YUTAKA KIKUCHI

Last Updated :2025/04/03

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Professor
Web Site
https://www.bio.hiroshima-u.ac.jp/devbio/
E-mail
yutakahiroshima-u.ac.jp

Basic Information

Academic Degrees

  • Doctor of Agriculture, The University of Tokyo

Research Fields

  • Informatics;Frontiers of informatics;Life / Health / Medical informatics
  • Biological Sciences;Oncology;Tumor biology
  • Biological Sciences;Genome science;Genome biology

Research Keywords

  • bioinformatics, imaging, cancer, epigenetics

Affiliated Academic Societies

  • The Molecular Biology Society of Japan
  • Japanese Cancer Association

Educational Activity

Course in Charge

  1. 2025, Liberal Arts Education Program1, 1Term, Fundamentals of Biology
  2. 2025, Undergraduate Education, 4Term, Introduction to Biological Sciences B
  3. 2025, Liberal Arts Education Program1, 2Term, Introductory Seminar for First-Year Students
  4. 2025, Undergraduate Education, Second Semester, English Seminar on Biological Science
  5. 2025, Undergraduate Education, 2Term, Advanced Biology
  6. 2025, Undergraduate Education, 2Term, Developmental Biology B
  7. 2025, Undergraduate Education, Second Semester, Seminar for Developmental Biology
  8. 2025, Undergraduate Education, First Semester, Special Study for Graduation
  9. 2025, Undergraduate Education, Second Semester, Special Study for Graduation
  10. 2025, Undergraduate Education, First Semester, Practice for Fundamental Biology III
  11. 2025, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
  12. 2025, Undergraduate Education, First Semester, Practice for Fundamental Biology IV
  13. 2025, Undergraduate Education, 4Term, Biological Informatics
  14. 2025, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Basic Biology
  15. 2025, Graduate Education (Master's Program) , 4Term, Cell Dynamics and Genomics
  16. 2025, Graduate Education (Master's Program) , First Semester, Exercises in Basic Biology A
  17. 2025, Graduate Education (Master's Program) , Second Semester, Exercises in Basic Biology B
  18. 2025, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  19. 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
  20. 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
  21. 2025, Graduate Education (Master's Program) , 3Term, Introduction to Disease Models
  22. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
  23. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
  24. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E

