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last update: Feb. 22. 2024


in reverse chronological order

[first-author (*) and corresponding author (#) papers from the lab. Lab members are shown in bold]
[Publications colored in yellow: projects started when PI was a trainee]  


88. Youk J*, Kwon HW*, Lim J*, Kim E*, Kim T*, …, Chang JH#, Kim KS#, Son TG#, Ju YS#. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. Cell Genomics. 2024 Feb 14;4(2):100499. PMID:38359788  

87. Lee SE, Park S, Yi S, Choi NR, Lim MA, ..., Kang YE. Unraveling the role of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer by multi-omics analyses. Nature Communications. 2024 Feb 8;15(1):1163. PMID:38331894


86. Kim YJ, Park HS, Youk J, Han JW, Byeon SH, ..., Lee CS. Subset of retinoblastoma tumours is associated with BRCA1/2 mutations. Br J Ophthalmol. 2023 Oct 13:bjo-2023-323388. PMID:37833038


85. Bruzos AL, Santamarina M, García-Souto D, Díaz S, Rocha S, …, Tubio JMC. Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma eduleNature Cancer. 2023 Nov;4(11):1575-1591. PMID:37783803

84. Cho S, Park S, Lee JS, Ju YS, Choi YJ, Lee S. Adenosine Deaminase 2 Deficiency Caused by Biallele Variants Including Splicing Variant: The First Case in Korea. J Rheum Dis. 2022 Oct 1;29(4):254-260. PMID:37476427

83. Nam CH*, Youk J*, Kim JY, Lim J, Park JW, ..., Kwon HW#, Kim MJ#, Ju YS#. Widespread somatic L1 retrotransposition in normal colorectal epithelium. Nature. 2023 May; 617(7961):540-547. PMID:37165195

82. Jikuya R, Johnson TA, Maejima K, An J, Ju YS, ..., Hasumi H. Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma. EBioMedicine. 2023 Jun;92:104596. PMID:37182269 

81. Hong Y, Kim HJ, Park S, Yi S, Lim MA, ..., Kang YE. Single Cell Analysis of Human Thyroid Reveals the Transcriptional Signatures of Aging. Endocrinology. 2023 Feb 11;164(4):bqad029. PMID:36791033

80. Kim JH, Park JH, Lee J, Park JW, Kim HJ, ..., Lee JH. Ultra-Low Level Somatic Mutations and Structural Variations in Focal Cortical Dysplasia Type II. Ann Neurol. 2023 Jun;93(6):1082-1093. PMID:36700525

79. Yoon C*, Kim S, Nam CH, Lee JH, Park JW, …, Griffith OL#, Ju YS#. Estimation of intrafamilial DNA contamination in family trio genome sequencing using Mendelian inconsistencies. Genome Res. 2022 Dec; 32(11-12):2134-2144. PMID:36617634

78. Kim T*, Min KI*, Yang J, Kim JW, Cho J, …, Na KJ#, Lee J-Y#, Ju YS#. Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells. iScience. 2022 Dec;25(12):105571. PMID:36406862

77. Sohn JI, Choi MH, Yi D, Menon VA, Kim YJ, …, Nam JW. Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets. Nat Biomed Eng. 2022 Dec 19. Online ahead of print. PMID:36536253

76. Lomakin A, Svedlund J, Strell C, Gataric M, Shmatko A, …, Yates LR. Spatial genomics maps the structure, nature and evolution of cancer clones. Nature. 2022 Nov;611(7936):594-602. Epub 2022 Nov 9. PMID:36352222

75. Park CS, Kim SH, Yang HY, Kim JH, Schermuly RT, …, Kim I. Sox17 Deficiency Promotes Pulmonary Arterial Hypertension via HGF/c-Met Signaling. Circ Res. 2022 Oct 28;131(10):792-806. PMID:36205124 

74. Johnson TA, Maekawa S, Fujita M, An J, Ju YS, …, Nakagawa H. Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis. Hum Mol Genet. 2022 Aug 18:ddac180. Online ahead of print. PMID:35981075

73. Kim IB, Lee T, Lee J, Kim J, Lee S, ..., Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry. 2022 Nov;27(11):4680-4694. PMID:35840799

72. Jeong D, Kim SM, Min BJ, Kim JH, Ju YS, …, Lee DS. Heterogeneous genetic landscape of congenital neutropenia in Korean patients revealed by whole exome sequencing: genetic, phenotypic and histologic correlations. Sci Rep. 2022 May 7;12(1):7515. PMID:35525891

