2017

Siwy Ling Yang, Louis DeFalco, Danielle E. Anderson, Yu Zhang, Ashley J Aw, Su Ying Lim, Xin Ni Lim, Kiat Yee Tan, Tong Zhang, Tanu Chawla, Yan Su, Alexander Lezhava, Andres Merits, Lin-Fa Wang*, Roland G. Huber*, Yue Wan*. Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions. Nature Communications, 2021 Aug 25;12(1):5113. doi: 10.1038/s41467-021-25357-1.

2013 and before

Publications

2016

Jong Ghut Ashley Aw, Shaun W. Lim, Jia Xu Wang, Finnlay R. P. Lambert, Wen Ting Tan, Yang Shen, Yu Zhang, Pornchai Kaewsapsak, Chenhao Li, Sarah B. Ng, Leah A. Vardy, Meng How Tan, Niranjan Nagarajan, Yue Wan. Determination of isoform-specific RNA structure with nanopore long reads. Nature biotechnology, doi:10.1038/s41587-020-0712-z

Bingbing Xu, Yanda Zhu, Changchang Cao, Hao Chen, Qiongli Jin, Guangnan Li, Junfeng Ma, Siwy Ling Yang, Jieyu Zhao, Jianghui Zhu, Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang, Yu Zhou. Recent advances in RNA structurome. Sci China Life Sci. 2022 Jun 14:1–40. doi: 10.1007/s11427-021-2116-2.

Yang SL, Ponti RD, Wan Y*, Huber RG*. Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses. Viruses. 2022 Aug 16;14(8):1795. doi: 10.3390/v14081795. PMID: 36016417; PMCID: PMC9415818.

Jiaxu Wang, Tong Zhang, Zhang Yu, Wen Ting Tan, Ming Wen, Yang Shen, Finnlay R.P. Lambert, Roland G. Huber, Yue Wan. Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks. Molecular Cell. 2021 Oct 12;S1097-2765(21)00796-6. doi: 10.1016/j.molcel.2021.09.027.

2019

Riccardo Delli Ponti, Jiaxu Wang, Yue Wan and Roland G. Huber. RNAvigator: A Pipeline to Identify Candidates for Functional RNA Structure Elements. Front.Virol. 2022 Jun 27:2:878679. doi: 10.3389/fviro.2022.878679

Wang J, Yang L, Cheng A, Tham CY, Tan W, Darmawan J, de Sessions PF, Wan Y. Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome. Nat Commun. 2024 Jan 11;15(1):481. doi: 10.1038/s41467-023-44656-3. PMID: 38212309; PMCID: PMC10784512.

Grzegorz Kudla, Yue Wan and Aleksandra Helwak. RNA Conformation Capture by Proximity Ligation. Annual Review of Genomics and Human Genetics. 2020. 21:14.1–14.20.

Cedric Chih Shen Tan, Sebastian Maurer-Stroh, Yue Wan, October M Sessions, Paola Florez de Sessions. A novel method for the capture-based purification of whole viral native RNA genomes. AMB express. 2019. 9:45.

Roland G. Huber, Xin Ni Lim, Wy Ching Ng, Adelene Y. L. Sim, Hui Xian Poh, Yang Shen, Su Ying Lim, Karin B. Sundstrom, Xuyang Sun, Jong Ghut Aw, Horng Khit Too, Peng Hee Boey, Andreas Wilm, Tanu Chawla, Ming M. Choy, Lu Jiang, Paola Florez de Sessions, Xian Jun Loh, Sylvie Alonso, Martin Hibberd, Niranjan Nagarajan, Eng Eong Ooi, Peter J. Bond, October M. Sessions, Yue Wan. Structure mapping of dengue and Zika viruses reveals functional long-range interactions. 2019. Nature Communications, Mar 29;10(1):1408.

Sidika Tapsin, Miao Sun, Yang Shen, Huibin Zhang, Xin Ni Lim, Teodorus Theo Susanto, Siwy Ling Yang, Gui Sheng Zeng, Jasmine Lee, Alexander Lezhava, Ee Lui Ang, Lian Hui Zhang, Yue Wang, Huimin Zhao, Niranjan Nagarajan, Yue Wan (2018) Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes. Nature Communications, 2018 Mar 29;9(1):1289.

Jong Ghut Ashley Aw, Yang Shen, Niranjan Nagarajan, Yue Wan (2017) Mapping RNA-RNA interactions globally using biotinylated psoralen. J Vis Exp. 2017 May 24;(123).

Minh N. Nguyen, Adelene Y. L. Sim, Yue Wan, M. S. Madhusudhan and Chandra Verma (2016) Topology independent comparison of RNA 3D structures using the CLICK algorithm. Nucleic Acids Research, doi: 10.1093/nar/gkw819

Jong Ghut Ashley Aw1*, Andreas Wilm2*, Miao Sun2*, Yang Shen2, Xin Ni Lim1, Kum-Loong Boon1, Yun-Shen Chan3, Tong Zhang4, Sidika Tapsin1, Teodorus Theo Susanto1, Niranjan Nagarajan2Ɨ, Yue Wan1Ɨ (2016) In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Molecular Cell 2016 May 19;62(4):603-17

Huibin Zhang, Teodorus T Susanto, Yue Wan, Swaine L. Chen (2016) Comprehensive mutagenesis of fimS reveals novel regulation of Type 1 pili in uropathogenic Escherichia coli. PNAS, 2016 Apr 12;113(15):4182-7.

Yue Wan*ᶧ, Kun Qu*, Qiangfeng Cliff Zhang, Ohad Manor, Zhenqgqing Ouyang, Jiajing Zhang, Michael P. Snyder, Eran Segal and Howard Y. Changᵼ. (2013) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 2014 Jan 30;505(7485):706-9. *These authors contributed equally. ᶧ Co-corresponding authors.

Ibrahim AvsarIIik, Jeffrey J Quinn, Plamen Georgiev, Filipe Tavares-Cadete, Daniel Maticzka, Sarah Toscano, Yue Wan, Robert C. Spitale, Nicholar Luscombe, Rolf Backofen, Howard Y. Chang and Asifa Akhtar. (2013) Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Molecular Cell 2013 Jul 25;51(2):156-73.

Yue Wan, Kun Qu, Zhengqing Ouyang and Howard Y. Chang. (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nature Protocols, 2013 May;8(5):849-69.

Man Zhang, Lili Li, Zhongfeng Wang, Huijuan Liu, Junlin Hou, Min Zhang, Aijun Hao, Yun Liu, Guang He, Yongyong Shi, Lin He, Xueying Wang, Yue Wan* and Baojie Li* (2012). A role for c-Abl in cell senescence and spontaneous immortalization. AGE10.1007/s11357-012-9452-4. *corresponding author

Yue Wan, Kun Qu, Michael Kertesz, Zhengqing Ouyang, Jun Li, Robert Tibshirani, Robert C. Nutter, Eran Segal, Howard Y. Chang. (2012) Genome-wide measurement of RNA folding energies. Molecular Cell 48(2):169-81.

Yue Wan, Michael Kertesz, Robert C. Spitale, Eran Segal and Howard Chang. (2011) Understanding the transcriptome through RNA structure. Nature Reviews Genetics12(9):641-55.

Yue Wan and Howard Chang. (2010) HOTAIR: Flight of noncoding RNAs in cancer metastasis. Cell Cycle 9(17):3391-2

Michael Kertesz*, Yue Wan*, Elad Mazor, John L. Rinn, Robert C. Nutter, Howard Y. Chang, Eran Segal. (2010) Genome-wide Measurement of RNA Secondary Structure in Yeast. Nature467(7311):103-7. * these authors contributed equally.

Miao-Chih Tsai, Ohad Manor, Yue Wan, Nima Mosammaparast, Jordan K. Wong, Fei Lan, Yang Shi, Eran Segal, Howard Y. Chang. (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689-93.

2022

2018

Liao KC, Xie X, Sundstrom AKB, Lim XN, Tan KK, Zhang Y, Zou J, Bifani AM, Poh HX, Chen JJ, Ng WC, Lim SY, Ooi EE, Sessions OM, Tay Y, Shi PY, Huber RG, Wan Y. Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells. Genome Biol. 2023 Dec 5;24(1):279. doi: 10.1186/s13059-023-03110-9. PMID: 38053173; PMCID: PMC10696742.

Wang J, Zhang Y, Zhang T, Tan WT, Lambert F, Darmawan J, Huber R, Wan Y. RNA structure profiling at single-cell resolution reveals new determinants of cell identity. Nat Methods. 2024 Jan 4. doi: 10.1038/s41592-023-02128-y. Epub ahead of print. PMID: 38177506.

Roland G Huber, Jan K Marzinek, Priscilla L S Boon, Wan Yue, Peter J Bond. Computational modelling of flavivirus dynamics: The ins and outs. Methods. 2021 Jan;185:28-38. doi: 10.1016/j.ymeth.2020.06.004. Epub 2020 Jun 8.

2020

2024

Zhu B, Finch-Edmondson M, Leong KW, Zhang X, V M, Lin QXX, Lee Y, Ng WT, Guo H, Wan Y, Sudol M, DasGupta R. LncRNA SFTA1P mediates positive feedback regulation of the Hippo-YAP/TAZ signaling pathway in non-small cell lung cancer. Cell Death Discov. 2021 Nov 29;7(1):369. doi: 10.1038/s41420-021-00761-0. PMID: 34845189; PMCID: PMC8630011.

Bowen Zhu, Mitheera V, Megan Finch-Edmondson, Yaelim Lee, Yue Wan, Marius Sudol, Ramanuj DasGupta. miR-582-5p Is a Tumor Suppressor microRNA Targeting the Hippo-YAP/TAZ Signaling Pathway in Non-Small Cell Lung Cancer. Cancers (Basel). 2021 Feb 11;13(4):756. doi: 10.3390/cancers13040756.

Rachel Patton McCord, Mikko Taipale, Sarah Teichmann, Rebecca Vorhees, Yue Wan, Cees Dekker, Neville E. Sanjana. Voices on technology: The molecular biologist’s ever-expanding toy box. Molecular Cell. 22 Jan 20;82(2):221-226. doi: 10.1016/j.molcel.2021.12.025.

Yue Zhao, Jiaxu Wang, Wai Nam Liu, Shin Yie Fong, Timothy Wai Ho Shuen, Min Liu, Sarah Harden, Sue Yee Tan, Jia Ying Cheng, Wilson Wei Sheng Tan, Jerry Kok Yen Chan, Cheng Ean Chee, Guan Huei Lee, Han Chong Toh, Seng Gee Lim, Yue Wan, Qingfeng Chen. Analysis and Validation of Human Targets and Treatments Using a Hepatocellular Carcinoma-Immune Humanized Mouse Model. Hepatology. 2021 Sep;74(3):1395-1410. doi: 10.1002/hep.31812.

2021

2023

WAN LAB

of RNA structuromics

Nguyen TA, Heng JWJ, Kaewsapsak P, Kok EPL, Stanojević D, Liu H, Cardilla A, Praditya A, Yi Z, Lin M, Aw JGA, Ho YY, Peh KLE, Wang Y, Zhong Q, Heraud-Farlow J, Xue S, Reversade B, Walkley C, Ho YS, Šikić M, Wan Y, Tan MH. Direct identification of A-to-I editing sites with nanopore native RNA sequencing. Nat Methods. 2022 Jul;19(7):833-844. doi: 10.1038/s41592-022-01513-3. Epub 2022 Jun 13. PMID: 35697834.