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Dongwon Lee, Ph.D.

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Biography
KAIST, Daejeon, South KoreaB.S.08/2007Computer Science
KAIST, Daejeon, South KoreaB.S.08/2007Biological Science
Johns Hopkins University, Baltimore, MD, USAPh.D.03/2013Biomedical Engineering
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USAPostdoctoral fellow03/2018Human Genetics
Center for Human Genetics & Genomics, New York University School of Medicine, New York, NY, USAPostdoctoral fellow08/2019Human Genetics
2012
TOP 10 Paper Award, RECOMB Conference on Regulatory and Systems Genomics 2012
2013
Nupur Dinesh Thekdi Award, Johns Hopkins University School of Medicine
2015
Top 10 Paper Award, RECOMB/ISCB Conference on Regulatory and Systems Genomics 2015

Overview
Our group studies disease-associated genetic variants using computational approaches with a specific focus on transcriptional regulatory mechanisms. We have developed several machine-learning based methods for predicting regulatory elements and regulatory variants (Lee et al., Nature Genetics 2015). We have shown that these predicted regulatory variants explain a significant proportion of heritability in a tissue-specific manner (Lee et al., Genome Research 2018). Our group will continue to develop computational methods to model regulatory control of human diseases, by incorporating improved machine-learning algorithms and single-cell multi-omic data (genomic, transcriptomic, and epigenomic.) New computational frameworks will help discover the molecular mechanisms driving the development and progression of human diseases.

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. 5R01HL141980-02 (CHAKRAVARTI, ARAVINDA) May 1, 2018 - Apr 30, 2020
    NIH
    Cardiac genetic effects across HLBS phenotypes
    Role: Co-Investigator
  2. 7R01HL128782-04 (CHAKRAVARTI, ARAVINDA) Aug 1, 2015 - Apr 30, 2019
    NIH
    Genomics of blood pressure-induced target organ damage
    Role: Co-Investigator
  3. 5R01HL086694-09 (CHAKRAVARTI, ARAVINDA) Sep 1, 2007 - Jan 31, 2022
    NIH
    From GWAS loci to blood pressure genes, variants & mechanisms
    Role: Co-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. Kapoor A, Lee D, Zhu L, Soliman EZ, Grove ML, Boerwinkle E, Arking DE, Chakravarti A. Multiple SCN5A variant enhancers modulate its cardiac gene expression and the QT interval. Proc Natl Acad Sci U S A. 2019 05 28; 116(22):10636-10645. PMID: 31068470.
    Citations:    
  2. Lee D, Kapoor A, Safi A, Song L, Halushka MK, Crawford GE, Chakravarti A. Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants. Genome Res. 2018 10; 28(10):1577-1588. PMID: 30139769.
    Citations:    
  3. Wang TY, Lee D, Fox-Talbot K, Arking DE, Chakravarti A, Halushka MK. Cardiomyocytes have mosaic patterns of protein expression. Cardiovasc Pathol. 2018 May - Jun; 34:50-57. PMID: 29677652.
    Citations:    
  4. Nandakumar P, Lee D, Richard MA, Tekola-Ayele F, Tayo BO, Ware E, Sung YJ, Salako B, Ogunniyi A, Gu CC, Grove ML, Fornage M, Kardia S, Rotimi C, Cooper RS, Morrison AC, Ehret G, Chakravarti A. Rare coding variants associated with blood pressure variation in 15?914 individuals of African ancestry. J Hypertens. 2017 07; 35(7):1381-1389. PMID: 28234671.
    Citations:    
  5. Kapoor A, Auer DR, Lee D, Chatterjee S, Chakravarti A. Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development. Hum Mol Genet. 2017 05 15; 26(10):1811-1820. PMID: 28334784.
    Citations:    
  6. Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS. Design of a synthetic yeast genome. Science. 2017 03 10; 355(6329):1040-1044. PMID: 28280199.
    Citations:    
  7. Chatterjee S, Kapoor A, Akiyama JA, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio LA, Chakravarti A. Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. Cell. 2016 Oct 06; 167(2):355-368.e10. PMID: 27693352.
    Citations:    
  8. Kapoor A, Bakshy K, Xu L, Nandakumar P, Lee D, Boerwinkle E, Grove ML, Arking DE, Chakravarti A. Rare coding TTN variants are associated with electrocardiographic QT interval in the general population. Sci Rep. 2016 06 20; 6:28356. PMID: 27321809.
    Citations:    
  9. Ghandi M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, Beer MA. gkmSVM: an R package for gapped-kmer SVM. Bioinformatics. 2016 07 15; 32(14):2205-7. PMID: 27153639.
    Citations: 9     Fields:    
  10. Lee D. LS-GKM: a new gkm-SVM for large-scale datasets. Bioinformatics. 2016 07 15; 32(14):2196-8. PMID: 27153584.
    Citations:    
  11. Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. 2015 Aug; 47(8):955-61. PMID: 26075791.
    Citations:    
  12. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. PMID: 25409824.
    Citations: 283     Fields:    Translation:HumansAnimalsCells
  13. Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. 2014 Dec; 24(12):1932-44. PMID: 25319996.
    Citations: 28     Fields:    Translation:AnimalsCells
  14. Ghandi M, Lee D, Mohammad-Noori M, Beer MA. Enhanced regulatory sequence prediction using gapped k-mer features. PLoS Comput Biol. 2014 Jul; 10(7):e1003711. PMID: 25033408.
    Citations:    
  15. Fletez-Brant C, Lee D, McCallion AS, Beer MA. kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. Nucleic Acids Res. 2013 Jul; 41(Web Server issue):W544-56. PMID: 23771147.
    Citations:    
  16. Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res. 2012 Nov; 22(11):2290-301. PMID: 23019145.
    Citations:    
  17. Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011 Dec; 21(12):2167-80. PMID: 21875935.
    Citations:    
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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.