YUTAKA KIKUCHI
Last Updated :2025/04/03
- Affiliations, Positions
- Graduate School of Integrated Sciences for Life, Professor
- Web Site
- E-mail
- yutaka
hiroshima-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
- 2025, Liberal Arts Education Program1, 1Term, Fundamentals of Biology
- 2025, Undergraduate Education, 4Term, Introduction to Biological Sciences B
- 2025, Liberal Arts Education Program1, 2Term, Introductory Seminar for First-Year Students
- 2025, Undergraduate Education, Second Semester, English Seminar on Biological Science
- 2025, Undergraduate Education, 2Term, Advanced Biology
- 2025, Undergraduate Education, 2Term, Developmental Biology B
- 2025, Undergraduate Education, Second Semester, Seminar for Developmental Biology
- 2025, Undergraduate Education, First Semester, Special Study for Graduation
- 2025, Undergraduate Education, Second Semester, Special Study for Graduation
- 2025, Undergraduate Education, First Semester, Practice for Fundamental Biology III
- 2025, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
- 2025, Undergraduate Education, First Semester, Practice for Fundamental Biology IV
- 2025, Undergraduate Education, 4Term, Biological Informatics
- 2025, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Basic Biology
- 2025, Graduate Education (Master's Program) , 4Term, Cell Dynamics and Genomics
- 2025, Graduate Education (Master's Program) , First Semester, Exercises in Basic Biology A
- 2025, Graduate Education (Master's Program) , Second Semester, Exercises in Basic Biology B
- 2025, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
- 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
- 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
- 2025, Graduate Education (Master's Program) , 3Term, Introduction to Disease Models
- 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
- 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
- 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E
Research Activities
Academic Papers
- ★, Microarray Transcriptome datasets of maternal-zygotic DNA methyltransferase 3aa−/− zebrafish during early developmental stages, Data in Brief, 47, 108967, 20230209
- ★, CHRNA1 and its correlated-myogenesis/cell cycle genes are
prognosis-related markers of metastatic melanoma, Biochemistry and Biophysics Reports, 33(3), 101425, 20230301
- Radiomic Analysis for Pretreatment Prediction of Recurrence Post-Radiotherapy in Cervical Squamous Cell Carcinoma Cancer, Diagnostics, 12(10), 2346, 20220928
- ★, Understanding Breast Cancers through Spatial and High-Resolution Visualization Using Imaging Technologies, Cancers, 14(17), 4080, 20220823
- ★, Methylome data derived from maternal-zygotic DNA methyltransferase 3aa−/− zebrafish, Data in Brief, in press, 20220805
- ★, Analysis of Melanoma Gene Expression Signatures at the Single-Cell Level Uncovers 45-Gene Signature Related to Prognosis, Biomedicines, 10(7), 1478, 20220622
- ★, 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
- ★, 3D in vitro co-culture disc for spatiotemporal image analysis of cancer-stromal cell interaction, BIOMATERIALS SCIENCE, 9(12), 4448-4458, 20210621
- ★, Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates., bioRxiv, 20210813
- Anticancer polymers designed for killing dormant prostate cancer cells, SCIENTIFIC REPORTS, 9, 20190131
- 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
- ★, Leucine/glutamine and v-ATPase/lysosomal acidification via mTORC1 activation are required for position-dependent regeneration., Scientific Reports, 8(1), 8278, 20180329
- 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
- Histone H3 lysine 27 trimethylation leads to loss of mesendodermal competence during gastrulation in zebrafish ectodermal cells., Zoological Science, 34, 64-71, 20170201
- Magnetically tunable control of light reflection in an unusual optical protein of squid., AIP ADVANCES, 7, 056722-056722-6, 201702
- A limited role for zebrafish Planar Cell Polarity during early endoderm morphogenesis., Biology Open, 6, 531-539, 201703
- Sfrp5 identifies murine cardiac progenitors for all myocardial structures except for the right ventricle., Nature Communications, 8, 14664, 201703
- ★, 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
- 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
- Expression patterns of dnmt3aa, dnmt3ab, and dnmt4 during development and fin regeneration in zebrafish, Gene Expression Patterns, 14(2), 105-110, 201403
- ★, Nipbl and Mediator Cooperatively Regulate Gene Expression to Control Limb Development, PLOS Genetics, 10(9), e1004671, 201409
