Biography
I am a postdoctoral scholar at Department of Statistics, Stanford University. I received my B.S degree in Biological Sciences from Tsinghua University (Beijing) in 2004. I received my doctorate degree in 2009 on Structural Biology, Oxford University, under Prof. David I. Stuart and Dr. Robert Esnouf's guidance. At the same year, I received my master degree in Statistics at Stanford University and continued my research on biostatistics/bioinformatics in Prof. Wing H. Wong's Lab till present. My current research interests focus on the following areas:
- RNA-seq (Alternative Splicing, isoform detection)
- Third Generation Sequencing
- Stem cell transcriptome analysis
- Proteomics (Protein identification and novel splice detections from high-throughput Mass Spec)
- Gene regulatory network
- RNA editing
Latest publication
Oct4-Sall4-Nanog network controls developmental progression in the preimplantation mouse embryo.
Tan, M.H.*, Au, Kin Fai*, Leong, D. E., Foygel K., Wong, W.H., Yao, M.W.M.
Molecular Systems Biology 2012. 632 doi:10.1038/msb.2012.65.[preprint]
* These authors contributed equally to this work
Improving PacBio long read accuracy by short read alignment.
Au, Kin Fai, Underwood, J., Lee, L., Wong, W.H.
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679 [preprint]
RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.
Tan, M.H.*, Au, Kin Fai*, Yablonovitch, A.L.*, Wills, A.E., Baker J.C.,
Wong, W.H., Li, J.B.
Genome Research, 2012. doi:10.1101/gr.141424.112 [preprint]
* These authors contributed equally to this work
Activation of Innate Immunity is Required for Efficient Nuclear Reprogramming
Lee, J., Sayed, N., Hunter, A., Au, Kin Fai, Wong, W.H., Mocarski, E., Pera, R.R., Yakubov, E., Cooke, J.P.
Cell, 2012 Oct; 151(3): 547-58. [preprint]
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Au, Kin Fai, Jiang, H., Lin, L., Xing, Y., Wong, W.H. Nucleic Acids Research, Aug;38(14):4570-8. 2010. [preprint]
Latest News
8-12-2012 - LSC 0.2.1 Released
LSC 0.2.1 fixes the bug of python path. Another bug of removing redundant reads is also fixed. LSC takes a long read data sets (>=100bp) and a short reads data sets (50 - 100bp) as input. They should be in FASTA format. Running time is almost linear with the the number of threads.
- Python (version 2.6 or higher) should be installed in the default user bin "#!/usr/bin/python"
- Novoalign should be in your default path. The version V2.07.10 is recommended.
- A new option of using nonredandunt reads that save ~40% running time
5-2-2012: LSC 0.2 Released
LSC 0.2 takes a long read data sets (>=100bp) and a short reads data sets (50 - 100bp) as input. They should be in FASTA format. Running time is almost linear with the the number of threads.
- More optional for raw data prefilter
- Multi-threading is available
- Reduced redundant temp files
6-5-2010: SpliceMap 3.2.2 Released
SpliceMap 3.2.2 is another minor release, it fixes some issues people had with compiling on the latest version of g++ (4.4.3). The next version will include some fixes to improve sensitivity with long reads (100bp+).
- Added some libraries
- Added better instructions on how to build from source (it seems that this is necessary for many non-mac users)
For detailed information about this release, please see the release notes.
LSC 0.2.1