Selected papers:
Ameres SL, Horwich MD, Hung J-H, Xu J, Ghildiyal M, Weng Z, Zamore PD. Target RNA–directed trimming and tailing of small silencing RNAs.Science. 328:1534-1539, 2010
Hung J-H, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biology.11:R23, 2010
Hung J-H, Yang TH, Hu Z, Weng Z, Delisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform. 2011 Sep 7.
Yildirim O, Li R, Hung J-H, Chen PB, Dong X, Ee L-Y, Weng Z, Rando OJ and Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. Volume 147, Issue 7, 1498-1510, 23 December 2011
Xie J, Ameres SL, Friedline R, Hung J-H, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, Weng Z, Flotte TR, Zamore PD, Gao G. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods, 2012 Mar 4;9(4):403-9
Ryuya Fukunaga, Bo W. Han, Hung J-H, Jia Xu, Zhiping Weng, Phillip D. Zamore Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell. 11 October 2012
Chou M.-T., Han B. W., Hsiao C.-P., Zamore P. D., Weng Z. and Hung J.-H.A Computational Framework for Detecting Non-Templated Tailing of Small Silencing RNAs.Nucleic Acids Research. Volume: 10. 1093. 2015.
Chang CH, Chou MT, Wu YC, Hong TW, Li YL, Yang CH,and Hung J-H. sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. Bioinformatics. July 2016
Y. Wu, C. Chang, J. Hung, C. Yang. A 135-mW Fully Integrated Data Processor for Next-Generation Sequencing. IEEE Transactions on Biomedical Circuits and Systems. 11: 1216-1225, 2017
Complete list:
Yi-Ching Lin, Wei-Chen Chien, Yu-Xuan Wang, Ying-Hau Wang, Feng-Shuo Yang, Li-Ping Tseng, Jui-Hung Hung*. PS2MS: A Deep Learning-Based Prediction System for Identifying New Psychoactive Substances Using Mass Spectrometry. Analytical Chemistry, March 2024. DOI: 10.1021/acs.analchem.3c05019
Yuan-Yu Chang, Sheng-Tang Wong, Emmanuel O Salawu, Ming-Hsuan Liao, Jui-Hung Hung*, Lee-Wei Yang*. Full-privacy secured search engine empowered by efficient genome-mapping algorithms. IEEE Journal of Biomedical and Health Informatics, Oct. 2023. DOI：10.1109/JBHI.2023.3300885
Chung-Hsuan Yang, Yi-Chung Wu, Yen-Lung Chen, Chao-Hsi Lee, Jui-Hung Hung*, Chia-Hsiang Yang*. An FM-index Based High-Throughput Memory-Efficient FPGA Accelerator for Paired-end Short-read Mapping. IEEE Transactions on Biomedical Circuits and Systems, July 2023. DOI：10.1016/j.omtn.2023.03.005
Tai-Heng Chen, Shih-Hsin Chang, Yu-Fu Wu, Ya-Ping Yen, Fang-Yu Hsu, Yen-Chung Chen, Yang Ming, Ho-Chiang Hsu, Yi-Ching Su, Sheng-Tang Wong, Jui-Hung Hung, Shih-Hwa Chiou, Yuh-Jyh Jong, Jun-An Chen. MiR34 Contributes to Spinal Muscular Atrophy and AAV9-mediated Delivery of MiR34a Ameliorates the Motor Deficits in SMA Mice. Molecular Therapy-Nucleic Acids, 2023. DOI:https://doi.org/10.1016/j.omtn.2023.03.005
Chung-Hsuan Yang, Yi-Chung Wu, Yen-Lung Chen, Chao-Hsi Lee, Jui-Hung Hung, Chia-Hsiang Yang. A 75.6M Base-pairs/s FPGA Accelerator for FM-index Based Paired-end Short-Read Mapping. 2022 IEEE Asian Solid-State Circuits Conference (A-SSCC). DOI: 10.1109/A-SSCC56115.2022.9980714
Chiao-Yu Hsieh, Ching-Chih Tu, Jui-Hung Hung. Estimating intraclonal heterogeneity and subpopulation changes from bulk expression profiles in CMap. Life Science Alliance, 2022. DOI: 10.26508/lsa.202101299
Jui-Hung Hung, Chia-Hsiang Yang, WU Yi-Chung. Method and system for DNA sequence alignment. US Patent 11,302,419, 2022. https://patents.google.com/patent/US11302419B2/en
Lee-Wei Yang, Jui-Hung Hung, Emmanuel Oluwatobi Salawu, Yuan-Yu Chang. Privacy-kept text comparison method, system and computer program product. US Patent 11,232,157, 2022. https://patents.google.com/patent/US11232157B2/en