71. Lee JH, Kim S, Han S, Min J, Caldwell B, …, Kim JK. p57Kip2 imposes the reserve stem cell state of gastric chief cells. Cell Stem Cell. 2022 May 5;29(5):826-839.e9. PMID:35523142

70. Seo J, Kim H, Min KI, Kim C, Kwon Y, …, Kim J. Weight-bearing activity impairs nuclear membrane and genome integrity via YAP activation in plantar melanoma. Nat Commun. 2022 Apr 25;13(1):2214. PMID:35468978

69. Kwon SG, Bae GH, Choi JH, Mali NM, Jun MS, …, Oh JW. Asymmetric Contribution of Blastomere Lineages of First Division of the Zygote to Entire Human Body Using Post-Zygotic Variants. Tissue Eng Regen Med. 2022 Aug;19(4):809-821. PMID:35438457

68. Cho YW, Min DW, Kim HP, An Y, Kim S, …, Kim TY. Patient-derived organoids as a preclinical platform for precision medicine in colorectal cancer. Mol Oncol. 2022 Jun;16(12):2396-2412. PMID:34850547

67. (Review) Youk J*, Kwon HW*, Kim R, Ju YS#. Cdissecting single-cell genomes through the clonal organoid technique. Exp Mol Med. 2021 Oct;53(10):1503-1511. PMID:34663940

66. Song U, Ryu YH, Hong K, Shim SY, Park S, …, Lee S. Severe protein C deficiency in a newborn caused by a homozygous pathogenic variant in the PROC gene: a case report. BMC Pediatr. 2021 Oct 16;21(1):453. PMID:34654403

65. Yi K*, Kim SY, Bleazard T, Kim T, Youk J, Ju YS#. Mutational spectrum on SARS-CoV-2 during the global pandemic. Exp Mol Med. 2021 Aug;53(8):1229-1237.  Epub 2021 Aug 27. PMID:34453107

64. Park S*, Mali NM, Kim R*, Choi J-W, Lee J, …, Oh JW#, Ju YS#. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 2021 Aug 25. Online ahead of print. PMID:34433967

63. Lee JS, Koh JY, Yi K*, Kim YI, Park SJ, …, Park SH. Single-cell transcriptome of bronchoalveolar lavage fluid reveals sequential change of macrophages during SARS-CoV-2 infection in ferrets. Nat Commun 2021 Jul 27;12(1):4567. PMID:34315893

62. Park HR, Kim TM, Lee Y, Kim S, Park S, …, Heo DS. Acquired resistance to third-generation EGFR tyrosine kinase inhibitors in patients with de novo EGFRT790M-mutant non-small cell lung cancer. J Thorac Oncol. 2021 Jul 6:S1556-0864(21)02254-1. Online ahead of print. PMID:34242789

61. (mini review) Kim T*, Lee JS, Ju YS#. Experimental Models for SARS-CoV-2 Infection. Mol Cells. 2021 Jun 30;44(6):377-383. PMID:34187969

60. Ahn JH, Kim J, Hong SP, Choi SY, Yang MJ, …, Koh GY. Nasal ciliated cells are primary targets for SARS-CoV-2 replication in the early stage of COVID-19. J Clin Invest. 2021 Jul 1;131(13):e148517. PMID:34003804

59. (spotlight) Ju YS#. A large-scale snapshot of intratumor heterogeneity in human cancer. Cancer Cell. 2021 Apr 12;39(4):463-465. PMID:33848477

58. Park S, Lee HY, Kim J, Park H, Ju YS, Kim EG, Kim J. Cerebral Cavernous Malformation 1 Determines YAP/TAZ Signaling-Dependent Metastatic Hallmarks of Prostate Cancer Cells. Cancers (Basel). 2021 Mar 5;13(5):1125. PMID:33807895

57. Park JH, Kim HJ, Kim CW, Kim HC, Jung Y, …, Lee HK. Tumor hypoxia represses γδ T cell-mediated antitumor immunity against brain tumors. Nat Immunol. 2021 Mar;22(3):336-346. PMID:33574616

56. Kim HD, Jeong S, Park S, Lee YJ, Ju YS, …, Park SH. Implication of CD69+ CD103+ tissue-resident-like CD8+ T cells as a potential immunotherapeutic target for cholangiocarcinoma. Liver Int. 2021 Apr;41(4):764-776. PMID:33548061

