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Jui-hung Hung, Ph.D. - Publications

Affiliations: 
2011 Boston University, Boston, MA, United States 
Area:
Bioinformatics Biology, Biomedical Engineering, Systematic Biology
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 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. locus-derived LncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. Elife. 7. PMID 30311912 DOI: 10.7554/Elife.38080  0.32
2016 Hung JH, Weng Z. Mapping Short Sequence Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574204 DOI: 10.1101/Pdb.Prot093161  0.544
2016 Hung JH, Weng Z. Mapping Billions of Short Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574203 DOI: 10.1101/Pdb.Top093153  0.521
2016 Hung JH, Weng Z. Designing Polymerase Chain Reaction Primers Using Primer3Plus. Cold Spring Harbor Protocols. 2016: pdb.prot093096. PMID 27574202 DOI: 10.1101/Pdb.Prot093096  0.457
2016 Hung JH, Weng Z. Analyzing Microarray Data. Cold Spring Harbor Protocols. PMID 27574201 DOI: 10.1101/Pdb.Prot093112  0.535
2016 Hung JH, Weng Z. Sequence Alignment and Homology Search. Cold Spring Harbor Protocols. PMID 27574200 DOI: 10.1101/Pdb.Top093070  0.583
2016 Hung JH, Weng Z. Discovering cis-Regulatory Motifs. Cold Spring Harbor Protocols. PMID 27574199 DOI: 10.1101/Pdb.Prot093203  0.511
2016 Hung JH, Weng Z. Visualizing Genomic Annotations with the UCSC Genome Browser. Cold Spring Harbor Protocols. PMID 27574198 DOI: 10.1101/Pdb.Prot093062  0.56
2016 Hung JH, Weng Z. Sequence Alignment and Homology Search with BLAST and ClustalW. Cold Spring Harbor Protocols. PMID 27574197 DOI: 10.1101/Pdb.Prot093088  0.505
2016 Hung JH, Weng Z. Peak-Finding Algorithms. Cold Spring Harbor Protocols. PMID 27574196 DOI: 10.1101/Pdb.Top093179  0.545
2016 Hung JH, Weng Z. Motif Finding. Cold Spring Harbor Protocols. PMID 27574195 DOI: 10.1101/pdb.top093195  0.446
2016 Hung JH, Weng Z. Analysis of Microarray and RNA-seq Expression Profiling Data. Cold Spring Harbor Protocols. PMID 27574194 DOI: 10.1101/Pdb.Top093104  0.563
2016 Hung JH, Weng Z. Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding). Cold Spring Harbor Protocols. PMID 27574193 DOI: 10.1101/Pdb.Prot093187  0.504
2016 Hung JH, Weng Z. Data Formats in Bioinformatics. Cold Spring Harbor Protocols. 2016: pdb.top093211. PMID 27480726 DOI: 10.1101/Pdb.Top093211  0.474
2016 Chang CH, Chou MT, Wu YC, Hong TW, Li YL, Yang CH, Hung JH. sBWT: Memory Efficient Implementation of the Hardware-acceleration-friendly Schindler Transform for the Fast Biological Sequence Mapping. Bioinformatics (Oxford, England). PMID 27412087 DOI: 10.1093/Bioinformatics/Btw419  0.322
2015 Reimão-Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Fariña-Lopez S, Ameres SL. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Molecular Cell. 59: 203-16. PMID 26145176 DOI: 10.1016/J.Molcel.2015.05.033  0.306
2015 Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Research. PMID 26007652 DOI: 10.1093/Nar/Gkv537  0.512
2014 Yildirim O, Hung JH, Cedeno RJ, Weng Z, Lengner CJ, Rando OJ. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. Plos Genetics. 10: e1004515. PMID 25102063 DOI: 10.1371/Journal.Pgen.1004515  0.515
2014 Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Developmental Cell. 30: 11-22. PMID 24998598 DOI: 10.1016/J.Devcel.2014.05.024  0.542
2013 Chen PB, Hung JH, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Hdac6 regulates Tip60-p400 function in stem cells. Elife. 2: e01557. PMID 24302573 DOI: 10.7554/Elife.01557  0.505
2013 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Research. 41: D171-6. PMID 23203885 DOI: 10.1093/Nar/Gks1221  0.528
2013 Wu-Chou YH, Chen YT, Yeh TH, Chang HC, Weng YH, Lai SC, Huang CL, Chen RS, Huang YZ, Chen CC, Hung J, Chuang WL, Lin WY, Chen CH, Lu CS. Genetic variants of SNCA and LRRK2 genes are associated with sporadic PD susceptibility: a replication study in a Taiwanese cohort. Parkinsonism & Related Disorders. 19: 251-5. PMID 23182315 DOI: 10.1016/j.parkreldis.2012.10.019  0.695
2013 Chen PB, Hung J, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Author response: Hdac6 regulates Tip60-p400 function in stem cells Elife. DOI: 10.7554/Elife.01557.035  0.458
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell. 151: 912. PMID 30360291 DOI: 10.1016/J.Cell.2012.10.029  0.401
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 151: 533-46. PMID 23063653 DOI: 10.1016/J.Cell.2012.09.027  0.428
2012 Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, et al. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods. 9: 403-9. PMID 22388288 DOI: 10.1038/Nmeth.1903  0.479
2012 Shigemizu D, Hu Z, Hung JH, Huang CL, Wang Y, DeLisi C. Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. Plos Computational Biology. 8: e1002347. PMID 22346740 DOI: 10.1371/Journal.Pcbi.1002347  0.71
2012 Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Briefings in Bioinformatics. 13: 281-91. PMID 21900207 DOI: 10.1093/Bib/Bbr049  0.718
2011 Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 147: 1498-510. PMID 22196727 DOI: 10.1016/J.Cell.2011.11.054  0.538
2011 Han BW, Hung JH, Weng Z, Zamore PD, Ameres SL. The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Current Biology : Cb. 21: 1878-87. PMID 22055293 DOI: 10.1016/J.Cub.2011.09.034  0.492
2011 Yang TH, Kon M, Hung JH, Delisi C. Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk. Bmc Medical Genomics. 4: 63. PMID 21827660 DOI: 10.1186/1755-8794-4-63  0.713
2011 Xie J, Xie Q, Zhang H, Ameres SL, Hung JH, Su Q, He R, Mu X, Seher Ahmed S, Park S, Kato H, Li C, Mueller C, Mello CC, Weng Z, et al. MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Molecular Therapy : the Journal of the American Society of Gene Therapy. 19: 526-35. PMID 21179009 DOI: 10.1038/Mt.2010.279  0.519
2011 Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research. 21: 203-15. PMID 21177969 DOI: 10.1101/Gr.116657.110  0.507
2011 Ameres SL, Hung JH, Xu J, Weng Z, Zamore PD. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. Rna (New York, N.Y.). 17: 54-63. PMID 21106652 DOI: 10.1261/Rna.2498411  0.486
2010 Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19 Proteins: Structure, Function and Bioinformatics. 78: 3104-3110. PMID 20936681 DOI: 10.1002/Prot.22764  0.468
2010 Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng Z, Zamore PD. Target RNA-directed trimming and tailing of small silencing RNAs. Science (New York, N.Y.). 328: 1534-9. PMID 20558712 DOI: 10.1126/Science.1187058  0.489
2010 Hung JH, 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. PMID 20187943 DOI: 10.1186/Gb-2010-11-2-R23  0.727
2009 Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, Delisi C. VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology Nucleic Acids Research. 37. PMID 19465394 DOI: 10.1093/Nar/Gkp406  0.751
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