Jui-Hung Hung, Chia-Hsiang Yang. Portable genome sequencing and genotyping device and operating method thereof. US Patent App. 17/114,455, 2022. https://patents.google.com/patent/US20220017955A1/en
Ching-Chih Tu, Jui-Hung Hung. Reliable and accurate gene expression quantification with subpopulation structure-aware constraints for single-cell RNA sequencing. bioRxiv, 2022. doi: https://doi.org/10.1101/2022.11.08.515740
Yuan-Yu Chang, Sheng-Tang Wong, Emmanuel O Salawu, Yu-Xuan Wang, Jui-Hung Hung, Lee-Wei Yang. Full-privacy secured search engine empowered by efficient genome-mapping algorithms. arXiv:2201.00696, 2021. https://doi.org/10.48550/arXiv.2201.00696
Wang, Ting-Hsuan; Huang, Cheng-Ching; Hung, Jui-Hung. EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences. Bioinformatics, Jul 2021. https://doi.org/10.1093/bioinformatics/btab025
Chang, C. Y., Hung, J. H., Huang, L. W., Li, J., Fung, K. S., Kao, C. F., & Chen, L. (2020). Epigenetic regulation of WNT3A enhancer during regeneration of injured cortical neurons. International journal of molecular sciences, 21(5), [1891]. https://doi.org/10.3390/ijms21051891
Yen, Y. P., Hsieh, W. F., Tsai, Y. Y., Lu, Y. L., Liau, E. S., Hsu, H. C., Chen, Y. C., Liu, T. C., Chang, M., Li, J., Lin, S. P., Hung, J. H., & Chen, J. A. (2020). Erratum: Correction: Dlk1-Dio3 locus-derived LncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity (eLife (2018) 7 PII: e55647). eLife, 9. https://doi.org/10.7554/eLife.55647
Wu, Y. C., Chen, Y. L., Yang, C. H., Lee, C. H., Yu, C. Y., Chang, N. S., Chen, L. C., Chang, J. R., Lin, C. P., Chen, H. L., Chen, C. S., Hung, J. H., & Yang, C. H. (2020). A Fully Integrated Genetic Variant Discovery SoC for Next-Generation Sequencing. 於 2020 IEEE International Solid-State Circuits Conference, ISSCC 2020 (頁 322-324). [9063002] (Digest of Technical Papers - IEEE International Solid-State Circuits Conference; 卷 2020-February). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISSCC19947.2020.9063002
Tsai, P. H., Chien, Y., Wang, M. L., Hsu, C. H., Laurent, B., Chou, S. J., Chang, W. C., Chien, C. S., Li, H. Y., Lee, H. C., Huo, T. I., Hung, J. H., Chen, C. H., & Chiou, S. H. (2019). Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network. Nucleic acids research, 47(19), 10115-10133. https://doi.org/10.1093/nar/gkz801
Hung, J-H. (2018). 用於基因定序資料的資料處理方法及系統. (專利號 I636372).
Yen, Y. P., Hsieh, W. F., Tsai, Y. Y., Lu, Y. L., Liau, E. S., Hsu, H. C., Chen, Y. C., Liu, T. C., Chang, M., Li, J., Lin, S. P., Hung, J-H., & Chen, J. A. (2018). Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. eLife, 7, [e38080]. https://doi.org/10.7554/eLife.38080
Wu, Y. C., Hung, J-H., & Yang, C. H. (2017). A 135mW fully integrated data processor for next-generation sequencing. 於 L. C. Fujino (編輯), 2017 IEEE International Solid-State Circuits Conference, ISSCC 2017 (頁 252-253). [7870356] (Digest of Technical Papers - IEEE International Solid-State Circuits Conference; 卷 60). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISSCC.2017.7870356
Hung, J-H., & Weng, Z. (2017). Analysis of microarray and RNA-seq expression profiling data. Cold Spring Harbor Protocols, 2017(3), 191-196. https://doi.org/10.1101/pdb.top093104
Hung, J-H., & Weng, Z. (2017). Analyzing microarray data. Cold Spring Harbor Protocols, 2017(3), 244-253. https://doi.org/10.1101/pdb.prot093112
Hung, J-H., & Weng, Z. (2017). Peak-finding algorithms. Cold Spring Harbor Protocols, 2017(3), 197-203. https://doi.org/10.1101/pdb.top093179
Hung, J-H., & Weng, Z. (2017). Discovering cis-regulatory motifs. Cold Spring Harbor Protocols, 2017(2), 173-181. https://doi.org/10.1101/pdb.prot093203
