Education

2006.03-2010.02 Ph. D., Biology Pusan National University, Republic of Korea, (Advisor: Heui-Soo Kim, Ph. D.) 

[Thesis Title: Retroposons and Low Copy Repeats Contribute to the Formation of Alternative Promoter during Primate Evolution]

1999.03-2006.02 B. S.,   Biology Pusan National University, Republic of Korea

Professional Experiences

2022.12-current Senior Researcher, Seoul National University (Advisor: Kwangsoo Kim, Ph. D.)

2022.08-2022.11 Research assistant Professor, Yonsei University 

2016.06-2022.07 Research Professor, Korea University (Advisor: Yoon Ki Kim, Ph. D.)

2012.03-2016.01 Post-doc Associate, Rutgers University (Advisor: Jinchuan Xing, Ph. D.)

2011.03-2012.02 Post-doc Fellow, Medical College of Georgia (current name: Georgia regents University) (Advisor: Dorothy Tuan, Ph. D.)

2010.03-2011.02 Post-doc Fellow, Research Institute for Basic Sciences at PNU

Research Grants, Fellowships

2022 Jun. -2025 May Support project for creative/challenging ₩70,000,000 x 3 years (PI)

2019 Jun. -2022 May. Support project for creative/challenging ₩50,000,000 x 3 years (PI)

2016 Nov. - 2019 Oct. Research Fellowship ₩50,000,000 x 3 years (PI)

2010 Agenda Program “Isolation and characterization of immune-related genes and development of the immunomodulated animal model”, total amount ₩240,000,000 (Co-PI, over 30% of budget) ₩75,000,000

2008 fall - 2009 spring National Graduate S&T Scholarship, ₩12,000,000.

Publications [https://orcid.org/0000-0002-0923-9187]

1. SCI(E)

* Authors contributed equally to this work

1.      Lee DH, Bae WH, Ha H, Kim WR, Park EG, Lee YJ, Kim JM, Shin HJ, Kim HS. The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p. Scientific Reports. 14(1):4723 2024 [IF: 4.6 (JCR 2023)]

2.      Park EG, Lee DH, Kim WR, Lee YJ, Bae WH, Kim JM, Shin HJ, Ha H, Yi JM, Cho SG, Choi YH, Leem SH, Cha HJ, Kim SW, Kim HS. Human Endogenous Retrovirus-H-Derived miR-4454 Inhibits the Expression of DNAJB4 and SASH1 in Non-Muscle-Invasive Bladder Cancer. Genes (Basel). 14(7):1410 2023 [IF: 3.5 (JCR 2022)]

3.      Park EG, Ha H, Lee DH, Kim WR, Lee YJ, Bae WH, Kim HS. Genomic Analyses of Non-coding RNAs Overlapping Transposable Elements and Its Implication to Human diseases. International Journal of Molecular Sciences. 23(16):8950, 2022 [IF: 6.208 (JCR 2021)] (Review)

4.      Boo SH, Ha H, Kim YK. m1A and m6A modifications function cooperatively to facilitate rapid mRNA degradation. Cell Reports. 40(10):111317, 2022 [IF: 9.995 (JCR 2021)]

5.      Lee DH*, Bae WH*, Ha H*, Park EG, Yun Ju Lee YJ, Kim WR, Kim HS. Long Terminal Repeats of HERV Families Containing Z-DNA Provide Alternative Promoter in Human Functional Genes. Molecules and Cells. 45(8):522-530, 2022 [IF: 4.254 (JCR 2021)] (Review)

6.      Boo SH*, Ha H*, Lee Y*, Shin MK, Lee S, Kim YK. UPF1 promotes rapid degradation of m6A-containing RNAs. Cell Reports. 39(8):110861, 2022 [IF: 9.995 (JCR 2021)]

7.      Hwang HJ*, Ha H*, Lee BS, Kim BH, Song HK, Kim YK. LC3B is an RNA-binding protein to promote autophagy. Nature Communications. 13(1):1436, 2022 [IF: 17.694 (JCR 2021)]

8.      Park J*, Chang J*, Hwang HJ, Jeong K; Lee HJ, Ha H; Park Y, Lim C, Woo JS, Kim YK. The pioneer round of translation ensures proper targeting of ER and mitochondrial proteins. Nucleic Acids Research. 49(21):12517-12534, 2021. [IF: 16.971 (JCR 2020)]

9.      Loh JW*, Ha H*, Lin T, Sun N, Burn KH, Xing J. Integrated Mobile element scanning (ME-Scan) method to identify multiple types of polymorphic mobile element insertions. Mobile DNA. 11:12, 2020 [IF: 3.630 (JCR 2019)]

10.   Feusier J, Watkins WS, Thomas J, Farrell A, Witherspoon DJ, Baird L, Ha H, Xing J, Jorde LB. Pedigree-based estimation of human mobile element retrotransposition rates. Genome Research. 29(10):1567-1577, 2019 [Cover article] [IF: 9.944 (JCR 2018)]

11.   Jeong K*, Ryu I*, Park J*, Hwang HJ, Ha H, Park Y, Oh ST, Kim YK. Staufen1 and UPF1 exert opposite actions on the replacement of the nuclear cap-binding complex by eIF4E at the 5' end of mRNAs. Nucleic Acids Research. 47(17):9313-9328, 2019 [recommended in F1000Prime] [IF: 11.147 (JCR 2018)]

12.   Shin JE, Ha H, Kim YK, Cho Y, DiAntonio A. DLK regulates a distinctive transcriptional regeneration program after peripheral nerve injury. Neurobiology of Disease. 127:178-192, 2019 [IF: 5.227 (JCR 2018)].

13.   Park OH*, Ha H*, Lee Y, Boo SH, Kwon DH, Song HK, Kim YK. Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex. Molecular Cell. 74(3):494-507, 2019 [IF: 14.248 (JCR 2018)].

14.   Ryu I*, Won YS*, Ha H, Kim E, Park Y, Kim MK, Kwon DH, Choe J, Song HK, Jung H, Kim YK. eIF4A3 Phosphorylation by CDKs Affects NMD during the Cell Cycle. Cell Reports. 26(8):2126-2139, 2019 [IF: 7.815 (JCR 2018)]

15.   Ryu I, Park Y, Seo JW, Park OH, Ha H, Nam JW, Kim YK. HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions. FASEB Journal. 33(2):2680-2693, 2019 [IF: 5.391 (JCR 2018)]

16.   Shin JE*, Ha H*, Cho EH, Kim YK, Cho Y. Comparative analysis of the transcriptome of injured nerve segments reveals spatiotemporal responses to neural damage in mice. Journal of Comparative Neurology. 526(7):1195-1208, 2018 [IF: 3.400 (JCR 2017)]

17.   Hu T, Pi W, Zhu X, Yu M, Ha H, Shi H, Choi JH, Tuan D. Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function. Nucleic Acids Research. 45(8):4479-4492, 2017. [IF: 10.162 (JCR 2016)]

18.   Ha H, Loh JW, Xing J. Identification of polymorphic SVA retrotransposons using a mobile element scanning method for SVA (ME-Scan-SVA). Mobile DNA. 7:15, 2016 [IF: 2.520 (JCR 2015)]

19.   Bruse S *, Xing J *, Moreau M *, Bromberg Y *, Jang JH, Wang N, Ha H, Picchi M, Lin Y, Langley R, Qualls C, Klensney-Tait J, Zabner J, Mao J, Belinsky S, Nyunoya T. Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility. Human genomics. 10:1, 2016 [IF: 1.598 (JCR 2015)]

20.   Parrish NF-*, Fujino K*, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa I, Nakano T, Siomi H, Honda T, Tomonaga K. piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals. RNA. 21(10):1691-1703, 2015 [IF: 4.940 (JCR 2014)]

