News

April 2023, Yunhao and our collaborators’ single-cell RNA m6A mapping study has been accepted in principle by Nature Biotechnology! Congratulations!

In this study, together with our collaborators Profs. Arne Klungland and John Arne Dahl, Dr. Yanjiao Li (co-first author), we develop a low-input RNA N6-methyladenosine (m6A) mapping approach picoMeRIP-seq that enables transcriptome-wide m6A profiling from as little as 100 picogram polyA-selected RNAs and 10 mouse embryonic stem cells, as well as single zebrafish zygote, single mouse oocyte and single mouse preimplantation embryos.

Feb 2023: Yunhao and our collaborators’ RNA m6A work was accepted in principle by Nature Structural & Molecular Biology! Congratulations!

In this work, together with our collaborators Profs. Arne Klungland and John Arne Dahl, Dr. Yanjiao Li (co-first author), we define the RNA N6-methyladenosine (m6A) landscape in mouse oocytes and early embryos using the low-input approach we have developed (another work which is now under review in another Nature sister journal). We find that m6A is widely deposited in key genes during the maternal-to-zygotic transition (i.e., the stage-specifically expressed transcription factor coding genes, the maternally-inherited transcripts to be degraded post fertilization, the zygotically-activated genes during zygotic genome activation), and the RNAs derived from the stage-specifically activated retrotransposons (e.g., MERVL, MTA).

Feb 2023: We are thrilled to join the Department of Computational Medicine and Bioinformatics at University of Michigan and start a new journey of more exciting researches!
We are also recruting talented students and postdoctoral scholars to join our team. For more information, please refer to our homepage and feel free to contact us!

July 2022: Kin Fai is appointed as the Vice Chair of Research at the Department of Biomedical Informatics. Congratulations!

May 2022: Dingjie and Haoran's latest manuscript of LRGASP project was accepted in principle by Nature Methods! Congratulations!

Oct. 12th, 2021: The Au Lab receives two NIH R01 grants from National Human Genome Research Institute and National Institute of General Medical Sciences to develop a series of bioinformatics tools to study gene isoforms and transposable elements in human stem cells and germ cells.

Jul. 15th, 2021: The Au Lab receives an NIH R01 grant from NATIONAL HUMAN GENOME RESEARCH INSTITUTE to develop a series of bioinformatics tools to analyze gene isoforms in human stem cells

Jul. 12th, 2021: Congratulation on Haoran's paper accepted by Bioinformatics!

Real-time mapping of nanopore raw signals.
Zhang, H.*, Li, H.*,Jain, C., Cheng, H., Au, K.F.**, Li, H.**, Aluru, S.**
Bioinformatics. 2021. [Manuscript]
* These authors contributed equally to this work.
** Co-corresponding author

Jul. 1st, 2021: Kin Fai serves a regular member at the NIH Genomics, Computational Biology and Technology Study Section.

Dec. 16th, 2020: Congrats! Kin Fai receives the OSU-BMI Award for Research Excellence!

Dec. 15th, 2020: Congratulations to Yunhao, Audrey, Diana and Yuru for their article accepted by Nature Biotechnology!

Nanopore sequencing technology, bioinformatics and applications.
Wang, Y., Zhao, Y., Bollas, A., Au, K.F.#
in press, Nature Biotechnology. 2020
# Corresponding author

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

Dec. 16th, 2020: Congrats! Kin Fai receives the OSU-BMI Award for Research Excellence!

Dec. 15th, 2020: Congratulations to Yunhao, Audrey, Diana and Yuru for their article accepted by Nature Biotechnology!

Nanopore sequencing technology, bioinformatics and applications.
Wang, Y., Zhao, Y., Bollas, A., Au, K.F.#
in press, Nature Biotechnology. 2020
# Corresponding author

Jun 10th, 2020: New Publications.

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

March, 2020: Congrats! Professor Au joined the editorial boards of the premier journals of genomics and bioinformatics.

Kinfai joined the editorial board of Genome Biology .

Kinfai joined the editorial board of Genome Research.

Jan 17th, 2020: New Publications.

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

Audrey presents our recent work at the Nanopore Community Meeting 2019.

Our genome has different levels of organization, and at the nucleosome level, DNA strands wrap around protein cores like beads on a string. Positioning of these nucleosomes and changes in chromatin status play important regulatory roles in gene expression. Our new method, MeSMLR-seq, aims to resolve the long-range dynamics that remain poorly understood at the single-molecule level. Briefly, two examples from the paper in Genome Research are discussed: 1) MeSMLR-seq can resolve differential nucleosome organization principles at the transcription start site of silent versus active genes; and 2) MeSMLR-seq can explore the coupled chromatin status of adjacent genes during transcriptional reprogramming. These methods offer promising utility to study multiple layers of epigenetics simultaneously.[Video]

Jun 14th, 2019: Our latest paper of identifying nucleosome occupancy and chromatin accessibility on single DNA molecule is selected as the cover of the August Issue of Genome Research.

Single-molecule long-read sequencing reveals the chromatin basis of gene expression.

Wang, Y., Wang, A., Liu, Z., Thurman, A., Powers, L.S., Zou, M., Hefel, A., Li, Y., Zabner, J., Au, K.F.
Genome Res. Cover photo of issue August 2019 . [Manuscript]

Combining methyltransferase treatment with nanopore sequencing, Wang et al. developed a new experimental approach “MeSMLR-seq” to map nucleosome occupancy and chromatin accessibility at single long DNA molecules. MeSMLR-seq shows consistent bulk-cell results with existing methods (e.g. MNase-seq and ATAC-seq), but more importantly it brings unprecedented power to capture the single-molecule epigenome. Thus, epigenome heterogeneity can be clearly resolved and subtle but meaningful epigenome differences at single molecules can be discovered. For instance, the MeSMLR-seq data provided the quantitative evidence for the correlation between promoter accessibility and transcription activity. The MeSMLR-seq long reads phased >300 nucleosomes and identified chromatin accessibility of up to 40 adjacent genes simultaneously at single molecules - e.g. the MeSMLR-seq data revealed the coupled chromatin status changes of the adjacent glucose transporter genes responding to the glucose concentration changes. It shows potential to study the association of multiple layers of epigenomes, including base modifications at the same molecules.

Jun 15th, 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)

Feb 23rd, 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]

University of Michigan, MI 48109.