Professor

Thomas H. Gosnell School of Life Sciences
College of Science
Graduate Director of Bioinformatics

Education

MS, Truman State University; Ph.D., Iowa State University; MD, Hunan Medical University (China)

fxcsbi@rit.edu
585-475-4115
Areas of Expertise
P53
Chromatin Organization
Machine Learning
Biological Data Visualization
Genomics

Select Scholarship

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.
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.
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.
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.
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.
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.
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.

Currently Teaching

BIOL-295
Biology Research
1 - 4 Credits
This course is a faculty-directed student project or research involving laboratory work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their first three years of study.
BIOL-298
Biology Independent Study
1 - 4 Credits
This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their first three years of study.
BIOL-301
Undergraduate Teaching Experience
1 - 4 Credits
This course allows students to assist in a class or laboratory for which they have previously earned credit. The student will assist the instructor in the operation of the course. Assistance by the student may include fielding questions, helping in workshops, and assisting in review sessions. In the case of labs, students may also be asked to help with supervising safety practices, waste manifestation, and instrumentation.
BIOL-327
Fundamental Bioinformatics Analysis
3 Credits
This course addresses the fundamental concepts of bioinformatics, focusing on computational analysis of nucleic acids and proteins. Utilization of computational programs for analysis of individual and multiple sequences for functional and evolutionary information will be discussed. The computational laboratory will highlight the applications available for analysis of molecular sequences.
BIOL-495
Advanced Biology Research
1 - 4 Credits
This course is a faculty-directed student project or research involving laboratory or field work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their final two years of study.
BIOL-498
Advanced Biology Independent Study
1 - 4 Credits
This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their final two years of study.
BIOL-689
Graduate Special Topics
1 - 4 Credits
This is a graduate course on a topic that is not part of the formal curriculum. This course is structured as an ordinary course and has specific prerequisites, contact hours, and examination procedures.
BIOL-790
Research and Thesis
1 - 6 Credits
Masters-level research by the candidate on an appropriate topic as arranged between the candidate and the research advisor.
BIOL-791
Continuation of Thesis
0 Credits
Continuation of Thesis
BIOL-798
Grad Biology Independent Study
1 - 4 Credits
This course is a faculty-directed, graduate level tutorial of appropriate topics that are not part of the formal curriculum.

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