Bao F, LoVerso PR, Fisk JN, Zhurkin VB, Cui F: p53 binding sites in normal and cancer cells are characterized by distinct chromatin context. Cell Cycle 2017, 16:2073-2085.
Ocampo J, Cui F, Zhurkin VB, Clark DJ: The proto-chromatosome: a fundamental subunit of chromatin? Nucleus 2016, 7:382-387.
Cole HA, Cui F, Ocampo J, Burke TL, Nikitina T, Nagarajavel V, Kotomura N, Zhurkin VB, Clark DJ: Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Res 2016, 44:573-81.
LoVerso PR, Cui F: Cell type-specific transcriptome profiling in mammalian brains. Front Biosci (Landmark) 2016, 21:973-985.
Norouzi D, Katebi A, Cui F, Zhurkin VB: Topological diversity of chromatin fibers: interplay between nucleosome repeat length, DNA linking number and the level of transcription. AIMS Biophysics 2015, 2:613-629.
LoVerso PR, Wachter CM, Cui F: Cross-species transcriptomic comparison of in vitro and in vivo mammalian neural cells. Bioinform Biol Insights 2015, 9:153-164.
LoVerso PR, Cui F: A computational pipeline for cross-species analysis of RNA-seq data using R and Bioconductor. Bioinform Biol Insights 2015, 9:165-174.
Cole HA, Cui F, Ocampo J, Burke TL, Nikitina T, Nagarajavel V, Kotomura N, Zhurkin VB, Clark DJ: Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acid Res 2016, 44:573-581.
Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB, Cui F: nuMap: a web platform for accurate prediction of nucleosome positioning. Genomics Proteomics Bioinformatics 2014, 12:249-253.
Cui F, Chen L, LoVerso PR, 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 inEscherichia 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 Direct2011, 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.