Kin Fai Au, PhD
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Center Memberships
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Center MemberCenter for Computational Medicine and Bioinformatics
Research Overview
Third Generation Sequencing (TGS, i.e., PacBio and Oxford Nanopore Technologies) is delivering ultra long reads, we now can have an unprecedented view on the genomic elements that remain poorly characterized by Next Generation Sequencing (NGS, i.e., Illumina) (please see details in our review article in Nature Biotechnology, 2021). We are not only in the midst of a new revolution in sequencing technology but also the next revolution in biomedical research. To timely and fully utilize the unique benefits of this technological breakthrough, my laboratory focuses on three layers of research:
1) As what we have been pioneering in the past 10 years, we will continue to develop innovative experimental approaches and data analytic methods based on TGS. Considering the diverse cell types in heterogeneous samples (e.g., over the early embryonic development and central nervous system), we are also extending the method development to the single-cell level;
2) With these new tools, we will investigate the complexity of transcriptome at the gene isoform level, as well as the transcription and epigenetic regulation of transposable elements (TEs) in the contexts of embryonic development and stem cell biology via intense collaborations with the corresponding experts; this has been supported by recent NIH funding to my group (three active R01s);
3) The long-term goal is to create a community that combines biological/clinical questions, TGS expertise and shared resources, including computational support. Toward this goal, we need to assemble and coordinate the TGS expertise and resources in the campus for extensive collaborations to facilitate the UM community to leverage the power of TGS in a broader range of biomedical areas.
Recent Publications
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Li H, Wang D, Gao Q, Tan P, Wang Y, Cai X, Li A, Zhao Y, Thurman AL, Malekpour SA, Zhang Y, Sala R, Cipriano A, Wei CL, Sebastiano V, Song C, Zhang NR, Au KF. Nature Biotechnology, 2026 Mar 1; 44 (3): 477 - 489.Journal ArticleImproving gene isoform quantification with miniQuant
DOI:10.1038/s41587-025-02633-9 PMID: 40461779 -
Li B, Li T, Wang D, Yang Y, Tan P, Wang Y, Yang YG, Jia S, Au KF. Nature Communications, 2025 Dec 1; 16 (1):Journal ArticleZygotic activation of transposable elements during zebrafish early embryogenesis
DOI:10.1038/s41467-025-58863-7 PMID: 40246845 -
Li Y, Wang Y, Cengiz A, Jin KX, Castroviejo BC, Lin X, Indahl M, Zuo R, Skuland T, Fosslie M, Biba M, Wu X, Fedorcsak P, Bjørås M, Filipczyk A, Dahl JA, Greggains GD, Au KF, Klungland A. EMBO Journal, 2025 Jul 15; 44 (14): 4150 - 4180.Journal ArticleThe RNA m6A landscape during human oocyte-to-embryo transition
DOI:10.1038/s44318-025-00474-5 PMID: 40467862 -
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Nature Methods, 2024 Jul 1; 21 (7): 1349 - 1363.Journal ArticleSystematic assessment of long-read RNA-seq methods for transcript identification and quantification
DOI:10.1038/s41592-024-02298-3 PMID: 38849569 -
Li Y, Wang Y, Vera-Rodriguez M, Lindeman LC, Skuggen LE, Rasmussen EMK, Jermstad I, Khan S, Fosslie M, Skuland T, Indahl M, Khodeer S, Klemsdal EK, Jin KX, Dalen KT, Fedorcsak P, Greggains GD, Lerdrup M, Klungland A, Au KF, Dahl JA. Nature Biotechnology, 2024 Apr 1; 42 (4): 591 - 596.Journal ArticleSingle-cell m6A mapping in vivo using picoMeRIP–seq
DOI:10.1038/s41587-023-01831-7 PMID: 37349523 -
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner M-M, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. bioRxiv, 2023 Jul 27;Journal ArticleSystematic assessment of long-read RNA-seq methods for transcript identification and quantification.
DOI:10.1101/2023.07.25.550582 PMID: PMC10402094 -
Wang Y, Li Y, Skuland T, Zhou C, Li A, Hashim A, Jermstad I, Khan S, Dalen KT, Greggains GD, Klungland A, Dahl JA, Au KF. Nature Structural and Molecular Biology, 2023 May 18;Journal ArticleThe RNA m6A landscape of mouse oocytes and preimplantation embryos
DOI:10.1038/s41594-023-00969-x -
Zhao Y, Yu L, Wu X, Li H, Coombes KR, Au KF, Cheng L, Li L. Bioinformatics, 2022 Dec 1; 38 (23): 5245 - 5252.Journal ArticleCEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression
DOI:10.1093/bioinformatics/btac668 PMID: 36250792
Featured News & Stories
Announcing DCMB/CCMB Fall 2025 seminar series
The Au lab developed a computational method that combines short- and long- RNA sequencing reads to study gene isoforms
DCMB welcomes new faculty
Kin Fai Au's interview in 'Genomeweb'
“Imagining the future” with long-read
