Eunjung (Alice) Lee

Publications

1. Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data. Bioinformatics. 2026 May 03; 42(5). View Abstract
2. Somatic cancer variants enriched in Alzheimer's disease microglia-like cells drive inflammatory and proliferative states. Cell. 2026 Apr 21. View Abstract
3. Somatic mosaicism in ALS and FTD identifies focal mutations associated with widespread degeneration. Nat Genet. 2026 May; 58(5):1019-1029. View Abstract
4. Inverted Alu repeats in loop-out exon skipping across hominoid evolution. Nucleic Acids Res. 2026 Mar 19; 54(6). View Abstract
5. Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter. Nucleic Acids Res. 2026 Jan 05; 54(1). View Abstract
6. Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy. Science. 2025 Oct 30; 390(6772):eadu1351. View Abstract
7. VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3K? activation. bioRxiv. 2025 Sep 18. View Abstract
8. STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features. bioRxiv. 2025 Sep 08. View Abstract
9. The Somatic Mosaicism across Human Tissues Network. Nature. 2025 07; 643(8070):47-59. View Abstract
10. Identifying kinematic biomarkers of the dystrophic phenotype in a zebrafish model of Duchenne muscular dystrophy. Skelet Muscle. 2025 06 20; 15(1):17. View Abstract
11. Cell-type-specific patterns and consequences of somatic mutation in development and aging brain. bioRxiv. 2025 May 31. View Abstract
12. Analysis of DNA from brain tissue on stereo-EEG electrodes reveals mosaic epilepsy-related variants. Brain Commun. 2025; 7(2):fcaf113. View Abstract
13. Inverted Alu repeats in loop-out exon skipping across hominoid evolution. bioRxiv. 2025 Mar 10. View Abstract
14. Multi-omic analysis of the ciliogenic transcription factor RFX3 reveals a role in promoting activity-dependent responses via enhancing CREB binding in human neurons. bioRxiv. 2025 Mar 01. View Abstract
15. Chromosomal rearrangements and instability caused by the LINE-1 retrotransposon. bioRxiv. 2024 Dec 17. View Abstract
16. High resolution kinematic approach for quantifying impaired mobility of dystrophic zebrafish larvae. bioRxiv. 2024 Dec 09. View Abstract
17. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nat Commun. 2024 09 27; 15(1):8268. View Abstract
18. Human cytomegalovirus harnesses host L1 retrotransposon for efficient replication. Nat Commun. 2024 09 02; 15(1):7640. View Abstract
19. Analysis of DNA from brain tissue on stereo-EEG electrodes reveals mosaic epilepsy-related variants. medRxiv. 2024 Jul 22. View Abstract
20. Analysis of REST binding sites with canonical and non-canonical motifs in human cell lines. BMC Med Genomics. 2024 04 17; 17(Suppl 1):92. View Abstract
21. Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia. bioRxiv. 2024 Jan 04. View Abstract
22. ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia. Cell Rep. 2024 01 23; 43(1):113622. View Abstract
23. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. medRxiv. 2023 Dec 27. View Abstract
24. Impaired neural stress resistance and loss of REST in bipolar disorder. Mol Psychiatry. 2024 01; 29(1):153-164. View Abstract
25. Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs. bioRxiv. 2023 Oct 19. View Abstract
26. Contribution and therapeutic implications of retroelement insertions in ataxia telangiectasia. Am J Hum Genet. 2023 11 02; 110(11):1976-1982. View Abstract
27. A framework for individualized splice-switching oligonucleotide therapy. Nature. 2023 07; 619(7971):828-836. View Abstract
28. Contribution of Somatic Ras/Raf/Mitogen-Activated Protein Kinase Variants in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy. JAMA Neurol. 2023 Jun 01; 80(6):578-587. View Abstract
29. Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders. Nat Commun. 2022 10 07; 13(1):5918. View Abstract
30. Somatic mutations in single human cardiomyocytes reveal age-associated DNA damage and widespread oxidative genotoxicity. Nat Aging. 2022 08; 2(8):714-725. View Abstract
31. A neurodevelopmental disorder caused by a novel de novo SVA insertion in exon 13 of the SRCAP gene. Eur J Hum Genet. 2022 09; 30(9):1083-1087. View Abstract
32. Somatic genomic changes in single Alzheimer's disease neurons. Nature. 2022 04; 604(7907):714-722. View Abstract
33. Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction. Nucleic Acids Res. 2022 03 21; 50(5):2700-2718. View Abstract
34. Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data. Front Aging. 2021; 2:800380. View Abstract
35. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA. 2021 Nov 27; 12(1):28. View Abstract
36. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA. 2021 Oct 18; 12(1):22. View Abstract
37. Molecular Signature Expands the Landscape of Driver Negative Thyroid Cancers. Cancers (Basel). 2021 Oct 15; 13(20). View Abstract
38. Rates and Patterns of Clonal Oncogenic Mutations in the Normal Human Brain. Cancer Discov. 2022 01; 12(1):172-185. View Abstract
39. Comprehensive identification of transposable element insertions using multiple sequencing technologies. Nat Commun. 2021 06 22; 12(1):3836. View Abstract
40. HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. Bioinformatics. 2021 05 23; 37(8):1045-1051. View Abstract
41. Novel Alzheimer's disease risk variants identified based on whole-genome sequencing of APOE e4 carriers. Transl Psychiatry. 2021 05 19; 11(1):296. View Abstract
42. Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas. Cancers (Basel). 2021 May 12; 13(10). View Abstract
43. Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. Curr Protoc Hum Genet. 2020 09; 107(1):e102. View Abstract
44. APP gene copy number changes reflect exogenous contamination. Nature. 2020 08; 584(7821):E20-E28. View Abstract
45. Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):13886-13895. View Abstract
46. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319. View Abstract
47. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 10 15; 20(1):209. View Abstract
48. Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. N Engl J Med. 2019 10 24; 381(17):1644-1652. View Abstract
49. An enhanced genetic model of colorectal cancer progression history. Genome Biol. 2019 08 15; 20(1):168. View Abstract
50. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics. 2018 Oct 16; 19(1):381. View Abstract
51. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 07 10; 24(2):515-527. View Abstract
52. Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. Genome Res. 2018 08; 28(8):1136-1146. View Abstract
53. Large-scale clinical validation of biomarkers for pancreatic cancer using a mass spectrometry-based proteomics approach. Oncotarget. 2017 Jun 27; 8(26):42761-42771. View Abstract
54. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types. Nucleic Acids Res. 2017 Jun 20; 45(11):e103. View Abstract
55. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 06 12; 31(6):820-832.e3. View Abstract
56. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science. 2017 04 28; 356(6336). View Abstract
57. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2016 11 17; 167(5):1310-1322.e17. View Abstract
58. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet. 2016 10; 12(10):e1006385. View Abstract
59. Next-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics. 2016 05 10; 17:342. View Abstract
60. Resolving rates of mutation in the brain using single-neuron genomics. Elife. 2016 Feb 22; 5. View Abstract
61. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15148-53. View Abstract
62. Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet. 2015 Nov; 47(11):1242-8. View Abstract
63. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 02; 350(6256):94-98. View Abstract
64. Cell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 07; 85(1):49-59. View Abstract
65. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. View Abstract
66. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 08; 26(3):319-330. View Abstract
67. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14; 158(4):929-944. View Abstract
68. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. View Abstract
69. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. View Abstract
70. Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39):15764-9. View Abstract
71. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26; 151(3):483-96. View Abstract
72. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27; 489(7417):519-25. View Abstract
73. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407):330-7. View Abstract
74. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71. View Abstract
75. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011 Nov 15; 108(46):E1128-36. View Abstract
76. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. View Abstract
77. Prediction of cancer prognosis with the genetic basis of transcriptional variations. Genomics. 2011 Jun; 97(6):350-7. View Abstract
78. Predicting disease phenotypes based on the molecular networks with condition-responsive correlation. Int J Data Min Bioinform. 2011; 5(2):131-42. View Abstract
79. Relationships between genetic polymorphisms and transcriptional profiles for outcome prediction in anticancer agent treatment. BMB Rep. 2010 Dec; 43(12):836-41. View Abstract
80. Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol. 2010 Jan; 17(1):97-105. View Abstract
81. Pathway level analysis by augmenting activities of transcription factor target genes. IET Syst Biol. 2009 Nov; 3(6):534-42. View Abstract
82. Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S2. View Abstract
83. Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S53. View Abstract
84. Inferring pathway activity toward precise disease classification. PLoS Comput Biol. 2008 Nov; 4(11):e1000217. View Abstract
85. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007; 3:140. View Abstract
Show All Publications Show Fewer Publications