cyinbox

PPI

Yin, C. & Yau, S. S.-T. (2017). A coevolution analysis for identifying protein-protein interactions by Fourier transform. PLoS ONE 12(4): e0174862.

iCGR

Yin, C. (2018). Encoding DNA sequences by integer Chaos Game Representation, Journal of Computational Biology

DNADU

Yin, C. (2017). Identification of repeats in DNA sequences using nucleotide distribution uniformity. Journal of Theoretical Biology, 412, 138-145.

GenomeSSR

The program for detecting the special genome-wide simple sequence repeats (SSR), the homopolymeric nucleotide repeats (HPs).

NGS

Yin., C., & Yau., S. S.-T (2019). Whole genome single nucleotide polymorphisms genotyping of Staphylococcus aureus. Communications in Information and Systems, Vol 19. No.1, 57-80

FPS

The Fourier spectrum at a fractional period is often examined when extracting features from biological sequences and time series. It reflects the inner information structure of the sequences. A fractional period is not uncommon in time series. A typical example is the 3.6 period in protein sequences, which determines the alpha-helix secondary structure. Computing the spectrum of a fractional period offers a high-resolution insight into a time series. It has thus become an important approach in genomic analysis. However, computing Fourier spectra of fractional periods by the traditional Fourier transform is computationally expensive. We propose here a novel, fast algorithm for directly computing the fractional period spectrum (FPS) of time series. The algorithm is based on the periodic distribution of signal strength at periodic positions of the time series. The analysis of computational complexity of the algorithm shows that the algorithm is much faster than traditional Fourier transform. Our algorithm can be applied directly in computing fractional periods in time series from extensive research fields.

GeneBow

Yin, C. (2017). GeneBow: A pipeline for detecting antibiotic resistance genes (ARGs)

Genome

Yin, C. & Yau, S. S. T. (2015). An improved model for whole genome phylogenetic analysis by Fourier transform. Journal of Theoretical Biology, 382, 99-110.

GenomeDFT

Yin, C., Chen, Y., & Yau, S. S. T. (2014). A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering. Journal of Theoretical Biology, 359, 18-28.

PPS

Yin, C. & Wang, J. (2016). Periodic power spectrum with applications in detection of latent periodicities in DNA sequences. Journal of Mathematical Biology, 73(5), 1053-1079.

machine_learning_notes

Notebooks on machine learning, generative AI, data analytics and visualization, and statistical inference.

periodicDNA

periodicDNA R package

ProteinData