Publications

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:

Yen YP, Hsieh WF, Tsai YY, Lu YL, Liau ES, Hsu HC, Chen YC, Liu TC, Chang M, Li J, Lin SP, Hung JH, Chen JA, Jun-An Chen. Dlk1-Dio3 locus-derived LncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. eLife 2018;7:e38080
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
Chang C.-H., Chou M.-T., Wu Y.-C., Hong T-.W., Li Y.-L., Yang C.-H.,and Hung J.-H. sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. Bioinformatics. July 2016
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.
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..Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Molecular Cell. Volume 59, Issue 2, Pages 203–216, 2015.
Tung Y.-T., Lu Y.-L., Peng K.-C., Yen Y.-P., Chang M., Li J., H. Jung, Thams S., Y.-P. Huang, Hung J.-H., and Chen J.-A.Mir-17~92 Governs Motor Neuron Subtype Survival by Mediating Nuclear PTEN.Cell Reports. Volume: 11 Pages:1–14. 2015
Li, Y.-L., Weng J.-C., Hsiao C.-C., Chou M.-T., Tseng C.-W. and Hung J.-H.PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. BMC Bioinformatics, 16:S2, 2015
Carone RB., Hung J-H, Sarah J. Hainer, Min-Te Chou, Dawn M. Carone, Zhiping Weng, Thomas G. Fazzio, Oliver J. Rando.High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm. Developmental Cell Vol: 30(1), 2014
Yildirim O., Hung J-H, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, Oliver J. Rando. A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters. PLoS Genetics, 10.1371, Aug. 2014
Chen PB, Hung J-H, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Hdac6 regulates Tip60-p400 function in stem cells. eLIFE, December 3, 2013
Chih-Hung Chou, Feng-Mao Lin, Min-Te Chou, Sheng-Da Hsu, Tzu-Hao Chang,Shun-Long Weng, Sirjana Shrestha, Chiung-Chih Hsiao, Hung J-H and Hsien-Da Huang. A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics, 14:S2, 2013. (Co-corresponding author)
Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moor, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Hung J-H and Zhiping Weng. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Research. 41(D1):D171-D176, 2013.
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
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
Shigemizu D , Hu Z , Hung J-H , Huang C-L , Wang Y , et al. Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer. PLoS Comput Biol 8(2): e1002347. doi:10.1371/journal.pcbi.1002347
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
Han B, Hung J-H, Weng Z, Zamore PD, Ameres SL. The 3’-to-5’ Exoribonuclease Nibbler Shapes the 3’ Ends of MicroRNAs Bound to Drosophila Argonaute1. Current Biology, November 2011.
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.
Yang T-H, Kon M, Hung J-H, DeLisi C. Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk. BMC Medical Genomics 2011, 4:63
Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung J-H, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster micro RNAs yields insights into their processing, modification, and emergence. Genome Res., 2011; Feb; 21(2):203-15
Ameres SL, Hung J-H, Xu J, Weng Z, Zamore PD. Target RNA-directed Tailing and Trimming purifies the sorting of endo-siRNA between the two Drosophila argonaute proteins. RNA. 2011; 17(1):54-63.
Xie J, Xie Q, Zhang H, Ameres SL, Hung J-H, Su Q, He R, Mu X, Seher Ahmed S, Park S, Kato H, Li C, Mueller C, Mello CC, Weng Z, Flotte TR, Zamore PD, Gao G. MicroRNA-regulated, Systemically Delivered rAAV9: A Step Closer to CNS-restricted Transgene Expression. Mol Ther (PMID: 21179009)
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. 320:1534-1539, 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
Hwang H, Vreven T, Pierce B, Hung J-H, Weng Z. Performance of ZDOCK and ZRANK in CAPRI round 13-19. Protein. 78(15):3104-10
Hu Z., Hung J-H, Chang Y-C, Huang C-L, Huyck M. and DeLisi C. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Research. 37: W115-W121, 2009
Hung J-H, Hung J-H, and Chen S-G. A systematic Optimized Comparison Algorithm for Fast LDPC Decoding. ICACT 10th. Vol. 3, pp. 1513-1526. 2008.
Hung J-H, Huang H-D, and Lee T-Y. ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Research. 34: W89-W94, 2006.
Lee T-Y, Huang H-D, Hung J-H, Yang Y-S, and Wang T-H. dbPTM: An Information Repository of Protein Post-Translational Modification. Nucleic Acids Research. 34: D622-D627. 2006.

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)