Soohyun Lee

Soohyun Lee, PhD

Senior Bioinformatics Scientist, Harvard Medical School
Park Lab

Soo Lee received her PhD in bioinformatics from Boston University in 2009 (PhD advisors: Zhiping Weng, Simon Kasif, Charles Cantor). She is currently working as part of the 4DNucleome Data Coordination and Integration Center, setting up automated genomic workflows on the Amazon Cloud using Docker, Common Workflow Language (CWL) and Workflow Description Language (WDL). She is a main developer of Tibanna, a workflow manager for AWS cloud. She also wrote Pairix, a fast random access tool for 2D genomic positions.

Previously, she developed EMSAR, a software program for quantifying mRNA transcripts from RNA-seq data. She also participated in the study of transcriptomics in various biological contexts such as comparison of embryonic stem cells and induced pluripotent stem cells, detecting translation initiation sites genomewide, or analysis of mutation rates in single neurons. Earlier, she developed software tools for analyzing high throughput-sequencing of small RNAs for the studies of siRNAs and piRNAs in fruit fly (2008-2009), in collaboration with Phil Zamore at UMMS.

Failure to replicate the STAP cell phenomenon.
Authors: De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQ.
Nature
View full abstract on Pubmed
Hallmarks of pluripotency.
Authors: De Los Angeles A, Ferrari F, Xi R, Fujiwara Y, Benvenisty N, Deng H, Hochedlinger K, Jaenisch R, Lee S, Leitch HG, Lensch MW, Lujan E, Pei D, Rossant J, Wernig M, Park PJ, Daley GQ.
Nature
View full abstract on Pubmed
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
Authors: Lee S, Seo CH, Alver BH, Lee S, Park PJ.
BMC Bioinformatics
View full abstract on Pubmed
Comparative analysis of metazoan chromatin organization.
Authors: Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.
Nature
View full abstract on Pubmed
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
Authors: Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB.
Proc Natl Acad Sci U S A
View full abstract on Pubmed
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization.
Authors: Lee S, Seo CH, Lim B, Yang JO, Oh J, Kim M, Lee S, Lee B, Kang C, Lee S.
Nucleic Acids Res
View full abstract on Pubmed
Relative codon adaptation index, a sensitive measure of codon usage bias.
Authors: Lee S, Weon S, Lee S, Kang C.
Evol Bioinform Online
View full abstract on Pubmed
The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.
Authors: Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A, Seitz H, Zamore PD, Weng Z, Theurkauf WE.
Cell
View full abstract on Pubmed
Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies.
Authors: Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM, Kittler EL, Zapp ML, Klattenhoff C, Schulz N, Theurkauf WE, Weng Z, Zamore PD.
Cell
View full abstract on Pubmed
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells.
Authors: Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z, Zamore PD.
Science
View full abstract on Pubmed