wu lab

bioengineering @ HKUST

Publications

Link to Angela Wu’s Google Scholar profile

*equal contribution; #corresponding author

Preprints

  1. The Tabula Microcebus Consortium. Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism. (Under Review, Nature). Preprint
  2. The Tabula Microcebus Consortium. Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution. (Under Review, Nature). Preprint

Publications

2023

  1. Sin Yen Tan, Xiaohan Feng, Lily Kwan Wai Cheng, Angela Ruohao Wu#. Vascularized Human Brain Organoid On-Chip. Lab on a Chip, 2023(Accepted).
  2. Jiarui Li*, Qiuyu Jing*, Jie Li*, Mingxi Hua*, Lin Di, Chuan Song, Yanyi Huang, Jianbin Wang, Chen Chen#, Angela Ruohao Wu#. Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection. Microbiome, 11 (1), 1-16, 2023.
  3. Lei Yu, Xinlei Wang, Quanhua Mu, Sindy Sing Ting Tam, Danson Shek Chun Loi, Aden Ka Yin Chan, Wai Sang Poon, Ho-Keung Ng, Danny Tat Ming Chan, Jiguang Wang, Angela Ruohao Wu#. scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors. Science Advances, 9(1), p.eabp8901, 2023. https://doi.org/10.1126/sciadv.abp8901

2022

  1. Xu Wang, Chao Yang, Xuejie Wang, Jinmin Miao, Weitao Chen, Yiren Zhou, Ying Xu, Yongyan An, Aifang Cheng, Wenkang Ye, Mengxian Chen, Dong Song, Xue Yuan, Jiguang Wang, Peiyuan Qian, Angela Ruohao Wu, Zhong-Yin Zhang, Kai Liu#. Driving axon regeneration by orchestrating neuronal and non-neuronal innate immune responses via the IFNγ-cGAS-STING axis. Neuron, 2022. doi.org/10.1016/j.neuron.2022.10.028
  2. Sin Yen Tan, Qiuyu Jing, Ziuwin Leung, Ying Xu, Lily Kwan Wai Cheng, Sindy Sing Ting Tam, Angela Ruohao Wu#. Transcriptomic Analysis of 3D Vasculature-On-A-Chip Reveals Paracrine Factors Affecting Vasculature Growth and Maturation. Lab on a Chip, 22(20), 3885-3897, 2022. doi.org/10.1039/D2LC00570K
  3. Qiuyu Jing*, Chi Hung Czarina Leung*, Angela Ruohao Wu#. Cell-free DNA as biomarker for sepsis by integration of microbial and host information. Clinical Chemistry, 68(9), 1184-1195, 2022. doi.org/10.1093/clinchem/hvac097
  4. Maik Herbig*, Akihiro Isozaki*, Dino Di Carlo, Jochen Guck, Nao Nitta, Robert Damoiseaux, Shogo Kamikawaji, Eigo Suyama, Hirofumi Shintaku, Angela Ruohao Wu, Itoshi Nikaido, Keisuke Goda#. Best practices for reporting throughput in biomedical research. Nature Methods 19, 633–634, 2022. doi.org/10.1038/s41592-022-01483-6 | PDF
  5. Jingsi Ming*, Zhixiang Lin*, Jia Zhao, Xiang Wan, Can Yang#, Angela Ruohao Wu#. FIRM: Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets. Briefings in Bioinformatics, 23(5), bbac167, 2022. doi.org/10.1093/bib/bbac167
  6. Jia Zhao*, Gefei Wang*, Jingsi Ming, Zhixiang Lin, Yang Wang, Tabula Microcebus Consortium, Angela Ruohao Wu#, Can Yang#. Portal: Adversarial domain translation networks enable fast and precise atlas-level single cell data integration. Nature Computational Science, 2, 317–330, 2022. doi.org/10.1038/s43588-022-00251-y
  7. Cheuk Wang Fung*, Shaopu Zhou*, Han Zhu*, Xiuqing Wei, Zhenguo Wu#, Angela Ruohao Wu#. Cell fate determining molecular switches and signaling pathways in Pax7-expressing somitic mesoderm. Cell Discovery, 8, 61, 2022. doi.org/10.1038/s41421-022-00407-0
  8. Katherine Li, Nicole Palmour, Stephan Beck, Alison Berner, Martin Hirst, Reiner Siebert, Angela Ruohao Wu, Yann Joly. Auditing the Editor: Epistemic and Ethical Issues in Epigenetic Editing. The CRISPR Journal, 5(2), 203-212, 2022. doi.org/10.1089/crispr.2021.0094
  9. Jiarui Li*, Pengcheng Du*, Lijiang Yang*, Ju Zhang*, Chuan Song*, Danying Chen*, Yangzi Song, Nan Ding, Mingxi Hua, Kai Han, Rui Song, Wen Xie, Zhihai Chen, Xianbo Wang, Jiangyuan Liu, Yanli Xu, Guiji Gao, Qi Wang, Lin Pu, Lin Di, Jie Li, Jingling Yue, Junyan Han, Xuesen Zhao, Yonghong Yan, Fengting Yu, Angela Ruohao Wu, Fujie Zhang, Yi Gao, Yanyi Huang^#, Jianbin Wang#, Hui Zeng#, Chen Chen#. Two-step fitness selection for intra-host variations in SARS-CoV-2. Cell Reports, 38(2), 110205, 2022. doi.org/10.1016/j.celrep.2021.110205

