- Accurate anchoring alignment of divergent sequencesWeichun Huang
Biostatistics Branch, The National Institute of Environmental Health Sciences NIH, Research Triangle Park, NC 27709, USA
Bioinformatics 22:29-34. 2006..Obtaining high quality alignments of divergent homologous sequences for cross-species sequence comparison remains a challenge...
- Optimized mixed Markov models for motif identificationWeichun Huang
Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
BMC Bioinformatics 7:279. 2006..Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availability of training samples...
- Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment toolsWeichun Huang
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Genome Biol 8:R225. 2007..As an alternative, we introduce a flexible new simulation system, Phylogenetic Simulation of Promoter Evolution (PSPE), designed to study functional site turnovers in regulatory sequences...
- EagleView: a genome assembly viewer for next-generation sequencing technologiesWeichun Huang
Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA
Genome Res 18:1538-43. 2008..EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView...