Aki Ushiki, PhD

Title(s)Associate Specialist, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street, #582
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0002-0889-4577 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of Tsukuba, JapanPh.D.2017
    Collapse Awards and Honors
    American Society of Human Genetics (ASHG) 2020 Virtual Meeting2020Reviewers’ Choice (the top 10% of all poster abstracts)
    American Society of Human Genetics (ASHG) 2020 Virtual Meeting2020Semi-Finalists of ASHG/Charles J. Epstein Trainee Awards
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan2017Dean’s Award for Excellence
    University of Tsukuba, Japan2012Valedictorian award of the College of Biological Sciences

    Collapse Overview 
    Collapse Overview
    My research focus aims to understand how gene-regulatory elements control gene expression in mammals, as it relates to the genetic basis of development, evolution and disease. I am working on several projects: elucidating the mechanism of congenital limb malformation (acheiropodia), dissecting factors involved in bat wing development and understanding the genetic cause of scoliosis.

    I am also developing novel in vivo high-throughput technologies combining my skills in mouse embryo manipulation and genomic techniques. I apply these technologies to evaluate the function of enhancers and disease-associated variants in mice. Employing these novel tools, I will be able to directly connect DNA sequence changes to their phenotypic impact on an organism. This project is currently supported by NHGRI K99 award.

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. Cell Rep. 2024 Mar 08; 43(3):113907. Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. PMID: 38461417.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    2. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. Elife. 2024 Jan 26; 12. Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng RR, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. PMID: 38277211; PMCID: PMC10945706.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    3. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. bioRxiv. 2023 Nov 22. Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng R, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. PMID: 37292598; PMCID: PMC10245954.
      View in: PubMed   Mentions: 1  
    4. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. bioRxiv. 2023 Apr 13. Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. PMID: 37090618; PMCID: PMC10120660.
      View in: PubMed   Mentions:
    5. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun. 2021 04 16; 12(1):2282. Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. PMID: 33863876; PMCID: PMC8052326.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    6. Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome. Hum Mol Genet. 2021 01 21; 29(22):3606-3615. Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N. PMID: 33179741; PMCID: PMC7823110.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    7. The cartilage matrisome in adolescent idiopathic scoliosis. Bone Res. 2020; 8:13. Wise CA, Sepich D, Ushiki A, Khanshour AM, Kidane YH, Makki N, Gurnett CA, Gray RS, Rios JJ, Ahituv N, Solnica-Krezel L. PMID: 32195011; PMCID: PMC7062733.
      View in: PubMed   Mentions: 14  
    8. Recapitulation of gametic DNA methylation and its post-fertilization maintenance with reassembled DNA elements at the mouse Igf2/H19 locus. Epigenetics Chromatin. 2020 01 14; 13(1):2. Matsuzaki H, Kuramochi D, Okamura E, Hirakawa K, Ushiki A, Tanimoto K. PMID: 31937365; PMCID: PMC6958606.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    9. Transvection-like interchromosomal interaction is not observed at the transcriptional level when tested in the Rosa26 locus in mouse. PLoS One. 2019; 14(2):e0203099. Tanimoto K, Matsuzaki H, Okamura E, Ushiki A, Fukamizu A, Engel JD. PMID: 30763343; PMCID: PMC6375575.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    10. Synthetic DNA fragments bearing ICR cis elements become differentially methylated and recapitulate genomic imprinting in transgenic mice. Epigenetics Chromatin. 2018 06 29; 11(1):36. Matsuzaki H, Okamura E, Kuramochi D, Ushiki A, Hirakawa K, Fukamizu A, Tanimoto K. PMID: 29958543; PMCID: PMC6027785.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    11. Homeostatic Response of Mouse renin Gene Transcription in a Hypertensive Environment Is Mediated by a Novel 5' Enhancer. Mol Cell Biol. 2018 04 01; 38(7). Ushiki A, Matsuzaki H, Fukamizu A, Tanimoto K. PMID: 29358217; PMCID: PMC5854831.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    12. Long-Range Control of Renin Gene Expression in Tsukuba Hypertensive Mice. PLoS One. 2016; 11(11):e0166974. Ushiki A, Matsuzaki H, Ishida J, Fukamizu A, Tanimoto K. PMID: 27861631; PMCID: PMC5115840.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    13. De novo DNA methylation through the 5'-segment of the H19 ICR maintains its imprint during early embryogenesis. Development. 2015 Nov 15; 142(22):3833-44. Matsuzaki H, Okamura E, Takahashi T, Ushiki A, Nakamura T, Nakano T, Hata K, Fukamizu A, Tanimoto K. PMID: 26417043.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    14. A mouse renin distal enhancer is essential for blood pressure homeostasis in BAC-rescued renin-null mutant mice. J Recept Signal Transduct Res. 2014 Oct; 34(5):401-9. Tanimoto K, Kanafusa S, Ushiki A, Matsuzaki H, Ishida J, Sugiyama F, Fukamizu A. PMID: 24734888.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
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