Publications

Last updated: June, 2025

2025

  • Nguyen CD, Lu CH, Chen YS, Lee HT, Lo SF, Wei AC, Ho TD, Yu SM. Mitochondrial AOX1a and an H2O2 feed-forward signalling loop regulate flooding tolerance in rice. Plant Biotechnol J. 2025 Feb;23(2):395-411. doi: 10.1111/pbi.14504.

  • Su JY, Wang YL, Hsieh YT, Chang YC, Yang CH, Kang Y, Huang YT, Lin CL. Multiplexed assays of human disease-relevant mutations reveal UTR dinucleotide composition as a major determinant of RNA stability. Elife. 2025 Feb 18;13:RP97682. doi: 10.7554/eLife.97682.

  • Song PY, Tsai CE, Chen YC, Huang YW, Chen PP, Wang TH, Hu CY, Chen PY, Ku C, Hsia KC, Ting SY. An interbacterial cysteine protease toxin inhibits cell growth by targeting type II DNA topoisomerases GyrB and ParE. PLoS Biol. 2025 May 27;23(5):e3003208. doi: 10.1371/journal.pbio.3003208.

  • Murashko ON, Morgan-Lang C, Yu CA, Lin HN, Kaberdina AC, Kung SY, Kaberdin VR, Lin-Chao S. Comprehensive analysis of repetitive extragenic palindrome sequences identified in Bacteria and Archaea using a new web-based tool, RepRanger. mSphere. 2025

  • Huang TN, Lin MH, Hsu TT, Yu CH, Hsueh YP. Abnormal synaptic proteomes, impaired neural ensembles, and defective behaviors in autism mouse models are ameliorated by dietary intervention with nutrient mixtures. bioRxiv. 2025 Jun 1:2025.05.29.656761. doi:10.1101/2025.05.29.656761.

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    2024

  • Chen PY, Chen YC, Chen PP, Lin KT, Sargsyan K, Hsu CP, Wang WL, Hsia KC, Ting SY. A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria. Nat Commun. 2024 Aug 3;15(1):6568. doi: 10.1038/s41467-024-51017-1.

  • Muzaffar A, Chen YS, Lee HT, Wu CC, Le TT, Liang JZ, Lu CH, Balasubramaniam H, Lo SF, Yu LC, Chan CH, Chen KT, Lee MH, Hsing YI, Ho TD, Yu SM. A newly evolved rice-specific gene JAUP1 regulates jasmonate biosynthesis and signalling to promote root development and multi-stress tolerance. Plant Biotechnol J. 2024 May;22(5):1417-1432. doi: 10.1111/pbi.14276.

  • Chu CH, Wu CT, Lin MG, Yen CY, Wu YZ, Hsiao CD, Sun YJ. Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB. Nucleic Acids Res. 2024 Jul 8;52(12):7321-7336. doi: 10.1093/nar/gkae450.

  • Li W-P, Su J-Y, Chang Y-C, Wang Y-L, Chiang H-L, Hsieh Y-T, Chiang Y-H, Ko Y-L, Chiang B-J, Yang C-H, Huang Y-T, Lin C-L. Massively parallel polyribosome profiling reveals translation defects of human disease-relevant UTR mutations. eLife. 2024;13:RP98814. doi: 10.7554/eLife.98814.1

  • Jovanska L, Lin IC, Yao JS, Chen CL, Liu HC, Li WC, Chuang YC, Chuang CN, Yu AC, Lin HN, Pong WL, Yu CI, Su CY, Chen YP, Chen RS, Hsueh YP, Yuan HS, Timofejeva L, Wang TF. DNA cytosine methyltransferases differentially regulate genome-wide hypermutation and interhomolog recombination in Trichoderma reesei meiosis. Nucleic Acids Res. 2024 Sep 9;52(16):9551-9573. doi: 10.1093/nar/gkae611.

  • Wang JP, Hung CH, Liou YH, Liu CC, Yeh KH, Wang KY, Lai ZS, Chatterjee B, Hsu TC, Lee TL, Shyu YC, Hsiao PW, Chen LY, Chuang TJ, Yu CA, Liao NS, Shen CJ. Long-term hematopoietic transfer of the anti-cancer and lifespan-extending capabilities of a genetically engineered blood system by transplantation of bone marrow mononuclear cells. Elife. 2024 May 16;12:RP88275. doi: 10.7554/eLife.88275.

  • Huang AC, Su JY, Hung YJ, Chiang HL, Chen YT, Huang YT, Yu CA, Lin HN, Lin CL. SpliceAPP: an interactive web server to predict splicing errors arising from human mutations. BMC Genomics. 2024 Jun 15;25(1):600. doi: 10.1186/s12864-024-10512-x.

  • Yeh CW, Hsu KL, Lin ST, Huang WC, Yeh KH, Liu CJ, Wang LC, Li TT, Chen SC, Yu CH, Leu JY, Yeang CH, Yen HS. Altered assembly paths mitigate interference among paralogous complexes. Nat Commun. 2024 Aug 21;15(1):7169. doi: 10.1038/s41467-024-51286-w.

  • Chen SW, Chu Y, Chu CH, Pham XT, Ng HP, Guo CL, Cheng PL. ECM29/proteasome-mediated self-antigen generation by CNS-resident neuroglia promotes regulatory T cell activation. Cell Rep. 2025 Jan 28;44(1):115161. doi: 10.1016/j.celrep.2024.115161.

  • Fang YL, Yen TL, Liu HC, Wang TF, Hsueh YP. Sex-biased zinc responses modulate ribosomal protein expression, protein synthesis and social defects in Cttnbp2 mutant mice. Neurobiol Dis. 2025 Jul;211:106932. doi: 10.1016/j.nbd.2025.106932.

  • Hsu FY, Yen YP, Fan HC, Chang M, Chen JA. Sertm2 is a conserved micropeptide that promotes GDNF-mediated motor neuron subtype specification. EMBO Rep. 2025 Apr;26(8):2013-2043. doi: 10.1038/s44319-025-00400-0.

  • Yang CH, Wang YW, Hsu CW, Chung BC. Zebrafish Foxl2l functions in proliferating germ cells for female meiotic entry. Dev Biol. 2025 Jan;517:91-99. doi: 10.1016/j.ydbio.2024.09.013.

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    2023

  • Kulkarni R, Kasani SK, Tsai CY, Tung SY, Yeh KH, Yu CA, Chang W. FAM21 is critical for TLR2/CLEC4E-mediated dendritic cell function against Candida albicans. Life Sci Alliance. 2023 Jan 30;6(4):e202201414. doi: 10.26508/lsa.202201414.

  • Wang CK, Chen TJ, Tan GYT, Chang FP, Sridharan S, Yu CA, Chang YH, Chen YJ, Cheng LT, Hwang-Verslues WW. MEX3A Mediates p53 Degradation to Suppress Ferroptosis and Facilitate Ovarian Cancer Tumorigenesis. Cancer Res. 2023 Jan 18;83(2):251-263. doi: 10.1158/0008-5472.CAN-22-1159.

  • Kao S, Kao CF, Chang W, Ku C. Widespread Distribution and Evolution of Poxviral Entry-Fusion Complex Proteins in Giant Viruses. Microbiol Spectr. 2023 Mar 13;11(2):e0494422. doi: 10.1128/spectrum.04944-22.

  • Liau ES, Jin S, Chen YC, Liu WS, Calon M, Nedelec S, Nie Q, Chen JA. Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. Nat Commun. 2023 Jan 3;14(1):46. doi: 10.1038/s41467-022-35574-x.

  • Lin YC, Tsay YF. Study of vacuole glycerate transporter NPF8.4 reveals a new role of photorespiration in C/N balance. Nat Plants. 2023 May;9(5):803-816. doi: 10.1038/s41477-023-01392-2.

  • Chen TH, Chang SH, Wu YF, Yen YP, Hsu FY, Chen YC, Ming Y, Hsu HC, Su YC, Wong ST, Hung JH, Chiou SH, Jong YJ, Chen JA. MiR34 contributes to spinal muscular atrophy and AAV9-mediated delivery of MiR34a ameliorates the motor deficits in SMA mice. Mol Ther Nucleic Acids. 2023 Mar 15;32:144-160. doi: 10.1016/j.omtn.2023.03.005.

  • Kao CF, Tsai MH, Carillo KJ, Tzou DL, Chang W. Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations. PLoS Pathog. 2023 Nov 10;19(11):e1011500. doi: 10.1371/journal.ppat.1011500.

  • Murashko ON, Yeh KH, Yu CA, Kaberdin VR, Lin-Chao S. Sodium Fluoride Exposure Leads to ATP Depletion and Altered RNA Decay in Escherichia coli under Anaerobic Conditions. Microbiol Spectr. 2023 Mar 20;11(2):e0415822. doi: 10.1128/spectrum.04158-22.

  • Lu SH, Wu YH, Su LY, Hsu ZT, Weng TH, Wang HY, Yu C, Hsu PW, Tsai SY. Cardiac myofibrillogenesis is spatiotemporally modulated by the molecular chaperone UNC45B. Stem Cell Reports. 2023 Jul 11;18(7):1405-1420. doi: 10.1016/j.stemcr.2023.05.006.

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    2022

  • Chiang HL, Chen YT, Su JY, Lin HN, Yu CA, Hung YJ, Wang YL, Huang YT, Lin CL. Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing. Nat Struct Mol Biol. 2022 Nov;29(11):1043-1055. doi: 10.1038/s41594-022-00844-1.

  • Swamy KBS, Lee HY, Ladra C, Liu CJ, Chao JC, Chen YY, Leu JY. Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast. Nat Commun. 2022 Jul 29;13(1):4394. doi: 10.1038/s41467-022-32107-4.

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    2021

  • Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barillà D, Sun YJ, Hsiao CD. Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly. Nucleic Acids Res. 2021 Dec 16;49(22):13150-13164. doi: 10.1093/nar/gkab1155.

  • Li WC, Lee CY, Lan WH, Woo TT, Liu HC, Yeh HY, Chang HY, Chuang YC, Chen CY, Chuang CN, Chen CL, Hsueh YP, Li HW, Chi P, Wang TF. Trichoderma reesei Rad51 tolerates mismatches in hybrid meiosis with diverse genome sequences. Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):e2007192118. doi: 10.1073/pnas.2007192118.

  • Yeh CW, Huang WC, Hsu PH, Yeh KH, Wang LC, Hsu PW, Lin HC, Chen YN, Chen SC, Yeang CH, Yen HS. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO J. 2021 Apr 1;40(7):e105846. doi: 10.15252/embj.2020105846.

  • Li WC, Lin TC, Chen CL, Liu HC, Lin HN, Chao JL, Hsieh CH, Ni HF, Chen RS, Wang TF. Complete Genome Sequences and Genome-Wide Characterization of Trichoderma Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions. Microbiol Spectr. 2021 Dec 22;9(3):e0066321. doi: 10.1128/Spectrum.00663-21.

  • Wang IF, Wang Y, Yang YH, Huang GJ, Tsai KJ, Shen CJ. Activation of a hippocampal CREB-pCREB-miRNA-MEF2 axis modulates individual variation of spatial learning and memory capability. Cell Rep. 2021 Aug 3;36(5):109477. doi: 10.1016/j.celrep.2021.109477.

  • Chen CY, Hung YF, Tsai CY, Shih YC, Chou TF, Lai MZ, Wang TF, Hsueh YP. Transcriptomic Analysis and C-Terminal Epitope Tagging Reveal Differential Processing and Signaling of Endogenous TLR3 and TLR7. Front Immunol. 2021 Jun 15;12:686060. doi: 10.3389/fimmu.2021.686060.

  • Hung YF, Hsueh YP. TLR7 and IL-6 differentially regulate the effects of rotarod exercise on the transcriptomic profile and neurogenesis to influence anxiety and memory. iScience. 2021 Mar 31;24(4):102384. doi: 10.1016/j.isci.2021.102384.

  • Yeh CW, Huang WC, Hsu PH, Yeh KH, Wang LC, Hsu PW, Lin HC, Chen YN, Chen SC, Yeang CH, Yen HS. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO J. 2021 Apr 1;40(7):e105846. doi: 10.15252/embj.2020105846.

  • Chang SH, Su YC, Chang M, Chen JA. MicroRNAs mediate precise control of spinal interneuron populations to exert delicate sensory-to-motor outputs. Elife. 2021 Mar 31;10:e63768. doi: 10.7554/eLife.63768.

  • Kulkarni R, Chen WC, Lee Y, Kao CF, Hu SL, Ma HH, Jan JT, Liao CC, Liang JJ, Ko HY, Sun CP, Lin YS, Wang YC, Wei SC, Lin YL, Ma C, Chao YC, Chou YC, Chang W. Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters. PLoS One. 2021 Sep 9;16(9):e0257191. doi: 10.1371/journal.pone.0257191.

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    2020

  • Hong GC, Tsai CH, Chang W. Experimental Evolution To Isolate Vaccinia Virus Adaptive G9 Mutants That Overcome Membrane Fusion Inhibition via the Vaccinia Virus A56/K2 Protein Complex. J Virol. 2020 May 4;94(10):e00093-20. doi: 10.1128/JVI.00093-20.

  • Li WC, Liu HC, Lin YJ, Tung SY, Wang TF. Third-generation sequencing-based mapping and visualization of single nucleotide polymorphism, meiotic recombination, illegitimate mutation and repeat-induced point mutation. NAR Genom Bioinform. 2020 Jul 29;2(3):lqaa056. doi: 10.1093/nargab/lqaa056.

  • Ko YC, Lai TY, Hsu SC, Wang FH, Su SY, Chen YL, Tsai ML, Wu CC, Hsiao JR, Chang JY, Wu YM, Robinson DR, Lin CY, Lin SF. Index of Cancer-Associated Fibroblasts Is Superior to the Epithelial-Mesenchymal Transition Score in Prognosis Prediction. Cancers (Basel). 2020 Jun 28;12(7):1718. doi: 10.3390/cancers12071718.

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