Soohyun Lee
Soohyun Lee, PhD
Senior Bioinformatics Scientist, Harvard Medical School

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.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.
Authors: Jain D, Chu C, Alver BH, Lee S, Lee EA, Park PJ.
Bioinformatics
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HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.
Authors: Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ.
Genome Biol
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Tibanna: software for scalable execution of portable pipelines on the cloud.
Authors: Lee S, Johnson J, Vitzthum C, Kirli K, Alver BH, Park PJ.
Bioinformatics
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HiGlass: web-based visual exploration and analysis of genome interaction maps.
Authors: Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N.
Genome Biol
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Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.
Authors: Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV.
Genome Res
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NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
Authors: Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ.
Nucleic Acids Res
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DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.
Authors: Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K.
Cell Stem Cell
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Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing.
Authors: Yang L, Lee MS, Lu H, Oh DY, Kim YJ, Park D, Park G, Ren X, Bristow CA, Haseley PS, Lee S, Pantazi A, Kucherlapati R, Park WY, Scott KL, Choi YL, Park PJ.
Am J Hum Genet
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A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.
Authors: Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K.
Nat Biotechnol
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Somatic mutation in single human neurons tracks developmental and transcriptional history.
Authors: 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.
Science
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