- RNA-seq and Third Generation Sequencing
- Stem cell transcriptome analysis
- We are interested in methodology research of Third Generation Sequencing (TGS) (especially for PacBio and Oxford Nanopore sequencing).
Au lab is working on both hybrid sequencing (Second Generation Sequencing (SGS) + TGS) and TGS-alone methodology research.
Our research interests include but not limited to alternative splicing, isoform construction, gene fusion and quantitative analysis.
- Au lab is applying the hybrid sequencing method on ESC, iPSC and preimplantation embryo, to deeply study the transcriptome differences between stem cells.
- Protein identification and novel splice detections from tandem Mass Spec are our research interests. Au lab is developing statistical methods for Integration of Mass Spec and sequencing data, in order to solve difficult proteomics problems.
CollaboratorsCurrently, we have very close ongoing collobrations with:
- Wing H. Wong's Lab at Stanford
Pacific Biosciences (PacBio)
Renee Reijo Pera's Lab at Stanford
Jack H. Wong's Lab at Houston Methodist Research Institute
A novel primate-specific noncoding RNA modulates human embryo- and pluripotent stem cell fate.
Durruthy-Durruthy J., Sebastiano V., Wossidlo M., Cepeda D., Cui J., Grow E.J., Davila J., Mall M., Wing W.H., Wysocka J., Au, K.F., Pera, R.R.
Nature Genetics. 2015. In press.
PacBio Sequencing and Its Applications.
Rhoads, A., Au, K.F.
Genomics, Proteomics, & Bioinformatics. 2015. In press.
Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
Weirather, J.*, Afshar, P.T.*, Clark, T., Tseng, E., Powers, L., Underwood, J.G., Zabner, J., Korlach, J., Wong, W.H., Au, K.F.
Nucleic Acids Research. 2015 [Manuscript]
* These authors contributed equally to this work
Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis.
Xu, Z., Peters, R.J., Weirather, Jason, Luo, H., Liao, B., Zhang, X., Zhu, Y., Ji, A., Zhang, B., Hu, S., Au, Kin Fai, Song, J., Chen, S.
The Plant Journal. 2015 Apr 24 [Manuscript]
The transcriptome of human pluripotent stem cells.
Au, Kin Fai*, Sebasiano, V.
Current Opinion in Genetics and Development. 2014 Oct 31. 28, 71-77 [Manuscript]
* Corresponding Author
08-18-2015: American Cancer Society (ACS) Seed Grants for Junior Faculty (IRG-77-004-34) is awarded
05-26-2015: IDP-fusion paper is released paper is releasedJason L. Weirather*, Pegah Tootoonchi Afshar*, Tyson A. Clark, Elizabeth Tseng, Linda S. Powers, Jason Underwood, Joseph Zabner, Jonas Korlach, Wing Hung Wong and Kin Fai Au
Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing [preprint]
*These authors contributed equally to this work.
02-02-2015: Minor updates and bug fixes to LSC 1.beta
Updating aligners default command options to gain better performance.
- Updated Novoalign command options (tested with >= novocraftV3.02.04 version)
- Updated RazerS3 command options to be compatible with latest version (razers3 3.1.1)
- Added extra clean_up option value to remove all generated intermiediate files in case of issues w/ disk space
- Fix a bug in generating full_LR.fa sequences causing some full read sequences to miss couple of bases