Hung, J-H., & Weng, Z. (2017). Identifying regions enriched in a chip-seq data set (Peak finding). Cold Spring Harbor Protocols, 2017(2), 165-172. https://doi.org/10.1101/pdb.prot093187
Hung, J-H., & Weng, Z. (2017). Mapping short sequence reads to a reference genome. Cold Spring Harbor Protocols, 2017(2), 158-164. https://doi.org/10.1101/pdb.prot093161
Hung, J-H., & Weng, Z. (2017). Motif finding. Cold Spring Harbor Protocols, 2017(2), 92-97. https://doi.org/10.1101/pdb.top093195
Hung, J-H., & Weng, Z. (2017). Mapping billions of short reads to a reference genome. Cold Spring Harbor Protocols, 2017(1), 14-17. https://doi.org/10.1101/pdb.top093153
Wu, Y. C., Hung, J-H., & Yang, C. H. (2017). A 135mW fully integrated data processor for next-generation sequencing. 於 L. C. Fujino (編輯), 2017 IEEE International Solid-State Circuits Conference, ISSCC 2017 (頁 252-253). [7870356] (Digest of Technical Papers - IEEE International Solid-State Circuits Conference; 卷 60). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISSCC.2017.7870356
Hung, J-H., & Weng, Z. (2016). Sequence alignment and homology search. Cold Spring Harbor Protocols, 2016(11), 937-940. https://doi.org/10.1101/pdb.top093070
Hung, J-H., & Weng, Z. (2016). Sequence alignment and homology search with BLAST and ClustalW. Cold Spring Harbor Protocols, 2016(11), 1016-1021. https://doi.org/10.1101/pdb.prot093088
Hung, J-H., & Weng, Z. (2016). Visualizing genomic annotations with the UCSC genome browser. Cold Spring Harbor Protocols, 2016(11), 1006-1015. https://doi.org/10.1101/pdb.prot093062
Hung, J-H., & Weng, Z. (2016). Designing polymerase chain reaction primers using Primer3Plus. Cold Spring Harbor Protocols, 2016(9), 821-826. https://doi.org/10.1101/pdb.prot093096
Hung, J-H., & Weng, Z. (2016). Data formats in bioinformatics. Cold Spring Harbor Protocols, 2016(8), 669-671. https://doi.org/10.1101/pdb.top09321
Chang, C. H., Chou, M. T., Wu, Y. C., Hong, T. W., Li, Y. L., Yang, C. H., & Hung, J-H. (2016). SBWT: Memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. Bioinformatics, 32(22), 3498-3500. https://doi.org/10.1093/bioinformatics/btw419
Tung, Y. T., Lu, Y. L., Peng, K. C., Yen, Y. P., Chang, M., Li, J., Jung, H., Thams, S., Huang, Y. P., Hung, J-H., & Chen, J. A. (2015). Mir-17~92 Governs Motor Neuron Subtype Survival by Mediating Nuclear PTEN. Cell Reports, 11(8), 1305-1318. https://doi.org/10.1016/j.celrep.2015.04.050
Li, Y. L., Weng, J. C., Hsiao, C. C., Chou, M. T., Tseng, C. W., & Hung, J-H. (2015). PEAT: An intelligent and efficient paired-end sequencing adapter trimming algorithm. BMC Bioinformatics, 16(1), [S2]. https://doi.org/10.1186/1471-2105-16-S1-S2
Chou, M. T., Han, B. W., Hsiao, C. P., Zamore, P. D., Weng, Z., & Hung, J-H. (2015). Tailor: A computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic acids research, 43(17), [e109]. https://doi.org/10.1093/nar/gkv537
Reimão-Pinto, M. M., Ignatova, V., Burkard, T. R., Hung, J-H., Manzenreither, R. A., Sowemimo, I., Herzog, V. A., Reichholf, B., Fariña-Lopez, S., & Ameres, S. L. (2015). Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Molecular Cell, 59(2), 203-216. https://doi.org/10.1016/j.molcel.2015.05.033
Yildirim, O., Hung, J-H., Cedeno, R. J., Weng, Z., Lengner, C. J., & Rando, O. J. (2014). A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters. PLoS Genetics, 10(8), [e1004515]. https://doi.org/10.1371/journal.pgen.1004515
Carone, B. R., Hung, J-H., Hainer, S. J., Chou, M. T., Carone, D. M., Weng, Z., Fazzio, T. G., & Rando, O. J. (2014).High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Developmental Cell, 30(1), 11-22. https://doi.org/10.1016/j.devcel.2014.05.024