55. Leem G, Park J, Jeon M, Kim ES, Kim SW, …, Park SH. 4-1BB co-stimulation further enhances anti-PD-1-mediated reinvigoration of exhausted CD39+ CD8 T cells from primary and metastatic sites of epithelial ovarian cancers. J Immunother Cancer. 2020 Dec;8(2):e001650. PMID:33335029

54. Bae K, Kim JH, Jung H, Kong SY, Kim YH, …, Yoon KA. A fusion of CD63-BCAR4 identified in lung adenocarcinoma promotes tumorigenicity and metastasis. Br J Cancer. 2021 Jan;124(1):290-298. PMID:33204025

53. Youk J*, Kim T*, Evans KV, Jeong Y-I, Hur Y, Hong SP, ..., Kim YT#, Koh GY#, Choi B-S#, Ju YS#, Lee JH#. Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2. Cell Stem Cell. 2020 Dec 3;27(6):905-919.e10. PMID:33142113


52. Lee JS, Yi K*, Ju YS, Shin EC. Effects of Cryopreservation and Thawing on Single-Cell Transcriptomes of Human T Cells. Immune Netw. 2020 Jul 15;20(4):e34. PMID: 32895621

51. Youk J*, An Y, Park S, Lee JK & Ju YS#. The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population. BMC Genomics. 2020 Mar 30;21(1):270. PMID: 32228436

50. Yang JM, Park CS, Kim SH, Noh TW, Kim JH, Park S, ..., Ju YS & Kim I. Dll4 Suppresses Transcytosis for Arterial Blood-Retinal Barrier Homeostasis. Circ Res. 2020 Mar 13;126(6):767-783. PMID:32078435

49. Yuan Y, Ju YS*, Kim Y, Li J, Wang Y, Yoon CJ, ..., Liang H & PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2020 Feb 05. (Epub ahead of print). PMID:32024997

48. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, ..., Tubio JMC & PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 Feb 05. (Epub ahead of print). PMID:32024998

47. (conference paper) Poirier JT, George J, Owonikoko TK, Berns A, Brambilla E, ... & Oliver TG. New approaches to small cell lung cancer therapy : from the laboratory to the clinic. J Thorac Oncol. 2020 Feb 01. (Epub ahead of print). PMID:32018053

46. Lee JS*, An Y*, Yoon CJ*, Kim JY, Kim KH, ..., Lee EY# & Ju YS#. Germline gain-of-function mutation of STAT1 rescued by somatic mosaicism in immune dysregulation-polyendocrinopathy-enteropathy-X-linked-like disorder. J Allergy Clin Immunol. 2019 Dec 02. (Epub ahead of print). PMID:31805313

45. Kim HD, Park S, Jeong S, Lee YJ, Lee H, ..., & Park SH. 4-1BB Delineates Distinct Activation Status of Exhausted Tumor-Infiltrating CD8+ T Cells in Hepatocellular Carcinoma. Hepatology. 2019 Jul 28. (Epub ahead of print) PMID:31353502

44. Lee JJ-K*, Park S*, Park H, Kim S, Lee J, ... , Ju YS# & Kim YT. Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma. Cell. 2019 Jun 13;177(7):1842-1857 PMID:31155235

43. Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, … , & Stratton MR. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis. Cell. 2019 Mar 7;176(6):1282-1294 PMID:30849372.

42. Park ES, Lee AR, Kim DH, Lee JH, Yoo JJ, …. & Kim KH. Identification of a quadruple mutation that confers tenofovir resistance in chronic hepatitis B patients. J Hepatol. 2019 Jun;70(6):1093-1102. PMID:30794889.

41. Choi W, Namkung J, Hwang I, Kim H, Lim A, ..., & Kim H. Serotonin signals through a gut-liver axis to regulate hepatic steatosis. Nat Commun. 2018 Nov 16;9(1):4824. PMID: 30446669

40. Kim HD, Song GW, Park S, Jung MK, Kim MH, ..., & Park SH. Association Between Expression Level of PD1 by Tumor-Infiltrating CD8+ T Cells and Features of Hepatocellular Carcinoma. Gastroenterology. 2018 Dec;155(6):1936-1950.e17. PMID:30145359

39. (review) Yi K*, Ju YS#. Patterns and mechanisms of structural variations in human cancer. Exp Mol Med. 2018 Aug 7;50(8):98. PMID:30089796

