IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.
Fu, S., Ma, Y., Yao, H., Xu, Z., Chen, S., Song, J., Au, K.F.

Bioinformatics. (Accepted)

Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale.
He, L., Fu, S. , Xu, Z., Yan, J., Xu, J., Zhou, H., Zhou, J., Chen, X., Li, Y., Au, K.F.#, Yao, H.#
Genes (Basel). 2017. [Manuscript]
# Corresponding authors

CF airway smooth muscle transcriptome reveals a role for PYK2.
Cook, D.P., Adam, R.J., Zarei, K., Deonovic, B., Stroik, M.R., Gansemer, N.D., Meyerholz, D.K., Au, K.F., Stoltz, D.A.
JCI Insight. 2017. [Manuscript]

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis [version 2; referees: 2 approved].
Weirather, J.L.*, de Cesare, M.*, Wang, Y.*, Piazza, P., Vittorio, S., Wang, X.J., Buck, D., Au, K.F.
F1000Research 2017, 6:100 [Manuscript]
* These authors contributed equally to this work

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
Sahraeian, S.M.E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar P.T., Au, K.F. , Bani Asadi, N., Gerstein, M.B., Wong, W.H., Snyder, M.P., Schadt, E., Lam, H.Y.K.
Nature Communications. 2017. [Manuscript]

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing.
Deonovic, B., Wang, Y., Weirather, J., Wang, X.J., Au, K.F.
Nucleic Acids Research. 2016. [Manuscript]

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. [Manuscript]

PacBio Sequencing and Its Applications.
Rhoads, A., Au, K.F.
Genomics, Proteomics, & Bioinformatics.
2015. [Manuscript]

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]

Accurate mapping of RNA-Seq data.
Au, Kin Fai
Methods in Molecular Biology 2015;1269:147-61. [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]

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 [Manuscript]

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 [Manuscript]
* 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 26. 151 (3):547-58 [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

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. [Manuscript]

Structures of an alanine racemase from Bacillus anthracis (BA0252) in the presence and absence of (R)-1-aminoethylphosphonic acid (L-Ala-P)
Au, Kin Fai, Ren, J., Walter, T.S., Harlos, K., Nettleshipa, J.E., Owens, R.J., Stuart, D.I., Esnouf, R.M.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 May 1;64(Pt 5):327-33. Aug;[Manuscript]

Application of high-throughput technologies to a structural proteomics-type analysis of Bacillus anthracis
Au, Kin Fai, Berrow, N.S., Blagova, E., Boucher, I.W., Boyle, M.P., Brannigan, J.A., Carter, L.G., Dierks, T., Folkers, G., Grenha, R., Harlos, K., Kaptein, R., Kalliomaa, A.K., Levdikov, V.M., Meier, C., Milioti, N., Moroz, O., Muller, A., Owens, R.J., Rzechorzek, N., Sainsbury, S., Stuart, D.I., Walter, T.S., Waterman, D.G., Wilkinson, A.J., Wilson, K.S., Zaccai, N., Esnouf, R.M., Fogg, M.J.
Acta Crystallogr D Biol Crystallogr. 2006 Oct;62(Pt 10):1267-75.[Manuscript]

Lysine methylation as a routine rescue strategy for protein crystallization
Walter, T.S., Meier, C., Assenberg, R., Au, Kin Fai, Ren, J., Vermaa, A., Nettleshipa, J.E., Owens, R.J., Stuart, D.I., Grimes, J.M..
Structure. 2006 Nov;14(11):1617-22.[Manuscript]