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• Short Direct Repeats in the 3' Untranslated Region Are Involved in Subgenomic Flaviviral RNA Production

  Zhang, Q. Y., Li, X. F., Niu, X., Li, N., Wang, H. J., Deng, C. L., Ye, H. Q., Huang, X. Y., Chen, Q., Xu, Y. P., Dong, H. L., Li, X. D., Zhao, H., Shi, P. Y., Yuan, Z. M., Gong, P., Fang, X., Qin, C. F. & Zhang, B., Feb 28 2020, In: Journal of virology. 94, 6

  Research output: Contribution to journal › Article › peer-review

  • Nucleic Acid Repetitive Sequences
  • 3' untranslated regions
  • 3' Untranslated Regions
  • RNA
  • Flavivirus
  3 Scopus citations

• Spike mutation D614G alters SARS-CoV-2 fitness

  Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., Zhang, X., Muruato, A. E., Zou, J., Fontes-Garfias, C. R., Mirchandani, D., Scharton, D., Bilello, J. P., Ku, Z., An, Z., Kalveram, B., Freiberg, A. N., Menachery, V. D., Xie, X., Plante, K. S. & 2 others, Weaver, S. C. & Shi, P. Y., 2020, (Accepted/In press) In: Nature.

  Research output: Contribution to journal › Article › peer-review

  • SARS Virus
  • Viral Vaccines
  • Mutation
  • Cricetinae
  • Viruses
  35 Scopus citations

• Stabilization of dengue virus polymerase in de novo initiation assay provides advantages for compound screening

  Niyomrattanakit, P., Wan, K. F., Chung, K. Y., Abas, S. N., Seh, C. C., Dong, H., Lim, C. C., Chao, A. T., Lee, C. B., Nilar, S., Lescar, J., Shi, P. Y., Beer, D. & Lim, S. P., Jul 1 2015, In: Antiviral research. 119, p. 36-46 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Dengue Virus
  • RNA Replicase
  • Enzymes
  • dengue virus NS5 protein
  • Heavy Ions
  13 Scopus citations

• Structural biology of dengue virus enzymes: Towards rational design of therapeutics

  Noble, C. G. & Shi, P. Y., Nov 1 2012, In: Antiviral research. 96, 2, p. 115-126 12 p.

  Research output: Contribution to journal › Review article › peer-review

  • Dengue Virus
  • Methyltransferases
  • Dengue
  • Enzymes
  • Peptide Hydrolases
  78 Scopus citations

• Structure-activity relationship of uridine-based nucleoside phosphoramidate prodrugs for inhibition of dengue virus RNA-dependent RNA polymerase

  Wang, G., Lim, S. P., Chen, Y. L., Hunziker, J., Rao, R., Gu, F., Seh, C. C., Ghafar, N. A., Xu, H., Chan, K., Lin, X., Saunders, O. L., Fenaux, M., Zhong, W., Shi, P. Y. & Yokokawa, F., Jul 15 2018, In: Bioorganic and Medicinal Chemistry Letters. 28, 13, p. 2324-2327 4 p.

  Research output: Contribution to journal › Article › peer-review

  • phosphoramidic acid
  • RNA Replicase
  • Uridine
  • Dengue Virus
  • Structure-Activity Relationship
  8 Scopus citations

• Synergistic suppression of dengue virus replication using a combination of nucleoside analogs and nucleoside synthesis inhibitors

  Yeo, K. L., Chen, Y. L., Xu, H. Y., Dong, H., Wang, Q. Y., Yokokawa, F. & Shi, P. Y., Apr 1 2015, In: Antimicrobial agents and chemotherapy. 59, 4, p. 2086-2093 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Dengue Virus
  • brequinar
  • Nucleosides
  • Virus Replication
  • Ribavirin
  39 Scopus citations

• Synthesis and antiviral activity of 4,6-disubstituted pyrimido[4,5-b]indole ribonucleosides

  Tichý, M., Pohl, R., Xu, H. Y., Chen, Y. L., Yokokawa, F., Shi, P. Y. & Hocek, M., Oct 15 2012, In: Bioorganic and Medicinal Chemistry. 20, 20, p. 6123-6133 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Ribonucleosides
  • indole
  • Antiviral Agents
  • stannane
  • Cross Reactions
  37 Scopus citations

• Targeting dengue virus NS4B protein for drug discovery

  Xie, X., Zou, J., Wang, Q. Y. & Shi, P. Y., Jun 2015, In: Antiviral research. 118, p. 39-45 7 p., 3603.

