Computer Science and Engineering, Biology
Genome3D: A Viewer-Model Framework for Integrating and Visualizing Multi-Scale Epigenomic Information within a Three-Dimensional Genome (with Thomas M. Asbury, Matt Mitman, and W. Jim Zheng), BMC Bioinformatics (2010)
Background
New technologies are enabling the measurement of many types of genomic and epigenomic information...
Using Jackknife to Assess the Quality of Gene Order Phylogenies (with Jian Shi, Yiwei Zhang, and Haiwei Luo), BMC Bioinformatics (2010)
Background
In recent years, gene order data has attracted increasing attention from both biologists and...
Gene Order Phylogeny and the Evolution of Methanogens (with Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, and Robert Friedman), PLoS ONE (2009)
Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets...
Gene Order Phylogeny of the Genus Prochlorococcus (with Haiwei Luo, Jian Shi, William Arndt, and Robert Friedman), PLoS ONE (2008)
Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved...
Improving Reversal Median Computation Using Commuting Reversals and Cycle Information (with William Arndt), Journal of Computational Biology (2008)
In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer...
Phylogenetic Reconstruction from Transpositions (with Feng Yue and Meng Zhang), BMC Genomics (2008)
Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost...
Gene Rearrangement Analysis and Ancestral Order Inference from Chloroplast Genomes with Inverted Repeat (with Feng Yue, Liying Cui, Claude W. dePamphilis, and Bernard M.E. Moret), BMC Genomics (2008)
Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes...
Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach (with Liying Cui, Jim Leebens-Mack, Li-San Wang, Linda Rymarquis, David B. Stern, and Claude W. dePamphilis), BMC Evolutionary Biology (2006)
Background
Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most...