38. Lee JH, Lee JE, Kahng JY, Kim SH, Park JS, ..., & Lee JH. Human glioblastoma arises from subventricular zone cells with lower-level driver mutations. Nature. 2018 Aug;560(7717):243-247. PMID:30069053 

37. Lee J, Lee AJ, Lee JK*, Park J, Kwon Y, Park S, Chun H, Ju YS# & Hong D#. MUTALISK: a web-based somatic MUTation AnaLysIS toolKit for genomic, transcriptional and epigenomic signatures. Nucleic Acids Res. 2018 Jul 2;46(W1):W102-W108. PMID:29790943

36. Cho SY, Sung CO, Chae J, Lee J, Na D, …, & Lee C. Alterations in the Rho pathway contribute to Epstein-Barr virus-induced lymphomagenesis in immunosuppressed environments. Blood. 2018 Apr 26;131(17):1931-1941. PMID:29475961

35. Kim IK, KIM K, Lee E, Oh DS, Park CS, .., & Kim I. Sox7 promotes high-grade glioma by increasing VEGFR2-mediated vascular abnormality. J Exp Med. 2018. Mar 5;215(3):963-983. PMID:29444818

34. (review) Ju YS#. The mutational signatures and molecular alterations of bladder cancer. Transl Cancer Res. 2017;6(Supple 4):S689-S701. pdf file

33. Lee JK*, Lee J, Kim S, Kim S, Youk J, ... Kim TM# & Ju YS#. Clonal history and genetic predictors of transformation into small-cell carcinomas from lung adenocarcinomas. J Clin Oncol. 2017 Sep 10;35(26):3065-3074. PMID:28498782
(Introduced by editorials in the issue of J Clin Oncol. link)

32. Ju YS*, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, ... & Stratton MR. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature. 2017 Mar 30;543(7647):714-718. PMID:28329761

31. Lee JK*, Louzada S, An Y, Kim SY, Kim S, Youk J, Park S, ... & Ju YS#. Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma. Ann Oncol. 2017 Feb 14. 28(4):890-897. PMID:28203693

30. Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, ... & Stratton MR. Mutational signatures associated with tobacco smoking in human cancer. Science. 2016 Nov 4;354(6312):618-622. PMID:27811275

29. Shlien A, Raine K, Fuligni F, Arnold R, Nik-Zainal S, Dronov S, Mamanova L, Rosic A, Ju YS, ... & Campbell PJ. Direct transcriptional consequences of somatic mutation in breast cancer. Cell Rep. 2016 Aug 16;16(7):2032-46. PMID:27498871

28. Kemper K, Krijgsman O, Kong X, Cornelissen-Steijger P, Shahrabi A, Weeber F, van der Velden DL, Bleijerveld OB, Kuilman T, Kluin RJ, Sun C, Voest EE, Ju YS, ... & Peeper DS. BRAF(V600E) kinase domain duplication identified in therapy-refractory melanoma patient-derived xenografts. Cell Rep. 2016 Jun 28;16(1):263-77. PMID:27320919

27. Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D,  Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, ... & Stratton MR. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. 2016 Jun 2;534(7605):47-54. PMID:27135926

26. (review) Ju YS#. Intracellular mitochondrial DNA transfers to the nucleus in human cancer cells. Curr Opin Genet Dev. 2016 Jun;38:23-30. PMID:27010587

25. Kim J, Kim S, Ko S, In YH, Moon HG, Ahn SK, Kim MK, Lee M, Hwang JH, Ju YS, ... & Han W. Recurrent fusion transcripts detected by whole-transcriptome sequencing of 120 primary breast cancer samples. Genes Chromosomes Cancer. 2015 Nov;54(11):681-91. PMID:26227178

24. Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H, Li Y, Ju YS, ... & Campbell PJ . Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015 Jul;21(7):751-9. PMID:26099045

23. Ju YS*, Tubio JM, Mifsud W, Fu B, Davies HR, ... & Stratton MR. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res. 2015 Jun;25(6):814-24. PMID:25963125 

22. Ju YS*, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, ... & Campbell PJ. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife. 2014 Oct 1;3. PMID:25271376

21. Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, ... & Campbell PJ. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014 Aug 1;345(6196):1251343. PMID:25082706

20. Go H, Jung YJ, Kang HW, Park IK, Kang CH, Lee JW, Ju YS, ... & Kim YT. Diagnostic method for the detection of KIF5B-RET transformation in lung adenocarcinoma. Lung Cancer. 2013 Oct;82(1):44-50. PMID:23932363