Hung, J-H. (2013). Gene set/pathway enrichment analysis. 於 H. Mamitsuka, M. Kanehisa, & C. DeLisi (編輯), Data Mining for Systems Biology: Methods and Protocols (頁 201-213). (Methods in Molecular Biology; 卷 939). https://doi.org/10.1007/978-1-62703-107-3-13
Chou, C. H., Lin, F. M., Chou, M. T., Hsu, S. H. D., Chang, T. H., Weng, S. L., Shrestha, S., Hsiao, C. C., Hung, J-H., & Huang, H. D. (2013). A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics, 14, [S2]. https://doi.org/10.1186/1471-2164-14-S1-S2
Wang, J., Zhuang, J., Iyer, S., Lin, X. Y., Greven, M. C., Kim, B. H., Moore, J., Pierce, B. G., Dong, X., Virgil, D., Birney, E., Hung, J-H., & Weng, Z. (2013). Factorbook.org: A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic acids research, 41(D1). https://doi.org/10.1093/nar/gks1221
Chen, P. B., Hung, J-H., Hickman, T. L., Coles, A. H., Carey, J. F., Weng, Z., Chu, F., & Fazzio, T. G. (2013). Hdac6 regulates Tip60-p400 function in stem cells. eLife, 2013(2), [e01557]. https://doi.org/10.7554/eLife.01557
Fukunaga, R., Han, B. W., Hung, J-H., Xu, J., Weng, Z., & Zamore, P. D. (2012). Erratum: Dicer partner proteins tune the length of mature miRNAs in flies and mammals (Cell (2012) 151 (533-546)). Cell, 151(4). https://doi.org/10.1016/j.cell.2012.10.029
Fukunaga, R., Han, B. W., Hung, J-H., Xu, J., Weng, Z., & Zamore, P. D. (2012). Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell, 151(3), 533-546. https://doi.org/10.1016/j.cell.2012.09.027
Hung, J-H., Yang, T. H., Hu, Z., Weng, Z., & DeLisi, C. (2012). Gene set enrichment analysis: Performance evaluation and usage guidelines. Briefings in Bioinformatics, 13(3), 281-291. [bbr049]. https://doi.org/10.1093/bib/bbr049
Xie, J., Ameres, S. L., Friedline, R., Hung, J-H., Zhang, Y., Xie, Q., Zhong, L., Su, Q., He, R., Li, M., Li, H., Mu, X., Zhang, H., Broderick, J. A., Kim, J. K., Weng, Z., Flotte, T. R., Zamore, P. D., & Gao, G. (2012). Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods, 9(4), 403-409. https://doi.org/10.1038/nmeth.1903
Shigemizu, D., Hu, Z., Hung, J-H., Huang, C. L., Wang, Y., & DeLisi, C. (2012). Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. PLoS Computational Biology, 8(2), [e1002347]. https://doi.org/10.1371/journal.pcbi.1002347
Hung, J-H., & Chen, S-G. (2011). CYCLIC COMPARISON METHOD FOR LOW-DENSITY PARITY-CHECK DECODER. (專利號 US 7,966,543 B2).
Hung, J-H., & Chen, S-G. (2011). SET-CYCLIC COMPARISON METHOD FOR LOW-DENSITY PARITY-CHECK DECODER.(專利號 US 7,945,839 B2).
Yang, T. H., Kon, M., Hung, J-H., & Delisi, C. (2011). Combinations of newly
confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to
increased disease risk. BMC Medical Genomics, 4, [63].
https://doi.org/10.1186/1755-8794-4-63
Berezikov, E., Robine, N., Samsonova, A., Westholm, J. O., Naqvi, A., Hung,
J-H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y., Zamore,
P. D., Hannon, G. J., Marra, M. A., Weng, Z., Perrimon, N., & Lai, E. C. (2011).
Deep annotation of Drosophila melanogaster microRNAs yields insights into their
processing, modification, and emergence. Genome Research, 21(2), 203-215.
https://doi.org/10.1101/gr.116657.110
Yildirim, O., Li, R., Hung, J-H., Chen, P. B., Dong, X., Ee, L. S., Weng, Z.,
Rando, O. J., & Fazzio, T. G. (2011). Mbd3/NURD complex regulates expression of
5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell, 147(7),
1498-1510. https://doi.org/10.1016/j.cell.2011.11.054
Xie, J., Xie, Q., Zhang, H., Ameres, S. L., Hung, J-H., Su, Q., He, R., Mu, X.,
Seher Ahmed, S., Park, S., Kato, H., Li, C., Mueller, C., Mello, C. C., Weng,
Z., Flotte, T. R., Zamore, P. D., & Gao, G. (2011). MicroRNA-regulated,
systemically delivered rAAV9: A step closer to CNS-restricted transgene
expression. Molecular Therapy, 19(3), 526-535.