  Research output: Contribution to journal › Review article › peer-review

  • Dengue virus NS4B protein
  • Drug Discovery
  • Flavivirus
  • Proteins
  • Antiviral Agents
  44 Scopus citations

• Targeting vesicle size

  Zou, J. & Shi, P. Y., Nov 1 2018, In: Nature Materials. 17, 11, p. 955-956 2 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  • blood-brain barrier
  • Peptides
  • viruses
  • Viruses
  • peptides

• Ten years of dengue drug discovery: Progress and prospects

  Lim, S. P., Wang, Q. Y., Noble, C. G., Chen, Y. L., Dong, H., Zou, B., Yokokawa, F., Nilar, S., Smith, P., Beer, D., Lescar, J. & Shi, P. Y., 2013, In: Antiviral research. 100, 2, p. 500-519 20 p.

  Research output: Contribution to journal › Review article › peer-review

  • Dengue Virus
  • Dengue
  • Drug Discovery
  • balapiravir
  • celgosivir
  241 Scopus citations

• Testing Antiviral Compounds in a Dengue Mouse Model

  Schul, W., Yip, A. & Shi, P. Y., Jul 18 2013, Antiviral Methods and Protocols. p. 269-281 13 p. (Methods in Molecular Biology; vol. 1030).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Dengue Virus
  • Dengue
  • Antiviral Agents
  • Virus Diseases
  • Active Immunotherapy
  3 Scopus citations

• The dengue virus NS5 protein as a target for drug discovery

  Lim, S. P., Noble, C. G. & Shi, P-Y., Jul 1 2015, In: Antiviral Research. 119, p. 57-67 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Viral Structural Proteins
  • RNA Replicase
  • Flavivirus
  • Dengue Virus
  • Methyltransferases
  101 Scopus citations

• The Interface between Methyltransferase and Polymerase of NS5 Is Essential for Flavivirus Replication

  Li, X. D., Shan, C., Deng, C. L., Ye, H. Q., Shi, P. Y., Yuan, Z. M., Gong, P. & Zhang, B., May 2014, In: PLoS neglected tropical diseases. 8, 5, e2891.

  Research output: Contribution to journal › Article › peer-review

  • RNA Replicase
  • Flavivirus
  • Methyltransferases
  • Japanese Encephalitis Virus
  • Reverse Genetics
  28 Scopus citations

• Therapeutics for Dengue: Recommendations for Design and Conduct of Early-Phase Clinical Trials

  Simmons, C. P., Wolbers, M., Nguyen, M. N., Whitehorn, J., Shi, P. Y., Young, P., Petric, R., Nguyen, V. V. C., Farrar, J. & Wills, B., Sep 2012, In: PLoS neglected tropical diseases. 6, 9, e1752.

  Research output: Contribution to journal › Article › peer-review
  25 Scopus citations

• Therapeutics for Neglected Infectious Diseases: Progress and Challenge

  Shi, P. Y., Smith, P. W. & Diagana, T. T., Jan 8 2015, In: ACS Infectious Diseases. 1, 1, p. 76-78 3 p.

  Research output: Contribution to journal › Short survey › peer-review
  7 Scopus citations

• The search for nucleoside/nucleotide analog inhibitors of dengue virus

  Chen, Y. L., Yokokawa, F. & Shi, P. Y., Aug 10 2015, In: Antiviral research. 122, p. 12-19 8 p., 3670.

  Research output: Contribution to journal › Review article › peer-review

  • Dengue Virus
  • Nucleosides
  • Antiviral Agents
  • Nucleotides
  • Sofosbuvir
  44 Scopus citations

• The stem region of premembrane protein plays an important role in the virus surface protein rearrangement during dengue maturation

  Zhang, Q., Hunke, C., Yau, Y. H., Seow, V., Lee, S., Tanner, L. B., Guan, X. L., Wenk, M. R., Fibriansah, G., Chew, P. L., Kukkaro, P., Biuković, G., Shi, P. Y., Shochat, S. G., Grüber, G. & Lok, S. M., Nov 23 2012, In: Journal of Biological Chemistry. 287, 48, p. 40525-40534 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Viruses
  • Dengue
  • Membrane Proteins
  • Exosomes
  • Dengue Virus
  32 Scopus citations

• The structural basis for serotype-specific neutralization of dengue virus by a human antibody

  Teoh, E. P., Kukkaro, P., Teo, E. W., Lim, A. P. C., Tan, T. T., Yip, A., Schul, W., Aung, M., Kostyuchenko, V. A., Leo, Y. S., Chan, S. H., Smith, K. G. C., Chan, A. H. Y., Zou, G., Ooi, E. E., Kemeny, D. M., Tan, G. K., Ng, J. K. W., Ng, M. L., Alonso, S. & 5 others, Fisher, D., Shi, P. Y., Hanson, B. J., Lok, S. M. & MacAry, P. A., Jun 20 2012, In: Science Translational Medicine. 4, 139, 139ra83.

  Research output: Contribution to journal › Article › peer-review

  • Dengue Virus
  • Serogroup
  • Antibodies
  • Immunity
  • Cryoelectron Microscopy
  165 Scopus citations

• Topoisomerase III-β is required for efficient replication of positive-sense RNA viruses

  Prasanth, K. R., Hirano, M., Fagg, W. S., McAnarney, E. T., Shan, C., Xie, X., Hage, A., Pietzsch, C. A., Bukreyev, A., Rajsbaum, R., Shi, P. Y., Bedford, M. T., Bradrick, S. S., Menachery, V. & Garcia-Blanco, M. A., Oct 2020, In: Antiviral research. 182, 104874.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • DNA topoisomerase III
  • Yellow fever virus
  • SARS Virus
  • Dengue Virus
  • RNA Viruses
  3 Scopus citations

• Treatment of human glioblastoma with a live attenuated Zika virus vaccine candidate

  Chen, Q., Wu, J., Ye, Q., Ma, F., Zhu, Q., Wu, Y., Shan, C., Xie, X., Li, D., Zhan, X., Li, C., Li, X. F., Qin, X., Zhao, T., Wu, H., Shi, P. Y., Man, J. & Qin, C. F., Sep 1 2018, In: mBio. 9, 5, e01683-18.

  Research output: Contribution to journal › Article › peer-review

  • Zika Virus
  • Glioblastoma
  • Vaccines
  • Glioma
  • Stem Cells
  32 Scopus citations

• Two distinct sets of NS2A molecules are responsible for dengue virus RNA synthesis and virion assembly

  Xie, X., Zou, J., Puttikhunt, C., Yuan, Z. & Shi, P. Y., 2015, In: Journal of virology. 89, 2, p. 1298-1313 16 p.

  Research output: Contribution to journal › Article › peer-review

  • Dengue virus
  • Dengue Virus
  • virion
  • Virion
  • RNA
  53 Scopus citations

• Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies

  Arora, R., Liew, C. W., Soh, T. S., Otoo, D. A., Seh, C. C., Yue, K., Nilar, S., Wang, G., Yokokawa, F., Noble, C. G., Chen, Y. L., Shi, P. Y., Lescar, J., Smith, T. M., Benson, T. E. & Lim, S. P., Dec 2020, In: Journal of virology. 94, 24, e01130-20.

  Research output: Contribution to journal › Article › peer-review

  • Dengue virus
  • Dengue Virus
  • RNA Replicase
  • RNA-directed RNA polymerase
  • RNA

• Type I and Type III interferons restrict SARS-CoV-2 infection of human airway epithelial cultures

  Vanderheiden, A., Ralfs, P., Chirkova, T., Upadhyay, A. A., Zimmerman, M. G., Bedoya, S., Aoued, H., Tharp, G. M., Pellegrini, K. L., Manfredi, C., Sorscher, E., Mainou, B., Lobby, J. L., Kohlmeier, J. E., Lowen, A. C., Shi, P. Y., Menachery, V. D., Anderson, L. J., Grakoui, A., Bosinger, S. E. & 1 others, Suthar, M. S., Oct 2020, In: Journal of virology. 94, 19, e00985-20.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Severe acute respiratory syndrome coronavirus
  • interferon type III
  • Coronavirus Infections
  • Severe Acute Respiratory Syndrome
  • interferons
  19 Scopus citations

• Type I interferon signals in macrophages and dendritic cells control dengue virus infection: Implications for a new mouse model to test dengue vaccines

  Züst, R., Toh, Y. X., Valdés, I., Cerny, D., Heinrich, J., Hermida, L., Marcos, E., Guillén, G., Kalinke, U., Shi, P. Y. & Fink, K., 2014, In: Journal of virology. 88, 13, p. 7276-7285 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Dengue Vaccines
  • Dengue virus
  • dendritic cells
  • dengue
  • Interferon Type I
  52 Scopus citations

• U18666A, an intra-cellular cholesterol transport inhibitor, inhibits dengue virus entry and replication

  Poh, M. K., Shui, G., Xie, X., Shi, P. Y., Wenk, M. R. & Gu, F., Jan 2012, In: Antiviral research. 93, 1, p. 191-198 8 p.

  Research output: Contribution to journal › Article › peer-review

  • 3-beta-(2-(diethylamino)ethoxy)androst-5-en-17-one
  • Anticholesteremic Agents
  • Virus Internalization
  • Dengue Virus
  • Virus Replication
  72 Scopus citations

• Unraveling a flavivirus enigma

  Shi, P. Y., Jan 1 2014, In: Science. 343, 6173, p. 849-850 2 p.

  Research output: Contribution to journal › Short survey › peer-review

  • Flavivirus
  • Proteins
  9 Scopus citations

• Using a virion assembly-defective dengue virus as a vaccine approach

  Shan, C., Xie, X., Zou, J., Züst, R., Zhang, B., Ambrose, R., Mackenzie, J., Fink, K. & Shi, P. Y., Nov 1 2018, In: Journal of virology. 92, 21, e01002.

  Research output: Contribution to journal › Article › peer-review

  • Defective Viruses
  • Dengue virus
  • Dengue Virus
  • virion
  • Virion
  10 Scopus citations

• Using next generation sequencing to study the genetic diversity of candidate live attenuated zika vaccines

  Collins, N. D., Shan, C., Nunes, B. T. D., Widen, S. G., Shi, P. Y., Barrett, A. D. T. & Sarathy, V. V., Apr 2020, In: Vaccines. 8, 2, 161.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Zika Virus
  • Attenuated Vaccines
  • Genetic Variation
  • Membranes
  • Flaviviridae
  2 Scopus citations

• Using recombination-dependent lethal mutations to stabilize reporter flaviviruses for rapid serodiagnosis and drug discovery

  Baker, C., Xie, X., Zou, J., Muruato, A., Fink, K. & Shi, P. Y., Jul 2020, In: EBioMedicine. 57, 102838.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Drug Discovery
  • Flavivirus
  • Viruses
  • Serologic Tests
  • Genetic Recombination
  4 Scopus citations

• Vesicular stomatitis virus and DNA vaccines expressing zika virus nonstructural protein 1 induce substantial but not sterilizing protection against zika virus infection

  Li, A., Xue, M., Attia, Z., Yu, J., Lu, M., Shan, C., Liang, X., Gao, T. Z., Shi, P. Y., Peeples, M. E., Boyaka, P. N., Liu, S. L. & Li, J., Sep 2020, In: Journal of virology. 94, 17, e00048-20.

  Research output: Contribution to journal › Article › peer-review

  • Zika virus
  • Zika Virus Infection
  • Zika Virus
  • recombinant vaccines
  • Vesiculovirus

• West Nile virus drug discovery

  Lim, S. P. & Shi, P. Y., Dec 3 2013, In: Viruses. 5, 12, p. 2977-3006 30 p.

  Research output: Contribution to journal › Review article › peer-review

  • West Nile virus
  • Drug Discovery
  • Antiviral Agents
  • Antibodies
  • Flaviviridae
  27 Scopus citations

• Zika structural genes determine the virulence of African and Asian lineages

  Nunes, B. T. D., Fontes-Garfias, C. R., Shan, C., Muruato, A. E., Nunes, J. G. C., Burbano, R. M. R., Vasconcelos, P. F. C., Shi, P. Y. & Medeiros, D. B. A., Jan 1 2020, In: Emerging Microbes and Infections. 9, 1, p. 1023-1033 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Zika Virus
  • Virulence
  • Viruses
  • Epidemics
  • Genes

• Zika virus infection elicits auto-antibodies to C1q

  Koma, T., Veljkovic, V., Anderson, D. E., Wang, L. F., Rossi, S. L., Shan, C., Shi, P. Y., Beasley, D. W., Bukreyeva, N., Smith, J. N., Hallam, S., Huang, C., Von Messling, V. & Paessler, S., Dec 1 2018, In: Scientific reports. 8, 1, 1882.

  Research output: Contribution to journal › Article › peer-review

  • Zika Virus Infection
  • Zika Virus
  • Antibodies
  • Complement C1q
  • Viral Structures
  10 Scopus citations

• Zika Virus Vaccine: Progress and Challenges

  Shan, C., Xie, X. & Shi, P. Y., Jul 11 2018, In: Cell Host and Microbe. 24, 1, p. 12-17 6 p.

  Research output: Contribution to journal › Review article › peer-review

  • Zika Virus
  • Vaccines
  • Eye Abnormalities
  • Flavivirus
  • Explosive Agents
  36 Scopus citations