Research Activities

Academic Papers

  1. ★, Microarray Transcriptome datasets of maternal-zygotic DNA methyltransferase 3aa−/− zebrafish during early developmental stages, Data in Brief, 47, 108967, 20230209
    Link to Paper Search Results by DOI
  2. ★, CHRNA1 and its correlated-myogenesis/cell cycle genes are prognosis-related markers of metastatic melanoma, Biochemistry and Biophysics Reports, 33(3), 101425, 20230301
    Link to Paper Search Results by DOI
  3. Radiomic Analysis for Pretreatment Prediction of Recurrence Post-Radiotherapy in Cervical Squamous Cell Carcinoma Cancer, Diagnostics, 12(10), 2346, 20220928
    Link to Paper Search Results by DOI
  4. ★, Understanding Breast Cancers through Spatial and High-Resolution Visualization Using Imaging Technologies, Cancers, 14(17), 4080, 20220823
    Link to Paper Search Results by DOI
  5. ★, Methylome data derived from maternal-zygotic DNA methyltransferase 3aa−/− zebrafish, Data in Brief, in press, 20220805
    Link to Paper Search Results by DOI
  6. ★, Analysis of Melanoma Gene Expression Signatures at the Single-Cell Level Uncovers 45-Gene Signature Related to Prognosis, Biomedicines, 10(7), 1478, 20220622
    Link to Paper Search Results by DOI
  7. ★, Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency, Genes & Genetic Systems, 97(3), 139-152, 20221018
    Link to Paper Search Results by DOI
  8. ★, 3D in vitro co-culture disc for spatiotemporal image analysis of cancer-stromal cell interaction, BIOMATERIALS SCIENCE, 9(12), 4448-4458, 20210621
    Link to Paper Search Results by DOI
  9. ★, Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates., bioRxiv, 20210813
    Link to Paper Search Results by DOI
  10. Anticancer polymers designed for killing dormant prostate cancer cells, SCIENTIFIC REPORTS, 9, 20190131
    Link to Paper Search Results by DOI
  11. The N-terminal domain of gastrulation brain homeobox 2 (Gbx2) is required for iridophore specification in zebrafish., Biochemical and Biophysical Research Communications, 502, 104-109, 20180701
    Link to Paper Search Results by DOI
  12. ★, Leucine/glutamine and v-ATPase/lysosomal acidification via mTORC1 activation are required for position-dependent regeneration., Scientific Reports, 8(1), 8278, 20180329
    Link to Paper Search Results by DOI
  13. Unusual light-reflecting pigment cells appear in the Xenopus neural tube culture system in the presence of guanosine., Tissue and Cell, 54, 55-58, 20180809
    Link to Paper Search Results by DOI
  14. Histone H3 lysine 27 trimethylation leads to loss of mesendodermal competence during gastrulation in zebrafish ectodermal cells., Zoological Science, 34, 64-71, 20170201
    Link to Paper Search Results by DOI
  15. Magnetically tunable control of light reflection in an unusual optical protein of squid., AIP ADVANCES, 7, 056722-056722-6, 201702
    Link to Paper Search Results by DOI
  16. A limited role for zebrafish Planar Cell Polarity during early endoderm morphogenesis., Biology Open, 6, 531-539, 201703
    Link to Paper Search Results by DOI
  17. Sfrp5 identifies murine cardiac progenitors for all myocardial structures except for the right ventricle., Nature Communications, 8, 14664, 201703
    Link to Paper Search Results by DOI
  18. ★, Nuclear movement regulated by non-Smad Nodal signaling via JNK is associated with Smad signal transduction during zebrafish endoderm specification., Development, 144(21), 4015-4025, 20171101
    Link to Paper Search Results by DOI
  19. Temporal effects of Notch signaling and potential cooperation with multiple downstream effectors on adenohypophysis cell specification in zebrafish, Gnens to Cells, 21(5), 492-504, 201603
    Link to Paper Search Results by DOI
  20. Expression patterns of dnmt3aa, dnmt3ab, and dnmt4 during development and fin regeneration in zebrafish, Gene Expression Patterns, 14(2), 105-110, 201403
    Link to Paper Search Results by DOI
  21. ★, Nipbl and Mediator Cooperatively Regulate Gene Expression to Control Limb Development, PLOS Genetics, 10(9), e1004671, 201409
    Link to Paper Search Results by DOI
  22. Decrease in cytosine methylation at CpG island shores and increase in DNA fragmentation during zebrafish aging, Age, 36(1), 103-115, 201402
    Link to Paper Search Results by DOI
  23. ★, Mechanistic target of rapamycin complex 1 signaling regulates cell proliferation, cell survival, and differentiation in regenerating zebrafish fins, BMC Developmental Biology, 14, 42, 20141206
    Link to Paper Search Results by DOI
  24. No Evidence for AID/MBD4-Coupled DNA Demethylation in Zebrafish Embryos, PLOS ONE, 9(12), e114816, 20141223
    Link to Paper Search Results by DOI
  25. ★, Ddx46 Is Required for Multi-Lineage Differentiation of Hematopoietic Stem Cells in Zebrafish, Stem Cells and Development, 22(18), 2532-2542, 20130915
    Link to Paper Search Results by DOI
  26. ★, Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin, Epigenetics, 8(9), 899-906, 20130901
    Link to Paper Search Results by DOI
  27. DEAD-Box Protein Ddx46 Is Required for the Development of the Digestive Organs and Brain in Zebrafish, PLOS ONE, 7(3), 20120319
    Link to Paper Search Results by DOI
  28. Expression patterns of lgr4 and lgr6 during zebrafish development, Gene Expression Patterns, 11(7), 378-383, 201110
    Link to Paper Search Results by DOI