https://doi.org/10.1038/mt.2010.279
Ameres, S. L., Horwich, M. D., Hung, J-H., Xu, J., Ghildiyal, M., Weng, Z., &
Zamore, P. D. (2010). Target RNA-directed trimming and tailing of small
silencing RNAs. Science, 328(5985), 1534-1539.
https://doi.org/10.1126/science.1187058
Han, B. W., Hung, J-H., Weng, Z., Zamore, P. D., & Ameres, S.
L. (2011). The
3′-to-5′ exoribonuclease nibbler shapes the 3′ ends of microRNAs bound to
drosophila argonaute1. Current Biology, 21(22), 1878-1887.
https://doi.org/10.1016/j.cub.2011.09.034
Chen, S-G., & Hung, J-H. (2010). 應用於低密度奇偶校驗解碼器之迴旋比較方法. (專利號 I328934).
Hung, J-H., & Chen, S-G. (2010). 應用於低密度奇偶校驗（ＬＤＰＣ）解碼器之集合迴旋比較方法. (專利號 I328933).
Hung, J-H., Whitfield, T. W., Yang, T. H., Hu, Z., Weng, Z., & DeLisi, C.
(2010). Identification of functional modules that correlate with phenotypic
difference: The influence of network topology. Genome Biology, 11(2), [r23].
https://doi.org/10.1186/gb-2010-11-2-r23
Hwang, H., Vreven, T., Pierce, B. G., Hung, J-H., & Weng, Z.
(2010). Performance
of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins: Structure, Function and
Bioinformatics, 78(15), 3104-3110. https://doi.org/10.1002/prot.22764
Ameres, S. L., Horwich, M. D., Hung, J-H., Xu, J., Ghildiyal, M., Weng, Z., &
Zamore, P. D. (2010). Target RNA-directed trimming and tailing of small
silencing RNAs. Science, 328(5985), 1534-1539.
https://doi.org/10.1126/science.1187058
Hu, Z., Hung, J-H., Wang, Y., Chang, Y. C., Huang, C. L., Huyck, M., & Delisi,
C. (2009). VisANT 3.5: Multi-scale network visualization, analysis and inference
based on the gene ontology. Nucleic acids research, 37(SUPPL. 2).
https://doi.org/10.1093/nar/gkp406
Hung, J. H., Hung, J-H., & Chen, S-G. (2008). A systematic optimized comparison
algorithm for LDPC decoder. 於 10th International Conference on Advanced
Communication Technology, ICACT 2008 - Proceedings (頁 1513-1516). [4494066]
(International Conference on Advanced Communication Technology, ICACT; 卷 3).
https://doi.org/10.1109/ICACT.2008.4494066
Lee, T. Y., Huang, H. D., Hung, J-H., Huang, H. Y., Yang, Y-S., & Wang, T. H.
(2006). dbPTM: an information repository of protein post-translational
modification. Nucleic acids research, 34(Database issue), D622-D627.
https://doi.org/10.1093/nar/gkj083
Hung, J-H., Huang, H. D., & Lee, T. Y. (2006). ProKware: Integrated software for
presenting protein structural properties in protein tertiary structures. Nucleic
Acids Research, 34(WEB. SERV. ISS.). https://doi.org/10.1093/nar/gkl235
Book Chapter:
Hung J-H, and Weng Z. Bioinformatics Essentials. Molecular Cloning: A Laboratory Manual, 4th ed. Cold Spring Harbor Laboratory ISBN-10: 1936113422 | ISBN-13: 978-1936113422.
International Conference:
Hung J-H, Hung J-H, and Chen S-G. A General Comparator Structure for LDPC Decoder by Novel Systematic Optimization Algorithms. ICASSP2007
Hung J-H, Wang W-G, and Huang H-D. Systematic Identification of RNA Editing Site in Human Genome. ICS2006
International Patent:
Hung J-H, Hung J-H, and Chen S-G. An Efficient Set-Cyclic Comparison IP for Low Density Parity Check Code. USA. (Patent No.: US 7945839B2)
Hung J-H, Hung J-H, and Chen S-G. An Efficient Cyclic Comparison IP for Low Density Parity Check Codes. USA. (Patent No.: US 7966543B2)
