1. A hidden Markov model for extracting nucleosome positions from tiling array data.

Reference: Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ.  Genome-scale identification of nucleosome positions in S. Cerevisiae.  Science 2005;309(5734):626-630 [paper]

Download MATLAB source code

2. N-score model: a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.


2a) Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology 2008. doi:10.1371/journal.pcbi.0040013.eor) [paper]

2b) Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol 2009 Feb;16(2):341-355. [paper]

Download the latest and faster version in python (written by Yijing Zhang and Luca Pinello)

Download MATLAB source code

Download predicted nucleosome position: This is based on the 2003 version of yeast genome (Download fasta files)

3. MIM (Motif-Independent Metric) for sequence specificity

Reference: Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12:408. [paper]

[Link to Github].

4. A hidden Markov model for identifying chromatin domains from multiple histone modificaiton data

Reference: Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12;11:557. [paper]

[ Download Matlab and R codes].

5. MAnorm: a robust model for quantitative comparison of ChIP-seq datasets

Reference: Shao Z, Zhang Y, Yuan GC., Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology. 2012 Mar 16;13(3):R16. [paper]

[Software page]

6. SCUBA: a method for single-cell gene expression analysis

Details will come soon.

[Link to Github]

7. PANDA: a message-passing method for gene regulatory network reconstruction

Reference: Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing Messages between Biological Networks to Refine Predicted Interactions. PLOS ONE. 2013 May 31, 8(5), e64832. [paper]

[Link to SourceForge]