M.D. Hunan Medical University, Changsha, Hunan, PR China
M.S. Truman State University, Kirksville, MO
Ph.D. Iowa State University, Ames, IA
Molecular Modeling and Proteomics
Genome-wide nucleosome positioning patterns
DNA motifs guiding nucleosome positioning
Nucleosomal DNA-binding proteins
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).