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Yoo Jin Ha

  CONTACT INFORMATION  

 

Translational Genome Informatics Laboratory

Dept. of Biomedical Systems Informatics

Yonsei University College of Medicine

50-1 Yonsei-ro, Seodaemun-gu,

Seoul 03722, South Korea.

Office: +82-2-2228-2487

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  RESEARCH AREAS  

Next-generation sequencing, Somatic mutation, Somatic mosaicism, Genetic disease analysis(including de novo variants), Method evaluation and development

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  SHORT BIOGRAPHY  

Youjin majored Genetic Engineering in Kyunghee University 2018 and joined Translational Genome Informatics Laboratory, Yonsei University on January 2018. She is studying happily more in depth of Bioinformatics with the attitude of scientist and working to develop useful algorithms that can be standardized and used universally in the community. She is especially interested in mosaicism and development of computational algorithms for its accurate detection.

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  EDUCATION & EXPERIENCE  

  • Ph.D. in Dept. of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea, August 2023
    (Thesis: Accurate detection of mosaic variants and application to disease genome analysis)

  • Visiting graduate student, Dept. of Neuroscience, UC San Diego (host: Joseph G. Gleeson), 2022/03-2023/02

  • LT (learn-by-teaching) lecturer, Yonsei Univ. College of Medicine
    - lectured ‘Genome Informatics’ (MES7594) - 2021 fall and 2022 fall
    class 1. Linux and shell script
    class 2. NGS analysis practice – short read mapping and SNV calling
    class 3. NGS analysis practice – CNV and Structural variation calling
    class 4. NGS analysis practice – Annotation and clinical application

  • Teaching assistant and lecturer, Data Science Workshop “Understanding and Analyzing Genomic Data”, Yonsei Univ. College of Medicine, 2019/01 and 2020/01

  • B.S. in Genetic Engineering, Kyunghee University, Yong-in, Korea, February 2018

  • Research Assistant, Systems Biology lab. in Kyunghee Univ. (2017.7 – 2017.12)

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  PUBLICATIONS  

Journal Papers (Peer reviewed)

    † These authors contributed equally to this work.

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  1. Ha Y-J, Kim J, Kang S, Kim J, Jo S-Y, and Kim S*, Comprehensive benchmarking and guidelines of mosaic variant calling strategies, Nature Methods 2023

  2. Ha Y-J†, Oh MJ†, Kim J, Kim J, Kang S, Kim HS*, and Kim S*, Establishment of reference
    standards for multifaceted mosaic variant analysis, Scientific Data 2022, 9, article number 35

  3. Wang L, Heffner C, Vong KI, Barrows C, Ha Y-J, Lee S, Lara-Gonzalez P, Jhamb I, Meer D, Loughman R, Parker R, Parker N, Sievert DM, Mittal S, Issa M, Andressen OA, Dale AM, Dobyns WB, Zaki MS, Murray SA, Gleeson JG*, TMEM161B modulates radial glial scaffolding in neocortical development, PNAS 2023 120 (4): e220998312)

  4. Kim JH †, Hwang S†, Son H, Kim D, Kim IB, Kim MH, Sim NS, Kim DS, Ha Y-J, Lee J, Kang H-C, Lee JH* and Kim S*, Analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development, PLoS Genetics 2022, 18(9):e1010404

  5. Kim TM, Yang IS, Seung BJ, Lee S, Kim D, Ha Y-J, Seo M-k, Kim K-K, Kim HS, Cheong J-H, Sur J-H, Nam H, and Kim S*, Cross-species Oncogenic Signatures of Breast Cancer in Canine Mammary Tumors, Nature Communications 2020 11, article number 3616

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CONFERENCES AND SEMINARS

International Conferences

  1. Ha Y-J et al, a robust benchmark for evaluating and improving mosaic variant calling strategies, RECOMB-GENETICS, May 20, 2022, San Diego (poster)
    *selected as lightning talk

  2. Ha Y-J et al, a robust benchmark for evaluating and improving mosaic variant calling strategies, AGBT Precision Health, Sep 08, 2022, San Diego (poster)

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  AWARDS  ​

  • Academic Award for Highest Achievement in Ph.D. degree, Yonsei University College of Medicine, Aug. 2023

  • Best Presentation Award, Yonsei University College of Medicine, Aug. 2022

  • Academic Excellence Award, KyungHee University, 2017

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  FUNDING GRANTED  ​

  • Grant awarded, ‘Biomedical Global Talent Nurturing Program (Ph.D. course)’, funded by Korea Health Industry Development Institute, USD 64,000

  • Scholarship awarded (full tuition), Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 2018.3-2023.8

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  SKILLS  

  • Experience in NGS DNA (including ~5000 samples analysis) including WGS

  • Experienced currently used mosaic variant detection tools (eleven tools/strategies that were developed or utilized for mosaic variants)

  • Somatic/Mosaic variant detection especially in low allele frequency

  • Long read sequencing (PacBio) data analysis

  • Single cell RNA sequencing data analysis and network analysis

  • Problem-solving skills with sequencing data

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Last Update: December 1, 2023

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