Current Environment: Development

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Dev

Publications

Full publications can be found on Dongwon's Google Scholar page.

Selected Publications

  1. Lee D†*, Han SK*, Yaacov O, Berk-Rauch H, Mathiyalagan P, Ganesh SK, Chakravarti A†. Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure. Cell Reports 42:113351 (2023)

  2. Han SK*, McNulty MT*, Benway CJ*, Wen P, Greenberg A, Onuchic-Whitford AC, NEPTUNE, Jang D, Flannick J, Burtt NP, Wilson PC, Humphreys BD, Wen X, Han Z†, Lee D†, Sampson MG†. Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs. Nature Communications 14:2229 (2023)

  3. Han SK, Muto Y, Wilson PC, Humphreys BD, Sampson MG, Chakravarti A†, Lee D†. Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model. Proceedings of the National Academy of Sciences 119: e2212810119 (2022)

  4. Lee D†, Kapoor A, Lee C, Mudgett M, Beer M, Chakravarti A†. Sequence-based correction of barcode bias in massively parallel reporter assays. Genome Research. 31(9): 1638-1645 (2021)

  5. Kapoor A*, Lee D*, Zhu L, Chakravarti A. Multiple SCN5A enhancers modulate cardiac gene expression and QT interval variation. Proceedings of the National Academy of Sciences 106(22):10636–10645 (2019) *co-first authors

  6. 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 Research 28: 1577–1588 (2018)

  7. Lee D. LS-GKM: a new gkm-SVM for large-scale datasets. Bioinformatics 32: 2196-2198 (2016)

  8. 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. Nature Genetics 47: 955-961 (2015)

  9. Ghandi M*, Lee D*, Mohammad-Noori M, Beer MA. Enhanced regulatory sequence prediction using gapped k-mer features. PLoS Computational Biology 10: e1003711 (2014)

  10. Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research 21:2167-2180 (2011)