Au Lab

Openings


Research Focus


Collaborators

Currently, we have very close ongoing collobrations with:


Latest Publications


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]


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 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]


News

06-15-2018: Shuhua Fu, Anqi Wang and Andrew Thurman are going to make presentations in ISMB 2018, July 7th, Chicago.

Topics:
IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing. (Shuhua Fu)
Theoretical analysis of graph-based and alignment-based hybrid error correction methods for error-prone long reads. (Anqi Wang)
Gene isoform abundance quantification with Third Generation transcriptome sequencing. (Andrew Thurman)

02-23-2018: IDP-denovo paper is published

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]

02-07-2016: AlignQC paper is released

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
You can also check out the Latest AlignQC Software here if you are interested in using it to assess long read alignments.

11-28-2016: IDP-ASE paper is released

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]

07-08-2016: AlignQC, a tool for analyzing alignment files and assessing errors in alignments, is released.

05-26-2016: IDP-ASE, a tool for haplotyping and quantifying allele-specific expression from Second Generation Sequencing and PacBio sequencing, is released.

04-11-2016: Update to LSC (version 2.0), the long read error correction tool, is released.

01-21-2016: HPAT Transcripts highlighted in Nature technology feature

"Finding function in mystery transcripts" by Kelly Rae Chi

08-18-2015: American Cancer Society (ACS) Seed Grants for Junior Faculty (IRG-77-004-34) is awarded

12-16-2015: PhRMA Foundation Research Starter Grant is awarded

http://www.phrmafoundation.org/2015-awards/research-starter-grants/informatics/

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

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.

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

Feature Updates:

Bug Fixes: