Feng Cui

Assistant Professor

Contact Information

OfficeGOS 1336
Phone(585) 475-4115

M.D. Hunan Medical University, Changsha, Hunan, PR China
M.S. Truman State University, Kirksville, MO
Ph.D. Iowa State University, Ames, IA

Job Responsibilities

Molecular Modeling and Proteomics
Bioinformatics Languages

Research Interests

Chromosome biology
Genome-wide nucleosome positioning patterns
DNA motifs guiding nucleosome positioning
Nucleosomal DNA-binding proteins
Next-generation sequencing

Selected Publications

Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB and Cui F. nuMap: a web platform for accurate prediction of nucleosome positioning. Genomics Proteomics Bioinformatics, 2014 12:249-253 (selected for the "GPB Editor's Choice").
Cui F, Chen L, LoVerso P and Zhurkin VB: Accurate prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy. BMC Bioinformatics 2014 15:313.
Cui F, Zhurkin VB: Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res 2014 42:836-847.

Cui F, Cole H, Clark DJ, Zhurkin VB: Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res 2012, 40:10735-10764.
Macvanin M, Edgar R, Cui F, Trostel A, Zhurkin VB, Adhya S: RNAs binding to the nucleoid protein HU in Escherichia coli. J Bacteriol 2012, 194:6046-6055.
Cui F, Sirotin MV, Zhurkin VB: Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct 2011, 6:2.
Cui F, Zhurkin VB: Structure-based analysis of DNA sequence patterns guiding nucleosome  
positioning in vitro. J Biomol Struct Dynam 2010, 27:821-841.
Cui F, Zhurkin VB: Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res 2009, 37:2818-2829.
Cui F, Mukhopadhyay K, Young MB, Jernigan RL, Wu Z: Refinement of under-determined loops of human prion protein by database-derived distance constraints. Int J Data Min Bioinform 2009, 3:454-468.
Cui F, Jernigan R, Wu Z: Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement. J Bioinform Comput Biol 2008, 6:283-300.
Wu D, Cui F, Jernigan R, Wu Z: PIDD: Database for protein inter-atomic distance distributions. Nucleic Acid Res 2007, 35:D202-207.
Cui F, Jernigan R, Wu Z: A knowledge-based, structural approach to the refinement of NMR-determined protein structure. J Bioinform Comput Biol 2005, 3:1315-1329.
Dietrick C, Cui F, Packila M, Li J, Ashlock D, Nikolau B, Schnable P: Maize Mu transposons are targeted to the 5’ un-translated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit non-random nucleotide composition throughout the genome. Genetics 2002, 160:697-716.
Xia JH, Tang XX, Tang TS, Cui F, Yu KP, Pan Q, Dai HP, Liao XD, Long ZG: Molecular cloning of human Oligophrenin-1-like gene. Progress in Natural Science 2000, 10:945-948 (in Chinese).
Xia JH, Liu CY, Ruan QG, Pan Q, Liao XD, Fu JJ, Cui F, Deng HX: Molecular cloning of one splicing form of human M6b cDNA. Yi Chuan Xue Bao 1999, 26:439-446 (in Chinese).
Cui F, Xia JH: On Research Progress of Pseudogenes. Life Science Research 1999, 3:203-209 (in Chinese).
Xia JH, Liu CY, Wang DA, Ruan QG, Cui F, Xie W, Pan Q, Liao XD, Dai HP, Deng HX: Molecular cloning and localization of human Atrophin-1-like gene. Progress in Natural Science 1999, 9:203-210.
Cui F, Liu CY, Xia JH: Identification and localization of four retro-pseudogenes of the human polypeptide chain elongation factor 1α. Hereditas (Beijing) 1998, 20:6-10 (in Chinese).