I have a mixed background of experimental and computational biology, as well as software development.
During my Ph.D., I have generated over 300 Illumina libraries for small RNA-seq, RNA-seq, ChIP-seq, GRO-seq, and Genomic sequencing from genetically engineered Drosophila and mice. In the meanwhile, I developed computational tools for their analyses.
I have more than 10 years of experience using C++ and Python for bioinformatics and algorithm development, and R for statistical calculation, machine learning and figure generation.
I also have experience with web development using Vue.js and Beego, as well as using it for data visualization with D3.js.
2008/09 - 2015/08
Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs
In 2008, I joined the Lab of Dr. Zamore to pursue my Ph.D in Biomedical Science to study the biogenesis of small RNAs (including microRNA and piRNA). Since then I have been leading or co-leading 3 experimental-computational hybrid projects—which were published on Science, Molecular Cell, and Current Biology— and 2 computational projects that were published in Nucleic Acids Research and Bioinformatics. The main approach I used in those projects is the combination of next generation sequencing and computational analysis. I have experience analyzing both the secondary generation sequencing (illumina) and the third generation sequencing data (pacBio) using both state-of-the-art tools as well as ad hoc tools developed in my own hands.
Other than my own projects, I constantly provided bioinformatics support for people in my lab and school, some of these works were published in Cell, Molecular Cell, and EMBO Journal.
Implemented an architecture to automatically execute pipelines (upon sequencing finishes or user triggers) using Vue.js, plain Go, MySQL, AWS parallel cluster, SGE, AWS SDK, and Docker.
Developed a Hidden Markov Model based PolyA trimming program with C++
Wrote a pipeline to combine illumina and PacBio data for transcriptome annotation and quantification
C++ 11 years
Python 10 years
R 10 years
Bash 10 years
HTML/CSS 6 years
MySQL 6 years
Go 4 year
A set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq, and genomic DNA sequencing
A Burrow-Wheeler Transform based short reads aligner specialized in capturing non-templated nucleotide addition to the 3′ ends of small RNAs
A Hidden Markov model based PolyA trimmer for third-generation sequencing data
Web-based small utilities
Wang W.*, Han B.W.*, Tipping C., Ge T., Zhang Z., Weng Z., and Zamore P.D. (2015). Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell. 59, 819–830.
Chou M.*, Han B.W.*, Hsiao C.-P., Zamore P.D., Weng Z., and Hung J.H. (2015). Tailor: A Computational Framework for Detecting Non-Templated Tailing of Small Silencing RNAs. Nucleic Acids Res. 43, e109.
Han B.W.*, Wang W.*, Li C., Weng Z., and Zamore P.D. (2015). Secondary piRNA-guided cleavage initiates Zucchini-dependent, phased, primary piRNA production. Science. 348, 817-821.
Wang W., Yoshikawa M., Han B.W., Izumi N., Tomari Y., Weng Z., and Zamore P.D. (2014). The Initial Uridine of Primary piRNAs Does not Create the Tenth Adenine That is the Hallmark of Secondary piRNAs. Mol Cell. 56, 708-716.
Han B.W.*, Wang W.*, Zamore P.D., and Weng Z. (2014). piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics. 31, 593-595.
Han B.W., and Zamore P.D. (2014). piRNAs. Curr Biol. 24, R730-R733.
Fukunaga R., Colpan C., Han B.W., and Zamore P.D. (2014). Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO J. 33, 371-384.
Li X.Z., Roy C.K., Dong X., Bolcun-Filas E., Wang J., Han B.W., Xu J., Moore M.J., Schimenti J.C., Weng Z. et al. (2013). An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell. 50, 67-81.
Fukunaga R., Han B.W., Hung J.H., Xu J., Weng Z., and Zamore P.D. (2012). Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 151, 533-546.
Han B.W., Hung J.H., Weng Z., Zamore P.D., and Ameres S.L. (2011). The 3′-to-5′ exoribonuclease Nibbler shapes the 3′ ends of microRNAs bound to Drosophila Argonaute1. Curr Biol. 21, 1878-1887.