Representa­tive Publications

An atlas of bacterial two-component systems reveals function and plasticity in signal transduction

Yingpeng Xie, Jingwei Li, Yiqing Ding, Xiaolong Shao, Yue Sun, Fangzhou Xie, Shiyi Liu, Shaojun Tang & Xin Deng. An atlas of bacterial two-component systems reveals function and plasticity in signal transduction. Cell Reports (2022) 41(3):111502 doi: 10.1016/j.celrep.2022.111502

Single-cell RNA-seq recognized the initiator of epithelial ovarian cancer recurrence

Tongtong Kan, Shupeng Zhang, Shengtao Zhou, Ya Zhang, Yun Zhao, Yinghua Gao, Tao Zhang, Feng Gao, Xin Wang, Linjie Zhao & Mengsu Yang. Single-cell RNA-seq recognized the initiator of epithelial ovarian cancer recurrence. Oncogene (2022) 41:895-906 doi: 10.1038/s41388-021-02139-z

Defect-enhanced selective ion transport in an ionic nanocomposite for efficient energy harvesting from moisture

Dong Lv, Shuang Zheng, Chunyan Cao, Kedi Li, Liqing Ai, Xin Li, Zhengbao Yang, Zhengtao Xu & Xi Yao. Defect-enhanced selective ion transport in an ionic nanocomposite for efficient energy harvesting from moisture. Engergy & Environmental Science (2022) 15:2601-2609 doi: 10.1039/D2EE00432A

Continuous Energy Harvesting from Ubiquitous Humidity Gradients using Liquid-Infused Nanofluidics

Shuang Zheng, Jiayue Tang, Dong Lv, Mi Wang, Xuan Yang, Changshun Hou, Bo Yi, Gang Lu, Ruiran Hao, Mingzhan Wang, Yanlei Wang, Hongyan He & Xi Yao. Continuous Energy Harvesting from Ubiquitous Humidity Gradients using Liquid-Infused Nanofluidics. Advanced Materials (2022) 34(4):2106410 doi: 10.1002/adma.202106410

Lung adenocarcinoma-related target gene prediction and drug repositioning

Rui Xuan Huang, Damrongrat Siriwanna, William C. Cho, Tsz Kin Wan, Yan Rong Du, Adam N. Bennett, Qian Echo He, Jun Dong Liu, Xiao Tai Huang & Kei Hang Katie Chan. Lung adenocarcinoma-related target gene prediction and drug repositioning. Frontiers in Pharmacology (2022) 13:936758 doi: 10.3389/fphar.2022.936758

Wetting ridge assisted programmed magnetic actuation of droplets on ferrofluid-infused surface

Jianqiang Zhang, Xuejiao Wang, Zhaoyue Wang, Shangfa Pan, Bo Yi, Liqing Ai, Jun Gao, Frieder Mugele & Xi Yao. Wetting ridge assisted programmed magnetic actuation of droplets on ferrofluid-infused surface. Nature Communications (2021) 12:7136 doi: 10.1038/s41467-021-27503-1

Attenuating innate immunity and facilitating β-coronavirus infection by NSP1 of SARS-CoV-2 through specific redistributing hnRNP A2/B1 cellular localization

Fanghang Zhou, Qianya Wan, Sheng Chen, Ying Chen, Pui-Hui Wang, Xi Yao & Ming-liang He. Attenuating innate immunity and facilitating β-coronavirus infection by NSP1 of SARS-CoV-2 through specific redistributing hnRNP A2/B1 cellular localization. Signal Transduction and Targeted Therapy (2021) 6:371 doi: 10.1038/s41392-021-00786-y

Deep RNA Sequencing Revealed Fusion Junctional Heterogeneity May Predict Crizotinib Treatment Efficacy in ALK-Rearranged NSCLC

Song Z, Lian S, Mak S, Chow M Z-Y, Xu C, Wang W, Keung H Y, Lu C, Kebede F T, Gao Y, Cheuk W, Cho W C S, Yang M, Zheng Z*. Deep RNA Sequencing Revealed Fusion Junctional Heterogeneity May Predict Crizotinib Treatment Efficacy in ALK-Rearranged NSCLC. Journal of Thoracic Oncology (2021) S1556-0864(21)03219-6 doi: 10.1016/j.jtho.2021.09.016

Pseudomonas syringae senses polyphenols via phosphorelay crosstalk to inhibit virulence

Xie Y, Ding Y, Shao X, Yao C, Li J, Liu J, Deng X*. Pseudomonas syringae senses polyphenols via phosphorelay crosstalk to inhibit virulence. EMBO Reports (2021) e52805 doi: 10.15252/embr.202152805

Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes

Wang P, Al Azad MAR, Yang X, Martelli PR, Cheung KY, Shi J*, Shen Y*. Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes. PNAS (2021) 118(23):e2024329118 doi: 10.1073/pnas.2024329118

Bioinspired Supramolecular Slippery Organogels for Controlling Pathogen Spread by Respiratory Droplets

Wang Z, Yi B, Wu M, Lv D, He ML*, Liu M*, Yao X*. Bioinspired Supramolecular Slippery Organogels for Controlling Pathogen Spread by Respiratory Droplets. Advanced Functional Materials (2021) 31:2102888 doi: 10.1002/adfm.202102888

PIM1 kinase facilitates Zika virus replication by suppressing host cells’ natural immunity

Zhou F, Wan Q, Chen Y, Chen S, He ML*. PIM1 kinase facilitates Zika virus replication by suppressing host cells’ natural immunity. Signal Transduction and Targeted Therapy (2021) 6(1):207 doi: 10.1038/s41392-021-00539-x

Berbamine inhibits SARS-CoV-2 infection by compromising TRPMLs-mediated endolysosomal trafficking of ACE2

Huang L, Yuen T, Ye Z, Liu S, Zhang G, Chu H*, Yue J*. Berbamine inhibits SARS-CoV-2 infection by compromising TRPMLs-mediated endolysosomal trafficking of ACE2. Signal Transduction and Targeted Therapy (2021) 6: 168 doi: 10.1038/s41392-021-00584-6

OCaMIR—A Noninvasive, Diagnostic Signature for Early-Stage Ovarian Cancer: A Multi-cohort Retrospective and Prospective Study

Kandimalla R, Wang W, Yu F, Zhou N, Gao F, Spillman M, Moukova L, Slaby O, Salhia B, Zhou S*, Wang X*, Goel A*. OCaMIR—A Noninvasive, Diagnostic Signature for Early-Stage Ovarian Cancer: A Multi-cohort Retrospective and Prospective Study. Clinical Cancer Research (2021) doi: 10.1158/1078-0432.CCR-21-0267

Vacuolin-1 inhibits endosomal trafficking and metastasis via CapZβ

Ye Z, Wang D, He Y, Yu J, Wei W, Chen C, Wang R, Zhang L, Zhang LH, Zhang LR, Le M, Cho W, M Yang, Zhang H, Yue J*. Vacuolin-1 inhibits endosomal trafficking and metastasis via CapZβ. Oncogene (2021) 40, 1775-1791 doi: 10.1038/s41388-021-01662-3

Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling

Huang H, Hu J, Maryam A, Huang Q, Zhang Y, Ramakrishnan S, Li J, Ma VW, Cheuk W, So GYK, Wang W, Cho WCS, Zhang L, Chan M, Wang X*, Chin YR*. Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling. Nature Communications (2021) 12:1–16 doi: 10.1038/s41467-021-22445-0

Systematic analysis of binding of transcription factors to noncoding variants

Yan J*, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, Sander M, Taipale J*, Ren B*. Systematic analysis of binding of transcription factors to noncoding variants. Nature (2021) 591:147-151 doi: 10.1038/s41586-021-03211-0

Covalent conjugation of extracellular vesicles with peptides and nanobodies for targeted therapeutic delivery

Pham TC, Jayasinghe MK, Pham TT, Yang Y, Wei L, Usman WM, Chen H, Pirisinu M, Gong J, Kim S, Peng B, Wang W, Chan C, Ma V, Nguyen NTH, Kappei D, Nguyen XH, Cho WC, Shi J*, Le MTN*. Covalent conjugation of extracellular vesicles with peptides and nanobodies for targeted therapeutic delivery. Journal of Extracellular Vesicles (2021) 10(4):e12057 doi: 10.1002/jev2.12057

Integrated regulatory network in Pseudomonas syringae reveals dynamics of virulence

Shao X, Tan M, Xie Y, Yao C, Wang T, Huang H, Zhang Y, Ding Y, Liu J, Han L, Hua C, Wang X*, Deng X*. Integrated regulatory network in Pseudomonas syringae reveals dynamics of virulence. Cell Reports (2021) 34:108920 doi: 10.1016/j.celrep.2021.108920

An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine

Chen Y, Wu T, Zhu Z, Huang H, Zhang L, Goel A, Yang M, Wang X*. An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Seminars in Cancer Biology (2021) doi: 10.1016/j.semcancer.2021.03.011

An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

Wang T, Sun W, Fan L, Hua C, Wu N, Fan S, Zhang J, Deng X*, Yan J.* An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence. eLife (2021) 10:e61885 doi: 10.7554/eLife.61885

Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices

Xie K, Wang Z, Qi L, Zhao X, Wang Y, Qu J, Huang L, Zhang W, Yang Y*, Wang X*, Shi P*. Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices. ACS Nano (2021) doi: 10.1021/acsnano.0c0967610.1021/acsnano.0c09676