21.   Gim JA, Hong CP, Kim DS, Moon JW, Choi Y, Eo J, Kwon YJ, Lee JR, Jung YD, Bae JH, Choi BH, Ko J, Song S, Ahn K, Ha HS, Yang YM, Lee HK, Park KD, Do KT, Han K, Yi JM, Cha HJ, Ayarpadikannan S, Cho BW, Bhak J, Kim HS. Genome-Wide Analysis of DNA Methylation before and after Exercise in the Thoroughbred Horse with MeDIP-Seq. Molecules and Cells. 38(3):210-220, 2015 [IF: 2.090 (JCR 2014)]

22.   Song J, Liu J, Schankenberg S, Ha H, Xing J, Chen KC. Variation in piRNA and transposable element content in strains of Drosophila melanogaster. Genome Biology and Evolution. 6(10):2786-27798, 2014 [IF: 4.532 (JCR 2013)]

23.   Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K,Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS. Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics. 15(1):598, 2014 [IF: 4.041 (JCR 2013)]

24.   Ha H*, Song J*, Wang S, Kapusta A, Feschotte C, Chen KC, Xing J. A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. BMC Genomics. 15(1):545, 2014 [IF: 4.041 (JCR 2013)]

25.   Jung YD, Lee JR, Kim YJ, Ha HS, Oh KB, Im GS, Choi BH, Kim HS. Promoter activity analysis and methylation characterization of LTR elements of PERVs in NIH miniature pig. Genes & Genetic Systems. 88(2):135-142, 2013 [IF: 1.132 (JCR 2012)]

26.   Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Research. 23(7):1170-1181, 2013 [IF: 14.397 (JCR 2012)]

27.   Jung YD, Ha HS, Park SJ, Oh KB, Im GS, Kim TH, Seong HH, Kim HS. Identification and promoter analysis of PERV LTR subtypes in NIH-Miniature pig. Molecules and Cells. 35(2):99-105, 2013 [IF: 2.210 (JCR 2012)]

28.   Ahn K, Gim JA, Ha HS, Han K, Kim HS. The novel MER transposon-derived miRNAs in human genome. Gene. 512(2):422-428, 2013 [IF: 2.196 (JCR 2012)]

29.   Ha HS*, Moon JW*, Gim JA, Jung YD, Ahn K, Oh KB, Kim TH, Seong HH, and Kim HS. Identification and characterization of transposable element chimeric transcripts from porcine Refseq and EST database. Genes & Genomics. 34(4):409-414, 2012 [IF: 0.442 (JCR 2011)]

30.   Ha HS*, Lee YC*, Park SJ, Jung YD, Ahn K, Moon JW, Han K, Oh KB, Kim TH, Seong HH, and Kim HS. In vitro CpG methylation and garcinol reduce PERV LTR promoter activity. Genes & Genomics. 34(2):217-222, 2012 [IF: 0.442 (JCR 2011)]

31.   Ha HS*, Chung WK*, Ahn K, Bae JH, Park SJ, Moon JW, Nam KH, Han K, Cho HG, Kim HS. Development of GEBRET: a web-based analysis tool for retroelements in primate genomes. Genes & Genomics. 33(6):679-684, 2011 [IF: 0.453 (JCR 2010)]

32.   Jung YD, Huh JW, Kim DS, Kim YJ, Ahn K, Ha HS, Lee JR, Yi JM, Moon JW, Kim TO, Song GA, Han K, Kim HS. Quantitative analysis of transcript variants of CHM gene containing LTR12C element in humans. Gene. 489(1):1-5, 2011 [IF: 2.67 (JCR 2010)]

33.   Ha HS, Huh JW, Han K and Kim HS. Transcriptional variations mediated by an alternative promoter of the FPR3 gene. Mammalian Genome. 22:621-633, 2011 [IF: 2.771 (JCR 2010)]

