Publications

Single-molecule long-read sequencing reveals a conserved selection mechanism determining intact long RNA and miRNA profiles in sperm.
Sun, Y.H.*, Wang, A.*,Song, C., Srivastava, R.K., Au, K.F.**, Li, X.Z.**
Nature Communications. 2020. [Manuscript]
* These authors contributed equally to this work.
** Co-corresponding author

A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.
Wang, D., Zou, X., Au, K.F.#
Methods. 2020. [Manuscript]
# Corresponding author

Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads.
Wang, A., Au, K.F.#
Genome Biology. 2020. [Manuscript]
# Corresponding author

2019

iASPP mediates p53 selectivity through a modularmechanism fine-tuning DNA recognition
Chen, S., Wu, J., Zhong, S., Li, Y., Zhang P., Ma, J., Ren, J., Tan, Y., Wang, Y., Au, K.F., Siebold, C., Bond, G.L., Chen, Z., Lu, M., Jones, E.Y. and Lu, X.
Proc. Natl. Acad. Sci. USA 2019 Aug 27. 116 (35), 17470-17479 [Manuscript]

Wang, Y.*, Wang, A.*, Liu, Z., Thurman, A., Powers, L.S., Zou, M., Zhao, Y., Hefel, A., Li, Y., Zabner, J., Au, K.F. Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Research. 2019 08; 29(8)1329-1342 * corresponding author [Manuscript]

Selected as the cover of the 2019 August Issue of Genome Research

Recommended by F1000prime as "exceptional" article

Media Report: Reported by GenomeWeb

A comparative evaluation of hybrid error correction methods for error-prone long reads
Fu, S., Wang, A., Au, K.F.#
Genome Biology. 2019. [Manuscript]
# Corresponding author

2018

EC coupling structural protein junctophilin-2 encodes a stress-adaptive transcription regulator.
Guo, A., Wang, Y., Chen, B., Wang, Y. ,Yuan, J., Zhang, L., Hall, D., Wu, J., Shi, Y., Zhu, Q., Chen, C., Thiel, W.H., Zhan, X., Weiss, R.M, Zhan, F., Musselman, C., Pufall, M., Zhu, W., Au, K.F. , Hong, J., Anderson, M.E., Grueter, C.E., Song, L.S.
Science. 2018. [Manuscript]

A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing.
Suzuki, Y., Wang, Y., Au, K.F., Morishita, S.
Genes. 2018. [Manuscript]
# Co-corresponding author

Single cell expression analysis of primate-specific retroviruses-derived HPAT lincRNAs in viable human blastocysts identifies embryonic cells co-expressing genetic markers of multiple lineages.
Glinsky, G., Durruthy-Durruthy, J., Wossidlo, M., Grow, E.J., Weirather, J.L., Au, K.F., Wysocka, J., Sebastiano, V.
Heliyon. 2018. [Manuscript]

Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations.
Zou, M., Jin, R., Au, K.F.#
Briefings in Bioinformatics. 2018. [Manuscript]
# Corresponding author

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. 2018. [Manuscript]
# Corresponding author

2017

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. 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 1; referees: awaiting peer review].
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
** Co-corresponding author

2016

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]
# Corresponding author

2015

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]
# Corresponding author

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
** Corresponding author

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]

2014

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]

2013

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

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]

2012

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]

2010

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]

2008

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]

2006

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]