Weichun Huang, Ph.D.
Biostatistics & Computational Biology Branch
- Weichun Huang, Ph.D.
My research is primarily in the interdisciplinary fields of statistics, biomedical sciences, and computer science and engineering. I'm interested in designing and using efficient informatic approaches to help undercover biological mechanisms underlying complex biological data. Currently, my research work focuses on the following two areas:
- Independent research in statistical methods and tools for next-generation sequencing data analysis.
- Collaborative research in biological data mining or analyses for new biology insights or discoveries.
- Stumpo D, Trempus C, Tucker CJ, Huang W, Li L, Kluckman K, Bortner DM, and Blackshear PJ. Deficiency of the placenta- and yolk sac-specific tristetraprolin family member ZFP36L3 identifies likely mRNA targets and an unexpected link to placental iron metabolism. Development. 143(8): 1424-33, 2016.
- Patial S., Stumpo D., Huang W., Flake G. and Blackshear PJ. Genetic deletion of AU-rich region in the tristetraprolin (TTP) transcript increases TTP stability and expression and provides protection against inflammatory diseases. The Journal of Immunology, vol.194 (1 Supplement). 56.10, 2015.
- Wells ML, Washington OL, Hicks SN, Nobile CJ, Hartooni N, Wilson GM, Zucconi BE, Huang W, Li L, Fargo DC, and Blackshear PJ. Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans. Molecular Microbiology. 95(6):1036-1053, 2015.
- Choi YJ, Lai WS, Fedic R, Stumpo DJ, Huang W, Li L, Perera L, Brewer BY, Wilson GM, Mason JM, and Blackshear PJ. The Drosophila Tis11 protein and its effects on mRNA expression in flies. Journal of Biological Chemistry. 289(51):35042-60, 2014.
- Niu L, Huang W, Umbach DM, Li L. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC Genomics. 15:862, 2014.
- Huang W, Loganantharaj R, Schroeder B, Fargo D, Li L. PAVIS: a tool for Peak Annotation and Visualization, Bioinformatics, 29(23): 3097-9, 2013.
- Li Y, Huang W, Niu L, Umbach DM, Covo S, Li L. Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes, BMC Genomics, 14: 553, 2013.
- Huang W, Li L, Myers JR, and Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 28(4): 593-594, 2012.
- Huang W, Umbach DM, Vincent Jordan N, Abell AN, Johnson GL, Li L. Efficiently identifying genome-wide changes with next-generation sequencing data. Nucleic Acids Research. 39(19): e130, 2011.
- Abell AN, Jordan NV, Huang W, Prat A, Midland AA, Johnson NL, Granger DA, Mieczkowski PA, Perou CM, Gomez SM et al. MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells. Cell Stem Cell. 8(5): 525-537, 2011.
- Huang W, with 1,000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 467(7319):1061-1073, 2010.
- Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W et al. 2008. Whole-genome sequencing and variant discovery in c. elegans. Nature Methods. 5(2): 183-188, 2008.
- Huang W, Marth GT. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Research. 18(9): 1538-1543, 2008.
- Huang Wξ, Nevins JR, Ohler U. Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biology. 8(10): R225, 2007.
- Huang W, Umbach DM, Li L. Accurate anchoring alignment of divergent sequences. Bioinformatics. 22(1): 29-34, 2006.
- Huang W, Umbach DM, Ohler U, Li L. Optimized mixed Markov models for motif identification. BMC Bioinformatics. 7: 279, 2006.
- ART: Next-Generation Sequencing Data Simulation
- EpiCenter: ChIP-seq and mRNA-seq Data Analysis
- EagleView: Integrated Genome Assembly, Genome Annotation, and Genetic Variation Viewer
- PSPE: Evolutionary Simulation of Gene Promoter Sequences and Regulatory Elements
- OMiMa: Model and Prediction of Biological Motifs
- ACANA: Accurate Pairwise Alignment of Divergent DNA Sequences