Ferric Ion Driven Assembly of Catalase-like Supramolecular Photosensitizing Nanozymes for Combating Hypoxic Tumors

Li Y, Sun P, Zhao L, Yan X*, Ng DKP*, Lo PC*. Ferric Ion Driven Assembly of Catalase-like Supramolecular Photosensitizing Nanozymes for Combating Hypoxic Tumors. Angew Chem Int Ed Engl. (2020) 59(51) 23228-23238 doi: 10.1002/anie.202010005

CRISPR-assisted detection of RNA–protein interactions in living cells

Yi W, Li J, Zhu X, Wang X, Fan L, Sun W, Liao L, Zhang J, Li X, Ye J, Chen F, Taipale J, Chan KM*, Zhang L*, Yan J*. CRISPR-assisted detection of RNA–protein interactions in living cells. Nature Methods (2020) 17(7) 685-688 doi: 10.1038/s41592-020-0866-0

A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae

Fan L, Wang T, Hua C, Sun W, Li X, Grunwald L, Liu J, Wu N, Shao X, Yin Y, Yan J*, Deng X*. A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae. Nature Communications (2020) 11:4947 doi: 10.1038/s41467-020-18744-7

Desuccinylation-Triggered Peptide Self-Assembly: Live Cell Imaging of SIRT5 Activity and Mitochondrial Activity Modulation

Yang L, Peltier R, Zhang M, Song D, Huang H, Chen G, Chen Y, Zhou F, Hao Q, Bian L, He ML*, Wang Z*, Hu Y*, Sun H*. Desuccinylation-Triggered Peptide Self-Assembly: Live Cell Imaging of SIRT5 Activity and Mitochondrial Activity Modulation. Journal of the American Chemical Society (2020) 142(42) 18150-18159 doi: 10.1021/jacs.0c08463

Wdr26 regulates nuclear condensation in developing erythroblasts

Zhen R, Moo C, Zhao Z, Chen M, Feng H, Zheng X, Zhang L, Shi J*, Chen C*. Wdr26 regulates nuclear condensation in developing erythroblasts. Blood (2020) 135(3) 208-219 doi: 10.1182/blood.2019002165

Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development

Wan Q, Song D, He B, Li H, He ML*. Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development. Signal Transduction and Targeted Therapy (2020) doi: 10.1038/s41392-020-00233-4.

Demyelination Regulates the Circadian Transcription Factor BMAL1 to Signal Adult Neural Stem Cells to Initiate Oligodendrogenesis

Huang S, Choi MH, Huang H, Wang X, Chang YC, Kim JY*. Demyelination Regulates the Circadian Transcription Factor BMAL1 to Signal Adult Neural Stem Cells to Initiate Oligodendrogenesis. Cell Reports (2020) 33:108394 doi: 10.1016/j.celrep.2020.108394

The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma

Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Lis J, Ishibashi T, Danko CG*, Wang X*, Chan KM*. The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma. Signal Transduction and Targeted Therapy (2020) 5:106 doi: 10.1038/s41392-020-00219-2

High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity

Wang Z, Qi L, Yang Y, Lu M, Xie K, Zhao X, Cheung EHC, Wang Y, Jiang X, Zhang W*, Huang L*, Wang X* & Shi P*. High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity. Science Advances (2020) 6:eaba4971 doi: 10.1126/sciadv.aba4971

Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes

Wan YCE, Leung TCS, Ding D, Sun X, Liu J, Zhu L, Kang TZE, Yang D, Zhang YC, Zhang J, Qian C, Huen MSY, Li Q, Chow MZY, Zheng Z, Han J, Goel A, Wang X*, Ishibashi T*, Chan KM*. Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes. Signal Transduction and Targeted Therapy (2020) 5:27 doi: 10.1038/s41392-020-0131-0

In vivo priming of human mesenchymal stem cells with hepatocyte growth factor-engineered mesenchymal stem cells promotes therapeutic potential for cardiac repair

Park BW, Jung SH, Das S, Lee SM, Park JH, Kim H, Hwang JW, Lee SH, Kim HJ, Kim HY, Jeong S, Cho DW, Jang J*, Ban K*, Park HJ*. In vivo priming of human mesenchymal stem cells with hepatocyte growth factor-engineered mesenchymal stem cells promotes therapeutic potential for cardiac repair. Science Advances (2020) 6(13) doi: 10.1126/sciadv.aay6994

Dual stem cell therapy synergistically improves cardiac function and vascular regeneration following myocardial infarction

