Lucy Jung, PhD

Lucy Jung, PhD

Research Fellow in Biomedical Informatics, Harvard Medical School
Park Lab
Mentor: Peter Park, PhD

Lucy Jung finished her PhD from Speech and Hearing program in the division of Health Science Technology at MIT. Since joining the Park lab at DBMI, she has shifted her research interest to epigenomics. Lucy has specialized in computational analysis of epigenetic data, especially for data from chromatin immunoprecipitation experiments followed by high-throughput sequencing (ChIP-seq). One of her main projects was to perform integrative analysis of various functional genomics datasets for the Drosophila modENCODE project. She also has worked closely with several experimental biologists around the Longwood area on analysis of chromatin data, on topics such as dosage compensation, Polycomb complex, and cellular reprogramming.

Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila.
Authors: Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI.
Genes Dev
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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
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Impact of sequencing depth in ChIP-seq experiments.
Authors: Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.
Nucleic Acids Res
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"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.
Authors: Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI.
Cell Rep
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Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters".
Authors: Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ.
Science
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Nature and function of insulator protein binding sites in the Drosophila genome.
Authors: Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V.
Genome Res
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Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.
Authors: Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC.
PLoS Genet
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Authors: Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.
Genome Res
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Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.
Authors: Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ.
PLoS Genet
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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
Authors: Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ.
Nature
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