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Bioinformatics Core Laboratory｜logoInstitute of Cellular and Organismic Biology, Academia Sinica

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Bioinformatics Core Laboratory

  • profile photo of Tsai-Ming Lu
    Tsai-Ming Lu Professor Tsai-Ming Lu Research ID Professor Tsai-Ming Lu ORCID
    Assistant Research Scientist
    • SpecialtyComparative Genomics & Transcriptomics, Phylogenomics, NGS data analysis
    • E-mailtmlu@gate.sinica.edu.tw
    • Tel02-2789-9532
    • LabR518/ICOB
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Lab IntroductionOpenClose
Experimental design consulting Custom-built analysis pipeline
Differential expression analysis
Gene family evolution analysis
Comparative genomic analysis
Phylogenetic analysis

The ICOB Bioinformatics Core is committed to integrating NGS approaches into diverse researches by providing bioinformatic analysis services. Bioinformatics Core manages the HPC server and covers up-to-date NGS analyses such as RNA-seq (including single-cell), ChIP-seq, ATAC-seq, and de novo genome assembly to facilitate researches across various topics from molecular mechanisms of cellular functions to developmental processes during evolution.

 

Services:
  1. Consulting services on NGS experimental design
  2. NGS data analysis
  3. Developing custom-built analysis pipelines
  4. Maintaining common software and testing new analysis tools
  5. Training course on basic bioinformatics to students

 

In addition to providing NGS analysis services, the Bioinformatics Core participates in xenacoelomorph genome projects and will apply single-cell sequencing approaches to work on Evolutionary Cell Biology, which is a fundamental part of acquiring a full picture of the cell differentiation process.

 

Research interests:
  1. Cell type differentiation and evolution
  2. Gene family evolution and adaptation
  3. Animal phylogeny

 

Ongoing projects:
  • Comparative genomics in Xenacoelomorpha
    Comparative genomics in Xenacoelomorpha

 

  • Cell differentiation in dicyemid
    Dicyema japonicum
Lab MemberOpenClose
Name Job Title Telephone Email Remark
Tsai-Ming Lu Assistant Research Scientist 02-2789-9532 tmlu@gate.sinica.edu.tw
Jia-Yang Su Bioinformatician 02-2787-1523 jys@gate.sinica.edu.tw
Shih-Han Wen Research Assistant 02-2787-1523 moonfish0515@gate.sinica.edu.tw
PublicationOpenClose
  1. Liao IJY*, Lu TM*, Chen ME and Luo YJ. (2023) Spiralian genomics and the evolution of animal genome architecture. Briefings in Functional Genomics 2023; elad029.

  2. Orús-Alcalde A, Lu TM, Børve A and Hejnol A. (2021) The evolution of the metazoan Toll receptor family and its expression during protostome development. BMC Ecology and Evolution 21:208.

  3. Yong LW, Lu TM, Tung CH, Chiou RJ, Li KL and Yu JK. (2021) Somite Compartments in amphioxus and its implications on the evolution of the vertebrate skeletal tissues. Front. Cell Dev. Biol. 9:607057.

  4. Lu TM✉️, Furuya H, Satoh N. (2019) Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts. Zoological Letters 5:32.

  5. Lu TM✉️, Kanda M, Furuya H, Satoh N. (2019) Dicyemid mesozoans: a unique parasitic lifestyle with reduced genome. Genome Biology and Evolution 11: 2232-2243.

  6. Nakashima K, Kimura S, Ogawa Y, Watanabe S, Soma S, Kaneko T, Yamada L, Sawada H, Tung CH, Lu TM, Yu JK, Villar-Briones A, Kikuchi S, Satoh N. (2018) Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota. Nature Communications 9: 3402.

  7. Guzman C, Shinzato C, Lu TM, Conaco C. (2018) Transcriptome analysis of the reef-building octocoral, Heliopora coerulea. Scientific Reports 8: 8397. 

  8. Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, Fujimoto S, Ishikawa M, Liu S, Sasagawa Y, Zhang G, Kuratani S, Yu JK, Kusakabe TG, Khaitovich P, Irie N, EXPANDE Consortium. (2017) Constrained vertebrate evolution by pleiotropic genes. Nature Ecology & Evolution 1: 1722-1730.

  9. Lu TM✉️, Kanda M, Satoh N, Furuya H. (2017) The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution. Zoological Letters 3:6.

  10. Kim JH, Lu TM. (2016) Bio-inspired Janus composite nanoscrolls for on-demand tumor targeting. RSC Advances 6: 17179-17187. 

  11. Soukup V, Yong LW, Lu TM, Huang SW, Kozmik Z, Yu JK. (2015) The Nodal signaling pathway controls left-right asymmetric development in amphioxus. EvoDevo 6:5. 

  12. Li KL, Lu TM, Yu JK. (2014) Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates. EvoDevo 5:20. 

  13. Lu TM, Luo YJ, Yu JK. (2012) BMP and Delta/Notch signaling control the development of amphioxus epidermal sensory neurons: insights into the evolution of the peripheral sensory system. Development 139: 2020-2030.