  29. Zebrafish Dmrta2 regulates neurogenesis in the telencephalon, Genes to Cells, 16(11), 1097-1109, 201111
    Link to Paper Search Results by DOI
  30. Cyp26 enzymes function in endoderm to regulate pancreatic field size, Proceedings of the National Academy of Sciences of the United States of America, 106(19), 7864-7869, 20090512
    Link to Paper Search Results by DOI
  31. Identification and characterization of nucleoplasmin 3 as a histone-binding protein in embryonic stem cells, Development Growth & Differentiation, 50(5), 307-320, 200806
    Link to Paper Search Results by DOI
  32. Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX, BMC Genomics, 9, 20080515
    Link to Paper Search Results by DOI
  33. ★, Sdf1/Cxcr4 signaling controls the dorsal migration of endodermal cells during zebrafish gastrulation, Development, 135(15), 2521-2529, 20080801
    Link to Paper Search Results by DOI
  34. Translational enhancement of recombinant protein synthesis in transgenic silkworms by a 5 '-untranslated region of polyhedrin gene of Bombyx mori Nucleopolyhedrovirus, Journal of Bioscience and Bioengineering, 105(6), 595-603, 200806
    Link to Paper Search Results by DOI
  35. Mtx2 directs zebrafish morphogenetic movements during epiboly by regulating microfilament formation., Developmental Biology, 12-22, 200802
    Link to Paper Search Results by DOI
  36. Identification and characterization of nucleoplasmin 3 as a histone-binding protein in embryonic stem cells, Development, growth & differentiation, 50(5), 307-320, 20080601
  37. Initial specification of the epibranchial placode in zebrafish embryos depends on the fibroblast growth factor signal., Developmental Dynamics, 236, 564-571, 200702
    Link to Paper Search Results by DOI
  38. Fgf signaling negatively regulates Nodal-dependent endoderm induction in zebrafish., Developmental biology, 300(2), 200612
    Link to Paper Search Results by DOI
  39. The yolk syncytial layer regulates myocardial migration by influencing extracellular matrix assembly in zebrafish., Development, 133(20), 4063-4072, 200610
    Link to Paper Search Results by DOI
  40. ★, Eomesodermin is a localized maternal determinant required for endoderm induction in zebrafish., Developmental Cell, 9, 523-533, 200510
    Link to Paper Search Results by DOI
  41. Notch signaling can regulate endoderm formation in zebrafish., Developmental Dynamics, 229(4), 756-762, 200404
    Link to Paper Search Results by DOI
  42. ★, The POU domain protein spg (pou2/Oct4) is essential for endoderm formation in cooperation with the HMG domain protein casanova., Developmental Cell, 6, 91-101, 200401
    Link to Paper Search Results by DOI
  43. ★, casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish., 15, 1493-1505, 200106
    Link to Paper Search Results by DOI
  44. Multiple roles for Gata5 in zebrafish endoderm formation., Development, 128, 125-135, 200101
  45. Functional repression of Islet-2 by disruption of complex with Ldb impairs pripheral axonal outgrowth in embryonic zebrafish., Neuron, 30, 423-436, 200103
  46. Molecular diversity in zebrafish NCAM family: three members with different VASE usage and distinct localization., Molecular and Cellular Neuroscience, 18, 119-130, 200107
    Link to Paper Search Results by DOI
  47. Two zebrafish (Danio rerio) antizymes with different expression and activities., Biochemical Journal, 345, 99-106, 200001
    Link to Paper Search Results by DOI
  48. ★, The zebrafish bonnie and clyde gene encodes a Mix family homeodomain protein that regulates the generation of endodermal precursors. , Genes & Development, 14, 1279-1289, 200005
    Link to Paper Search Results by DOI
  49. Compartmentalized expression of zebrafish ten-m3 and ten-m5, homologues of the Drosophila tenm/odd Oz gene, in the central nervous system., Mechanisms of Development, 87, 223-227, 199909
    Link to Paper Search Results by DOI
  50. ★, Ocular and cerebellar defects in zebrafish induced by overexpression of the LIM domains of the Islet-4 LIM/homeodomain protein., Neuron, 18, 369-382, 199703
    Link to Paper Search Results by DOI
  51. Mermaid : A family of short interspersed repetitive elements widespread in vertebrates., Biochemical and Biophysical Research Communications, 220, 226-232, 199603
    Link to Paper Search Results by DOI
  52. Mermaid, A family of short interspersed repetitive element, is useful for the zebrafish genome mapping., Biochemical and Biophysical Research Communications, 220, 233-237, 199603
    Link to Paper Search Results by DOI
  53. Pseudomonas fluorescens KKL101, a benzoic acid degrader in a mixed culture that degrades biphenyl and polychlorinated biphenyls., Bioscience, Biotechnology, and Biochemistry, 59, 2303-2304, 199512
  54. Identification of the bphA and bphB genes of Pseudomonas sp. strain KKS102 involved in degradation of biphenyl and polychlorinated biphenyls., Biochemical and Biophysical Research Communications, 202, 850-856, 199407
    Link to Paper Search Results by DOI
  55. ★, Identification of the bphA4 gene encoding ferredoxin reductase involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102., Journal of Bacteriology, 176, 1689-1694, 199403
    Link to Paper Search Results by DOI
  56. ★, Nucleotide sequence and functional analysis of the meta-cleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102., Journal of Bacteriology, 176, 4269-4276, 199407
    Link to Paper Search Results by DOI

