Nelson Hayes

Last Updated :2025/06/10

Affiliations, Positions
Graduate School of Biomedical and Health Sciences(Medicine), Associate Professor
Self-introduction
I am a bioinformatician and Java programmer using a data science approach to investigate viral hepatitis and liver diseases. I use a supercomputer to analyze next-generation sequencing data and analyze experimental data using statistics and machine learning. I also develop relational and NoSQL database approaches for data management and build web applications using Java and Angular. Recently I have begun to focus on deep learning and graph analytics to identify host factors implicated in hepatitis B and C infection. In 2003, I received a PhD in biology from the Pennsylvania State University, where I studied evolutionary ecology of mating systems. In 2005, I became a postdoctoral fellow in the Kanehisa Laboratory in the Bioinformatics Center at Kyoto University, where I developed the varDB antigenic variation database to examine mechanisms of immune escape in Plasmodium falciparum and other human pathogens.

Basic Information

Major Professional Backgrounds

  • 2009/10/01, 2010/05/31, Hiroshima University Hospital, Researcher
  • 2010/06/01, 2012/03/31, Hiroshima University, Graduate School of Biomedical Sciences, Assistant Professor (Special Appointment)
  • 2012/04/01, 2013/03/31, Hiroshima University, Institute of Biomedical & Health Sciences, Assistant Professor (Special Appointment)
  • 2013/04/01, 2014/03/31, Hiroshima University, Institute of Biomedical & Health Sciences, Lecturer (Special Appointment)
  • 2014/04/01, 2014/12/31, Hiroshima University, Institute of Biomedical & Health Sciences, Associate Professor (Special Appointment)
  • 2015/01/01, 2019/03/31, Hiroshima University, Institute of Biomedical & Health Sciences, Associate Professor
  • 2003/09/01, 2004/12/31, The Pennsylvania State University, Biology Department, multimedia support assistant
  • 2005/01/01, 2005/10/15, The Pennsylvania State University, Biology Department, Instructor
  • 2005/10/16, 2009/09/30, Kyoto University, Bioinformatics Center, postdoctoral researcher (JSPS)

Educational Backgrounds

  • The Pennsylvania State University, Biology Department, Biology, U.S.A., 1996/08, 2003/12
  • Washington & Jefferson College, Biology Department, Biology, U.S.A., 1992/08, 1996/06

Academic Degrees

  • Doctor of Philosophy, The Pennsylvania State University

Research Fields

  • Medicine,dentistry, and pharmacy;Basic medicine;Virology
  • Medicine,dentistry, and pharmacy;Basic medicine;Human genetics
  • Biological Sciences;Genome science;Medical genome science
  • Informatics;Computing Technologies;Software
  • Informatics;Computing Technologies;High performance computing
  • Biology;Basic biology;Evolutionary biology
  • Biology;Basic biology;Ecology / Environment

Research Keywords

  • hepatitis
  • virology
  • liver
  • Java
  • next generation sequencing
  • supercomputer
  • database

Educational Activity

Course in Charge

  1. 2025, Graduate Education (Doctoral Program) , First Semester, English Presentation
  2. 2025, Graduate Education (Doctoral Program) , First Semester, English Presentation

Research Activities

Academic Papers

  1. Analysis of the treatment outcome of duodenal varices: A retrospective case series of 15 patients from a single institution, DEN OPEN, 5(1), 202504
    Link to Paper Search Results by DOI
  2. Usefulness of serum HBV RNA levels for predicting antiviral response to entecavir treatment in patients with chronic hepatitis B, JOURNAL OF GASTROENTEROLOGY, 60(4), 469-478, 202504
    Link to Paper Search Results by DOI
  3. Real-world data analysis for factors influencing the quality check status in FoundationOne CDx cancer genomic profiling tests, SCIENTIFIC REPORTS, 15(1), 20250212
    Link to Paper Search Results by DOI
  4. Serum IL-6 concentration is a useful biomarker to predict the efficacy of atezolizumab plus bevacizumab in patients with hepatocellular carcinoma, JOURNAL OF GASTROENTEROLOGY, 60(3), 328-339, 202503
    Link to Paper Search Results by DOI
  5. Multiomics Analysis of Liver Molecular Dysregulation Leading to Nonviral-Related Hepatocellular Carcinoma Development, JOURNAL OF PROTEOME RESEARCH, 24(3), 1102-1117, 20250221
    Link to Paper Search Results by DOI
  6. Impact of viral eradication by direct-acting antivirals on clinical outcomes after curative treatment for hepatitis C virus-associated hepatocellular carcinoma, THERAPEUTIC ADVANCES IN GASTROENTEROLOGY, 18, 2025
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  7. A case of complete response to radiotherapy combined with durvalumab and tremelimumab in a patient with unknown primary hepatocellular carcinoma arising in the lumbar spine, CLINICAL JOURNAL OF GASTROENTEROLOGY, 18(1), 107-113, 202502
    Link to Paper Search Results by DOI
  8. Prediction of Hepatocellular Carcinoma After Hepatitis C Virus Sustained Virologic Response Using a Random Survival Forest Model, JCO CLINICAL CANCER INFORMATICS, 8, 202412
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  9. From Omics to Multi-Omics: A Review of Advantages and Tradeoffs, GENES, 15(12), 202412
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  10. Significance of changes in tumor markers in patients treated with durvalumab plus tremelimumab combination therapy as a surrogate marker for tumor response to unresectable hepatocellular carcinoma, HEPATOLOGY RESEARCH, 55(1), 149-154, 202501
    Link to Paper Search Results by DOI
  11. Alteration of Gene Expression After Entecavir and Pegylated Interferon Therapy in HBV-Infected Chimeric Mouse Liver, VIRUSES-BASEL, 16(11), 202411
    Link to Paper Search Results by DOI
  12. The Hepatitis B Virus PreS1/HBsAg Ratio Is a Predictive Marker for the Occurrence of Hepatocellular Carcinoma, LIVERS, 4(3), 364-376, 202409
    Link to Paper Search Results by DOI
  13. Useful Predictor for Exacerbation of Esophagogastric Varices after Hepatitis C Virus Eradication by Direct-Acting Antivirals, LIVERS, 4(3), 352-363, 202409
    Link to Paper Search Results by DOI
  14. The Prevalence and Genotype Distribution of Hepatitis C Virus in Kenya: A Systematic Review and Meta-Analysis, JOURNAL OF EPIDEMIOLOGY AND GLOBAL HEALTH, 14(3), 677-689, 202409
    Link to Paper Search Results by DOI
  15. Real-world efficacy and safety of durvalumab-tremelimumab as second-line systemic therapy after atezolizumab-bevacizumab in unresectable hepatocellular carcinoma, MEDICINE, 103(34), 20240823
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  16. Multi-omics analysis of a fatty liver model using human hepatocyte chimeric mice, SCIENTIFIC REPORTS, 14(1), 20240209
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  17. Peripheral T Cell Subpopulations as a Potential Surrogate Biomarker during Atezolizumab plus Bevacizumab Treatment for Hepatocellular Carcinoma, CANCERS, 16(7), 202404
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  18. Comprehensive genomic profiling testing in Japanese castration-resistant prostate cancer patients: results of a single-center retrospective cohort study, JAPANESE JOURNAL OF CLINICAL ONCOLOGY, 54(2), 175-181, 20240207
    Link to Paper Search Results by DOI
  19. Clinicopathological and genomic features of superficial esophageal squamous cell carcinomas in nondrinker, nonsmoker females, CANCER MEDICINE, 13(4), 202402
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  20. Lenvatinib activates anti-tumor immunity by suppressing immunoinhibitory infiltrates in the tumor microenvironment of advanced hepatocellular carcinoma, COMMUNICATIONS MEDICINE, 3(1), 20231025
    Link to Paper Search Results by DOI
  21. Serum interleukin-6 level predicts the prognosis for patients with alcohol-related acute-on-chronic liver failure, HEPATOLOGY INTERNATIONAL, 17(5), 1225-1232, 202310
    Link to Paper Search Results by DOI
  22. Correlation between serum pro-inflammatory cytokine levels and the prognosis of the patients with acute liver failure, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 38(9), 1637-1646, 202309
    Link to Paper Search Results by DOI
  23. Association of Hepatobiliary Phase of Gadoxetic-Acid-Enhanced MRI Imaging with Immune Microenvironment and Response to Atezolizumab Plus Bevacizumab Treatment, CANCERS, 15(17), 202309
    Link to Paper Search Results by DOI
  24. HBV with precore and basal core promoter mutations exhibits a high replication phenotype and causes ER stress-mediated cell death in humanized liver chimeric mice, HEPATOLOGY, 78(3), 929-942, 202309
    Link to Paper Search Results by DOI
  25. Deficiency of SCAP inhibits HBV pathogenesis via activation of the interferon signaling pathway, VIROLOGY, 585, 248-258, 202308
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  26. Impact and usefulness of the transition to the new MAFLD classification for non-B, non-C HCC: a retrospective cohort study, BMC GASTROENTEROLOGY, 23(1), 20230628
    Link to Paper Search Results by DOI
  27. Hepatitis B Virus (HBV) Upregulates TRAIL-R3 Expression in Hepatocytes Resulting in Escape From Both Cell Apoptosis and Suppression of HBV Replication by TRAIL, JOURNAL OF INFECTIOUS DISEASES, 227(5), 686-695, 20230301
    Link to Paper Search Results by DOI
  28. A novel cDNA-uPA/SCID/Rag2(-/-)/Jak3(-/-) mouse model for hepatitis virus infection and reconstruction of human immune system, JOURNAL OF VIRAL HEPATITIS, 30(3), 262-272, 202303
    Link to Paper Search Results by DOI
  29. The burden of Hepatitis B virus infection in Kenya: A systematic review and meta-analysis, FRONTIERS IN PUBLIC HEALTH, 11, 20230126
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  30. Prevalence of immune-related adverse events and anti-tumor efficacy following immune checkpoint inhibitor therapy in Japanese patients with various solid tumors, BMC CANCER, 22(1), 20221129
    Link to Paper Search Results by DOI
  31. The presence of vessels encapsulating tumor clusters is associated with an immunosuppressive tumor microenvironment in hepatocellular carcinoma, INTERNATIONAL JOURNAL OF CANCER, 151(12), 2278-2290, 20221215
    Link to Paper Search Results by DOI
  32. Road to elimination of HCV: Clinical challenges in HCV management, LIVER INTERNATIONAL, 42(9), 1935-1944, 202208
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  33. Untying relaxed circular DNA of hepatitis B virus by polymerase reaction provides a new option for accurate quantification and visualization of covalently closed circular DNA, JOURNAL OF GENERAL VIROLOGY, 103(2), 2022
    Link to Paper Search Results by DOI
  34. Construction of an anti-hepatitis B virus preS1 antibody and usefulness of preS1 measurement for chronic hepatitis B patients Anti-HBV PreS1 antibody, JOURNAL OF INFECTION, 84(3), 391-399, 202203
    Link to Paper Search Results by DOI
  35. Underestimation of impaired glucose tolerance and usefulness of a continuous glucose monitoring system in chronic liver disease, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 37(3), 592-599, 202203
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  36. Identification of novel HCV deletion mutants in chronic hepatitis C patients, ANTIVIRAL THERAPY, 17(8), 1551-1561, 2012
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  37. Common variation of IL28 affects gamma-GTP levels and inflammation of the liver in chronically infected hepatitis C virus patients, JOURNAL OF HEPATOLOGY, 53(3), 439-443, 201009
    Link to Paper Search Results by DOI
  38. Elimination of hepatitis C virus by short term NS3-4A and NS5B inhibitor combination therapy in human hepatocyte chimeric mice, JOURNAL OF HEPATOLOGY, 54(5), 872-878, 201105
    Link to Paper Search Results by DOI
  39. Rapid Emergence of Telaprevir Resistant Hepatitis C Virus Strain from Wildtype Clone In Vivo, HEPATOLOGY, 54(3), 781-788, 201109
    Link to Paper Search Results by DOI
  40. Predictive value of the IL28B polymorphism on the effect of interferon therapy in chronic hepatitis C patients with genotypes 2a and 2b, JOURNAL OF HEPATOLOGY, 54(3), 408-414, 201103
    Link to Paper Search Results by DOI
  41. Prediction of Response to Peginterferon-Alfa-2b Plus Ribavirin Therapy in Japanese Patients Infected With Hepatitis C Virus Genotype 1b, JOURNAL OF MEDICAL VIROLOGY, 83(6), 981-988, 201106
    Link to Paper Search Results by DOI
  42. Common Genetic Polymorphism of ITPA Gene Affects Ribavirin-Induced Anemia and Effect of Peg-Interferon Plus Ribavirin Therapy, JOURNAL OF MEDICAL VIROLOGY, 83(6), 1048-1057, 201106
    Link to Paper Search Results by DOI
  43. IL-28B predicts response to chronic hepatitis C therapy - fine-mapping and replication study in Asian populations, JOURNAL OF GENERAL VIROLOGY, 92, 1071-1081, 201105
    Link to Paper Search Results by DOI
  44. IL28 variation affects expression of interferon stimulated genes and peg-interferon and ribavirin therapy, JOURNAL OF HEPATOLOGY, 54(6), 1094-1101, 201106
    Link to Paper Search Results by DOI
  45. ME3738 enhances the effect of interferon and inhibits hepatitis C virus replication both in vitro and in vivo, JOURNAL OF HEPATOLOGY, 55(1), 11-18, 201107
    Link to Paper Search Results by DOI
  46. IL28B But Not ITPA Polymorphism Is Predictive of Response to Pegylated Interferon, Ribavirin, and Telaprevir Triple Therapy in Patients With Genotype 1 Hepatitis C, JOURNAL OF INFECTIOUS DISEASES, 204(1), 84-93, 2011
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  47. Effects of Hepatitis B Virus Infection on the Interferon Response in Immunodeficient Human Hepatocyte Chimeric Mice, JOURNAL OF INFECTIOUS DISEASES, 204(2), 224-228, 2011
    Link to Paper Search Results by DOI
  48. Inverse Association of IL28B Genotype and Liver mRNA Expression of Genes Promoting or Suppressing Antiviral State, JOURNAL OF MEDICAL VIROLOGY, 83(9), 1597-1607, 201109
    Link to Paper Search Results by DOI
  49. Variation in the DEPDC5 locus is associated with progression to hepatocellular carcinoma in chronic hepatitis C virus carriers, NATURE GENETICS, 43(8), 797-U108, 201108
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  50. Hepatitis C Virus Infection Suppresses the Interferon Response in the Liver of the Human Hepatocyte Chimeric Mouse, PLOS ONE, 6(8), 2011
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  51. Impact of Viral Amino Acid Substitutions and Host Interleukin-28B Polymorphism on Replication and Susceptibility to Interferon of Hepatitis C Virus, HEPATOLOGY, 54(3), 764-771, 201109
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  52. Serum PAI-1 is a novel predictor for response to pegylated interferon-a-2b plus ribavirin therapy in chronic hepatitis C virus infection, JOURNAL OF VIRAL HEPATITIS, 19(2), E126-E133, 201202
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  53. Hepatocellular carcinoma: Towards personalized medicine, CANCER SCIENCE, 103(5), 846-850, 201205
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  54. Toward the Establishment of a Prediction System for the Personalized Treatment of Chronic Hepatitis C, JOURNAL OF INFECTIOUS DISEASES, 205(2), 204-210, 2012
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  55. Genetics of IL28B and HCV-response to infection and treatment, NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY, 9(7), 406-417, 201207
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  56. Severe necroinflammatory reaction caused by natural killer cell-mediated Fas/Fas ligand interaction and dendritic cells in human hepatocyte chimeric mouse, HEPATOLOGY, 56(2), 555-566, 201208
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  57. Impact of interleukin-28B genotype on in vitro and in vivo systems of hepatitis C virus replication, HEPATOLOGY RESEARCH, 42(9), 841-853, 201209
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  58. IL28B polymorphism is associated with fatty change in the liver of chronic hepatitis C patients, JOURNAL OF GASTROENTEROLOGY, 47(7), 834-844, 201207
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  59. Hepatitis B Virus-Specific miRNAs and Argonaute2 Play a Role in the Viral Life Cycle, PLOS ONE, 7(10), 2012
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  60. Treatment of chronic hepatitis C virus infection in Japan: update on therapy and guidelines, JOURNAL OF GASTROENTEROLOGY, 48(1), 1-12, 201301
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  61. Interleukin-28B polymorphisms and hepatitis C virus clearance, GENOME MEDICINE, 5, 2013
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  62. Circulating microRNA-22 correlates with microRNA-122 and represents viral replication and liver injury in patients with chronic hepatitis B, JOURNAL OF MEDICAL VIROLOGY, 85(5), 789-798, 201305
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  63. HLA-DQB1*03 Confers Susceptibility to Chronic Hepatitis C in Japanese: A Genome-Wide Association Study, PLOS ONE, 8(12), 2013
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  64. A Nonsynonymous Polymorphism in Semaphorin 3A as a Risk Factor for Human Unexplained Cardiac Arrest with Documented Ventricular Fibrillation, PLOS GENETICS, 9(4), 201304
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  65. Combination therapies with NS5A, NS3 and NS5B inhibitors on different genotypes of hepatitis C virus in human hepatocyte chimeric mice, GUT, 62(7), 1055-1061, 201307
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  66. A Translational Study of Resistance Emergence Using Sequential Direct-Acting Antiviral Agents for Hepatitis C Using Ultra-Deep Sequencing, AMERICAN JOURNAL OF GASTROENTEROLOGY, 108(9), 1464-1472, 201309
    Link to Paper Search Results by DOI
  67. Serum HBV RNA and HBeAg are useful markers for the safe discontinuation of nucleotide analogue treatments in chronic hepatitis B patients, JOURNAL OF GASTROENTEROLOGY, 48(10), 1188-1204, 201310
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  68. Dental infection of Porphyromonas gingivalis exacerbates high fat diet-induced steatohepatitis in mice, JOURNAL OF GASTROENTEROLOGY, 48(11), 1259-1270, 201311
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  69. A novel TK-NOG based humanized mouse model for the study of HBV and HCV infections, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 441(1), 230-235, 2013
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  70. Ultradeep Sequencing Study of Chronic Hepatitis C Virus Genotype 1 Infection in Patients Treated with Daclatasvir, Peginterferon, and Ribavirin, ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 58(4), 2105-2112, 201404
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  71. Effect of vitamin D supplementation on pegylated interferon/ribavirin therapy for chronic hepatitis C genotype 1b: a randomized controlled trial, JOURNAL OF VIRAL HEPATITIS, 21(5), 348-356, 201405
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  72. Human microRNA hsa-miR-1231 suppresses hepatitis B virus replication by targeting core mRNA, JOURNAL OF VIRAL HEPATITIS, 21(9), E89-E97, 201409
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  73. IFNL4/IL-28B haplotype structure and its impact on susceptibility to hepatitis C virus and treatment response in the Japanese population, JOURNAL OF GENERAL VIROLOGY, 95, 1297-1306, 201406
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  74. New Insight Into the Enhanced Effect of Pegylated Interferon-alpha, HEPATOLOGY, 60(4), 1435-1437, 201410
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  75. Emergence of resistant variants detected by ultra-deep sequencing after asunaprevir and daclatasvir combination therapy in patients infected with hepatitis C virus genotype 1, JOURNAL OF VIRAL HEPATITIS, 22(2), 158-165, 201502
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  76. Predictive value of the IFNL4 polymorphism on outcome of telaprevir, peginterferon, and ribavirin therapy for older patients with genotype 1b chronic hepatitis C, JOURNAL OF GASTROENTEROLOGY, 49(12), 1548-1556, 201412
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  77. Emerging treatments for chronic hepatitis C, JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION, 114(3), 204-215, 201503
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  78. Differences in serum microRNA profiles in hepatitis B and C virus infection, JOURNAL OF INFECTION, 70(3), 273-287, 201503
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  79. Interferon lambda 4 polymorphism affects on outcome of telaprevir, pegylated interferon and ribavirin combination therapy for chronic hepatitis C, HEPATOLOGY RESEARCH, 44(14), E447-E454, 201412
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  80. Effect of prolonged administration of pegylated interferon/ribavirin therapy in genotypes 2a and 2b: Propensity score-matched analysis, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 30(2), 337-344, 201502
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  81. Ribavirin dose reduction during telaprevir/ribavirin/peg-interferon therapy overcomes the effect of the ITPA gene polymorphism, JOURNAL OF VIRAL HEPATITIS, 22(2), 166-174, 201502
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  82. Optimizing triple therapy and IFN/RBV-free regimens for hepatitis C virus infection, EXPERT REVIEW OF GASTROENTEROLOGY & HEPATOLOGY, 9(1), 21-30, 201501
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  83. Hepatitis C Virus (HCV) Reactivation Caused by Steroid Therapy for Dermatomyositis, INTERNAL MEDICINE, 53(23), 2689-2693, 2014
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  84. Two Patients Treated With Simeprevir Plus Pegylated-Interferon and Ribavirin Triple Therapy for Recurrent Hepatitis C After Living Donor Liver Transplantation: Case Report, TRANSPLANTATION PROCEEDINGS, 47(3), 809-814, 201504
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  85. Novel Robust in Vitro Hepatitis B Virus Infection Model Using Fresh Human Hepatocytes Isolated from Humanized Mice, AMERICAN JOURNAL OF PATHOLOGY, 185(5), 1275-1285, 201505
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  86. Rapid, Sensitive, and Accurate Evaluation of Drug Resistant Mutant (NS5A-Y93H) Strain Frequency in Genotype 1b HCV by Invader Assay, PLOS ONE, 10(6), 2015
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  87. Association between variants in the interferon lambda 4 locus and substitutions in the hepatitis C virus non-structural protein 5A, JOURNAL OF HEPATOLOGY, 63(3), 554-563, 201509
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  88. Human Cytotoxic T Lymphocyte-Mediated Acute Liver Failure and Rescue by Immunoglobulin in Human Hepatocyte Transplant TK-NOG Mice, JOURNAL OF VIROLOGY, 89(19), 10087-10096, 201510
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  89. Long term persistence of NS5A inhibitor-resistant hepatitis C virus in patients who failed daclatasvir and asunaprevir therapy, JOURNAL OF MEDICAL VIROLOGY, 87(11), 1913-1920, 201511
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  90. HCV Drug Resistance Challenges in Japan: The Role of Pre-Existing Variants and Emerging Resistant Strains in Direct Acting Antiviral Therapy, VIRUSES-BASEL, 7(10), 5328-5342, 201510
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  91. Effect of tenofovir disoproxil fumarate on drug-resistant HBV clones, JOURNAL OF INFECTION, 72(1), 91-102, 201601
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  92. Early events in hepatitis B virus infection: From the cell surface to the nucleus, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 31(2), 302-309, 201602
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  93. Elimination of HCV via a non-ISG-mediated mechanism by vaniprevir and BMS-788329 combination therapy in human hepatocyte chimeric mice, VIRUS RESEARCH, 213, 62-68, 2016
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  94. MicroRNAs as Biomarkers for Liver Disease and Hepatocellular Carcinoma, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 17(3), 201603
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  95. HBV culture and infectious systems, HEPATOLOGY INTERNATIONAL, 10(4), 559-566, 201607
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  96. Hepatitis C virus dynamics and cellular gene expression in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy, JOURNAL OF VIRAL HEPATITIS, 23(9), 708-717, 201609
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  97. Daclatasvir and asunaprevir treatment improves liver function parameters and reduces liver fibrosis markers in chronic hepatitis C patients, HEPATOLOGY RESEARCH, 46(8), 758-764, 201607
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  98. Improvement of renal dysfunction in a patient with hepatitis C virus-related liver cirrhosis by daclatasvir and asunaprevir combination therapy: A case report, HEPATOLOGY RESEARCH, 46(9), 944-948, 201608
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  99. Three patients treated with daclatasvir and asunaprevir for recurrent hepatitis C after liver transplantation: Case report, HEPATOLOGY RESEARCH, 46(7), 707-712, 201606
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  100. Antiviral effects of anti-HBs immunoglobulin and vaccine on HBs antigen seroclearance for chronic hepatitis B infection, JOURNAL OF GASTROENTEROLOGY, 51(11), 1073-1080, 201611
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  101. Effects of ITPA polymorphism on decrease of hemoglobin during simeprevir, peg-interferon, and ribavirin combination treatment for chronic hepatitis C, HEPATOLOGY RESEARCH, 46(12), 1256-1263, 201611
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  102. Combination therapies with daclatasvir and asunaprevir on NS3-D168 mutated HCV in human hepatocyte chimeric mice, ANTIVIRAL THERAPY, 21(4), 307-315, 2016
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  103. Hepatitis C virus treatment update - A new era of all-oral HCV treatment, ADVANCES IN DIGESTIVE MEDICINE, 3(4), 153-160, 201602
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  104. Protease Inhibitor Resistance Remains Even After Mutant Strains Become Undetectable by Deep Sequencing, JOURNAL OF INFECTIOUS DISEASES, 214(11), 1687-1694, 2016
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  105. The practical management of chronic hepatitis C infection in Japan - dual therapy of daclatasvir plus asunaprevir, EXPERT REVIEW OF GASTROENTEROLOGY & HEPATOLOGY, 11(2), 103-113, 201702
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  106. Interferon Stimulated Genes and Innate Immune Activation Following Infection With Hepatitis B and C Viruses, JOURNAL OF MEDICAL VIROLOGY, 89(3), 388-396, 201703
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  107. Efficacy and Safety of Daclatasvir Plus Asunaprevir Therapy for Chronic Hepatitis C Patients With Renal Dysfunction, JOURNAL OF MEDICAL VIROLOGY, 89(4), 665-671, 201704
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  108. Interferon alpha treatment stimulates interferon gamma expression in type I NKT cells and enhances their antiviral effect against hepatitis C virus, PLOS ONE, 12(3), 2017
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  109. The relationship between HBcrAg and HBV reinfection in HBV related post-liver transplantation patients, JOURNAL OF GASTROENTEROLOGY, 52(3), 366-375, 201705
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  110. Real-world efficacy and safety of daclatasvir and asunaprevir therapy for hepatitis C virus-infected cirrhosis patients, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 32(3), 645-650, 201705
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  111. IFNL4 polymorphism effects on outcome of simeprevir, peginterferon, and ribavirin therapy for older patients with genotype 1 chronic hepatitis C, HEPATOLOGY RESEARCH, 47(3), E5-E13, 201705
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  112. Safety and efficacy of dual therapy with daclatasvir and asunaprevir for older patients with chronic hepatitis C, JOURNAL OF GASTROENTEROLOGY, 52(4), 504-511, 201704
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  113. Why highly effective drugs are not enough: the need for an affordable solution to eliminating HCV, EXPERT REVIEW OF CLINICAL PHARMACOLOGY, 10(6), 583-594, 2017
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  114. ITPA polymorphism effects on decrease of hemoglobin during sofosbuvir and ribavirin combination treatment for chronic hepatitis C, JOURNAL OF GASTROENTEROLOGY, 52(6), 746-753, 201706
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  115. Development of a Novel Site-Specific Pegylated Interferon Beta for Antiviral Therapy of Chronic Hepatitis B Virus, ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 61(6), 201706
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  116. Usefulness of humanized cDNA-uPA/SCID mice for the study of hepatitis B virus and hepatitis C virus virology, JOURNAL OF GENERAL VIROLOGY, 98(5), 1040-1047, 201705
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  117. The risks of hepatocellular carcinoma development after HCV eradication are similar between patients treated with peg-interferon plus ribavirin and direct-acting antiviral therapy, PLOS ONE, 12(8), 2017
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  118. Emergence of drug resistance-associated variants and changes in serum lipid profiles in sofosbuvir plus ledipasvir-treated chronic hepatitis C patients, JOURNAL OF MEDICAL VIROLOGY, 89(11), 1963-1972, 201711
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  119. Three patients treated with sofosbuvir plus ledipasvir for recurrent hepatitis C after liver transplantation, CLINICAL JOURNAL OF GASTROENTEROLOGY, 10(2), 179-184, 201704
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  120. Wisteria floribunda agglutinin positive Mac-2-binding protein level increases in patients with acute liver injury, JOURNAL OF GASTROENTEROLOGY, 52(12), 1252-1257, 201712
    Link to Paper Search Results by DOI
  121. Serum HMGB1 concentrations at 4 weeks is a useful predictor of extreme poor prognosis for advanced hepatocellular carcinoma treated with sorafenib and hepatic arterial infusion chemotherapy, JOURNAL OF GASTROENTEROLOGY, 53(1), 107-118, 201801
    Link to Paper Search Results by DOI
  122. Involvement of Porphyromonas gingivalis in the progression of non-alcoholic fatty liver disease, JOURNAL OF GASTROENTEROLOGY, 53(2), 269-280, 201802
    Link to Paper Search Results by DOI
  123. Efficacy and safety of ledipasvir/sofosbuvir with ribavirin in chronic hepatitis C patients who failed daclatasvir/asunaprevir therapy: pilot study, JOURNAL OF GASTROENTEROLOGY, 53(4), 548-556, 201804
    Link to Paper Search Results by DOI
  124. Persistent Loss of Hepatitis B Virus Markers in Serum without Cellular Immunity by Combination of Peginterferon and Entecavir Therapy in Humanized Mice, ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 61(9), 201709
    Link to Paper Search Results by DOI
  125. Prevalence of NS5A resistance associated variants in NS5A inhibitor treatment failures and an effective treatment for NS5A-P32 deleted hepatitis C virus in humanized mice, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 500(2), 152-157, 20180602
    Link to Paper Search Results by DOI
  126. Limitations of daclatasvir/asunaprevir plus beclabuvir treatment in cases of NS5A inhibitor treatment failure, JOURNAL OF GENERAL VIROLOGY, 99(8), 1058-1065, 201808
    Link to Paper Search Results by DOI
  127. Chromosomal Abnormalities in Human Lymphocytes after Computed Tomography Scan Procedure, RADIATION RESEARCH, 190(4), 424-432, 201810
    Link to Paper Search Results by DOI
  128. Advanced liver fibrosis effects on the response to sofosbuvir-based antiviral therapies for chronic hepatitis C, JOURNAL OF MEDICAL VIROLOGY, 90(12), 1834-1840, 201812
    Link to Paper Search Results by DOI
  129. Molecular Mechanisms of Hepatocarcinogenesis Following Sustained Virological Response in Patients with Chronic Hepatitis C Virus Infection, VIRUSES-BASEL, 10(10), 201810
    Link to Paper Search Results by DOI
  130. CTL-associated and NK cell-associated immune responses induce different HBV DNA reduction patterns in chronic hepatitis B patients, JOURNAL OF VIRAL HEPATITIS, 25(12), 1555-1564, 201812
    Link to Paper Search Results by DOI
  131. Endoplasmic reticulum-mediated induction of interleukin-8 occurs by hepatitis B virus infection and contributes to suppression of interferon responsiveness in human hepatocytes, VIROLOGY, 525, 48-61, 201812
    Link to Paper Search Results by DOI
  132. The association between serum cytokine and chemokine levels and antiviral response by entecavir treatment in chronic hepatitis B patients, ANTIVIRAL THERAPY, 23(3), 239-248, 2018
    Link to Paper Search Results by DOI
  133. Real-world efficacy of glecaprevir plus pibrentasvir for chronic hepatitis C patient with previous direct-acting antiviral therapy failures, JOURNAL OF GASTROENTEROLOGY, 54(3), 291-296, 201903
    Link to Paper Search Results by DOI
  134. Reduction of hepatitis B surface antigen in sequential versus add-on pegylated interferon to nucleoside/nucleotide analogue therapy in HBe-antigen-negative chronic hepatitis B patients: a pilot study, ANTIVIRAL THERAPY, 23(8), 639-646, 2018
    Link to Paper Search Results by DOI
  135. Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy, CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY, 1(5), 516-534, 201509
    Link to Paper Search Results by DOI
  136. Regulation of the Hepatitis B virus replication and gene expression by the multi-functional protein TARDBP, SCIENTIFIC REPORTS, 9, 20190611
    Link to Paper Search Results by DOI
  137. Comparison of intracellular responses between HBV genotype A and C infection in human hepatocyte chimeric mice, JOURNAL OF GASTROENTEROLOGY, 54(7), 650-659, 201907
    Link to Paper Search Results by DOI
  138. Efficacy of glecaprevir and pibrentasvir treatment for genotype 1b hepatitis C virus drug resistance-associated variants in humanized mice, JOURNAL OF GENERAL VIROLOGY, 100(7), 1123-1131, 201907
    Link to Paper Search Results by DOI
  139. Management of HCV patients in cases of direct-acting antiviral failure, EXPERT REVIEW OF GASTROENTEROLOGY & HEPATOLOGY, 13(9), 839-848, 20190902
    Link to Paper Search Results by DOI
  140. Genomic landscape of epithelium with low-grade atypia on gastric cancer after Helicobacter pylori eradiation therapy, JOURNAL OF GASTROENTEROLOGY, 54(10), 907-915, 201910
    Link to Paper Search Results by DOI
  141. Pruritus in patients with chronic liver disease and serum autotaxin levels in patients with primary biliary cholangitis, BMC GASTROENTEROLOGY, 19(1), 20191024
    Link to Paper Search Results by DOI
  142. Regression of Idiopathic Thrombocytopenic Purpura in a Patient With Eradication of Hepatitis C Virus by Direct-Acting Antivirals, HEPATOLOGY, 71(1), 389-391, 202001
    Link to Paper Search Results by DOI
  143. Successful retreatment with 12 weeks of glecaprevir and pibrentasvir for a genotype 2a HCV-infected hemodialysis patient who failed to respond to 8 weeks of prior glecaprevir and pibrentasvir therapy, CLINICAL JOURNAL OF GASTROENTEROLOGY, 13(2), 267-270, 202004
    Link to Paper Search Results by DOI
  144. Genomic Characterization of Non-Invasive Differentiated-Type Gastric Cancer in the Japanese Population, CANCERS, 12(2), 202002
    Link to Paper Search Results by DOI
  145. Circulating cytokines and angiogenic factors based signature associated with the relative dose intensity during treatment in patients with advanced hepatocellular carcinoma receiving lenvatinib, THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY, 12, 202005
    Link to Paper Search Results by DOI
  146. Tumor Fibroblast Growth Factor Receptor 4 Level Predicts the Efficacy of Lenvatinib in Patients With Advanced Hepatocellular Carcinoma, CLINICAL AND TRANSLATIONAL GASTROENTEROLOGY, 11, 202005
  147. Risk factors for histological progression of non-alcoholic steatohepatitis analyzed from repeated biopsy cases, JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, 35(8), 1412-1419, 202008
    Link to Paper Search Results by DOI
  148. Liver fibrosis assessments using FibroScan, virtual-touch tissue quantification, the FIB-4 index, and mac-2 binding protein glycosylation isomer levels compared with pathological findings of liver resection specimens in patients with hepatitis C infection, BMC GASTROENTEROLOGY, 20(1), 20200925
    Link to Paper Search Results by DOI
  149. Impact of viral eradication by direct-acting antivirals on the risk of hepatocellular carcinoma development, prognosis, and portal hypertension in hepatitis C virus-related compensated cirrhosis patients, HEPATOLOGY RESEARCH, 50(11), 1222-1233, 202011
    Link to Paper Search Results by DOI
  150. Real-word efficacy of sofosbuvir, velpatasvir plus ribavirin therapy for chronic hepatitis patients who failed to prior DAA therapy with NS5A-P32 deletion mutated HCV infection, CLINICAL JOURNAL OF GASTROENTEROLOGY, 13(6), 1233-1238, 202012
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  151. Real-world efficacy of sofosbuvir plus velpatasvir therapy for patients with hepatitis C virus-related decompensated cirrhosis, HEPATOLOGY RESEARCH, 50(11), 1234-1243, 202011
    Link to Paper Search Results by DOI
  152. PNPLA3andHLA-DQB1polymorphisms are associated with hepatocellular carcinoma after hepatitis C virus eradication, JOURNAL OF GASTROENTEROLOGY, 55(12), 1162-1170, 202012
    Link to Paper Search Results by DOI
  153. Abatacept treatment for patients with severe acute hepatitis caused by hepatitis B virus infection-Pilot study, JOURNAL OF VIRAL HEPATITIS, 28(2), 400-409, 202102
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  154. Signal Activation of Hepatitis B Virus-Related Hepatocarcinogenesis by Up-regulation of SUV39h1, JOURNAL OF INFECTIOUS DISEASES, 222(12), 2061-2070, 20201215
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  155. A case with life-threatening secondary sclerosing cholangitis caused by nivolumab, CLINICAL JOURNAL OF GASTROENTEROLOGY, 14(1), 283-287, 202102
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  156. Clinical Usefulness of Serum Autotaxin for Early Prediction of Relapse in Male Patients with Type 1 Autoimmune Pancreatitis, DIGESTIVE DISEASES AND SCIENCES, 66(4), 1268-1275, 202104
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  157. Efficacy of Lusutrombopag for Thrombocytopenia in Patients with Chronic Liver Disease Scheduled to Undergo Invasive Procedures, INTERNAL MEDICINE, 60(6), 829-837, 2021
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  158. A case of acute liver failure with echovirus infection diagnosed by a multi-virus real-time PCR system, IDCASES, 23, 2021
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  159. yRibavirin induces hepatitis C virus genome mutations in chronic hepatitis patients who failed to respond to prior daclatasvir plus asunaprevir therapy, JOURNAL OF MEDICAL VIROLOGY, 92(2), 210-218, 202002
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  160. Novel drug resistance-associated substitutions against pibrentasvir emerged in genotype 1b hepatitis C virus-infected human hepatocyte transplanted mice, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 559, 78-83, 20210625
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  161. Identification and monitoring of mutations in circulating cell-free tumor DNA in hepatocellular carcinoma treated with lenvatinib, JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH, 40(1), 20210626
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  162. Serum PreS1 and HBsAg ratio reflects liver fibrosis and predicts the development of hepatocellular carcinoma in chronic hepatitis B patients, JOURNAL OF VIRAL HEPATITIS, 28(9), 1304-1311, 202109
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Publications such as books

  1. 2019/10/24, Hepatocellular Carcinoma, Hepatocellular carcinoma (HCC), the most common form of liver cancer, has become a major global health problem. Although the risk factors for HCC development are well known and great advances have been made through HBV vaccinations, direct-acting antivirals for HCV treatment, and aflatoxin eradication programs, the overall incidence and mortality rates of HCC are still rising. To tackle the burden of HCC, it is essential to understand the principle molecular and cellular processes as well as fundamental clinical challenges. This book provides an overview on several important disease aspects. Chapter 1 reviews recent studies assessing the potential cellular origins of HCC. Chapter 2 describes the newly discovered regulatory roles of the tumor microenvironment on tumor growth and progression. Chapters 3 and 4 outline the most commonly used in vitro systems and animal models of chronic liver disease and HCC in detail. Chapter 5 provides an overview of metabolic reprogramming and dysregulation of lipid metabolism as a newly recognized hallmark of HCC. Chapter 6 details the currently accepted standards and challenges for the surgical management of HCC, while Chapter 7 provides an overview of the recent developments in the field of tyrosine kinase inhibitors. Chapter 8 discusses multidrug resistance to chemotherapy and potential approaches to overcome this clinical obstacle. The book, written by experts from several countries, addresses each topic in sophisticated detail. It will be a valuable resource for clinicians and investigators who are interested in HCC., Chapter 5. The Role of Lipids in Hepatocellular Carcinoma, Codon Publications, 2019, 2019, Scholarly Book, Joint work, English, C. Nelson Hayes, Peiyi Zhang, and Kazuaki Chayama.
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Invited Lecture, Oral Presentation, Poster Presentation

  1. Multi-omics analysis of a human hepatocyte chimeric mouse fatty liver model and automating clinical trial matching and report generation in a cancer genome expert panel, 2024/09/27, With Invitation, English
  2. Of mice and men: Multi-omics analysis in a human hepatocyte chimeric mouse model and tumor genome profiling at a cancer genome expert panel in Japan, 2024/06/13, With Invitation, English, CIPHER: Center for Computational Intelligence to Predict Health and Environmental Risks, University of North Carolina, Charlotte
  3. Joint transcriptomic and metabolomic analysis in a chimeric mouse fatty liver model, Glyco-core Symposium 2024, 2024/07/16, Without Invitation, English, iGCORE: Institute for Glyco-core Research, Nagoya University, Toyoda Auditorium
  4. Transcriptomic and metabolomic analysis of growth hormone response in a fatty liver model using human hepatocyte chimeric mice, Liver Meeting, 2022/11/05, Without Invitation, English, American Association for the Study of Liver Diseases
  5. A comparison of male and female responses to inbreeding in Cucurbita texana. Poster., Hayes, C.N., Winsor, J.A., Stephenson, A.G., Symposium: Frontiers in Sexual Plant Reproduction in Honor of Prof. Joseph Mascarenhas, 2001/01/05, Without Invitation, English
  6. Inbreeding depression in male and female functions in Cucurbita texana., Hayes, C.N., Winsor, J.A., Stephenson, A.G., 16th Annual Penn State Symposium in Plant Physiology: Plant Reproduction 2002: From evolutionary and physiological analyses to molecular genetic studies, 2002/05/01, Without Invitation, English
  7. Male vs. female inbreeding depression in Cucurbita texana, Hayes, C.N., Winsor, J.A., Stephenson, A.G., Ecological Society of America Annual Meeting, 2002/08/01, Without Invitation, English
  8. Assessing undergraduate learning in web-based biology instruction, Cyr, R., Harris, S., Hayes, C.N. Woodward, D, National Association for Research in Science Teaching, 2002/10/01, Without Invitation, English
  9. Inbreeding depression in male and female functions in Cucurbita texana., Hayes, C.N., Winsor, J.A., Stephenson, A.G., Royal Society Discussion Meeting on Mechanisms Regulating Gene Flow in Flowering Plants. London, UK., 2002/12/15, Without Invitation, English
  10. varDB: a sequence database of protein families involved in antigenic variation in pathogens., Hayes, C.N., Diez, D., Kanehisa, M., Wahlgren, M., Wheelock, C., Goto, S., Genome Informatics Workshop 2007. Singapore, SINGAPORE., 2007/12/10, Without Invitation, English
  11. Tools for investigating mechanisms of antigenic variation: new extensions to varDB, Hayes CN, Diez D, Joannin N, Kanehisa M, Wahlgren M, Wheelock CE, Goto S, Genome Informatics Workshop 2009, Yokohama, Japan, 2009/12/06, Without Invitation, English
  12. Serum miRNAs and the hepatitis B virus life cycle, C. Nelson Hayes, Sakura Akamatsu, Masataka Tsuge, Daiki Miki, Nobuhiko Hiraga, Michio Imamura, Shoichi Takahashi, Hidenori Ochi, Kazuaki Chayama, AASLD, 2012/11/05, Without Invitation, English
  13. Early and late changes in gene expression profiles following infection with hepatitis B or C virus in human hepatocyte chimeric mice, Hayes, C. Nelson, Sakura Akamatsu, Masataka Tsuge, Daiki Miki, Nobuhiko Hiraga, Hiromi Abe, Michio Imamura1, Shoichi Takahashi, Hidenori Ochi, Kazuaki Chayama, AALSD 2013, 2013/11/04, Without Invitation, English
  14. Challenges in somatic mutation calling in virus-induced hepatocellular carcinoma, C. Nelson Hayes, Atsushi Ono, Sakura Akamatsu, Eisuke Murakami, Hiroshi Aikata, Michio Imamura, Daiki Miki, Hidenori Ochi, and Kazuaki Chayama, JCUP V, 2014/06/14, With Invitation, English
  15. Hepatitis B virus infection leads to activation of interferon-stimulated genes in primary cultured human hepatocytes, but infection efficiency decreases monotonically with decreasing cell density, C. Nelson Hayes, Hiromi Abe, Sakura Akamatsu, Nobuhiko Hiraga, Michio Imamura, Masataka Tsuge, Daiki Miki, Hiroshi Aikata, , Hidenori Ochi, Yuji Ishida, Chise Tateno, and Kazuaki Chayama, HBV Single topic conference 2014, 2014/11/18, Without Invitation, English
  16. Hepatitis B virus infection efficiency and immune response decreases with cell density in primary cultured hepatocytes, C. Nelson Hayes, Hiromi Abe, Sakura Akamatsu, Nobuhiko Hiraga, Michio Imamura, Masataka Tsuge, Daiki Miki, Hiroshi Aikata, , Hidenori Ochi, Yuji Ishida, Chise Tateno, and Kazuaki Chayama, AASLD, 2014/11/14, Without Invitation, English
  17. Characterizing the early immune response to hepatitis B virus infection using the human hepatocyte chimeric mouse model, C. Nelson Hayes, Sakura Akamatsu, Masataka Tsuge, Daiki Miki, Hiromi Abe-Chayama, Michio Imamura, Hidenori Ochi, Kazuaki Chayama, AASLD, 2017/10/22, Without Invitation, English
  18. Estimating HBV gene expression levels based on RNAseq data in a human hepatocyte chimeric mouse mode, Drug discovery research on HBV elimination using highly efficient infected cell line and long-lasting hepatitis mouse model, 2017/12/08, Without Invitation, English
  19. Prediction of hepatitis B virus co-receptors using semi-supervised learning, Peiyi Zhang, Kazuaki Chayama, AASLSD conference 2019, 2019/11/09, Without Invitation, English, American Association for the Study of Liver Diseases, Hynes Conference Center

Awards

  1. 1992/09/01, Presidential Scholarship, Washington and Jefferson College
  2. 1999/08/01, J. Ben and Helen D. Hill graduate student award, Pennsylvania State University
  3. 1999/07/15, Eberly College of Science Braddock Fellowship, Pennsylvania State University
  4. 2002/05/15, Graduate Assistant Outstanding Teaching Award, Pennsylvania State University
  5. 2006/04/01, Japan Society for the Promotion of Science Fellowship, Japan Society for the Promotion of Science
  6. 2009/12/16, Best paper award, Genome Informatics Workshop
  7. 2019/11/09, Presidential poster of distinction, American Association for the Study of Liver Diseases

External Funds

Acceptance Results of Competitive Funds

  1. KAKENHI, Tracking the emergence of escape mutants during triple therapy for hepatitis C virus infection, 2012, 2013
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Social Activities

History as Peer Reviews of Academic Papers

  1. 2025, Biomedicines, Others, peer reviewer
  2. 2025, Clinical and Experimental Medicine, Others, peer reviewer, 1
  3. 2025, Viruses, Others, peer reviewer, 1
  4. 2024, Cell Reports Medicine, Others, peer reviewer, 1
  5. 2024, Infectious Diseases and Therapy, Others, peer reviewer
  6. 2024, Hepatology Research, Others, peer reviewer, 1
  7. 2024, Cancer Science, Others, reviewer
  8. 2024, Gut Pathogens, Others, reviewer
  9. 2024, Communications Biology, reviewer, 1
  10. 2024, BioMed Research International, Others, reviewer, 1
  11. 2023, Scientific Reports, Others