Researcher Profile and Settings

Master

Affiliation (Master)

• Institute for Genetic Medicine　Pathophysiology

Affiliation (Master)

• Institute for Genetic Medicine　Pathophysiology

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Profile and Settings

Affiliation

• Hokkaido University, Institute for Genetic Medicine, Specially Appointed Assistant Professor

Degree

• PhD in Cell and Molecular Biology（2022/07 The Chinese University of Hong Kong）

Profile and Settings

• Name (Japanese)

  Chung

• Name (Kana)

  Claire Yik-Lok

• Name

  202201006914603233

Alternate Names

https://www.linkedin.com/in/claire-chung/?locale=ja_JP
https://www.linkedin.com/in/claire-chung/

Affiliation

• Hokkaido University, Institute for Genetic Medicine, Specially Appointed Assistant Professor

Achievement

Research Interests

• bioinformatics   genome structure   chromatin   genomics   genomics structural variations   

Research Areas

• Life sciences / Genomics
• Life sciences / Molecular biology
• Informatics / Biological, health, and medical informatics

Research Experience

• 2022/09 - Today Hokkaido University Institute for Genetic Medicine Specially Appointed Assistant Professor

Education

• 2015/08 - 2022/07  The Chinese University of Hong Kong  Division of Life Sciences  PhD Cell and Molecular Biology

Published Papers

• A role for condensin-mediator interaction in mitotic chromosomal organization.

  Osamu Iwasaki, Sanki Tashiro, Claire Chung, Tomomi Hayashi, Hideki Tanizawa, Xuebing Wang, Shinya Ohta, Yuko Fujioka, Joseph Han, Gabrielle Tabor, Mikihiro Kawagoe, Ronen Marmorstein, Nobuo N Noda, Ken-Ichi Noma

  bioRxiv : the preprint server for biology 2024/06/28 

  Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensinmediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation.
• Chemo-Senolytic Therapeutic Potential against Angiosarcoma

  Xuebing Wang, Claire Yik-Lok Chung, Ai Yoshioka, Shinya Hashimoto, Haruki Jimbo, Hideki Tanizawa, Shinya Ohta, Takeshi Fukumoto, Ken-ichi Noma

  Journal of Investigative Dermatology 2024/04 [Refereed][Not invited]
  
• Accurate identification of structural variations from cancer samples

  Le Li, Chenyang Hong, Jie Xu, Claire Yik-Lok Chung, Alden King-Yung Leung, Delbert Almerick T Boncan, Lixin Cheng, Kwok-Wai Lo, Paul B S Lai, John Wong, Jingying Zhou, Alfred Sze-Lok Cheng, Ting-Fung Chan, Feng Yue, Kevin Y Yip

  Briefings in Bioinformatics 25 (1) 1467-5463 2023/11/22 [Refereed][Not invited]
   

  Abstract Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.
• A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization

  Hongbo Wang, Hin Ting Wan, Bin Wu, Jianbo Jian, Alice H M Ng, Claire Yik-Lok Chung, Eugene Yui-Ching Chow, Jizhou Zhang, Anderson O L Wong, Keng Po Lai, Ting Fung Chan, Eric Lu Zhang, Chris Kong-Chu Wong

  GigaScience 2022/12/08 [Refereed][Not invited]
  
• Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication

  Wang, X., Li, M.-W., Wong, F.-L., Luk, C.-Y., Chung, C.Y.-L., Yung, W.-S., Wang, Z., Xie, M., Song, S., Chung, G., Chan, T.-F., Lam, H.-M.

  Plant Journal 107 (6) 1365-313X 2021/07/10 [Refereed]
  
• Whole genome assembly in a Japanese strawberry cultivar, ‘Reikou’, and comparison with wild Fragaria genomes

  K. Shirasawa, C. Chung, D. Boncan, H. Hirakawa, F. Maeda, T. Wada, T.F. Chan, S. Isobe

  Acta Horticulturae 1309 (1309) 175 - 180 0567-7572 2021/04 [Refereed]
   

  Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, which chromosome number is 2n=8x=56. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese cultivar. Genomes of diploid Fragaria species were re-sequenced and compared with the most similar chromosome-scale scaffolds to investigate possible progenitor of each subgenomes. The Illumina short reads derived from paired-end, mate pair and 10X Genomics libraries were obtained from a Japanese cultivar, 'Reikou'. The scafffolds assembled using Denovo MAGIC 3.0 consisted of 32,715 sequences with a total length of 1.4 Gb and N50 length of 3.9 Mb. The scaffolds were aligned onto the 'Reikou' S1 linkage maps with IStraw90 Axiom SaNP array and ddRAD-Seq for pseudomolecule construction.
• Monochorionic twins with selective fetal growth restriction: insight from placental whole-transcriptome analysis

  Wei Li, Claire Yik Lok Chung, Chi Chiu Wang, Ting Fung Chan, Maran Bo Wah Leung, Oi Ka Chan, Ling Wu, Kubi Appiah, Piya Chaemsaithong, Yvonne Kwun Yue Cheng, Liona Chiu Yee Poon, Tak Yeung Leung

  American Journal of Obstetrics and Gynecology 223 (5) 749.e1 - 749.e16 0002-9378 2020/11 [Refereed][Not invited]
  
• Advances in optical mapping for genomic research

  Yuan, Y., Chung, C.Y.-L., Chan, T.-F.