34.   Park SJ, Huh JW, Kim DS, Ha HS, Jung YD, Ahn K, Oh KB, Park EW, Chang KT, Kim HS. Analysis of the molecular and regulatory properties of active porcin endogenous retrovirus gamma-1 long terminal repeats in kidney tissues of the NIH-miniature pig. Molecules and Cells. 30:319-325, 2010 [IF: 1.878 (JCR 2009)]

35.   Ahn K, Huh JW, Kim DS, Ha HS, Kim YJ, Lee JR, Kim HS. Quantitative analysis of alternative transcripts of human PCDH11X/Y genes. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics. 153B(3):736-744, 2010 [IF: 3.481 (JCR 2009)]

36.   Huh JW, Kim DS, Noh YN, Park SJ, Ha HS, Kim CG, Lee YH, Kang CK, Chang KT, Kim HS. Dynamic evolution of tRNAThr-Derived HpaI SINEs and effect on genomes of oncorhynchus species. Genes & Genomics. 31(3):217-226, 2009 [IF: 0.148 (JCR 2009)]

37.   Lee JR, Huh JW, Kim DS, Ha HS, Ahn K, Kim YJ, Chang KT, Kim HS. Lineage specific evolutionary events on SFTPB gene: Alu recombination-mediated deletion (ARMD), exonization, and alternative splicing events. Gene. 435(1-2):29-35, 2009 [IF: 2.578 (JCR 2008)]

38.   Kim YJ, Huh JW, Kim DS, Bae MI, Lee JR, Ha HS, Ahn K, Kim TO, Song GA, Kim HS. Molecular characterization of the DYX1C1 gene and its application as a cancer biomarker. Journal of Cancer Research and Clinical Oncology. 135(2):265-270, 2009 [IF: 2.217 (JCR 2008)]

39.   Huh JW, Kim DS, Ha HS, Ahn K, Chang KT, Cho BW, Kim HS. Identification and molecular characterization of PERV gamma1 long terminal repeats. Molecules and Cells. 27(1):119-123, 2009 [IF: 2.023 (JCR 2008)]

40.   Huh JW, Kim DS, Ha HS, Lee JR, Kim YJ, Ahn K, Lee SR, Chang KT, Kim HS. Cooperative exonization of MaLR and AluJo elements contributed an alternative promoter and novel splice variants of RNF19. Gene. 424(1-2):63-70, 2008 [IF: 2.871 (JCR 2008)]

41.   Ahn K, Huh JW, Park SJ, Kim DS, Ha HS, Kim YJ, Lee JR, Chang KT, Kim HS. Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues. BMC Molecular Biology. 9:78 2008 [IF: 3.371 (JCR 2007)]

42.   Huh JW*, Ha HS*, Kim DS, Kim HS. Placenta-restricted expression of LTR-derived NOS3. Placenta. 29(7):602-608, 2008 [IF: 3.238 (JCR 2007)]

43.   Huh JW, Kim DS, Kang DW, Ha HS, Ahn K, Noh YN, Min DS, Chang KT, Kim HS. Transcriptional regulation of GSDML gene by antisense-oriented HERV-H LTR element. Archives of Virology. 153(6):1201-1205, 2008 [IF: 1.850 (JCR 2006)]

44.   Huh JW, Cho BW, Kim DS, Ha HS, Noh YN, Yi JM, Lee WH, Kim HS. Long terminal repeats of porcine endogenous retroviruses in Sus scrofa. Archives of Virology. 152(12):2271-2276, 2007 [IF: 1.839 (JCR 2007)]

45.   Ha HS*, Huh JW*, Kim DS, Kang DW, Cho BW, Kim HS. Promoter activity of the long terminal repeats of porcine endogenous retroviruses of the Korean domestic pig. Molecules and Cells. 24(1):148-151, 2007 [IF: 1.872 (JCR 2006)]

