Au Lab

Research Focus


Currently, we have very close ongoing collobrations with:

Latest Publications

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

Human tRNA synthetase catalytic nulls with diverse functions.
Lo, W.S., Gardiner E., Xu, Z., Lau C.F., Wang, F., Zhou, J.J., Mendlein, J.D., Nangle, L.A., Chiang, K.P., Yang, X.L., Au, Kin Fai, Wong, W.H., Guo, M., Zhang, M., Schimmel, P.
Science. 2014 Jul 18. 345 (6194), 328-32 [Manuscript]

ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects
Qiu H., Lee S., Shang Y., Wang W.Y., Au, Kin Fai, Kamiya S., Barmada S.J., Finkbeiner S., Lui H., Carlton C.E., Tang A.A., Oldham M.C., Wang H., Shorter J., Filiano A.J., Roberson E.D., Tourtellotte W.G., Chen B., Tsai L.H., Huang E.J.
The Journal of clinical investigation. 2014 Feb 10. 124 (3), 0-0 [Manuscript]

Characterization of the human ESC transcriptome by hybrid sequencing
Au, Kin Fai, Sebastiano V., Afshar P.T., Durruthy J.D., Lee L., Williams B.A., Bakel H.V., Schadt E., Pera R.A.R., Underwood J., Wong W.H.
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830 [Manuscript]

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. 2013. 9:632. [Manuscript]
* These authors contributed equally to this work


05-26-2015: IDP-fusion paper is released paper is released

Jason 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.

In press

02-02-2015: Minor updates and bug fixes to LSC 1.beta

Feature Updates:

Bug Fixes:

08-04-2014 - Major Update to IDP

This is a major update to IDP and update includes changes to software requirements, additional features, and bug fixes.

08-01-2014 - Preparing long read outputs of LSC for use in IDP

Please concatenate the LSC outputs: corrected.fa with full.fa, and use this new fasta file as your long read inputs for IDP.

The reason is that corrected.fa will lose some flanking sequences on the long reads that were not corrected by short reads, and there still may be some informative junctions in that region. If we used only corrected.fa, we could lose this information. full.fa includes those flanking regions in addition to the corrections that were made. However, if we used only full.fa, it is likely the IDP algorithm could throw out many of those long reads for failing to find short read support for junctions in those regions. If you combine the two datasets, you will not suffer any loss of information, and any redundancies will be handled by IDP.

04-24-2014 - IDP 0.1.2 minor update is released

This minor update fixes several bugs.

04-17-2014 - IDP 0.1.1 minor update is released

This minor update fixes several bugs fixes to and is accompanied by a convenient, small-sized, test dataset available in the tutorial.

12-01-2013: Faster and much less memory-required LSC 1.alpha is released

In the LSC 0.3.0 or 0.3.1, we optimized the setting of bowtie2 and BWA to get much more short read alignment, which improve the the accuracy of error correction a lot/ However, the increase of alignments also requires much more running time (on both alignment and the following error correction step) and memory usage. Therefore, a few users met difficulty of running LSC 0.3.0 or 0.3.1.

In LSC 1.alpha, we apply probabilistic algorithm ("SCD" option) to select ""enough" short read alignment for error correction. LSC 1.alpha does NOT sacrifice the error correction performace (sensitivity and specificity). Please see Thus, we save running time and memory usage significantly. The running time is 30-50% of LSC 0.3.1. The peak memory usage decreases to ~10G regardless of the data size.

New features:

Miscellaneous changes:

If you want to see the manual and tutorial of the old LSC (before 1.alpha), we keep the links of its the Old manual and Old tutorial in the right side bar.

11-26-2013 - IDP 0.1 and the manual and a tutorial are released

IDP integrates short reads (e.g. Illumina data) and long reads (e.g. PacBio data) to identify gene isoforms (transcripts) from transcriptome (see Figure above).

11-26-2013: Hompage of hESC transcriptome identified by SpliceMap-LSC-IDP pipline is released.

The homepage of hESC transcriptome (H1 cell line) is released. You can also find novel genes, novel isoforms of existing genes (including pluripency markers) and novel ncRNA in this website:

The details of this hESC transcriptome can be in our publication: Characterization of the human ESC transcriptome by hybrid sequencing [preprint]

11-26-2013: IDP and hESC transcriptome paper is released

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing [preprint]
In press

09-30-2013: More robust and faster LSC 0.3.1

In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.

New features:

Miscellaneous changes:

08-07-2013: Big changes in LSC 0.3

In LSC 0.3, we have a few updates. They are very IMPORTANT updates, new features and small fixes

Very IMPORTANT updates:

New features

Small bug fixed