Au Lab

Our lab has moved to the Department of Biomedical Informatics, the Ohio State University in August 2018. This homepage will be redirected to a new URL at Ohio State University in the near future.

Openings


Latest Publications


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. (in press) [Link]
# 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]


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]


Research Focus


Collaborators

Currently, we have very close ongoing collobrations with:



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.