Park S, Kim RY, Park BW, Lee S, Choi SW, Park JH, Choi JJ, Kim SW, Jang J, Cho DW, Chung HM, Moon SH, Ban K*, Park HJ*. Dual stem cell therapy synergistically improves cardiac function and vascular regeneration following myocardial infarction. Nature Communications (2019) 10(1):3123 doi: 10.1038/s41467-019-11091-2

Supramolecular silicone coating capable of strong substrate bonding, readily damage healing, and easy oil sliding

Liu M, Wang Z, Liu P, Wang Z, Yao H, Yao X*. Supramolecular silicone coating capable of strong substrate bonding, readily damage healing, and easy oil sliding. Science Advances (2019) 5:eaaw5643 doi: 10.1126/sciadv.aaw5643

Bio-Inspired Elastic Liquid-Infused Material for On-Demand Underwater Manipulation of Air Bubbles

Zhang J, Liu P, Yi B, Wang Z, Jiang L, Yao X*. Bio-Inspired Elastic Liquid-Infused Material for On-Demand Underwater Manipulation of Air Bubbles. ACS Nano (2019) 13:10596-10602 doi: 10.1021/acsnano.9b04771

Directional pumping of water and oil microdroplets on slippery surface

Jiang J, Gao J, Zhang H, He W, Zhang J, Dan D, Yao X*. Directional pumping of water and oil microdroplets on slippery surface. PNAS (2019) 116:2482-2487 doi: 10.1073/pnas.1817172116

An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa

Huang H, Shao X, Xie Y, Wang T, Zhang Y, Wang X*, Deng X*. An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa. Nature Communications (2019) 10:2931 doi: 10.1038/s41467-019-10778-w

Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-Risk T1 Colorectal Cancers

Kandimalla R, Ozawa T, Gao F, Wang X*, Goel A* and the T1 Colorectal Cancer Study Group. Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-Risk T1 Colorectal Cancers. Gastroenterology (2019) doi: 10.1053/j.gastro.2019.02.027

Long-Read RNA Sequencing Identifies Alternative Splice Variants in Hepatocellular Carcinoma and Tumor-Specific Isoforms

Chen H, Gao F , He M, Ding XF, Wong AM, Sze SC, Yu AC, Sun T, Chan AWH, Wang X*, Wong N*. Long-Read RNA Sequencing Identifies Alternative Splice Variants in Hepatocellular Carcinoma and Tumor-Specific Isoforms. Hepatology (2019) doi: 10.1002/hep.30500

Saikosaponin D suppresses enterovirus A71 infection by inhibiting autophagy

Li C, Huang L, Sun W, Chen Y, He ML*, Yue J*, Ballard H*. Saikosaponin D suppresses enterovirus A71 infection by inhibiting autophagy. Signal Transduction and Targeted Therapy (2019) doi: 10.1038/s41392-019-0037-x

AAV cis-regulatory sequences are correlated with ocular toxicity

Xiong W*, Wu DM, Xue Y, Wang SK, Chung MJ, Ji X, Rana P, Zhao SR, Mai S, Cepko CL*. AAV cis-regulatory sequences are correlated with ocular toxicity. PNAS (2019) 116(12): 5785-5794 doi: 10.1073/pnas.1821000116

Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity

Tan Y, Chu HY, Bao S, Hoang DA, Kebede TF, Xiong W, Ji M, Shi J*, Zheng Z*. Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. PNAS (2019) doi: 10.1073/pnas.1906843116

Super-enhancers in transcriptional regulation and genome organization

Wang X, Cairns MJ, Yan J*. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Research (2019) 47(22) 11481-11496 doi: 10.1093/nar/gkz1038

Chemical Probes Reveal Sirt2’s New Function as a Robust Eraser of Lysine Lipoylation

Xie Y, Chen L, Wang R, Wang J, Li J, Xu W, Li Y, Yao SQ, Zhang L*, Hao Q*, Sun H*. Chemical Probes Reveal Sirt2’s New Function as a Robust Eraser of Lysine Lipoylation. Journal of the American Chemical Society (2019) 141(46) 18428-18436 doi: 10.1021/jacs.9b06913

Cholecystokinin release triggered by NMDA receptors produces LTP and sound-sound associative memory

Chen X, Li X, Wong YT, Zheng XJ, Wang HT, Peng YJ, Feng HM, Feng JY, Baibado JT, Jesky R, Wang ZD, Xie H, Sun WJ, Zhang ZC, Zhang X, He L, Zhang N, Zhang ZJ, Tang P, Su JF, Hu LL, Liu Q, He XB, Tan AL, Sun X, Li M, Wong K, Wang XY, Cheung HY, Shum DKY, Yung KK, Chan YS, Tortorella M, Guo YP, Xu FQ, He JF*. Cholecystokinin release triggered by NMDA receptors produces LTP and sound-sound associative memory. PNAS (2019) 116(13): 6397-6406 doi: 10.1073/pnas.1816833116