46.   Huh JW*, Ha HS*, Kim DS, Cho BW, Kim HS. Transient transfection analysis of long terminal repeats of porcine endogenous retroviruses in sus scrofa coreanus. Korean Journal of Genetics. 29(3):403-407, 2007 ⊙

47.   Sin HS, Huh JW, Kim WY, Kim DS Ahn, K, Ha HS, Kim HS. Long terminal repeats of human endogenous retrovirus H family provide alternative polyadenylation signals to NADSYN1 Gene. Korean Journal of Genetics. 29(3):395-401, 2007 ⊙

48.   Huh JW*, Ha HS*, Kim YJ, Lee JR, Kim DS, Cho BW, Kim HS. Methylation and promoter activity of long terminal repeats from porcine endogenous retroviruses in the pig, sus scrofa. Korean Journal of Genetics. 29(2):171-176, 2007 ⊙

49.   Huh JW, Kim DS, Ha HS, Kim TH, Kim W, Kim HS. Formation of a new solo-LTR of the human endogenous retrovirus H family in human chromosome 21. Molecules and Cells. 22(3):360-363, 2006 [IF: 1.677 (JCR 2005)]

50.   Sin HS, Huh JW, Kim DS, Kang DW, Min DS, Kim TH, Ha HS, Kim HH, Lee SY, Kim HS. Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells. Archives of Virology. 151(10):1985-1994, 2006 [IF: 1.819 (JCR 2005)]

51.   Sin HS, Huh JW, Kim DS, Kim TH, Ha HS, Kim WY, Park HK, Kim CM, Kim HS. Endogenous retrovirus-related sequences provide an alternative transcript of MCJ genes in human tissues and cancer cells. Genes & Genetic Systems. 81(5):333-339, 2006 [IF: 1.677 (JCR 2005)]

⊙ Korean Journal of Genetics(~2007)→ genes & genomics(2008~)

3. Book Chapter International

• Ha H, Wang N, Xing J. Library Construction for High-Throughput Mobile Element Identification and Genotyping. Methods in Molecular Biology. 1589:1-15, 2015

2. Non-SCIE International

• Gim JA*, Ha HS*, Ahn K*, Kim DS, Kim HS. Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements. 

Genomics & Informatics. 12(4):261-267, 2014

3. Domestic [in Korean]

1.   Ha HS, Huh JW, Kim DS, Park SJ, Bae JH, Ahn K, Yun SE, Kim HS. 배아줄기세포에서 트랜스 스플라이싱 전사체의 분석 (Analysis of Trans-splicing Transcripts in Embryonic Stem Cell). 생명과학회지. 19(4): 549-552. 2009 [KCI 등재]

2.   Huh JW, Kim WY, Kim DS, Ha HS, Lee JR, Choi OH, Nam KM, Bae HJ, Choi J, Kim HS. 47,XXY와 46,XY 핵형을 가진 한국인 불임남성의 Y 염색체의 미세결실에 대한 비교 분석 (Comparative analysis of Y chromosomal microdeletions in Korean infertile men of 47,XXY and 46,XY karyotypes). 생명과학회지. 17(6):741-747. 2007 [KCI 등재]

3.  Huh JW, Kim WY, Kim DS, Ha HS, Park NC, Choi OH, Nam KM, Choi J, Kim HS. 한국 불임남성에 있어서 RBMY1, CDY1 그리고 VCY2 유전자의 발현 분석 (Expression analysis of RBMY1, CDY1, and VCY2 genes in Korean male infertility). 생명과학회지. 7(5):613-618. 2007 [KCI 등재]

4.   Kim DS, Huh JW, Ha HS, Kim TH, Jo UJ, Kim HS. 치매환자에서 transposable elements에 의한 유전자 발현조절의 생물정보 분석 (Bioinformatics analysis of gene expression regulation by transposable elements in dementia patient). 생명과학회지. 16(7):1188-1194. 2006 [KCI 등재]