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Ken Yamada PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentRNA Therapeutics Institute
AddressUMass Chan Medical School
368 Plantation Street
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentRNA Therapeutics Institute


    Collapse Biography 
    Collapse education and training
    Tokyo Institute of Technology, Tokyo, , JapanBS
    Tokyo Institute of Technology, Tokyo, , JapanMS
    Tokyo Institute of Technology, Tokyo, , JapanPHD

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Matsuoka Y, Katsumata Y, Chu PS, Morikawa R, Nakamoto N, Iguchi K, Takahashi K, Kou T, Ito R, Taura K, Yazumi S, Terajima H, Honjo G, Ichihara G, Muramoto Y, Sato K, Maeda R, Hata K, Toriu N, Yanagita M, Tajima M, Fagarasan S, Yamada KI, Sugiura Y. Monitoring ferroptosis in vivo: Iron-driven volatile oxidized lipids as breath biomarkers. Redox Biol. 2025 Oct; 86:103858. PMID: 40925124.
      Citations:    
    2. Davis SM, Hildebrand S, MacMillan HJ, Monopoli KR, Buchwald J, Sousa J, Cooper D, Ly S, Echeverria D, McHugh N, Ferguson C, Coles A, Hariharan VN, O'Reilly D, Tang Q, Furgal R, Yamada K, Alterman JF, Gilbert JW, Knox E, Pineda Y, Weston CN, Baer CE, Pai AA, Khvorova A. Systematic analysis of siRNA and mRNA features impacting fully chemically modified siRNA efficacy. Nucleic Acids Res. 2025 Jun 20; 53(12). PMID: 40548938.
      Citations:    
    3. Weiss A, Gilbert JW, Rivera Flores IV, Belgrad J, Ferguson C, Dogan EO, Wightman N, Mocarski K, Echeverria D, Harkins AL, Summers A, Bramato B, McHugh N, Furgal R, Yamada N, Cooper D, Monopoli K, Godinho BMDC, Hassler MR, Yamada K, Greer P, Henninger N, Brown RH, Khvorova A. RNAi-mediated silencing of SOD1 profoundly extends survival and functional outcomes in ALS mice. Mol Ther. 2025 Aug 06; 33(8):3917-3938. PMID: 40349108.
      Citations:    
    4. Furusho T, Das R, Hakui H, Sairavi A, Adachi K, Galbraith-Liss MS, Rajagopal P, Horikawa M, Luo S, Li L, Yamada K, Andeen N, Dissen GA, Nakai H. Enhancing gene transfer to renal tubules and podocytes by context-dependent selection of AAV capsids. Nat Commun. 2024 12 30; 15(1):10728. PMID: 39737896.
      Citations:    
    5. Miller R, Paquette J, Barker A, Sapp E, McHugh N, Bramato B, Yamada N, Alterman J, Echeveria D, Yamada K, Watts J, Anaclet C, DiFiglia M, Khvorova A, Aronin N. Preventing acute neurotoxicity of CNS therapeutic oligonucleotides with the addition of Ca2+ and Mg2+ in the formulation. Mol Ther Nucleic Acids. 2024 Dec 10; 35(4):102359. PMID: 39554992.
      Citations:    
    6. Yamada K, Hariharan VN, Caiazzi J, Miller R, Ferguson CM, Sapp E, Fakih HH, Tang Q, Yamada N, Furgal RC, Paquette JD, Biscans A, Bramato BM, McHugh N, Summers A, Lochmann C, Godinho BMDC, Hildebrand S, Jackson SO, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Enhancing siRNA efficacy in vivo with extended nucleic acid backbones. Nat Biotechnol. 2025 Jun; 43(6):904-913. PMID: 39090305.
      Citations:    
    7. Gilbert JW, Kennedy Z, Godinho BMDC, Summers A, Weiss A, Echeverria D, Bramato B, McHugh N, Cooper D, Yamada K, Hassler M, Tran H, Gao FB, Brown RH, Khvorova A. Identification of selective and non-selective C9ORF72 targeting in?vivo active siRNAs. Mol Ther Nucleic Acids. 2024 Sep 10; 35(3):102291. PMID: 39233852.
      Citations:    
    8. Allen S, O'Reilly D, Miller R, Sapp E, Summers A, Paquette J, Echeverria Moreno D, Bramato B, McHugh N, Yamada K, Aronin N, DiFiglia M, Khvorova A. mRNA Nuclear Clustering Leads to a Difference in Mutant Huntingtin mRNA and Protein Silencing by siRNAs In Vivo. Nucleic Acid Ther. 2024 08; 34(4):164-172. PMID: 39023561.
      Citations:    
    9. Weiss A, Gilbert JW, Flores IVR, Belgrad J, Ferguson C, Dogan EO, Wightman N, Mocarski K, Echeverria D, Summers A, Bramato B, McHugh N, Furgal R, Yamada N, Cooper D, Monopoli K, Godinho BMDC, Hassler MR, Yamada K, Greer P, Henninger N, Brown RH, Khvorova A. RNAi-mediated silencing of SOD1 profoundly extends survival and functional outcomes in ALS mice. bioRxiv. 2024 Jun 25. PMID: 38979291.
      Citations:    
    10. Belgrad J, Tang Q, Hildebrand S, Summers A, Sapp E, Echeverria D, O'Reilly D, Luu E, Bramato B, Allen S, Cooper D, Alterman J, Yamada K, Aronin N, DiFiglia M, Khvorova A. A programmable dual-targeting siRNA scaffold supports potent two-gene modulation in the central nervous system. Nucleic Acids Res. 2024 Jun 24; 52(11):6099-6113. PMID: 38726879.
      Citations:    
    11. Miller R, Paquette J, Barker A, Sapp E, McHugh N, Bramato B, Yamada N, Alterman J, Echeveria D, Yamada K, Watts J, Anaclet C, DiFiglia M, Khvorova A, Aronin N. Preventing acute neurotoxicity of CNS therapeutic oligonucleotides with the addition of Ca2+ and Mg2+ in the formulation. bioRxiv. 2024 Jun 08. PMID: 38895198.
      Citations:    
    12. Hariharan VN, Nakamura T, Shin M, Tang Q, Sontakke V, Caiazzi J, Hildebrand S, Khvorova A, Yamada K. Phosphatidylcholine head group chemistry alters the extrahepatic accumulation of lipid-conjugated siRNA. Mol Ther Nucleic Acids. 2024 Jun 11; 35(2):102230. PMID: 38938759.
      Citations:    
    13. Yamada N, Karasawa T, Ito J, Yamamuro D, Morimoto K, Nakamura T, Komada T, Baatarjav C, Saimoto Y, Jinnouchi Y, Watanabe K, Miura K, Yahagi N, Nakagawa K, Matsumura T, Yamada KI, Ishibashi S, Sata N, Conrad M, Takahashi M. Inhibition of 7-dehydrocholesterol reductase prevents hepatic ferroptosis under an active state of sterol synthesis. Nat Commun. 2024 Mar 12; 15(1):2195. PMID: 38472233.
      Citations:    
    14. Rana J, Herzog RW, Mu?oz-Melero M, Yamada K, Kumar SRP, Lam AK, Markusic DM, Duan D, Terhorst C, Byrne BJ, Corti M, Biswas M. B cell focused transient immune suppression protocol for efficient AAV readministration to the liver. Mol Ther Methods Clin Dev. 2024 Mar 14; 32(1):101216. PMID: 38440160.
      Citations:    
    15. Bo T, Nohara H, Yamada KI, Miyata S, Fujii J. Ascorbic Acid Protects Bone Marrow from Oxidative Stress and Transient Elevation of Corticosterone Caused by X-ray Exposure in Akr1a-Knockout Mice. Antioxidants (Basel). 2024 Jan 25; 13(2). PMID: 38397750.
      Citations:    
    16. Belgrad J, Tang Q, Hildebrand S, Summers A, Sapp E, Echeverria D, O'Reilly D, Luu E, Bramato B, Allen S, Cooper D, Alterman J, Yamada K, Aronin N, DiFiglia M, Khvorova A. A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system. bioRxiv. 2023 Dec 19. PMID: 38187561.
      Citations:    
    17. Miao MZ, Su QP, Cui Y, Bahnson EM, Li G, Wang M, Yang Y, Collins JA, Wu D, Gu Q, Chubinskaya S, Diekman BO, Yamada KM, Loeser RF. Redox-active endosomes mediate a5?1 integrin signaling and promote chondrocyte matrix metalloproteinase production in osteoarthritis. Sci Signal. 2023 10 31; 16(809):eadf8299. PMID: 37906629.
      Citations:    
    18. Syed F, Krishnan P, Chang G, Langlais SR, Hati S, Yamada K, Lam AK, Talware S, Liu X, Sardar R, Liu J, Mirmira RG, Evans-Molina C. ? Cell microRNAs Function as Molecular Hubs of Type 1 Diabetes Pathogenesis and as Biomarkers of Diabetes Risk. bioRxiv. 2023 Jun 15. PMID: 37398133.
      Citations:    
    19. Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. Res Sq. 2023 Jun 01. PMID: 37398145.
      Citations:    
    20. Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BMDC, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. bioRxiv. 2023 May 26. PMID: 37292886.
      Citations:    
    21. Hildebrand SR, Hedger AK, Yamada K, Watts JK, Khvorova A. Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors. RNA. 2023 07; 29(7):1077-1083. PMID: 37059467.
      Citations:    Fields:    
    22. Hariharan VN, Shin M, Chang CW, O'Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A. 2023 03 14; 120(11):e2219523120. PMID: 36893269.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    23. Bertolini TB, Herzog RW, Kumar SRP, Sherman A, Rana J, Kaczmarek R, Yamada K, Arisa S, Lillicrap D, Terhorst C, Daniell H, Biswas M. Suppression of anti-drug antibody formation against coagulation factor VIII by oral delivery of anti-CD3 monoclonal antibody in hemophilia A mice. Cell Immunol. 2023 03; 385:104675. PMID: 36746071.
      Citations:    
    24. Lee B, An HJ, Kim DH, Lee MK, Jeong HH, Chung KW, Go Y, Seo AY, Kim IY, Seong JK, Yu BP, Lee J, Im E, Lee IK, Lee MS, Yamada KI, Chung HY. SMP30-mediated synthesis of vitamin C activates the liver PPARa/FGF21 axis to regulate thermogenesis in mice. Exp Mol Med. 2022 11; 54(11):2036-2046. PMID: 36434042.
      Citations:    
    25. Conroy F, Miller R, Alterman JF, Hassler MR, Echeverria D, Godinho BMDC, Knox EG, Sapp E, Sousa J, Yamada K, Mahmood F, Boudi A, Kegel-Gleason K, DiFiglia M, Aronin N, Khvorova A, Pfister EL. Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in Huntington's disease models. Nat Commun. 2022 10 03; 13(1):5802. PMID: 36192390.
      Citations: 3     Fields:    Translation:Animals
    26. Kojima I, Onomoto K, Zuo W, Ozawa M, Okuya K, Naitou K, Izumi F, Okajima M, Fujiwara T, Ito N, Yoneyama M, Yamada K, Nishizono A, Sugiyama M, Fujita T, Masatani T. The Amino Acid at Position 95 in the Matrix Protein of Rabies Virus Is Involved in Antiviral Stress Granule Formation in Infected Cells. J Virol. 2022 09 28; 96(18):e0081022. PMID: 36069552.
      Citations:    
    27. Butterfield JSS, Yamada K, Bertolini TB, Syed F, Kumar SRP, Li X, Arisa S, Pi?eros AR, Tapia A, Rogers CA, Li N, Rana J, Biswas M, Terhorst C, Kaufman RJ, de Jong YP, Herzog RW. IL-15 blockade and rapamycin rescue multifactorial loss of factor VIII from AAV-transduced hepatocytes in hemophilia A mice. Mol Ther. 2022 12 07; 30(12):3552-3569. PMID: 35821634.
      Citations:    
    28. Yamada K, Hildebrand S, Davis SM, Miller R, Conroy F, Sapp E, Caiazzi J, Alterman JF, Roux L, Echeverria D, Hassler MR, Pfister EL, DiFiglia M, Aronin N, Khvorova A. Structurally constrained phosphonate internucleotide linkage impacts oligonucleotide-enzyme interaction, and modulates siRNA activity and allele specificity. Nucleic Acids Res. 2021 12 02; 49(21):12069-12088. PMID: 34850120.
      Citations: 2     Fields:    Translation:Humans
    29. Matsuoka Y, Takahashi M, Sugiura Y, Izumi Y, Nishiyama K, Nishida M, Suematsu M, Bamba T, Yamada KI. Structural library and visualization of endogenously oxidized phosphatidylcholines using mass spectrometry-based techniques. Nat Commun. 2021 11 03; 12(1):6339. PMID: 34732715.
      Citations:    
    30. Yamada K, Kuribayashi K, Inomata N, Noguchi K, Kimitsuki K, Demetria CS, Saito N, Inoue S, Park CH, Kaimori R, Suzuki M, Saito-Obata M, Kamiya Y, Manalo DL, Quiambao BP, Nishizono A. Validation of serum apolipoprotein A1 in rabies virus-infected mice as a biomarker for the preclinical diagnosis of rabies. Microbiol Immunol. 2021 Oct; 65(10):438-448. PMID: 34270107.
      Citations:    
    31. Ishii N, Homma T, Takeda Y, Aung NY, Yamada KI, Miyata S, Asao H, Yamakawa M, Fujii J. Developmental retardation in neonates of aldehyde reductase (AKR1A)-deficient mice is associated with low ascorbic acid and high corticosterone levels. J Nutr Biochem. 2021 05; 91:108604. PMID: 33549889.
      Citations:    
    32. Homma T, Takeda Y, Nakano T, Akatsuka S, Kinoshita D, Kurahashi T, Saitoh S, Yamada KI, Miyata S, Asao H, Goto K, Watanabe T, Watanabe M, Toyokuni S, Fujii J. Defective biosynthesis of ascorbic acid in Sod1-deficient mice results in lethal damage to lung tissue. Free Radic Biol Med. 2021 01; 162:255-265. PMID: 33096250.
      Citations:    
    33. Takahashi T, Inukai M, Sasaki M, Potratz M, Jarusombuti S, Fujii Y, Nishiyama S, Finke S, Yamada K, Sakai H, Sawa H, Nishizono A, Sugiyama M, Ito N. Genetic and Phenotypic Characterization of a Rabies Virus Strain Isolated from a Dog in Tokyo, Japan in the 1940s. Viruses. 2020 08 20; 12(9). PMID: 32825306.
      Citations:    
    34. Yamada K, Herzog RW. When Immune Suppression Goes Wrong. Mol Ther. 2020 06 03; 28(6):1381-1382. PMID: 32416057.
      Citations:    
    35. Levasseur EM, Yamada K, Pi?eros AR, Wu W, Syed F, Orr KS, Anderson-Baucum E, Mastracci TL, Maier B, Mosley AL, Liu Y, Bernal-Mizrachi E, Alonso LC, Scott D, Garcia-Oca?a A, Tersey SA, Mirmira RG. Hypusine biosynthesis in ? cells links polyamine metabolism to facultative cellular proliferation to maintain glucose homeostasis. Sci Signal. 2019 12 03; 12(610). PMID: 31796630.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    36. Rattila S, Dunk CEE, Im M, Grichenko O, Zhou Y, Yanez-Mo M, Blois SM, Yamada KM, Erez O, Gomez-Lopez N, Lye SJ, Hinz B, Romero R, Cohen M, Dveksler G. Interaction of Pregnancy-Specific Glycoprotein 1 With Integrin ?5?1 Is a Modulator of Extravillous Trophoblast Functions. Cells. 2019 10 31; 8(11). PMID: 31683744.
      Citations:    
    37. Ganapathi M, Padgett LR, Yamada K, Devinsky O, Willaert R, Person R, Au PB, Tagoe J, McDonald M, Karlowicz D, Wolf B, Lee J, Shen Y, Okur V, Deng L, LeDuc CA, Wang J, Hanner A, Mirmira RG, Park MH, Mastracci TL, Chung WK. Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder. Am J Hum Genet. 2019 02 07; 104(2):287-298. PMID: 30661771.
      Citations:    
    38. Rajendren S, Manning AC, Al-Awadi H, Yamada K, Takagi Y, Hundley HA. A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme. Nucleic Acids Res. 2018 10 12; 46(18):9647-9659. PMID: 30202880.
      Citations:    
    39. Huang H, Konduru K, Solovena V, Zhou ZH, Kumari N, Takeda K, Nekhai S, Bavari S, Kaplan GG, Yamada KM, Dhawan S. Therapeutic potential of the heme oxygenase-1 inducer hemin against Ebola virus infection. Curr Trends Immunol. 2016; 17:117-123. PMID: 28133423.
      Citations:    
    40. Matsumoto K, Yamasaki T, Nakamura M, Ishikawa J, Ueno M, Nakanishi I, Sekita A, Ozawa Y, Kamada T, Aoki I, Yamada K. Brain contrasting ability of blood-brain-barrier-permeable nitroxyl contrast agents for magnetic resonance redox imaging. Magn Reson Med. 2016 09; 76(3):935-45. PMID: 26414669.
      Citations:    
    41. Zhou ZH, Kumari N, Catalano J, Nekhai S, Wise J, Yamada KM, Dhawan S. Heme oxygenase-1-mediated host cell response inhibits the susceptibility of prostate cancer cells to retroviral infection and retards their proliferation. Curr Trends Immunol. 2013 Jan; 14:53-56. PMID: 25620854.
      Citations:    
    42. Maehr R, Hang HC, Mintern JD, Kim YM, Cuvillier A, Nishimura M, Yamada K, Shirahama-Noda K, Hara-Nishimura I, Ploegh HL. Asparagine endopeptidase is not essential for class II MHC antigen presentation but is required for processing of cathepsin L in mice. J Immunol. 2005 Jun 01; 174(11):7066-74. PMID: 15905550.
      Citations: 42     Fields:    Translation:AnimalsCells
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