2021

  1. Sean Agbor-Enoh, Michael Oellerich, Angela Ruohao Wu, Philip F. Halloran, Iwijn De Vlaminck, Michael Keller. Molecular Approaches to Transplant Monitoring; Is the Horizon Here?. Clinical Chemistry, 67(11), 1443-1449, 2021. doi.org/10.1093/clinchem/hvab183
  2. Julia Eve Olivieri*, Roozbeh Dehghannasiri*, Peter Wang, SoRi Jang, Antoine de Morree, Serena Y. Tan, Jingsi Ming, Angela Ruohao Wu, Tabula Sapiens Consortium, Stephen R. Quake, Mark A. Krasnow, Julia Salzman#. RNA splicing programs define tissue compartments and cell types at single-cell resolution. eLife, 10:e70692, 2021. doi.org/10.7554/eLife.70692
  3. Xinlei Wang, Lei Yu, Angela Ruohao Wu#. The effect of methanol fixation on single-cell RNA sequencing data. BMC Genomics, 22 (1), 1-16, 2021. doi.org/10.1186/s12864-021-07744-6
  4. Danson Shek Chun Loi, Lei Yu, Angela Ruohao Wu#. Effective rRNA depletion for single-cell total RNA-seq by scDASH. PeerJ, 9, e10717, 2021. doi.org/10.7717/peerj.10717
  5. Ju Zhang*, Nan Ding*, Lili Ren*, Rui Song*, Danying Chen*, Xuesen Zhao, Budong Chen, Junyan Han, Jiarui Li, Yangzi Song, Lin Di, Kai Han, Fengting Yu, Ruming Xie, Zhihai Chen, Wen Xie, Jingyuan Liu, Shan Cen, Yuhai Bi, Angela Ruohao Wu#, Fujie Zhang#, Chen Chen#, Hui Zeng#. COVID-19 reinfection in the presence of neutralizing antibodies. National Science Review, 8: nwab006, 2021. doi.org/10.1093/nsr/nwab006

2020

  1. Chen Chen*, Jizhou Li*, Lin Di*, Qiuyu Jing*, Pengcheng Du*, Chuan Song, Jiarui Li, Qiong Li, Yunlong Cao, X Sunney Xie, Angela Ruohao Wu#, Hui Zeng#, Yanyi Huang#, Jianbin Wang#. MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples. Molecular Cell, 80 (6), 1123-1134. e4, 2020. doi.org/10.1016/j.molcel.2020.11.030
  2. Pengcheng Du*, Nan Ding*, Jiarui Li*, Fujie Zhang*, Qi Wang*, Zhihai Chen*, Chuan Song, Kai Han, Wen Xie, Jingyuan Liu, Linghang Wang, Lirong Wei, Shanfang Ma, Mingxi Hua, Fengting Yu, Lin Wang, Wei Wang, Kang An, Jianjun Chen, Haizhou Liu, Guiju Gao, Sa Wang, Yanyi Huang, Angela Ruohao Wu, Jianbin Wang#, Di Liu#, Hui Zeng#, Chen Chen#. Genomic surveillance of COVID-19 cases in Beijing. Nature Communications, 11, 5503, 2020.
  3. Ryan HP Siu, Yang Liu, Kaitlin HY Chan, Clara Ridzewski, Liane Siu Slaughter#, Angela Ruohao Wu#. Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis. Talanta, 221, 121593, 2021. doi.org/10.1038/s41467-020-19345-0
  4. Cheuk Wang Fung, Shek Nga Chan, Angela Ruohao Wu#. Microfluidic single-cell analysis – Toward integration and total on-chip analysis. Biomicrofluidics, 14 (2), 021502, 2020. doi.org/10.1063/1.5131795
  5. Sin Yen Tan, Ziuwin Leung, Angela Ruohao Wu#. Recreating Physiological Environments In Vitro: Design Rules for Microfluidic‐Based Vascularized Tissue Constructs. Small, 16 (9), 1905055, 2020. doi.org/10.1002/smll.201905055

