Au Lab

Opening positions

            The lab is seeking candidates for two postdoctoral research scholar positions to work on sequencing analyses:

1)      Postdoctoral Research Scholar in bioinformatics method development: We are looking for a postdoctoral scholar to develop statistical and computational/algorithmic methods for high-throughput sequencing data analyses, such as RNA-seq using PacBio and Oxford Nanopore Technologies.

2)      Postdoctoral Research Scholar in computational biology: We are looking for a computational biology postdoctoral scholar to conduct cutting-edge research in the fields of transcriptome/epigenetics bioinformatics. He/she will apply bioinformatics methods to large-scale genomic and transcriptomic datasets to elucidate biological insights from stem cell biology and cancer biology.

Strong ability in statistical analysis or computer programming (python/perl, C/C++, R, Matlab) is desirable.

The postdoctoral research scholars will have the opportunity to collaborate with internationally recognized biomedical scientists at University of Iowa Carver College of Medicine, Stanford University, University of Oxford and Pacific Biosciences.

 

Research Focus

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.

In addition, we are interested in the methodology research of gene regulatory network and RNA editing.

 

Collaborators

Currently, we have very close ongoing collaborations with:

Wing H. Wong's Lab at Stanford
Pacific Biosciences (PacBio)
Bina Technologies
Renee Reijo Pera's Lab at Stanford
Jack H. Wong's Lab at Houston Methodist Research Institute
Vittorio Sebastiano's Lab at Stanford
David Buck and the Oxford Genomics Centre at the Wellcome Trust Centre for Human Genetics
Xiujie Wang's Lab at Beijing Institute of Genomics, Chinese Academy of Sciences
Yungui Yang's Lab at Institute for Genetics and Developmental Biology, Chinese Academy of Sciences
Xin Zhiguo Li's Lab at University of Rochester

 

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. (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]

 

News

02-19-2018: IDP-denovo paper is accepted

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.

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: