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Eunjung Alice Lee, Ph.D.

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Overview
E. Alice Lee is a faculty member of the Division of Genetics and Genomics at Boston Children's Hospital and Havard Medical School. She runs a research program that studies somatic mutation and aberration of repetitive DNA, such as transposable elements, in various human diseases using computational genomic and bioinformatic approaches. Her research group specializes in the development of computational methods for next-generation sequencing data and in the integrative analysis of large-scale genomic and transcriptomic data.

Lee Lab webpage: https://compgen.hms.harvard.edu/

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. Child Health Research Award (LEE, EUNJUNG ALICE) Jul 1, 2019 - Jun 30, 2021
    Charles H. Hood Foundation
    Role: Principal Investigator
  2. K01AG051791 (LEE, EUNJUNG) Aug 1, 2016 - Apr 30, 2021
    NIH
    The role of somatic mutation in neurodegenerative disease
    Role: Principal Investigator
  3. William Randolph Hearst Fund (LEE, EUNJUNG) Apr 1, 2015 - Mar 31, 2016
    Harvard Medical School
    Single-cell analysis of cerebellar degeneration in Ataxia-Telangiectasia
    Role: Principal Investigator
  4. Eleanor and Miles Shore Fellowship (LEE, EUNJUNG) Jun 1, 2014 - May 31, 2015
    Harvard Medical School
    Dysregulation of repetitive DNA and its impact on genomic stability in cancer
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Kang Y, Nam SH, Park KS, Kim Y, Kim JW, Lee E, Ko JM, Lee KA, Park I. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics. 2018 Oct 16; 19(1):381. PMID: 30326846.
    Citations:    Fields:    Translation:Humans
  2. Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJ. 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. PMID: 29996110.
    Citations:    Fields:    
  3. Jung H, Choi JK, Lee EA. Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. Genome Res. 2018 08; 28(8):1136-1146. PMID: 29970450.
    Citations: 1     Fields:    Translation:HumansCells
  4. Park J, Lee E, Park KJ, Park HD, Kim JW, Woo HI, Lee KH, Lee KT, Lee JK, Park JO, Park YS, Heo JS, Choi SH, Choi DW, Jang KT, Lee SY. Large-scale clinical validation of biomarkers for pancreatic cancer using a mass spectrometry-based proteomics approach. Oncotarget. 2017 Jun 27; 8(26):42761-42771. PMID: 28514751.
    Citations: 4     Fields:    Translation:Humans
  5. Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ. 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. PMID: 28369524.
    Citations: 1     Fields:    Translation:Humans
  6. Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 06 12; 31(6):820-832.e3. PMID: 28528867.
    Citations: 22     Fields:    Translation:HumansCells
  7. McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science. 2017 04 28; 356(6336). PMID: 28450582.
    Citations: 17     Fields:    Translation:HumansCells
  8. Yu VWC, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2016 11 17; 167(5):1310-1322.e17. PMID: 27863245.
    Citations: 24     Fields:    Translation:AnimalsCells
  9. Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet. 2016 10; 12(10):e1006385. PMID: 27788131.
    Citations: 11     Fields:    Translation:HumansCellsCTClinical Trials
  10. Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. Next-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics. 2016 05 10; 17:342. PMID: 27161561.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  11. Evrony GD, Lee E, Park PJ, Walsh CA. Resolving rates of mutation in the brain using single-neuron genomics. Elife. 2016 Feb 22; 5. PMID: 26901440.
    Citations: 22     Fields:    Translation:HumansCells
  12. Bersani F, Lee E, Kharchenko PV, Xu AW, Liu M, Xega K, MacKenzie OC, Brannigan BW, Wittner BS, Jung H, Ramaswamy S, Park PJ, Maheswaran S, Ting DT, Haber DA. 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. PMID: 26575630.
    Citations: 19     Fields:    Translation:HumansCells
  13. Jung H, Lee D, Lee J, Park D, Kim YJ, Park WY, Hong D, Park PJ, Lee E. Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet. 2015 Nov; 47(11):1242-8. PMID: 26437032.
    Citations: 46     Fields:    Translation:HumansCells
  14. Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 02; 350(6256):94-98. PMID: 26430121.
    Citations: 70     Fields:    Translation:HumansCells
  15. Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CA. Cell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 07; 85(1):49-59. PMID: 25569347.
    Citations: 47     Fields:    Translation:HumansCells
  16. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. PMID: 25417114.
    Citations: 349     Fields:    Translation:Humans
  17. Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 08; 26(3):319-330. PMID: 25155756.
    Citations: 133     Fields:    Translation:HumansCells
  18. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Benz CC, Perou CM, Stuart JM. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14; 158(4):929-944. PMID: 25109877.
    Citations: 290     Fields:    Translation:HumansCells
  19. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. PMID: 24120142.
    Citations: 850     Fields:    Translation:HumansCells
  20. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849.
    Citations: 799     Fields:    Translation:Humans
  21. Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39):15764-9. PMID: 24014587.
    Citations: 19     Fields:    Translation:HumansAnimals
  22. Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26; 151(3):483-96. PMID: 23101622.
    Citations: 169     Fields:    Translation:HumansCells
  23. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27; 489(7417):519-25. PMID: 22960745.
    Citations: 992     Fields:    Translation:HumansCells
  24. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407):330-7. PMID: 22810696.
    Citations: 1934     Fields:    Translation:HumansCells
  25. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71. PMID: 22745252.
    Citations: 252     Fields:    Translation:HumansCells
  26. Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. 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. PMID: 22065754.
    Citations: 79     Fields:    Translation:Humans
  27. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. PMID: 21720365.
    Citations: 1929     Fields:    Translation:HumansCells
  28. Paik H, Lee E, Park I, Kim J, Lee D. Prediction of cancer prognosis with the genetic basis of transcriptional variations. Genomics. 2011 Jun; 97(6):350-7. PMID: 21419214.
    Citations: 1     Fields:    Translation:HumansCells
  29. Lee S, Lee E, Lee KH, Lee D. Predicting disease phenotypes based on the molecular networks with condition-responsive correlation. Int J Data Min Bioinform. 2011; 5(2):131-42. PMID: 21544951.
    Citations: 1     Fields:    Translation:Humans
  30. Paik H, Lee E, Lee D. Relationships between genetic polymorphisms and transcriptional profiles for outcome prediction in anticancer agent treatment. BMB Rep. 2010 Dec; 43(12):836-41. PMID: 21189162.
    Citations: 2     Fields:    Translation:Humans
  31. Jung J, Ryu T, Hwang Y, Lee E, Lee D. Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol. 2010 Jan; 17(1):97-105. PMID: 20078400.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  32. Jung H, Lee E, Kim JW, Lee D. Pathway level analysis by augmenting activities of transcription factor target genes. IET Syst Biol. 2009 Nov; 3(6):534-42. PMID: 19947779.
    Citations:    Fields:    Translation:HumansCells
  33. Lee E, Jung H, Radivojac P, Kim JW, Lee D. Analysis of AML genes in dysregulated molecular networks. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S2. PMID: 19761572.
    Citations: 9     Fields:    Translation:Humans
  34. Won HH, Park I, Lee E, Kim JW, Lee D. 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. PMID: 19208156.
    Citations: 1     Fields:    Translation:Cells
  35. Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol. 2008 Nov; 4(11):e1000217. PMID: 18989396.
    Citations: 153     Fields:    Translation:HumansCells
  36. Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007; 3:140. PMID: 17940530.
    Citations: 550     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.