Invited Lecture, Oral Presentation, Poster Presentation

  1. Correlation between nuclear membrane-less organelle positioning in the nucleus and chromatin rheology., Takuya Nara, Haruko Takahashi, Yutaka Kikuchi, The 2021 Annual Conference of the Japanese Society for Bioinformatics, 2022/09/15, With Invitation, Japanese, The Japanese Society for Bioinformatics, Osaka
  2. Engineering-assisted muscle-tendon assemble organoids (assembloids) for analysis of musculotendinous junction formation mechanism., Haruko Takahashi, Shin-Yu Lee, Ikkei Kumoyama, Ruolin Hao, Hikaru Ikeda, Mingcong Xu, Mototsugu Eiraku, Yutaka Kikuchi, The 45th Annual Meeting of the Molecular Biology Society of Japan, 2021/12/03, With Invitation, English
  3. Integrative understanding of musculotendinous junction formation and maturation during musculoskeletal system development in mammals, Haruko Takahashi, Yasuhisa Yamamoto, Ikkei Kumoyama, Hikaru Ikeda, Mingcong Xu, Yutaka Kikuchi, MBSJ2020, 2020/12/04, With Invitation, English, The Molecular Biology Society of Japan, Online
  4. Tissue-constructive approach for understanding the tumor micro-environment by 3D in vitro culture system, Haruko Takahashi, Yutaka Kikuchi, MBSJ2019, 2019/12/03, With Invitation, Japanese, The Molecular Biology Society of Japan, Fukuoka International Congress Center, Fukuoka sunpalace hotel & hall, Marine Messe Fukuoka
  5. Control of cell proliferation in zebrafish fin regeneration -Position-dependent cell proliferation-, Yutaka Kikuchi, 2018/09/12, With Invitation, English
  6. Study on function of melanoma cell expressing neuroendocrine genes in tumorigenesis of melanoma, Shunya Hozumi, Hiroya Katayama, Yukiya Haraoka, Tohru Ishitani, Yutaka Kikuchi, 2018/09/11, With Invitation, English