2019

  1. Winston Koh, Angela Ruohao Wu, Lolita Penland, Barbara Treutlein, Norma F Neff, Gary L Mantalas, Yair J Blumenfeld, Yasser Y El-Sayed, David K Stevenson, Gary M Shaw, Stephen R Quake#. Single Cell Transcriptomes Derived from Human Cervical and Uterine Tissue during Pregnancy. Advanced Biosystems, 3 (11), 1800336, 2019. doi.org/10.1002/adbi.201800336
  2. Xiannian Zhang*, Yang Peng *, Chunmei Li, Qianxi Li, Zhilong Yu, Yuhong Pang, Angela Ruohao Wu, Yanyi Huang#, Hang Li#. Genomic heterogeneity and branched evolution of early stage primary acral melanoma shown by multiregional microdissection sequencing. Journal of Investigative Dermatology. 139 (7), 1526-1534, 2019. doi.org/10.1016/j.jid.2019.01.019
  3. Jianbin Wang#, Angela Ruohao Wu#. A head-to-toe makeover for classical sequencing-by-synthesis helps users to squeeze more out of each base. National Science Review, 6 (1), 3-4, 2019. doi.org/10.1093/nsr/nwy013

2017

  1. Angela Ruohao Wu#, Jianbin Wang#, Aaron M Streets#, Yanyi Huang#. Single-Cell Transcriptional Analysis. Annual Review of Analytical Chemistry, 10 (1), 2017. doi.org/10.1146/annurev-anchem-061516-045228
  2. Lei Yu, Angela Ruohao Wu#. There’s Plenty of Room at the Bottom of a Cell. AIChE Chemical Engineering Progress, 113(10), 47-51, 2017. Link to the article

2016

  1. Hendrik G Stunnenberg et al. The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell, 167 (5), 1145-1149, 2016. doi.org/10.1016/j.cell.2016.11.007
  2. Angela Ruohao Wu, Stephen R Quake#. Microfluidics technologies for low cell number chromatin immunoprecipitation. Cold Spring Harbor Protocols. 2016 (4), pdb.prot084996, 2016. doi.org/10.1101/pdb.prot084996

2015

  1. Olivia Padovan-Merhar, Gautham P Nair, Andrew G Biaesch, Andreas Mayer, Steven Scarfone, Shawn W Foley, Angela Ruohao Wu, L Stirling Churchman, Abhyudai Singh, Arjun Raj#. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular cell, 58 (2), 339-352, 2015. doi.org/10.1016/j.molcel.2015.03.005

2014

  1. Barbara Treutlein*, Doug G Brownfield*, Angela Ruohao Wu, Norma F Neff, Gary L Mantalas, F Hernan Espinoza, Tushar J Desai, Mark A Krasnow#, Stephen R Quake#. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature, 509 (7500), 371-375, 2014. doi.org/10.1038/nature13173
  2. Angela Ruohao Wu, Norma F Neff, Tomer Kalisky, Piero Dalerba, Barbara Treutlein, Michael E Rothenberg, Francis M Mburu, Gary L Mantalas, Sopheak Sim, Michael F Clarke, Stephen R Quake#. Quantitative assessment of single-cell RNA-sequencing methods. Nature methods, 11 (1), 41-46, 2014. doi.org/10.1038/nmeth.2694

2012 and earlier

  1. Angela Ruohao Wu, Tiara LA Kawahara, Nicole A Rapicavoli, Jan Van Riggelen, Emelyn H Shroff, Liwen Xu, Dean W Felsher, Howard Y Chang, Stephen R Quake#. High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. Lab on a Chip, 12 (12), 2190-2198, 2012 doi.org/10.1039/C2LC21290K
  2. Tiara LA Kawahara, Nicole A Rapicavoli*, Angela Ruohao Wu*, Kun Qu, Stephen R Quake, Howard Y Chang#. Dynamic chromatin localization of Sirt6 shapes stress-and aging-related transcriptional networks. PLoS Genetics, 7 (6), e1002153, 2011 doi.org/10.1371/journal.pgen.1002153
  3. Angela Ruohao Wu, Joseph B Hiatt, Rong Lu, Joanne L Attema, Neethan A Lobo, Irving L Weissman, Michael F Clarke, Stephen R Quake#. Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab on a Chip, 9 (10), 1365-1370, 2009 doi.org/10.1039/B819648F
  4. Adrian Y Lau, Paul J Hung, Angela Ruohao Wu, Luke P Lee#. Open-access microfluidic patch-clamp array with raised lateral cell trapping sites. Lab on a Chip, 6 (12), 1510-1515, 2006. doi.org/10.1039/B608439G

Conference Publications

  1. Sin Yen Tan, Angela Ruohao Wu#. Human Microvasculature On-a-Chip. Proceedings of the 13th IEEE International Conference on Nano/Molecular Medicine & Engineering, Nov 21-24, 2019, Gwangju, Korea