Available to mentor
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Center MemberCenter for Computational Medicine and Bioinformatics
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.
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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 J-L, 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 M-M, 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. Nat Methods, 2024 Jul; 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 K-X, Dalen KT, Fedorcsak P, Greggains GD, Lerdrup M, Klungland A, Au KF, Dahl JA. Nat Biotechnol, 2024 Apr; 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: 37546854 -
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. Nat Struct Mol Biol, 2023 May; 30 (5): 703 - 709.Journal ArticleThe RNA m6A landscape of mouse oocytes and preimplantation embryos.
DOI:10.1038/s41594-023-00969-x PMID: 37081317 -
Zhao Y, Yu L, Wu X, Li H, Coombes KR, Au KF, Cheng L, Li L. Bioinformatics, 2022 Nov 30; 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 -
Au KF. Genome Biol, 2022 Jan 12; 23 (1): 21Journal ArticleThe blooming of long-read sequencing reforms biomedical research.
DOI:10.1186/s13059-022-02604-2 PMID: 35022055 -
Sun YH, Wang A, Song C, Shankar G, Srivastava RK, Au KF, Li XZ. Nat Commun, 2021 Mar 1; 12 (1): 1361Journal ArticleSingle-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm.
DOI:10.1038/s41467-021-21524-6 PMID: 33649327 -
Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nat Biotechnol, 2021 Nov; 39 (11): 1348 - 1365.Journal ArticleNanopore sequencing technology, bioinformatics and applications.
DOI:10.1038/s41587-021-01108-x PMID: 34750572