  Computational and Structural Biotechnology Journal 18 2051 - 2062 2001-0370 2020/08/01 [Refereed]
  
• AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed

  Sachiko Isobe, Yuki Matsumoto, Claire Chung, Mika Sakamoto, Ting-Fung Chan, Hideki Hirakawa, Genki Ishihara, Hon-Ming Lam, Shinobu Nakayama, Shigemi Sasamoto, Yasuhiro Tanizawa, Akiko Watanabe, Kei Watanabe, Masaru Yagura, Yasukazu Nakamura

  bioRxiv 2020/05/19 [Not refereed][Not invited]
   

  Abstract The domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat, Felis catus genome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and ab initio gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.
• Construction and comparison of three reference‐quality genome assemblies for soybean

  Babu Valliyodan, Steven B. Cannon, Philipp E. Bayer, Shengqiang Shu, Anne V. Brown, Longhui Ren, Jerry Jenkins, Claire Y.‐L. Chung, Ting‐Fung Chan, Christopher G. Daum, Christopher Plott, Alex Hastie, Kobi Baruch, Kerrie W. Barry, Wei Huang, Gunvant Patil, Rajeev K. Varshney, Haifei Hu, Jacqueline Batley, Yuxuan Yuan, Qijian Song, Robert M. Stupar, David M. Goodstein, Gary Stacey, Hon‐Ming Lam, Scott A. Jackson, Jeremy Schmutz, Jane Grimwood, David Edwards, Henry T. Nguyen

  The Plant Journal 100 (5) 1066 - 1082 0960-7412 2019/10/28 [Refereed][Not invited]
   

  Summary We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
• A reference-grade wild soybean genome

  Min Xie, Claire Yik-Lok Chung, Man-Wah Li, Fuk-Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden King-Yung Leung, Tin-Hang Wong, Suk-Wah Tong, Zhixia Xiao, Kejing Fan, Ming-Sin Ng, Xinpeng Qi, Linfeng Yang, Tianquan Deng, Lijuan He, Lu Chen, Aisi Fu, Qiong Ding, Junxian He, Gyuhwa Chung, Sachiko Isobe, Takanari Tanabata, Babu Valliyodan, Henry T. Nguyen, Steven B. Cannon, Christine H. Foyer, Ting-Fung Chan, Hon-Ming Lam

  Nature Communications 10 (1) 2041-1723 2019/03/14 [Refereed][Not invited]
  
• Genome maps across 26 human populations reveal population-specific patterns of structural variation

  Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, Le Li, Alden K. Y. Leung, Jennifer McCaffrey, Eleanor Young, Ernest T. Lam, Alex R. Hastie, Karen H. Y. Wong, Claire Y. L. Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene Y. C. Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao, Pui-Yan Kwok

  Nature Communications 10 (1) 2019/03/04 [Refereed][Not invited]
   

  Abstract Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.
• Systematic Selection of Reference Genes for the Normalization of Circulating RNA Transcripts in Pregnant Women Based on RNA-Seq Data

  CHIM, Siu Chung Stephen, WONG, Ka Wing Karen, CHUNG, Yik Lok, LAM, Ka Wai, KWOK, Sui Lam, LAI, Chit Ying, CHENG, Kwun Yue Yvonne, CHAN, Oi Ka Catherine, TSUI, Kwok Wing, CHAN, Ting Fung Philos, LEUNG, Tak Yeung

  International Journal of Molecular Sciences 18 1709 - 1709 2017/08 [Refereed][Not invited]
  

Books etc

• Matplotlib for Python developers : effective techniques for data visualization with Python

  Yim, Aldrin, Chung, Claire, Yu, Allen 
  Packt Publishing 2018 (ISBN: 9781788625173) v, 287 p.
• Matplotlib 2.x By Example: Multi-dimensional charts, graphs, and plots in Python

  Allen Yu, Claire Chung, Aldrin Yim 
  Packt Publishing 2017/08 (ISBN: 1788295269) 334

Presentations

• Large-scale repetitive genome structure finding using optical mapping  [Not invited]

  Claire Yik-Lok Chung, Ting-Fung Chan

  The 94th Annual Meeting of the Genetics Society of Japan
• OMACASE: A modular web-based Python package for optical map data quality report and repeat motif analyses  [Not invited]

  Claire Chung

  The 44th Annual Meeting of the Molecular Biology Society of Japan  2021/12
• Pan-genome Analysis of Wild;cultivated Soybean Germplasms to Investigate Large Genomics Structural Variations  [Invited]

  International Meeting on Multiomics Platform Dvelopment cum AoE Symposium
• Multiple Alignment of Optical Mapping Facilitates Typing in Complex Regions

  Claire Yik-Lok Chung, Alden King-Yung Leung, Ting-Fung Chan

  International Plant & Animal Genome (PAG) XXV

Teaching Experience

Techniques in Biocomputing (TA)Techniques in Biocomputing (TA) The Chinese University of Hong Kong
Techniques in NGS Sequencing Library Preparation (TA)Techniques in NGS Sequencing Library Preparation (TA) The Chinese University of Hong Kong
Cell and Molecular Biology Laboratory (TA)Cell and Molecular Biology Laboratory (TA) The Chinese University of Hong Kong

Association Memberships

• Japanese Society for Bioinformatics   The Genetics Society of Japan   The Molecular Biology Society of Japan   

Academic Contribution

• Frontiers in Bioinformatics - Network Bioinformatics Review Editor

  Date (from-to) :2024/06-Today

  Role: Peer review

  Type: Peer review etc

  Organizer, responsible person: Patrick Aloy
• Research in Computational Molecular Biology (RECOMB)

  Date (from-to) :2017/05/03-2017/05/07

  Role: Planning etc

  Type: Academic society etc
• Computational and Structural Biotechnology Journal

  Role: Peer review

  Type: Peer review etc

  Organizer, responsible person: Gianni Panagiotou