- Decrease in cytosine methylation at CpG island shores and increase in DNA fragmentation during zebrafish aging, Age, 36(1), 103-115, 201402
- ★, Mechanistic target of rapamycin complex 1 signaling regulates cell proliferation, cell survival, and differentiation in regenerating zebrafish fins, BMC Developmental Biology, 14, 42, 20141206
- No Evidence for AID/MBD4-Coupled DNA Demethylation in Zebrafish Embryos, PLOS ONE, 9(12), e114816, 20141223
- ★, Ddx46 Is Required for Multi-Lineage Differentiation of Hematopoietic Stem Cells in Zebrafish, Stem Cells and Development, 22(18), 2532-2542, 20130915
- ★, 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
- DEAD-Box Protein Ddx46 Is Required for the Development of the Digestive Organs and Brain in Zebrafish, PLOS ONE, 7(3), 20120319
- Expression patterns of lgr4 and lgr6 during zebrafish development, Gene Expression Patterns, 11(7), 378-383, 201110
- Zebrafish Dmrta2 regulates neurogenesis in the telencephalon, Genes to Cells, 16(11), 1097-1109, 201111
- 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
- Identification and characterization of nucleoplasmin 3 as a histone-binding protein in embryonic stem cells, Development Growth & Differentiation, 50(5), 307-320, 200806
- Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX, BMC Genomics, 9, 20080515
- ★, Sdf1/Cxcr4 signaling controls the dorsal migration of endodermal cells during zebrafish gastrulation, Development, 135(15), 2521-2529, 20080801
- 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
- Mtx2 directs zebrafish morphogenetic movements during epiboly by regulating microfilament formation., Developmental Biology, 12-22, 200802
- Identification and characterization of nucleoplasmin 3 as a histone-binding protein in embryonic stem cells, Development, growth & differentiation, 50(5), 307-320, 20080601
- Initial specification of the epibranchial placode in zebrafish embryos depends on the fibroblast growth factor signal., Developmental Dynamics, 236, 564-571, 200702
- Fgf signaling negatively regulates Nodal-dependent endoderm induction in zebrafish., Developmental biology, 300(2), 200612
- The yolk syncytial layer regulates myocardial migration by influencing extracellular matrix assembly in zebrafish., Development, 133(20), 4063-4072, 200610
- ★, Eomesodermin is a localized maternal determinant required for endoderm induction in zebrafish., Developmental Cell, 9, 523-533, 200510
- Notch signaling can regulate endoderm formation in zebrafish., Developmental Dynamics, 229(4), 756-762, 200404
- ★, 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
- ★, casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish., 15, 1493-1505, 200106
- Multiple roles for Gata5 in zebrafish endoderm formation., Development, 128, 125-135, 200101
- Functional repression of Islet-2 by disruption of complex with Ldb impairs pripheral axonal outgrowth in embryonic zebrafish., Neuron, 30, 423-436, 200103
- Molecular diversity in zebrafish NCAM family: three members with different VASE usage and distinct localization., Molecular and Cellular Neuroscience, 18, 119-130, 200107
- Two zebrafish (Danio rerio) antizymes with different expression and activities., Biochemical Journal, 345, 99-106, 200001
- ★, 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
- 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
- ★, 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
- Mermaid : A family of short interspersed repetitive elements widespread in vertebrates., Biochemical and Biophysical Research Communications, 220, 226-232, 199603
- Mermaid, A family of short interspersed repetitive element, is useful for the zebrafish genome mapping., Biochemical and Biophysical Research Communications, 220, 233-237, 199603
- 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
- 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
- ★, 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
- ★, 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
Invited Lecture, Oral Presentation, Poster Presentation
- 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
- 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
- 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
- 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
- Control of cell proliferation in zebrafish fin regeneration
-Position-dependent cell proliferation-, Yutaka Kikuchi, 2018/09/12, With Invitation, English
- 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