19. Kim HJ, Yoo YJ, Ju YS, Lee S, Cho SI, ... & Seo JS. Combined linkage and association analyses identify a novel locus for obesity near PROX1 in Asians. Obesity (Silver Spring). 2013 Nov;21(11):2405-12. PMID:23818313

18. Hong D, Lee J, Bleazard T, Jung H, Ju YS, ... & Seo JS. TIARA genome database: update 2013. Database (Oxford). 2013 Mar 20;2013:bat003. PMID:23515433

17. Bleazard T, Ju YS, Sung J & Seo JS. Fine-scale mapping of meiotic recombination in Asians. BMC Genet. 2013 Mar 8;14:19. PMID:23510153

16. Park H, Kim HJ, Lee S, Yoo YJ, Ju YS, ... & Seo JS. A family-based association study after genome-wide linkage analysis identified two genetic loci for renal function in a Mongolian population. Kidney Int. 2013 Feb;83(2):285-92. PMID:23254893

15. Park H, Lee S, Kim HJ, Ju YS, Shin JY, ... & Seo JS. Comprehensive genomic analyses associate UGT8 variants with musical ability in a Mongolian population. J Med Genet. 2012 Dec;49(12):747-52. PMID:23118445

14. Seo JS*, Ju YS*, Lee WC*, Shin JY, Lee JK, ..., Kim YT. The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res. 2012 Nov;22(11):2109-19. PMID:22975805

13. Hong D, Rhie A, Park SS, Lee J, Ju YS, ... & Seo JS. FX: an RNA-Seq analysis tool on the cloud. Bioinformatics. 2012 Mar 1;28(5):721-3. PMID:22257667

12. Paik SH, Kim HJ, Son HY, Lee S, Im SW, Ju YS, ... & Kim JI. Gene mapping study for constitutive skin color in an isolated Mongolian population. Exp Mol Med. 2012 Mar 31;44(3):241-9. PMID:22198297

11. Ju YS*, Lee WC, Shin JY, Lee S, Bleazard T, ... & Seo JS. A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res. 2012 Mar;22(3):436-45. PMID:22194472

10. Paik SH, Kim HJ, Lee S, Im SW, Ju YS, ... & Kwon OS. Linkage and association scan for tanning ability in an isolated Mongolian population. BMB Rep. 2011 Nov;44(11):741-6. PMID:22118541

9. Ju YS*, Kim JI*, Kim S*, Hong D, Park H, ... & Seo JS. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet. 2011 Jul 3;43(8):745-52. PMID:21725310

8. Hong D*, Park SS*, Ju YS*, Kim S, Shin JY, ... & Seo JS. TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology. Nucleic Acids Res. 2011 Jan;39(Database issue):D883-8. PMID:21051338

7. (research highlight) Ju YS*, Yoo YJ, Kim JI & Seo JS. The first Irish genome and ways of improving sequence accuracy. Genome Biol. 2010;11(9):132. PMID:20815917

6. Ju YS*, Hong D*, Kim S*, Park SS, Kim S, ... & Seo JS. Reference-unbiased copy number variant analysis using CGH microarrays. Nucleic Acids Res. 2010 Nov;38(20):e190. PMID:20802225

5. Park H*, Kim JI*, Ju YS*, Gokcumen O, Mills RE, ... & Seo JS. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet. 2010 May;42(5):400-5. PMID:20364138

4. Kim JI*, Ju YS*, Park H, Kim S, Lee S, ... & Seo JS. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009 Aug 20;460(7258):1011-5. PMID:19587683

3. Lee JE, Park H, Ju YS, Kwak M, Kim JI, ... & Seo JS. Higher mitochondrial DNA copy number is associated with lower prevalence of microalbuminuria. Exp Mol Med. 2009 Apr 30;41(4):253-8. PMID:19299914

2. Ju YS*, Park H, Lee MK, Kim JI, Sung J, ... & Seo JS. A genome-wide Asian genetic map and ethnic comparison: the GENDISCAN study. BMC Genomics. 2008 Nov 25;9:554. doi: 10.1186/1471-2164-9-554. PMID:19025666

1. Gombojav B, Park H, Kim JI, Ju YS, Sung J, ... & Seo JS. Heritability and linkage study on heart rates in a Mongolian population. Exp Mol Med. 2008 Oct 31;40(5):558-64. PMID:18985014

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